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Cornell Initiative for Digital Agriculture (CIDA) 3rd Annual Cornell Initiative for Digital Agriculture Workshop

CURRICULUM VITAE – CORNELL UNIVERSITY GRADUATE STUDENTS AND POSTDOCS

phone: (607) 255-5173

e-mail : carrillo@cornell.edu

Carlos M. Carrillo Research Associate, Dept. of Earth and Atmospheric Sciences, Cornell University

1121 Bradfield Hall, Ithaca, NY 14853 Professional Preparation 2010-2014 Ph.D. Atmospheric Sciences, University of Arizona. 2007-2010 M.S. Meteorology, Iowa State University. 1992-1996 B.S. Physics, San Marcos University, Peru. Professional Appointments 2019-present Research Associate, Department of Earth and Atmospheric Sciences, Cornell

University, Ithaca, New York. 2016-2019 Postdoctoral Researcher, Department of Earth and Atmospheric Sciences,

Cornell University, Ithaca, New York. 2015-2016 Postdoctoral Researcher, Biological System Engineering Department, University

of Nebraska-Lincoln, Lincoln, Nebraska. Products Five most recent publications: Carrillo CM, Ault RT, Wilks DS, 2018. Spring Onset Predictability in the North American

Multimodel Ensemble. Journal of Geophysical Research. https://doi.org/10.1029/2018JD028597

Carrilo CM, Castro CL, Garfin G, Chang C, Bukosky M.Mearns LO, 2018. Pacific sea surface temperature related influences on North American monsoon precipitation within North American Regional Climate Change Assessment Program models. International Journal of Climatology. https://doi.org/10.1002/joc.5561

Carrillo CM, Castro CL, Chang H, Luong T. 2017. Multi-year climate variability in the Southwestern United States within a context of a dynamically downscaled twentieth century reanalysis. Climate Dynamics. doi: 10.1007/s00382-017-3569-1

Carrillo CM, Castro CL, Woodhouse CA, Griffin D. 2016. Low-frequency variability of precipitation in the North American monsoon as region as diagnosed through earlywood and latewood tree-ring chronologies in the southwestern U.S. International Journal of Climatology. doi:10.1002/joc.4493.

Mazon J., Castro C, Adams D, Chang HI, Carrillo CM, Brost J. 2016. Objective Climatological Analysis of Extreme Weather Events in Arizona during the North American Monsoon. Journal of Applied Meteorology and Climatology. https://doi.org/10.1175/JAMC-D-16-0075.1 Five other relevant publications: Ault TR, St. George S, Smerdon JE, Coats S, Mankin JS, Carrillo CM, Cook BI, Stevenson S,

2018. A robust null hypothesis for the potential causes of megadrought in Western North America. Journal of Climate. https://doi.org/10.1175/JCLI-D-17-0154.1

Bukovsky, M. S., C.M. Carrillo, D.J. Gochis, D.M. Hammerling, R.R. McCrary, L.O. Mearns, 2015: Towards Assessing NARCCAP Regional Climate Model Credibility for the North American Monsoon: Future Climate Simulations. Journal of Climate. doi: http://dx.doi.org/10.1175/JCLI-D-14-00695.1

D. Griffin, C.A. Woodhouse, D.M. Meko, D.W. Stahle, H.L. Faulstich, C. Carrillo, R. Touchan, C.L. Castro and S.W. Leavitt, 2013: North American monsoon precipitation reconstructed from tree-ring latewood. Geophysical Research Letters, doi: 10.1002/grl.50184.

Ciancarelli, B., C.L. Castro, C. Woodhouse, F. Dominguez, H. Chang, C. Carrillo, and D. Griffin, 2013. Influence of Large-scale Teleconnection on Dominant Patterns of Warm Season Precipitation Variability in a Fine Resolution Observational Record. Int. J. Climatol. DOI:10.1002/joc.3716.

Castro, C.L., H. Chang, F. Dominguez, C. Carrillo, J. Kyung-Schemm, H. H-M. Juang, 2012. Can a regional climate model improve warm season forecasts in North America? J. Climate, 25, 8212-8237.

Synergistic Activities

1. Technical skills: a) Atmospheric models: ETA, Community Climate Model (CCM) version 3, Community Atmosphere model (CAM), Regional Atmosphere Modeling System (RAMS), Hybrid Particle And Concentration Transport (HYPACT), Weather Research and Forecasting (WRF), and Ocean Land Atmosphere Model (OLAM); b) Other models: The Community Land Model (CLM), Land surface hydrology model VIC, Stochastic Weather Generator (WeaGETS); c) Programming Languages: C, Fortran, Matlab, Pascal, GrADS, Python, UNIX scripts (awk, bash, csh); d) Statistical analysis tools: Empirical Orthogonal Functions (EOF), EMOS (Ensemble Model Output Statistics), Canonical Correlation Analysis (CCA), Multi-Taper Method Singular Value Decomposition (MTM-SVD), and Spectral Analysis tools.

2. Awards: a) Water Sustainability Program Graduate Student Scholarship (2013/14); b) Galileo Circle Scholar (2013); c) Travel Grant Award (Graduate and Professional Student Consul – GPSC, 2012); d) Graduate Incentives for Growth Award (GIGA) in Hydrometeorology related research (2010).

3. Community services: a) Article reviewer for Climate Research journal (2016); b) Student Ambassador at the Atmospheric Science Department (U AZ, 2013/14); c) Grant reviewer for the Graduate and Professional Student Council (U AZ and U NE; 2013/14 and 2015).

Christine Yao-Yun Chang Curriculum Vitae (Updated October 27, 2019)

cyc54@cornell.edu | Skype : yaoyun.chang

Research Interests: • Understanding impacts of climate change and abiotic stresses on forest and crop physiology • Developing tower-based and airborne (UAV) platforms for remote sensing of chlorophyll fluorescence

and hyperspectral reflectance

Education: Sept 2010 – Oct 2016 Ph.D. in Plant Physiology, University of Toronto, Mississauga, ON, Canada

Sept 2005 – Feb 2009 B.A. in Biology, Barnard College, Columbia University, New York, NY, USA

Honors and Awards: 2018-2020 USDA-NIFA Postdoctoral Fellowship 2018 Robert E. Musgrave Award for Excellence in Agronomy 2013 Center for Global Change Science Graduate Research Award 2010 Zoology International Scholarship 2009 Constance Von Wahl Award for Excellence in Biology 2007 Amgen Summer Scholarship for Independent Scientific Research 2007 Dean’s List, Barnard College 2006 Howard Hughes Pipeline Project Internship 2006 Dean’s List, Barnard College

Publications: Chang C. Y., Zhou R., Kira O., Marri S., Skovira J., Gu L., Sun Y. An Unmanned Aerial System (UAS) for

concurrent measurements of sun-induced chlorophyll fluorescence and hyperspectral reflectance to improve crop monitoring and stress detection. In preparation for submission to Agriculture and Forest Meteorology, November 2019.

Chang C. Y., Bräutigam K., Hüner N. P. A., Ensminger I. How Evergreen Conifers Overwinter: Ecophysiology and Molecular Regulation. In preparation for submission to New Phytology, November 2019.

Chang C. Y., Guanter L., Frankenberg C., Köhler P., Gu L., Sun Y. Systematic assessment of retrieval methods for ground solar-induced chlorophyll fluorescence (SIF) using high-frequency automated field spectroscopy. Journal of Geophysical Research: Biogeosciences (under review).

Fréchette E., Chang C. Y., Ensminger I. Variation in the phenology of photosynthesis among eastern white pine provenances in response to warming. Global Change Biology (under review).

Wen J., Köhler P., Duveiller G., Parazoo N. C., Yu L., Chang C. Y., Sun Y. Generating a long-term record of high-resolution global solar-induced chlorophyll fluorescence (SIF) by harmonizing multiple satellite instruments: A case study for fusing GOME-2 and SCIAMACHY. Remote Sensing of Environment (under review).

Gu L., Han J., Wood J. D., Chang C. Y., Sun Y. (2019) Sun-Induced Chl fluorescence and its importance for biophysical modeling of photosynthesis based on light reactions. New Phytol. 223: 1179-1191. doi: 10.1111/nph.15796

Yu L., Wen J., Chang C. Y., Frankenberg C., Sun Y. (2019) High-resolution global contiguous SIF of OCO-2. Geophys. Res. Lett. 46: 1449-1458. doi: 10.1029/2018GL081109

Gu L., Wood J. D., Chang C. Y., Sun Y., Riggs J. S. (2019) Advancing Terrestrial Ecosystem Science with a Novel Automated Measurement System for Sun-Induced Chlorophyll Fluorescence for Integration with Eddy Covariance Flux Networks. J. Geophys. Res. Biogeosciences 124: 127-146. doi: 10.1029/2018JG004742

Chang C. Y., Fréchette E., Unda F., Mansfield S. D., Ensminger I. (2016) Elevated temperature and CO2 stimulate late-season photosynthesis but impair cold hardening in pine. Plant Physiol. 172: 802-818. doi: 10.1104/pp.16.00753

Fréchette E., Chang C. Y., Ensminger I. (2016) Photoperiod and temperature constraints on the relationship between the photochemical reflectance index and the light use efficiency of photosynthesis in Pinus strobus. Tree Physiol. 36: 311-324. doi: 10.1093/treephys/tpv143

Chang C. Y., Unda F., Zubilewich A., Mansfield S. D., Ensminger I. (2015) Sensitivity of cold acclimation to elevated autumn temperature in field-grown Pinus strobus seedlings. Front. Plant Sci., 6: 165. doi: 10.3389/fpls.2015.00165

Fréchette E., Wong C. Y. S., Junker L. V., Chang C. Y., Ensminger I. (2015) Zeaxanthin-independent energy quenching and alternative electron sinks cause a decoupling of the relation between the photochemical reflectance index (PRI) and photosynthesis in an evergreen conifer during spring. J. Exp. Bot. 66: 7309-7323. doi: 10.1093/jxb/erv427

Ensminger I., Chang C. Y., Bräutigam K. (2015) Tree responses to environmental cues. In: A.-F. Adam-Blondon, C. Plomion (volume eds.), J.-P. Jacquot, & P. Gadal (serial eds.), Advances in Botanical Research Vol. 74 (p. 229-264), London: Elsevier Ltd. doi: 10.1016/bs.abr.2015.05.003

Conference Presentations:

Chang C. Y., Zhou R., Skovira J., Sun Y. (2019) An Unmanned Aerial System (UAS) for concurrent measurements of sun-induced chlorophyll fluorescence and hyperspectral reflectance to improve crop monitoring and stress detection. National Association of Plant Breeders Annual Meeting, August 25, Pine Mountain, Georgia, USA.

Chang C. Y., Gu L., Melkonian J., Riha S. J., LeVonne J., Wen J., Yu L., Wang C., Sun Y. (2018) Exploring diurnal dynamics of solar-induced chlorophyll fluorescence and photosynthesis in a maize canopy. American Geophysical Union Fall Meeting, December 12, Washington, D.C., USA.

Chang C.Y., Gu L., Melkonian J., Riha S.J., Sun Y. (2017) Tracking seasonal and diurnal photosynthesis in maize using sun-induced chlorophyll fluorescence (SIF) and GPP. American Geophysical Union Fall Meeting, December 14, New Orleans, Louisiana, USA.

Chang C.Y., Gu L., Melkonian J., Riha S.J., Sun Y. (2017) Revealing the relationship between solar-induced chlorophyll fluorescence (SIF) and gross primary production (GPP) from diurnal to seasonal scales at a corn field in upstate New York. Potsdam Greenhouse Gas Workshop: From Photosystems to Ecosystems, October 24-26, Potsdam, Germany.

Fréchette E., Chang C., Ensminger I. (2014) Facultative and constitutive changes in pigment composition affect the relationship of the photosynthetic light-use efficiency and the photochemical reflectance index of Eastern white pine (Pinus strobus L.). Canadian Society of Plant Biologists Eastern Regional Meeting, November 29, Guelph, Ontario, Canada.

Chang C., Fréchette E., Ensminger I. (2013) Sensitivity of autumn cold acclimation to elevated temperature in Pinus strobus. Canadian Society of Plant Biology Eastern Regional Meeting, December 7, Mississauga, Ontario, Canada.

Fréchette, E., Chang, C., Ensminger, I. (2013) The photochemical index (PRI) as an indicator of photochemical efficiency in Pinus strobus during the autumn. Canadian Society of Plant Biologists Eastern Regional Meeting, December 7, Mississauga, Ontario, Canada.

Chang C., Fréchette E., Ensminger I. (2013) Temperature, Photoperiod and CO2: Effects of simulated climate change on autumn photosynthesis and freezing tolerance in Pinus strobus. Canadian Society of Plant Biology Annual Meeting, June 28, Québec City, Québec, Canada.

Chang C., Fréchette E., Bin Yameen T., Ensminger I. (2012) Effects of simulated future climate on autumn freezing tolerance of Pinus strobus. Canadian Society of Plant Biologists Eastern Regional Meeting, December 1, Waterloo, Ontario, Canada.

Chang C., Fréchette E., Bin Yameen T., Ensminger I. (2012) Impact of simulated future climate on autumn photosynthesis and cold hardening in Pinus strobus. Canadian Society of Plant Biologists Annual Meeting, June 25-27, Edmonton, Alberta, Canada.

Fréchette E., Chang C., Ensminger I. (2012) Temperature affects the spectral properties of Eastern white pine during the autumn downregulation of photosynthesis. Canadian Society of Plant Physiology annual meeting, June 25, Edmonton, Alberta, Canada.

Chang C., Weisser A., Wildhagen H., Ensminger I. (2011) Physiological performance reveals different responses to drought in Douglas-fir provenances adapted to contrasting environments. American Society of Plant Biology Annual Meeting, August 6-8, Minneapolis, Minnesota, USA.

Ahamed T., Bari K., Chang C., Wallenfang M. (2007) Effects of oxidative damage on male germline stem cell cycle activity. Drosophila Annual Conference, March 7-11, Philadelphia, Pennsylvania, USA.

Other Presentations:

Chang C. Y. (2019) Probing photosynthesis using remote sensing of solar-induced chlorophyll fluorescence (SIF): From leaf to globe. Life Sciences Lecture Series, Cornell Initiative for Digital Agriculture Mini-Symposium, September 13. Ithaca, NY, USA.

Chang C. Y. (2018) Solar-induced chlorophyll fluorescence: Potentially revolutionizing the remote sensing of photosynthesis. Phi Tau Phi Scholastic Honor Society Annual Meeting, November 24. Flushing, NY, USA.

Chang C. Y. (2018) Exploring the diurnal dynamics of solar-induced chlorophyll fluorescence (SIF) in relationship to photosynthesis. Departmental seminar for School of Integrative Plant Sciences (SIPS) Soil and Crop Sciences Section, November 1. Cornell University, Ithaca, NY, USA.

Chang C. Y. (2017) Impacts of short photoperiod, elevated temperature and CO2 on cold hardening in Eastern white pine. Departmental seminar for Atmospheric and Earth Sciences, March 9. Cornell University, Ithaca, NY, USA.

Chang C. (2016) Impacts of short photoperiod, elevated temperature and CO2 on cold hardening in Eastern white pine. Ph.D. Thesis Defense, September 7. University of Toronto Mississauga, Mississauga, Ontario, Canada.

Chang C., Fréchette E., Unda F., Mansfield S. D., Ensminger I. (2015) Autumn simulations reveal sensitivity of Eastern white pine seedlings to photoperiod, temperature, and elevated CO2. Graduate Research Colloquium. May 4. University of Toronto Mississauga, Mississauga, Ontario, Canada.

Chang C., Fréchette E., Ensminger I. (2013) Effects of simulated climate change on autumn photosynthesis and freezing tolerance in Pinus strobus. Graduate Seminar for Department of Cell and Systems Biology, November 6. University of Toronto, Toronto, Ontario, Canada.

Chang C., Ensminger I. (2012) Effects of future climate change on autumn cold acclimation in Pinus strobus. Department of Plant Biology Seminar, March 20. University of Toronto Mississauga, Mississauga, Ontario, Canada.

Chang C., Ensminger I. (2012) Examining the effects of future climate change on autumn cold acclimation in Pinus strobus. PhD Transfer Day, February 24. University of Toronto, Toronto, Ontario, Canada.

Chang C., Wallenfang M. (2008) The effects of aging on somatic stem cells in the Drosophila melanogaster testis. Senior Thesis Symposium, December 14. Barnard College, New York City, New York, USA.

Chang C., Wallenfang M. (2008) Effects of aging on somatic stem cells in the Drosophila melanogaster testis. Senior Thesis Poster Session, April 22. Barnard College, New York City, New York, USA.

Chang C., Wallenfang M. (2007) Investigating a mysterious overproliferation of aged germ cells in D. melanogaster. SURF/Amgen Research Symposium, January 21. Columbia University, New York City, New York, USA.

Research Experience:

March 2017-present Postdoctoral project: Using solar-induced chlorophyll fluorescence (SIF) to monitor crop productivity and response to water availability PI: Ying Sun, Cornell University Collaborators: Jeff Melkonian, Susan Riha, Joseph Skovira - Cornell University; Lianhong Gu – Oak Ridge National Laboratory In 2017-2018 I designed a solar-powered, tower-based system for continuous monitoring of SIF. In 2018-2019 I coordinated with teams of engineering students to continue development of SIF tower components. In 2018-2019 I led two teams of electrical and computer engineering and agricultural engineering students to develop a platform for remote sensing of SIF and hyperspectral reflectance using an unmanned aerial vehicle (UAV). I also designed and led three summer field experiments (2017-2019) to assess seasonal and diurnal dynamics of SIF in a rain-fed maize field using a combination of tower, ground and (in 2019) airborne measurements.

September 2010 – PhD project: Impacts of short photoperiod, elevated temperature and September 2016 elevated CO2 on cold hardening in Eastern white pine PI: Ingo Ensminger, University of Toronto In this project, I assessed whether elevated temperature and CO2 will impair cold hardening during autumn and expose conifer seedlings to winter freezing damage. I demonstrated that in a warmer, CO2-enriched climate, Eastern white pine seedlings benefit from enhanced photosynthetic productivity but develop impaired freezing tolerance. Our results indicated that Eastern white pine seedlings growing in Ontario are unlikely to increase risk of winter freezing damage under projected future conditions.

December 2013 Research internship: Training in extraction and HPLC analysis of nonstructural carbohydrates from pine needle tissue

PI: Shawn Mansfield, University of British Columbia I devoted two weeks to learning a protocol for HPLC analysis of non-structural carbohydrates established by host lab, transferred the technique to my home lab, and set up a productive research collaboration which resulted in two research papers.

May 2009 – Research internship: Method development for telomerase activity assay in Pinus August 2009 sylvestris buds PI: Tuija Aronen, Finnish Forestry Research Institute I devoted four months to learning and optimizing a protocol to assess telomerase activity in Scots pine using a PCR-based telomere repeat amplification protocol (TRAP). I also trained research station personnel on gel electrophoresis, protein and DNA extraction techniques.

September 2005 – Independent research, Amgen research fellowship, and senior thesis April 2009 project: Assessing effects of aging on somatic stem cell populations in Drosophila melanogaster testes PI: Matthew Wallenfang, Barnard College, Columbia University I assessed the lifespan and division rates of somatic stem cells in aging Drosophila melanogaster testes. I demonstrated that Drosophila mutants overexpressing superoxide dismutase exhibit reduced cell loss in the testis gonal region, in support of the oxidative stress theory of aging.

Teaching Experience:

March 2019 Guest Lecturer Cornell University, Ithaca, NY, USA PLSCS 4200: Geographic Information Systems (GIS): Concepts and Application Lecture title: UAV applications for remote sensing

August 2010 – Laboratory Teaching Assistant April 2015 University of Toronto Mississauga, Mississauga, ON, Canada BIO203: Introductory Plant Morphology and Physiology (course development: Fall 2014) BIO204: Introduction to Physiology (section leader: Fall 2010, 2011, 2013) BIO205: Introduction to Ecology (section leader: Summer 2012) BIO312: Plant Physiology (course development: Fall 2012; section leader: Winter 2013, 2014, 2015) BIO409: Advanced Physiology (section leader: Winter 2011, 2012)

October 2013 Guest Lecturer University of Toronto Mississauga, Mississauga, ON, Canada BIO 312: Plant Physiology Lecture title: Flowering and Senescence

November 2011 Guest Lecturer University of Toronto Mississauga, Mississauga, ON, Canada BIO 204: Introductory Physiology Lecture title: Light Stress in Plants

Journal Reviews (number of reviews)

- Tree Physiology (1) - Physiologia Plantarum (1) - Journal of Geophysical Research: Biogeosciences (2) - Remote Sensing of Environment (1)

Professional Affiliations:

- American Geophysical Union - American Society of Plant Biology - American Association for the Advancement of Science - Phi Tau Phi Scholastic Honors Society

Professional Skills: Data analysis and programming:

- Statistical analysis: Matlab, Python, R, Graphpad Prism, Microsoft Excel - Visualization: Matlab, Python, Graphpad Prism, R, TMEV, Cluster 3.0, Java Treeview, Figtree, ImageJ,

Microsoft Excel, Microsoft Powerpoint - Peptide analysis: PEAKS, Jalview - Sequence alignment: BLAST, ClustalW, MUSCLE - Computer Languages: Python, Matlab, R, C, C++, CRBasic, HTML - Tools: mySQL, BASH, Git, Vim

Plant physiology techniques: - Photosynthetic gas exchange: Walz GFS-3000, Li-Cor 6400XT - Leaf chlorophyll fluorescence: Walz Dual-PAM, Junior-PAM - Shoot freezing tolerance, assessed using chlorophyll fluorescence - Xylem water potential

Molecular and biochemistry techniques:

- HPLC and spectrophotometric analysis of photosynthetic pigments - HPLC analysis of non-structural carbohydrates - SDS-PAGE, Western blot, PCR - Confocal microscopy: Zeiss LSM 510

Mentoring: - Coordinated a team of 1 high school student, 3 graduate students and a postdoc to conduct field

campaigns including ground-based measurements and UAV flights (Summer 2019) - Led a team of 1 undergraduate student and 4 graduate students to improve designs of tower and UAV

based platforms for remote detection of SIF and reflectance using hyperspectral sensors (Fall 2018/Spring 2019)

- Trained and led a team of diverse students (1 high school student, 2 undergraduate students, and 6 graduate students to perform measurements of chlorophyll fluorescence, gas exchange, leaf water potential in crops (Summer 2017, 2018)

- Mentored 3 graduate students to develop a preliminary UAV-based platform for monitoring canopy reflectance using a hyperspectral sensor (Spring 2018)

- Trained 3 undergraduate students and 1 graduate student to perform extractions of photosynthetic pigments, carbohydrates, and proteins from conifer needle tissues (2013-2015)

- Trained 2 undergraduate students to perform measurements of chlorophyll fluorescence, leaf water potential in conifers (Fall 2013, 2014)

Project management and maintenance: - Trained and supervised 2-5 person teams in laboratory and field settings - Managed multiple concurrent projects - Provided troubleshooting and maintenance service for the lab’s computer, electronic, and mechanical

equipment (Sun, Ensminger and Wallenfang labs) - Laboratory and field management: initial setup of new lab, initial setup of field site, inventory orders,

equipment monitoring and maintenance, datalogger programming, field campaign coordination

Other Skills: I am fluent in English and conversational in French and Mandarin Chinese.

Outside of my research, I volunteered from 2006-2017 as a writer and content creator for Abandoned Realms,

an online multiplayer text-based roleplaying game. This provided me with experience in managing team projects, creative writing, providing technical support, and maintaining a positive community environment for the playerbase. In 2014, I was promoted to a coding position in which I began to create content and debug using the C programming language, as well as automating some workflow using Python scripts. Through this experience I became familiar with using Vim, Git repositories, and mySQL.

I completed three online courses, CS50x, Using Python for Research and Hidden Messages in DNA (Bioinformatics I), from October-December 2016. These courses improved my fluency in C and Python, which greatly facilitated my programming-based work (data analysis, tower and UAV development) during my postdoctoral research.

Eric S. Fabio

School of Integrative Plant Science Horticulture Section Cornell AgriTech at the New York State Agricultural Experiment Station

630 West North Street Geneva, NY 14456 Phone: 315-787-2491 Email: esf56@cornell.edu

ACADEMIC BACKGROUND:

2017 Ph.D., Horticulture, Cornell University 2006 M.S., Forestry, University of Kentucky 2000 B.S., Biology, University of South Carolina Upstate PROFESSIONAL EXPERIENCE: Aug 2017 – present

Postdoctoral Associate, Horticulture Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station. Project management for a USDA NIFA CAP grant focused on using drone imagery to assess nutritional status and pest and disease pressure in shrub willow biomass crops. (Supervisor: Dr. Larry Smart; phone: 315-787-2490; email: lbs33@cornell.edu)

Jan 2013 – Jul 2017

Graduate Research Assistant, Field of Horticulture, Cornell University, NYS Agricultural Experiment Station, Geneva, NY 14456. Research focuses on understanding the influence of soils and climate on yield, and selecting cultivars for high yield and nutrient use efficiency in Northeastern soils. (Advisor: Dr. Larry Smart; phone: 315-787-2490; email: lbs33@cornell.edu)

Mar 2010 – Dec 2012

Senior Research Support Specialist, SUNY College of Environmental Science & Forestry, Dept. Forest & Nat. Res. Management, Syracuse, NY 13210. Managed field data collection for research investigating the use of shrub willow as a dedicated bioenergy crop. Organized and analyzed large volumes of field data, operated power tools and farm equipment and ordered field and lab supplies. (Supervisor: Dr. Timothy Volk; phone: 315-470-6774; email: tavolk@esf.edu)

April 2007 – Oct 2009

Research Support Specialist I, Cornell University, Dept. Ecol. & Evol. Biology, Ithaca, NY 14853. Provided technical support for field and laboratory research investigating causes of geographic range limits. Collected demographic data on natural and experimental plant populations, reared plants in the greenhouse, maintained databases and supervised undergraduate research assistants in lab and field settings. (Supervisor: Dr. Monica Geber; phone: (607) 254-4208; email: mag9@cornell.edu)

Jan 2004 – Aug 2006

Graduate Research Assistant, University of Kentucky, Dept. of Forestry, Lexington,

KY 40503. Examined spatial variation in nitrogen cycling rates, soil solution N and decomposition rates in eastern forests, in relation to moisture regime and tree species. (Major advisor: Dr. Mary Arthur; Phone: (859) 257-2852; Email: marthur@uky.edu)

April 2003 – Sept 2003

Biological Science Technician, GS-7, National Park Service Shenandoah National Park Luray, VA 22835. Served as crew leader for a project validating a habitat map for plant species threatened by poaching (Supervisor: Wendy Cass)

Oct 2002 – Mar 2003

Biological Field Technician, Louisiana State University, Everglades National Park, Florida City, FL 33034. Sole field technician for a study characterizing the effects of fire and hurricane disturbance on south Florida slash pine (Pinus elliottii var. densa) demography. (Supervisor: Dr. Brian Beckage)

June 2002 – Sept 2002

Biological Science Technician, GS-5, U. S. Geological Survey BRD, Sequoia-Kings Canyon Research Office, Three Rivers, CA 93271. Provided field support for research comparing the effects of early- and late-season prescribed burning on fuel consumption and forest ecology. (Supervisor: Eric Knapp)

April 2001 – Oct 2001

Biological Science Technician, GS-5, National Park Service, Great Smoky Mountains National Park, Gatlinburg, TN 37738. Served as lead technician providing botanical support for a project studying the reintroduction of elk into the park. (Supervisor: Janet Rock)

June 2000 – Sept 2000 Resource Assistant, Student Conservation Association, Great Smoky Mountains National Park, Gatlinburg, TN. Worked with the park botanist to monitor 25 rare plant species comprising approximately 40 populations, occurring in a range of habitats throughout the park. (Supervisor: Janet Rock)

UNDERGRADUATE RESEARCH: Research Assistant, University of South Carolina Upstate, Spartanburg, SC 29303.Assisted in mapping the distribution of nine populations of the federally endangered plant, Sagittaria fasciculate. (Supervisor: Dr. Gillian Newberry) Independent Research Internship, University of South Carolina Upstate, Spartanburg, SC 29303. Located and mapped populations of the federally threatened plant, Hexastylis nanaflora. (Advisor: Dr. Gillian Newberry) TEACHING:

Teaching assistant, The Nature of Plants, Spring 2014, Horticulture Section, Cornell University. Teaching assistant, Forest Ecology, Fall 2005, Dept of Forestry, University of Kentucky. STUDENT MENTORSHIP: Kavya Krishnan – 2013 NEWBio Summer Research Scholar (SUNY-ESF, 2014) Carlie Leary – 2016 NEWBio Summer Research Scholar (The New School, 2019) Jeremy Feinstein – 2018 Cornell AgriTech Summer Research Scholar (Oberlin College, 2019) Jonathan Berlingeri – 2019 Cornell AgriTech Summer Research Scholar (Cornell University, 2020) PUBLICATIONS: Fabio, E.S., Leary, C.J. and Smart, L.B. (2019) Tolerance of novel inter-specific shrub willow hybrids to water stress. Trees 33 (4):1015-1026. (DOI: 10.1007/s00468-019-01835-4). Fabio, E.S. and Smart, L.B. (2018) Differential growth response to fertilization of ten elite shrub willow (Salix spp.) bioenergy cultivars. Trees, 32(4): 1061-1072 (DOI: 10.1007/s00468-018-1695-y). Fabio, E.S. and Smart, L.B. (2018) Effects of nitrogen fertilization in shrub willow short rotation coppice production – a quantitative review. GCB Bioenergy, 10(8): 548-564 (DOI: 10.1111/gcbb.12507). Volk, T.A., Berguson, B., Daly, C., Halbleib, M.D., Miller, R., Rials, T.G., Abrahamson, L.P., Buchman, D., Buford, M., Cunningham, M.W., Eisenbies, M., Fabio, E.S., Hallen, K., Heavey, J., Johnson, G.A., Kuzovkina, Y.A., Liu, B., Mcmahon, B., Rousseau, R., Shi, S., Shuren, R., Smart, L.B., Stanosz, G., Stanton, B., Stokes, B., and Wright, J. (2018) Poplar and shrub willow energy crops in the United States: field trial results from the multiyear regional feedstock partnership and yield potential maps based on the PRISM-ELM model. GCB Bioenergy, 10(2): 735-751 (DOI: 10.1111/gcbb.12498). Fabio, E.S., Volk, T.A., Miller, R.O., Serapiglia, M.J., Kuzovkina, J.A., Kling, G.J. and Smart, L.B. (2017) Contributions of environment and genotype to variation in shrub willow biomass composition. Industrial Crops and Products, 108: 149-161 (DOI: 10.1016/j.indcrop.2017.06.030). Fabio, E.S., Kemanian, A.R., Montes, F., Miller, R.O. and Smart, L.B. (2017) A mixed model approach for evaluating yield improvements in interspecific hybrids of shrub willow, a dedicated bioenergy crop. Industrial Crops and Products, 96: 57-70 (DOI: 10.1016/j.indcrop.2016.11.019). Fabio, E.S., Volk, T.A., Miller, R.O., Serapiglia, M.J., Gauch, H.G., Johnson, G.A., van Rees, K.C.J., Labrecque, M., Amichev, B.Y., Hangs, R.D., Kuzovkina, Y.A., Ewy, R.G., Kling, G.J. and Smart, L.B. (2016) Genotype by environment interactions analysis of North American shrub

willow yield trials confirms superior performance of triploid hybrids. GCB Bioenergy, 9(2): 445-459 (DOI: 10.1111/gcbb.12344). Sleight, N. J., Volk, T. A., Johnson, G. A., Eisenbies, M. H., Shi, S., Fabio, E. S., & Pooler, P. S. (2016) Change in yield between first and second rotations in willow (Salix spp.) biomass crops is strongly related to the level of first rotation yield. BioEnergy Research, 9(1), 270-287. Stoof, C.R., Richards, B.K., Woodbury, P.B., Fabio, E.S., Brumbach, A.R., Cherney, J., Das, S., Geohring, L., Hansen, J., Hornesky, J., Mayton, H., Mason, C., Ruestow, G., Smart, L.B., Volk and T.A., Steenhuis, T.S., (2015) Untapped potential: Opportunities and challenges for sustainable bioenergy production from marginal lands in the Northeast USA. Bioenergy Research 8, 482-501. Gould B., Moeller D.A., Eckhart V.M., Tiffin P., Fabio E.S., Geber M.A. (2014) Local adaptation and range boundary formation in response to complex environmental gradients across the geographical range of Clarkia xantiana ssp xantiana. Journal of Ecology, 102, 95-107. Pacaldo, R.S., Volk T.A., Briggs R.D., Abrahamson L.P., Bevilacqua E., Fabio E.S. (2014) Soil CO2 effluxes, temporal and spatial variations, and root respiration in shrub willow biomass crops fields along a 19-year chronosequence as affected by regrowth and removal treatments. GCB Bioenergy, 6, 488-498. Volk, T.A., Abrahamson, L.P., Cameron, K.D., Castellano, P., Corbin, T., Fabio, E., Johnson, G., Kuzovkina-Eischen, Y., Labrecque, M., Miller, R., Sidders, D., Smart, L.B., Staver, K., Stanosz, G.R. and Van Rees, K.C.J., (2011) Yields of willow biomass crops across a range of sites in North America. Aspects of Applied Biology 112, 67-74. Eckhart, V.M., Geber, M.A., Morris, W.F., Tiffin, P., Fabio, E.S. and Moeller, D.A. (2011) The geography of demography: Long-term demographic studies and species distribution models reveal a species border limited by adaptation. American Naturalist, 178: S26-S43. Fabio E.S., Arthur, M.A. and Rhoades, C.C. (2009) Influence of moisture regime and tree species composition on nitrogen cycling dynamics in hardwood forests of Mammoth Cave National Park, Kentucky, USA. Canadian Journal of Forest Research, 39, 330-341. PRESENTATIONS: Smart, L.B., Fabio, E.S., Kemanian, A.R., Richards, B.K., Feinstein, J., Carlson, C.H. and Montes, F. Optimizing nutrient uptake in shrub willow and switchgrass to provide multiple ecosystem services. Oral presentation given at the 2018 Mid-Atlantic Bioenergy Conference & Expo, Sept. 12-14, 2018, Philadelphia, PA, USA. Fabio, E.S. and Smart, L.B. Genetic and Environmental Effects on Variability in First-rotation Shrub Willow Bark and Wood Elemental Composition. Oral presentation given at the 2018 Woody Crops International Conference, July 23-25, 2018, Rhinelander, WI, USA.

Fabio, E.S. and Smart, L.B. Genetic and environmental effects on variability in first rotation shrub willow bark and wood elemental composition. Poster presented at the 2017 Mid-Atlantic Biomass Conference and Expo, Sept. 13, 2017, Pennsylvania State University. Fabio, E.S., Volk, T.A., Miller, R.O., Serapiglia, M.J., Kemanian, A.R., Montes, F., Hangs, R.D., Kuzovkina, J.A., Kling, G.J. and Smart, L.B. Genetic and environmental effects on variability in first rotation shrub willow biomass composition. Poster presented at the 2016 NEWBio Annual Meeting, July 27, 2016, Pennsylvania State University. Fabio, E.S., Volk, T.A., Kemanian, A.R., Montes, F., Miller, R.O. and Smart, L.B. Progress in shrub willow feedstock improvement. Research highlight presentation given at the 2016 NEWBio Annual Meeting, July 27, 2016, Pennsylvania State University. Fabio, E.S., Volk, T.A., Miller, R.O., Serapiglia, M.J., Gauch, H.G., Johnson, G.A., van Rees, K.C.J., Labrecque, M., Amichev, B.Y., Hangs, R.D., Kuzovkina, Y.A., Ewy, R.G., Kling, G.J. and Smart, L.B. Genotype by environment interactions analysis of North American shrub willow yield trials confirms superior performance of triploid hybrids. Oral presentation given to the Bioenergy Systems Community at the 2015 ASA, CSSA and SSSA International Annual Meeting, November 16, 2015, Minneapolis, MN. Fabio, E.S., Reiners, S., Ryan, M.R., and Smart, L.B. Can cover crops play a role in shrub willow establishment for weed and nutrient management? Monthly webinar series hosted by the AFRI sponsored Bioenergy CAP, NEWBio, March 10, 2015. Fabio, E.S., Gouker, F.G., Kemanian, A.R., Montes, F., Carlson, J.E., Miller, R.O, Volk, T.A., Herr, J.R., and Smart, L.B. Variation in first-year biomass growth and wood composition among 23 shrub willow genotypes across a range of environments. Poster presented at the International Poplar Symposium VI, July 21-23, 2014, Vancouver, BC. Fabio, E.S., Reiners, S., Ryan, M.R., and Smart, L.B. Sustainable shrub willow establishment using fall-seeded cover crops for weed and nutrient management. Poster presented at the 10th biennial Short Rotation Woody Crops Operations Working Group meeting, July 17-19, 2014, Seattle, WA. Fabio, E.S. and Arthur, M.A. Stand-level control of nitrogen cycling and decomposition by oak and sugar maple at Mammoth Cave National Park. Poster presented at the 90th annual meeting of the Ecological Society of America, Aug 8-12, 2005, Montreal, Canada. Fabio, E.S. and Arthur, M.A. Influence of moisture regime and species composition on nitrogen cycling at Mammoth Cave National Park, KY. Poster presented at the annual meeting of the American Society of Agronomy, Crops Science Society of America, and Soils Science Society of America, Oct 31 - Nov 4, 2004, Seattle, WA. Fabio, E.S. and Arthur, M.A. Forest stand-level control on nitrogen cycling and decomposition at Mammoth Cave National Park. Oral presentation given at the 2005 Center for Ecology,

Evolution and Behavior Research Symposium, May 12-13, 2005, Lexington, KY. EXTENSION ACTIVITIES: Factsheets: Gouker, F.E., Fabio, E.S., and Smart, L.B. (2015) Willowpedia Fact Sheet: ‘Fabius’ Salix viminalis x S. miyabeana, Cornell University, College of Agriculture and Life Sciences, Geneva, NY. Gouker, F.E., Fabio, E.S., and Smart, L.B. (2015) Willowpedia Fact Sheet: ‘Preble’ Salix viminalis x S. miyabeana, Cornell University, College of Agriculture and Life Sciences, Geneva, NY. Fabio, E.S., Frazier, L. and Smart, L.B. (2013) Field tour fact sheet. Demonstrating yield of shrub willow bioenergy crops-Big Flats, NY. Fabio, E.S., Frazier, L. and Smart, L.B. (2013) Field tour fact sheet. Demonstrating yield of shrub willow bioenergy crops-Willsboro Research Farm. Presentations: Fabio, E.S. An introduction to soils. Presentation given to the Cornell Cooperative Extensive of Onondaga County Master Gardeners, June 4, 2016, Liverpool, NY Public Library. Fabio, E.S. and Smart, L.B. Demonstrating yield of shrub willow bioenergy crops. Field tour presentation given to at the USDA-NRCS Big Flats Plant Materials Center Perennial Biofeedstock Energy Field Day, July, 31, 2013. Fabio, E.S. and Smart, L.B. Demonstrating yield of shrub willow bioenergy crops. Field tour presentation given to at the Willsboro Research Farm Field Day, July 10, 2013. HONORS AND AWARDS: Barbara McClintock Graduate Student Award, Cornell University, 2017 First place, graduate student poster competition, NEWBio CAP Annual Meeting, The Pennsylvania State University, July 28, 2016 NEWBio Graduate Distance Education Scholarship, Fall 2013, Spring 2014

Outstanding Biology Major Award, University of South Carolina Spartanburg, 2000 South Carolina Life Scholarship, 1997-2000

USCS Quality Scholarship, 1997-2000

Joseph Gage175 Biotechnology Building, Cornell University

Phone: 860–455–8435; email: joseph.l.gage@gmail.com

Employment

2020- NSF Postdoctoral Research Fellow Cornell University2018-2020 Postdoctoral Researcher USDA-ARS, Ithaca, NY

Education

2018 PhD, Plant Breeding and Plant Genetics, University of Wisconsin – MadisonMS, Biometry, University of Wisconsin – Madison

2011 BS, Plant Sciences, Cornell UniversityBS, Communcations, Cornell University

Publications

Sumbitted for Review

• Gage, J., E. Richards, N. Lepak, N. Kaczmar, C. Soman, G. Chowdhary, M.A. Gore, E.S. Buckler.“In-field whole plant maize architecture characterized by Latent Space Phenotyping.” Submitted July2019. https://www.biorxiv.org/content/10.1101/763342v1

In Print

2019 • Gage, J., B. Vaillancourt, J. Hamilton, N. Manrique-Carpintero, T. Gustafson, K. Barry, A.Lipzen, W. Tracy, S. Kaeppler, C.R. Buell, N. de Leon. “Multiple maize reference genomes im-pact the identification of variants by GWAS in a diverse inbred panel.” The Plant Genome, doi:10.3835/plantgenome2018.09.0069. Chosen as the featured article for the July 2019 issue.

• Marand, A., S. Jansky, J. Gage, A. Hamernik, N. de Leon, J. Jiang. “Residual heterozygosity andepistatic interactions underlie the complex genetic architecture of yield in diploid potato.” Genetics.doi: 10.1534/genetics.119.302036

• Mazaheri, M., M. Heckwolf, B. Vaillancourt, J. Gage, B. Burdo, S. Heckwolf, K. Barry, A. Lipzen, C.B.Ribeiro, T. Kono, H. Kaeppler, E. Spalding, C. Hirsch, C.R. Buell, N. de Leon, S. Kaeppler. “Genome-wide association analysis of stalk biomass and anatomical traits in maize.” BMC Plant Biology. doi:10.1186/s12870-019-1653-x

2018 • Gage, J.L., N. de Leon, M. Clayton. “Comparing genome-wide association study results from differentmeasurements of an underlying phenotype.” G3. doi: 10.1534/g3.118.200700

• Gage, J.L., M.R. White, J. Edwards, S. Kaeppler, N. de Leon.“Selection signatures underlyingdramatic male inflorescence transformation during modern hybrid maize breeding.” Genetics. doi:10.1534/genetics.118.301487

2017 • Gage, J.L., D. Jarquin, M.C. Romay, A. Lorenz, E.S. Buckler, S. Kaeppler, N. Alkhalifah, M. Bohn,D. Campbell, J. Edwards, D. Ertl, S. Flint-Garcia, J. Gardiner, B. Good, C. Hirsch, J. Holland, D.Hooker, J. Knoll, J. Kolkman, G. Kruger, N. Lauter, C. Lawrence-Dill, E. Lee, J. Lynch, S. Murray,R. Nelson, J. Petzoldt, T. Rocheford, J. Schnable, P. Schnable, B. Scully, M. Smith, N. Springer, S.Srinivasan, R. Walton, T. Weldekidan, R. Wisser, W. Xu, J. Yu, N. de Leon. “The effect of artificialselection on phenotypic plasticity in maize.” Nature Communications. doi: 10.1038/s41467-017-01450-2

• Gage, J.L., N. Miller, E. Spalding, S. Kaeppler, N. de Leon. “TIPS: a system for automated image-based phenotyping of maize tassels”. Plant Methods. doi: 10.1186/s13007-017-0172-8.

Publications (continued)

2013 • Spindel J, M. Wright, C. Chen, J. Gage, S. Harrington, M. Lorieux, N. Ahmadi, S. McCouch. “Bridg-ing the genotype gap: using genotyping by sequencing (GBS) to add high-density SNP markers andnew value to traditional bi-parental mapping and breeding populations.” Theor Appl Genet. doi:10.1007/s00122-013-2166-x.

Patents

2017 • Gage, D.J., L.M. Shor, J. Gage, J.L. Micciulla, R.L. Rubenstein. “Microbial carriers for targeteddelivery of agricultural payloads.” US Patent 9,603,368. 2017.

Talks

2019 • In-field whole plant architecture characterized by scalable, affordable robots. Corn Breeding ResearchMeeting. St. Louis, MO March 14, 2019.

2018 • TIPS: A System for Automated Image-Based Phenotyping of Maize Tassels. CyVerse - Software, Tools,and Services for Data-Driven Discovery Workshop, Plant and Animal Genome XXVI Conference. SanDiego, CA January 15, 2018.

2017 • Mapping variants associated with phenotypic stability in maize. Gordon Research Seminar. Galveston,TX February 26, 2017.

2016 • Genomic Prediction Within and Between Subpopulations of the USA National Maize Inbred Collection.Corn Breeding Research Meeting. Jacksonville, FL March 16, 2016.

2015 • Genome-Wide Association Analysis of Tassel Size and Branch Number in the Wisconsin Diverse Asso-ciation Panel. Corn Breeding Research Meeting, St. Charles, IL March 11, 2015.

Service

Outreach

2019 Showcased robotic phenotyping on local news WSYR (https://youtu.be/o6vKlVMBv14).Delivered guest lecture about robotic phenotyping to undergraduate Digital Agriculture class.

Teaching Assistant: University of Wisconsin – Madison

2017 Agronomy 772 – Advanced Applications in ANOVAAgronomy 811 – Biometric Procedures in Plant Breeding

2016 Agronomy 875 – Selection Theory for Quantitative Traits in Plants2015 Agronomy 811 – Biometric Procedures in Plant Breeding

Statistical Consultant

2018 Statistical Consulting Lab at the University of Wisconsin – Madison

Community Involvement

2019 Discussion Leader for Gordon Research Seminar in Quantitative Genetics and Genomics

Peer Review

Reviewed for Nature Biotechnology, Heredity, The Plant Genome, Crop Science, Field Crops Research, BioEnergyResearch, Molecular Genetics and Genomics.

Awards & Achievements

2019 Awarded NSF Postdoctoral Research Fellowship in Biology2017 Selected to talk at the Gordon Research Seminar in Quantitative Genetics and Genomics

Awards & Achievements (continued)

G.O. Mott Meritorious Graduate Student Award2016 O.N. Allen Graduate Scholarship

Scholarship to attend the Summer Institute in Statistical Genetics at the University of WashingtonG.O. Mott Meritorious Graduate Student Award

2015 Irwin Smith Wisconsin Distinguished Graduate FellowshipRoyce Bringhurst Memorial ScholarshipLarry Darrah Award for Best Student Research PresentationVice President, Plant Sciences Graduate Student Council, University of Wisconsin

2012 Intern at DuPont Pioneer, Johnston IA2009-2011 Dean’s List – Cornell University

Perialis Prize for Persuasive Oratory

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Anju Giri Postdoctoral researcher, Buckler lab Institute of Genomics Diversity Cornell University ag2484@cornell.edu 443-240-7125 I am a plant scientist with a training on plant genetics, physiology, and breeding. I am interested in working to make agricultural sustainable and maximize crop performance with the expertise I have gained over the years. I am always looking for the opportunity to learn addition new skill while honing the existing skill I own. Education: Ph. D: Agronomy (Plant Breeding and Genetics), Kansas State University, Kansas (2015- 2019)

Dissertation: Wheat Improvement for Heat and Drought Stress Tolerance M.S: Biology, The University of Toledo, Ohio (Jan 2012-Dec 2013)

Thesis: Effect of heat stress on nutrient uptake by tomato roots B.S: Agriculture, Institute of Agriculture and Animal Science, Tribhuvan University, Nepal (Oct 2006-Dec 2010)

Publications: Giri A., Fritz A. (2019). Heat tolerance screening of Triticum turgidum ssp. Dicoccoides. Crop

Science (manuscript in preparation).

Giri A., Fritz A., Jagadish SVK., & Poland J (2019). Selection for Water Soluble Carbohydrates

in diverse breeding population in bread wheat (manuscript in preparation)

Giri, A., Heckathorn, S., Mishra, S., & Krause, C. (2017). Heat Stress Decreases Levels of

Nutrient-Uptake and-Assimilation Proteins in Tomato Roots. Plants, 6(1), 6.

Lamsal, A., Welch, S.M., Jones, J.W., Boote, K.J., Asebedo, A., Crain, J., Wang, X., Boyer, W.,

Giri, A., Frink, E. and Xu, X. (2017). Efficient crop model parameter estimation and site

characterization using large breeding trial data sets. Agricultural Systems, 157, 170-184.

Giri, A., Armstrong, B. and Rajashekar, C. (2016) Elevated Carbon Dioxide Level Suppresses

Nutritional Quality of Lettuce and Spinach. American Journal of Plant Sciences, 7(1),

246-258.

Rajashekar, C., Fu, J. and Giri, A. (2014) Exogenous Vitamin K3 and Peroxides Can Alleviate

Hypoxia in Bean Seedlings (Phaseolus vulgaris L.). American Journal of Plant Sciences,

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5 (22), 3396-3407.

Lamsal A., Amgain LP., Giri A. 2013. Modeling the Sensitivity of CERES-Rice Model: An

Experience of Nepal, Agronomy Journal of Nepal, 3:11-22.

Heckathorn, S. A., Giri, A., Mishra, S., & Bista, D. (2013). Heat stress and roots. Climate change and plant abiotic stress tolerance, 109-136.

Presentation on Scientific Meetings: Giri A, Aiken RM, Dowell F, Fritz A, Jagadish SVK, and Poland J. Water-soluble carbohydrate accumulation in the wheat stem in relation to yield and yield components. CORTEVA Plant Center Spring Symposium, University of Georgia, 2018 (oral) Giri A, Aiken RM, Dowell F, Fritz A, Jagadish SVK, and Poland J. Analysis of water-soluble carbohydrates accumulation in wheat stem using NIR Spectroscopy. American Society of Agronomy (ASA), Crop Science Society of America (CSSA), Soil Science Society of America (SSSA), Tampa, Florida, 2017 (oral). Giri A and Fritz, A. Screening of Triticum turgidum ssp. Dicoccoides (Wild emmer wheat) for post anthesis heat tolerance. ASA, CSSA, SSA, Tampa, Florida, 2017 (poster). Giri A, Aiken RM, Dowell F, Fritz A, Jagadish SVK, and Poland J. Analysis of water-soluble carbohydrates accumulation in wheat stem using NIR Spectroscopy. National Association of Plant Breeders (NAPB) annual meeting, Davis, California, 2017 (poster). Giri A, Fritz A, Aiken RM, Poland J, Jagadish SVK, and Wang Xu. Selection of Drought Tolerant Wheat Under Water-Limited Condition Using High Throughput-Phenotyping Platform. ASA, CSSA, SSA, Phoenix, Arizona, 2016 (poster). Giri A and Rajashekar CB. Elevated Carbon dioxide decreases mineral nutrient composition in lettuce and spinach. Kansas State Research Forum, Kansas State University, Kansas, 2015 (oral). Giri A, Heckathorn SA, and Mishra S. Effect of abrupt heat stress and recovery on nutrient transporter protein efficiency in tomato roots. Botanical Society of America Conference, New Orleans, Louisiana, 2013 (Oral). Giri A, Mishra S, and Heckathorn SA. Effects of abrupt heat stress on nutrient uptake by plant roots. Ohio Plant Biotechnology Consortium, Columbus, Ohio, 2013 (Poster). Giri A, Heckathorn, SA. Effects of acute and chronic heat stress on nutrient uptake protein at different levels of Nitrogen. Ohio Plant Biotechnology Consortium, Toledo, Ohio, 2013 (Oral). Giri A, Mishra S, Heckathorn SA. 2013. Effect of acute heat stress in nutrient uptake by plant roots. Midwest Graduate Research Symposium, Toledo, Ohio, 2013 (Poster).

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Frantz J, Heckathorn SA, Mishra S, and Giri A. 2012. Characterizing the physiological response of tomato to phosphorus deficiency and recovery. American Society of Horticultural Sciences Conference, Miami, Florida, 2012 (Poster). Scholarship, Awards, and Achievements:

• CORTEVA Plant Center Spring Symposium, University of Georgia Student Travel Scholarship (2018)

• Future Leaders in Science Award, American Society of Agronomy (2018) • Prestigious travel award, graduate school Kansas State University (2017) • Crop Science Society of America Graduate Student Scholarship (2017) • Nunemacher scholarship, Kansas State University (2017) • Top 8 finalist in 3-MT (3-Minutes Thesis Competition), Kansas State University (2017) • First position, International Student talent show, Kansas State University (2017) • Kansas State Research and Extension Team award as a member of Western Kansas UAS

and Canopy Imaging Team (2016) • Second Position Elevator Speech Contest for graduate students and postdocs, ASA,

CSSA, SSA, Phoenix, AZ (2016) • Don. C Warren Genetics Scholarship, Kansas State University (2016) • International Student Scholarship, K-State Alumni (2016) • Ruby New Hall Memorial Scholarship, Pilot International (2015) • Tribhuvan University (Nepal) Merit Scholarship for B.SC. Ag entrance (2007) • The honor of “certificate of excellence” in my intermediate level of study (2004-2006) • Scholarship award during my two years of high school (1993-2003)

Professional membership:

• National Association of Plant Breeders (2016-Present) • American Society of Agronomy (2016-Present) • Crop Science Society of America (2016-Present) • Soil Science Society of America (2016- Present) • Graduate Student Association, Kansas State University, Kansas (2014-2019) • Nepalese Student Association, Manhattan, Kansas (2014-2019) • Botanical Society of America (2012-2014) • Graduate Student Association, University of Toledo, Ohio (2012-2013) • Nepalese Student Association, Toledo, Ohio (2012-2013)

Workshop: • Cereal Genomics Workshop, Cold Spring Harbor Laboratory, NY (October 2019) • Graduate Student Leadership Workshop ASA, CSSA, SSSA, Tampa, Fl (October 2018) • Gene Expression Analysis (RNA-Seq) Workshop, Integrated Genomics Facility, Kansas

State University, Kansas (June 2014)

Volunteering and Leadership activities: • Treasurer: Agronomy Graduate Student Association (AGSA) 2017- 2018

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• Organizing committee member: Nepal Night, 2016 and 2018, • Treasurer: Nepalese Student Association (NSA) (2014-2015) • Speaker: International Student Coffee hour series organized by International Student and

Scholar Services (ISSS) (Spring 2015) • Volunteer: International Student and Scholar Services (ISSS) welcome program (Fall,

2014) • Judge: High school Poster Presentation, Lake Erie Center, The University of Toledo,

Ohio (May 2013) • Volunteer: Botanical Society of America Annual Meeting, Columbus, Ohio (July 2012) • Volunteer: Midwest Graduate Research Symposium, The University of Toledo, Ohio

(April 2012) • Volunteer: Syangja Youth Club, Nepal to collect and distribute clothes and food to needy

and poor people of the western developmental region, Nepal (2004-2006) Teaching Experiences:

• Teaching assistant in Plant Propagation, Kansas State University, Kansas (2015-Spring semester)

• Teaching assistant in Introductory Horticulture, Kansas State University, Kansas (2014-Fall semester)

• Teaching assistant in Botany course, University of Toledo, Ohio (2013-Spring semester) • Teaching assistant in Environmental Problems Lab, University of Toledo, Ohio (2012-

Fall semester) • High school teacher in Syangja Higher Secondary School, Syangja, Nepal (2010-2011) • Lectured junior agriculture technician in Kantipur Medical School, Chitwan, Nepal

(2007-2010)

Research Experiences: • Research assistant, Department of Agronomy, Kansas State University, Kansas (Aug

2015-present) • Research assistant, Department of Horticulture, Forestry and Recreation Resources,

Kansas State University, Kansas (Jan 2014- May 2015) • Research assistant, Department of Environmental Science, The University of Toledo,

Ohio (Jan 2012-Dec 2013) • Assisted on USDA research project “Characterizing the Physiological Response of

Tomato to Phosphorus Deficiency and Recovery” (summer, 2012) • Research associate, Nepal Agricultural Research Council (NARC) in Department of

Horticulture, Nepal (2010) • Completed group research on Integrated Pest Management (IPM) in Rampur, Nepal

(2009)

Computer Skills: • Experience in programming/coding with R, Python, Linux • Capable of using different statistical and remote sensing software SAS, SigmaPlot,

ArcGIS, TASSEL 4, TASSEL 5, QGIS, and Microsoft Office • Experience working with Linux, Docker, Git, and APIs

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References: Dr. Edward Buckler Research Geneticist USDA-ARS Adjunct Professor Cornell University 159 Biotechnology Building Ithaca, NY 14853 Phone: 607-255-4520 ed.buckler@ars.usda.gov esb33@cornell.edu

Dr. Allan K. Fritz Professor Department of Agronomy 4012 Throckmorton PSC Kansas State University Manhattan, KS 66506 Phone: 785-532-7245 Fax: 785-532-6094 akf@ksu.edu

Dr. Jesse Poland Associate Professor Department of Plant Pathology 4702 Throckmorton PSC Kansas State University Manhattan, KS 66506 Phone: 785-532-2709 Fax: 785-532-5692 jpoland@ksu.edu

Dr. Scott A. Heckathorn Professor Department of Environmental Sciences University of Toledo, 2801 W Bancroft Street, MS 604 Toledo, OH 43606 Phone: 419 530 4328 scott.heckathorn@utoledo.edu

Mayank Kaashyap 2250 N. Triphammer Road, Lansing West Apt P1B, Ithaca 14850. NY, USA. Mobile: +1(607)-279-4394 Email: mayankkaashyap@gmail.com Career objective To apply my creative energy and strong research potential in a scientist position at a fast-evolving research industry, utilizing my tertiary knowledge and demonstrated history in research together with skills in Genomics, organization and teamwork. Area of Expertise Next-Generation Sequencing, Functional Genomics, Molecular Biology, Computational Biology, Molecular Genetics and High-throughput techniques.

Teaching Experience: Semester Mar to June 2018 Casual Academic Teacher at RMIT University, Australia. Lecturing Plant Tissue Culture – Micropropagation. Research Experience: August 2018 – to date Postdoctoral Associate Rose lab, Cornell University, USA Responsibilities:

• Study global cell-type specific gene atlas to identify conserved molecular systems and gene duplication events.

• Study the role of cutin and pectin genes in cell wall modification in response to drought in fruits.

• Write grant proposal. • Review manuscripts submitted to Plant Physiology.

Achievements: • Successfully generated RNA-seq data from specific leaf cell-types. • Developed interpersonal, communication and networking skills. • Training on proteome studies.

Feb 2014 - Dec 2017 PhD Student RMIT University, Australia Responsibilities:

• To grow the plants in greenhouse and record physiological parameters in response to salt stress.

• RNA isolation, RNA-Sequencing library preparation and perform deep sequencing on Ion-proton (Life Technologies) and HiSeq3000 (Illumina, Inc).

• Analyze the transcriptomic data to identify the differentially expressed genes in flowers and roots using bioinformatics tools.

• Develop ab initio transcriptome assembly and identify the long noncoding RNA and their potential role in regulating the gene expression.

• Study phenomenon like Alternative splicing, Motif identification, Variant calling, and Gene network.

• Perform qRT-PCR analysis to validate the gene expression.

• Study the ion-compartmentalization using Transmission Electron Microscope (TEM)

(JEOL1010, JEOL2100) and Scanning Electron Microscope (SEM)-EDX. • Writing project reports and research articles.

Achievements: • Identified 5022 differentially expressed genes regulating cell wall morphogenesis during

the root development in response to the salt stress. • Identified 7000 long noncoding RNA and their putative functions in gene expression. • Published research articles. • Accorded with 3MT thesis winner 2015.

Oct 2010 – May 2013 Research Fellow International Crops Research Institute for Semi-Arid Tropics (ICRISAT), India and University of California – Davis, USA Responsibilities:

• To grow the plants in fields and record physiological parameters in response to drought and nitrogen fixation across the evolutionary gradient of Cicer arietinum.

• Study the flowering C-locus mutation, SNP genotyping, hairy root transformation, identify nif candidate genes, analyzing marker genotypic data for genetic mapping, QTL analysis, and gene expression analysis.

• Isolate and inoculate Mesorhizobium strain from nodules, inoculate the plants with strain to study impact of domestication on nitrogen fixation efficiency, and metagenomics study of Mesorhizobium strains.

• Writing reports, articles and discussing the project briefings. • Attend International delegates, involved in organizing conferences and meetings, and

teamwork. • Achievements: • Successfully conducted multi-location trials of chickpea in India and at UC-Davis. • Established phylogeny among the potential Mesorhizobium strains involved in nitrogen

fixation. • Successfully established the hairy root protocol in chickpea.

Feb 2006 – Sep 2010 Research Associate Indian Institute of Pulses Research, India Responsibilities:

• Growing and phenotyping 196 Recombinant Inbred Lines (RILs) for Fusarium wilt resistance.

• DNA/RNA isolation, PCR, qPCR, cDNA synthesis, cDNA library, EST-SSR development, mapping Fusarium wilt resistance.

• Study marker conservation across the species, parental polymorphism, genetic diversity, allele detection, and SNP detection deploying RAPD, SSR, ISSR molecular markers.

• Isolation and cloning of Protease Inhibitor gene in chickpea. • Help and train Master of Science students. • Write the project reports, research articles, review the research articles and students

dissertation reports and any other job given by my supervisor. Achievements:

• Established marker conservation across the genera in chickpea. • Development SSR in chickpea to overcome molecular marker paucity.

• Established working protocols like DNA/RNA isolation, cloning, PCRs and NTSYS software for the first time in the laboratory.

• Proved to be an efficient troubleshooter, writer, reviewer, team mate and team leader.

Education

• Feb 2014 to Dec 2017 PhD (Applied biology and biotechnology) RMIT University, Melbourne, Australia.

• July 2003 to June 2005 MSc (Biotechnology) Jiwaji University, India.

• July 2000 to June 2003 BSc (Biotechnology) Jiwaji University, India.

• April 1997 to Mar 1999 10+2 ISC Board, India.

• April 1996 to Mar 1997 10th ICSE Board, India.

Publication(s): 15 peer reviewed research articles Social website link(s): https://www.linkedin.com/in/mayank-kaashyap-4b499421/ https://www.facebook.com/mayank.kaashyap

Referees Prof. Jocelyn Rose Cornell University, NY, USA jr286@cornell.edu Contact: (+1) 607-2554781 Prof. Nitin Mantri RMIT University, Melbourne nitin.mantri@rmit.edu.au Contact: +61 3 9925 7152 Prof. Eddie Pang RMIT University, Melbourne, eddie.pang@rmit.edu.au Contact: +61 3 9925 7137

Prof. Rebecca Ford Griffith University, Brisbane Rebecca.Ford@griffith.edu.au Contact: +61- 413585439 Dr. Rajeev Varshney ICRISAT, India r.k.varshney@cgiar.org Contact:+91 40 3071 3305

Dr. Subhojit Datta IIPR, India subhojit@email.com Contact: +91-9415478829

PUBLICATION HIGHLIGHTS

Journal Publications

2019

Abhishek Bohra,……, Mayank Kaashyap, et al. Genomic Interventions to Improve Resilience of Pigeonpea in Changing Climate. Genomic Designing of Climate-Smart Pulse Crops. Springer Nature Switzerland AG 2019. C. Kole (ed.),Genomic Designing of Climate-Smart Pulse Crops. 107-134. 978-3-319-96931-2.

2018

Mayank Kaashyap, Rebecca Ford, Himabindu Kudapa, Mukesh Jain, Dave Edwards, Rajeev Varshney, Nitin Mantri. Differential regulation of genes involved in root morphogenesis and cell wall modification is associated with salinity tolerance in chickpea. Scientific Reports 8, 4855. doi:10.1038/s41598-018-23116-9.

2017

Mayank Kaashyap, Rebecca Ford, Abhishek Bohra and Nitin Mantri. Improving Salt Tolerance of Chickpea using Modern Genomics Tools and Molecular Breeding. Current Genomics, 18(6): 557-567. doi: 10.2174/1389202918666170705155252.

A. Bohra, S. Pareek, R. Jha, R. K. Saxena, I. P. Singh, G. Pandey, R. K. Mishra, F. Singh, M. Kaashyap, R. Joshi, Rajeev K. Varshney. 2017. Modern genomic tools for pigeonpea improvement: Status and Prospects. Book: The Pigeonpea Genome. Editors: Rachit Saxena, Scott Jackson and Rajeev Varshney. Book series: Compendium of plant genomes. Publisher: Springer.

2016 Datta S, Gupta P, Kaashyap M, Kumar S. Genetic Diversity Analysis of Lentil (Lens culinaris Medik) Cultivars Using

Inter Simple Sequence Repeats Markers. Molecular Plant Breeding, 2016: 7(23). doi: 10.5376/mpb.2016.07.0023 2015 Datta S, M. Kaashyap, P. Gupta: Development of EST derived microsatellite markers in chickpea and their validation in

diversity analysis. Indian Journal of Biotechnology 01/2015; 14(1).

Lal N., Datta J., Kaashyap M., Gupta P.P.: Efficiency of three PCR-based marker systems for detecting DNA polymorphism in Cicer arietinum L. and Cajanus cajan L. Millspaugh. Genetic Engineering and Biotechnology Journal 08/2015; 5.

Saini M, P. Nandeesha, Mayank Kaashyap, Prasoonpal Gupta, Mukesh Mohan, Subhojit Datta: Cloning and characterization of protease inhibitor genes from some legumes. Legume Research 04/2015; 38(2). doi:10.5958/0976-0571.2015.00079.X

2014 Kim DH, M. Kaashyap, A Rathore, RR Das, S Parupalli, HD Upadhyaya, S Gopalakrishnan, PM Gaur, Sarvjeet Singh, J

Kaur, M Yasin, RK Varshney: Phylogenetic diversity of Mesorhizobium in chickpea. Journal of Biosciences 06/2014; 39(3).

DEVI R a, P. NANDEESHA a, M. KAASHYAPa, S. KUMARa, S. DATTA: Phylogenetic Analysis of Pulse Crops using RAPD and Seed Storage Protein Markers. Indian Journal of Agricultural Biochemistry 01/2014; 27(1).

2013 Md. Shamim, A Singh, M Kaashyap, R. P. Saxena, Deepti Srivastava, Pramila Pandey, N. A. Khan, K. N. Singh: The basis

of nonhost resistance for future genetic engineering to find out durable resistance in agricultural crops. African journal of microbiology research 06/2013; 7(40). DOI:10.5897/AJMR12.1729.

2012

Datta S, M. Kaashyap, P. Singh, P. Gupta, T. Anjum K., S. Mahfooz, Sanjeev Gupta: Conservation of microsatellite regions across legume genera enhances marker repertoire and genetic diversity study in Phaseolus genotypes. Plant Breeding 04/2012; 131(2). DOI:10.1111/j.1439-0523.2011.01892.x

Patil P, S Datta, I P Singh, A Das, K R Soren, M Kaashyap, A K Choudhary, S K Chaturvedi, N Nadarajan: Phylogenetic analysis of pigeonpea (Cajanus cajan) genotypes using Panzee retrotransposon-based SSAP markers. Indian Journal of Agricultural Sciences 07/2012; 82(12).

Datta S, S Gangwar, S Kumar, S Gupta, R Rai, M Kaashyap, P Singh, Chaturvedi SK, Singh BB, Nagaswamy Nadarajan: Genetic Diversity in Selected Indian Mungbean [ Vigna radiata (L.) Wilczek] Cultivars Using RAPD Markers. American Journal of Plant Sciences 01/2012; 3(08). DOI:10.4236/ajps.2012.38130.

2010

Datta S, S. Tiwari, M. Kaashyap, Prasoon P. Gupta, Choudhary PR, Jyoti Kumari, Shiv Kumar: Genetic similarity analysis of lentil (Lens culinaris Medik. Subsp. Culinaris) using cross genera legume STMS markers. Crop Science 01/2011; 51(6). DOI:10.2135/cropsci2010.12.0743.

2009 S. Datta, M. Kaashyap, S. Kumar: Amplification of chickpea-specific STMS primers in Cajanus species and their validity

in diversity analysis. Plant Breeding 06/2009; 129(3). DOI:10.1111/j.1439-0523.2009.01678.x.

2007

Datta S, Rai R, Tiwari K, Kashyap M, Hena, Kumar S: Phylogenetic analysis of pulse crops using RAPD markers. Indian Journal Of Food Legumes. 2007; 20(9).

Conference Proceedings

2014

Alex Greenspan, Dong Hyun Kim, Peter Chang, Aamir W. Khan, Emily M. Bergmann, Vanessa Sanchez, Lisa Vance, Klara Scharnagl, Mayank Kaashyap, Mohammad Yasin, Jagmeet Kaur, Sarvjeet Singh, Hari D. Upadhyaya, Pooran M. Gaur, R. Varma Penmetsa, Eric von Wettberg, Rajeev Varshney, Douglas R. Cook: The Impact of Domestication on Nitrogen Fixation in Chickpea: Parallel Shifts in Bacterial Genome Structure and Host Selectivity. International Plant and Animal Genome Conference XXII 2014; 01/2014.

2013

Dong Hyun Kim, Mayank Kaashyap, Alex Greenspan, R. Varma Penmetsa, Eric von Wettberg, Pooran M. Gaur, Abhishek Rathore, Hari D. Upadhyaya, Roma R. Das, Aamir W. Khan, Sarvjeet Singh, Jagmeet Kaur, Mohammad Yasin, Douglas R. Cook, Rajeev Varshney: Analysis of Rhizobium Haplotypes Based on Whole Genome Sequences and Relationship with Chickpea Phenotypes. International Plant and Animal Genome Conference XXI 2013; 01/2013.

2012

DH Kim, M Kashyap, A Greenspan, RV Penmetsa, E von Wettberg, PM Gaur, A Rathore, HD Upadhyaya, RR Das, S Singh, J Kaur, M Yasin, DR Cook, RK Varshney: Examination of relationship of Rhizobium sequences and chickpea traits for efficient nitrogen fixation. VI International Conference on Legume Genetics and Genomics’ (ICLGG), October 2-7, 2012, Hyderabad, India, Hyderabad, India; 10/2012.

Penmetsa RV, Carrasquilla - Garcia N, Bergmann EM, Vance LC, Castro BM, Dubey A, Gujaria N, Sarma BK, Kassa MT, Kaashyap M, Gaur PM, Datta S, Baek JM, Woodward JE, Farmer AD, Coyne CJ, Wettberg EJB, Varshney RK, Cook DR: Multi - locus molecular phylogeny and allelic variation in a transcription factor gene suggest the multiple independent origins of kabuli chickpea - locus molecular phylogeny and allelic variation in a transcription factor gene suggest the multiple independent origins of kabuli chickpea. VI ICLGG 2012; 10/2012.

2011

PR Varma, DH Kim, E Wettberg, M Kassa, N Carrasquilla-Garcia, E Bergmann, PM Gaur, M Kaashyap, HD Upadhyaya, Sarvjeet Singh, Y Mohammad, RK Varshney, DR Cook: Overcoming the Domestication Bottleneck for Symbiotic Nitrogen Fixation in Legumes. 2nd Annual NSF-BREAD Meeting, July 13-15, 2011, Seattle, USA., Seattle, USA.; 07/2011

RATHINA KUMAR SHANMUGA KANI

College of Human Ecology

Cornell University, Ithaca – 14853

New York, USA

E-mail: rs876@cornell.edu; Mobile: +1-6072162194

rathinabiotech@gmail.com

EDUCATION

Ph.D., Medical Science: Osaka University, Japan (2014-2018)

M.Tech., Biotechnology (First Class): VIT University, India (2010-2012)

B.Tech., Biotechnology (First Class with Distinction): Anna University, India (2006-2010)

RESEARCH EXPERIENCE

2018-present: Postdoctoral Associate, Cornell University, USA

➢ Isothermal amplification-based rapid diagnostics for MDR-TB

➢ Development of a point of care and sample sparing technique for assessing the

functionality of immune cells

2014-2018: Graduate Researcher, Osaka University, Japan

➢ Development of rapid diagnostics for MDROs (CRE, VRE, MRSA, MDRAB) directly

in clinical specimens

➢ Application of monoclonal antibodies for inhibiting drug resistance in vivo

➢ Genomic characterization of colistin- and carbapenem-resistant Enterobacteriaceae

➢ Molecular analysis of new carbapenemase variants

2012-2013: Junior Research Fellow, SRM Research Institute, India

➢ Role of SUMOylation in the molecular pathways of diabetes

2012 (Jan-Jun): Graduate Researcher (Semester Abroad Program), Tuscia University, Italy

➢ In vitro and in vivo evaluation of chemopreventive activity of functional foods on

carcinogen-induced DNA damage

2010-2012: Graduate Researcher, VIT University, India

➢ Universal primer designing for the detection of Shigella sp. ➢ Understanding bacterial adherence using salt aggregation test and hemagglutination assay ➢ Genetic polymorphisms in catfish

2009-2010: Graduate Researcher, Arulmigu Kalasalingam College of Engineering, India

➢ Epitope driven vaccine for Ebola virus: Computational prediction of Ebola CTL epitopes ➢ Bacteriophage as therapeutic agents for salmonellosis in poultry

PRODUCT DEVELOPMENT

➢ GeneFields®CPE (Kurabo Industries Ltd., Japan): Nucleic acid chromatography

diagnostic kit for rapid detection of carbapenemase genes directly from clinical

specimens

GRANTS AND AWARDS

➢ Grant-in-Aid for Education and Research

(Osaka University, Japan, FY 2017-18)

➢ Internship Abroad Grant, intern at Ramathibodi Hospital, Thailand

(IPBS, Osaka University, Japan, Jan-Feb 2018)

➢ APSIC Travel Award for the presentation of best abstract

(The 8th International APSIC Congress, Thailand, Feb 2017)

➢ Internship Abroad Grant, intern at Ramathibodi Hospital, Thailand

(IPBS, Osaka University, Japan, Jan-Feb 2017)

➢ Ph.D. stipend

(IPBS, Osaka University, Japan, 2014-2018)

➢ Semester Abroad Program Grant, Master’s thesis project at Tuscia University, Italy

(VIT University, India, Jan-Jun 2012)

TECHNICAL SKILLS

➢ Microbiology

• Bacterial cell culturing/identification, phenotypic/genotypic characterization, AST

• Clinical data analysis

➢ Molecular Biology

• Plasmid and genomic DNA isolation, conjugation

• PFGE, southern blotting

➢ Genomics/Genetic Engineering

• Whole genome sequencing

• Molecular cloning, RT-PCR

• Protein expression/purification – HPLC, SDS-PAGE, western blotting

➢ Molecular diagnostics

• PCR-based dipstick/lateral flow tests

• Isothermal amplification techniques - LAMP, HDA

➢ Immunology

• Hybridoma technology, ELISA, MAb purification

• Immunoelectrophoresis, immunodiffusion, hemagglutination

➢ Imaging

• Confocal microscopy

➢ Genetic Toxicology

• In vitro chromosomal aberration test

• DNA damage assays – comet assay, micronucleus assay (in vitro/in vivo)

➢ Bioinformatics

• Whole genome sequencing data analysis

• Epitope mapping

➢ Animal model handling

• Mice, rat

TRAININGS/COURSES/WORKSHOPS

➢ Interdisciplinary Program for Biomedical Sciences, Osaka University, Japan, 2014-

2018

➢ ESCMID Postgraduate Education Course on “Principles of Molecular

Microbiological Diagnostics”, The Netherlands, Jan 2018

➢ Training on “Next-Generation Sequencing”, Osaka University, Japan, Nov 2016

➢ Training on “NGS and Bioinformatics analysis of plasmids carrying carbapenemase

genes”, National Institute of Infectious Diseases, Japan, Aug–Sep 2015

➢ Post Graduate Diploma in Nanobiotechnology, Life Science Foundation of India,

India, Jan 2009-Jan 2010

➢ Workshop on “Nanoscience and Technology”, Kamaraj College of Engineering and

Technology, India, Mar 2009

➢ Summer training on “Bioinformatics”, Loyola Institute of Vocational Education, India,

May 2008

CONFERENCE PRESENTATIONS

➢ International: oral - 3; poster - 6

(including ECCMID, IDWeek, APSIC Congress)

➢ National: oral - 5; poster - 4

INVITED TALKS

➢ Lecture on “A new rapid detection technique for carbapenem-resistant

Enterobacteriaceae in clinical specimens”, Tuscia University, Italy, Apr 2017

PROFESSIONAL ACTIVITES IN JOURNALS

➢ Editorial Board member, Journal of Community Medicine and Public health

➢ Editorial Board member, International Journal of Infectious Diseases and Therapy

➢ Reviewer, Journal of Infectious Diseases Diagnosis and Treatment

➢ Reviewer, African Journal of Microbiology Research

PROFESSIONAL ASSOCIATIONS

➢ European Society of Clinical Microbiology and Infectious Diseases

➢ Infectious Diseases Society of America

➢ International Society for Infectious Diseases

PUBLICATIONS

➢ Shanmugakani RK., et al. Point-of-care diagnostics for antimicrobial resistance. In

revision.

➢ Shanmugakani RK., et al. blaOXA-731, a new chromosome-encoded blaOXA-48-like

variant in Shewanella sp. from the aquatic environment in Myanmar. In revision.

➢ Shanmugakani RK., et al. Rapid and multiplex detection of methicillin-resistant

Staphylococcus aureus and vancomycin-resistant Enterococcus from positive blood

cultures using PCR-dipstick technique. In revision.

➢ Shanmugakani RK., et al. PCR-dipstick-oriented surveillance and characterization of

mcr-1- and carbapenemase-carrying Enterobacteriaceae in a Thai hospital. Front

Microbiol. 2019. 10: 149.

➢ Shanmugakani RK., et al. PCR-dipstick chromatography for differential detection of

carbapenemase genes directly in stool specimens. Antimicrob Agents Chemother. 2017.

61(6): e00067-17.

➢ Sugawara Y., Hagiya H., Akeda Y., Aye MM., Win HPM., Sakamoto N.,

Shanmugakani RK., et al. Dissemination of carbapenemase-producing

Enterobacteriaceae harboring blaNDM or blaIMI in local market foods of Yangon,

Myanmar. Sci Rep. 2019. 9(1): 14455.

➢ Hagiya H., Aoki K., Akeda Y., Yamamoto N., Shanmugakani RK., et al. In-vitro

effectiveness of cefmetazole and meropenem combination treatment against KPC-2-

producing Enterobacteriaceae. Microb Drug Resist. 2019. 25(6): 839-845.

➢ Sugawara Y., Akeda Y., Hagiya H., Sakamoto N., Takeuchi D., Shanmugakani RK., et

al. Spreading patterns of NDM-producing Enterobacteriaceae in clinical and

environmental settings in Yangon, Myanmar. Antimicrob Agents Chemother. 2018.

63(3): e01924-18.

➢ Takeuchi D., Akeda Y., Sugawara Y., Sakamoto N., Yamamoto N., Shanmugakani

RK., et al. Establishment of a dual-wavelength spectrophotometric method for analyzing

and detecting carbapenemase-producing Enterobacteriaceae. Sci Rep. 2018. 8(1):

15689.

➢ Takeuchi D., Akeda Y., Yoshida H., Hagiya H., Nishi I., Yoshioka N., Sugawara Y.,

Sakamoto N., Shanmugakani RK., et al. Genomic reorganization by IS26 in a blaNDM-

5-bearing FII plasmid of Klebsiella pneumoniae isolated from a patient in Japan. J Med

Microbiol. 2018. 67(9): 1221-1224.

➢ Hagiya H., Yamamoto N. Kawahara R., Akeda Y., Shanmugakani RK., et al. Risk

factors for fecal carriage of IMP-6-producing Enterobacteriaceae at a long-term care

hospital in Japan: A follow-up report from the northern Osaka multicenter study group.

J Infect Chemother. 2018. 24(9): 769-772.

➢ Yamamoto N., Asada R., Kawahara R., Hagiya H., Akeda Y., Shanmugakani RK., et

al. Prevalence of, and risk factors for, carriage of carbapenem-resistant

Enterobacteriaceae among hospitalized patients in Japan. J Hosp Infect. 2017. 97(3):

212-217.

➢ Yamamoto N., Kawahara R., Akeda Y., Shanmugakani RK., et al. Development of

selective medium for IMP-type carbapenemase-producing Enterobacteriaceae in stool

specimens. BMC Infect Dis. 2017. 17(1): 229.

➢ Pepe G., Grossi MR., Berni A., Filippi S., Shanmugakani RK., et al. Effect of

blueberries (BB) on micronuclei induced by N-methyl-N’-nitro-N-nitrosoguanidine

(MNNG) and 7,12-dimethylbenz(α)anthracene (DMBA) in mammalian cells, assessed

in in vitro and in vivo assays. Mutat Res. 2013. 758(1-2): 6-11.

➢ Sireesh D., Bhakkiyalakshmi E., Ramkumar KM., Rathinakumar S., et al. Targeting

SUMOylation cascade for diabetes management. Curr Drug Targets. 2014. 15(12):

1094-1106.

➢ Shanmugakani RK., and Ghosh AR. Single primer designed for detection of Shigella

species. Afr J Microbiol Res. 2012. 6(25): 5288-5293.

➢ Mythreyi N., Rathina Kumar S., et al. Salt Aggregation Test and Hemagglutination

Assay for understanding bacterial adherence. J Pharm Res. 2011. 4(11): 4055-4056.

REFERENCES

Prof. Dr. Kazunori Tomono Assoc. Prof. Yukihiro Akeda

Division of Infection Control and Prevention Research Institute for Microbial Diseases

Graduate School of Medicine Graduate School of Medicine

Osaka University Osaka University

Osaka – 565-0871, Japan Osaka – 565-0871, Japan

E-mail: tomono@hp-infect.med.osaka-u.ac.jp E-mail: akeda@biken.osaka-u.ac.jp

Tel: +81-668795093 Tel: +81-668794254

Assoc. Prof. Saurabh Mehta

Division of Nutritional Sciences

College of Human Ecology

Cornell University

Ithaca – 14853, USA

E-mail: smehta@cornell.edu

Tel: +1-6072552640

1

Oz Kira | (607)-279-8998 | ok78@cornell.edu

*Actively looking for a faculty or research position

Education

Ph.D. Environmental Engineering 2016

The Department of Environmental, Water, and Agriculture Engineering, Faculty of Civil and Environmental

Engineering, Technion, Israel Institute of Technology, Haifa, Israel

Advisors: Prof. Yael Dubowski, and Prof. Raphael Linker

Thesis: Monitoring Pesticide Drift Using Open-Path FTIR

M.Sc Environmental Engineering 2012

The Department of Environmental, Water, and Agriculture Engineering, Faculty of Civil and Environmental

Engineering, Technion, Israel Institute of Technology, Haifa, Israel

Advisors: Prof. Avi Shaviv, and Prof. Raphael Linker

Thesis: New and Innovative Measuring Method Combining FTIR-ATR Spectroscopy and Stable Isotopes to

Investigate the Kinetics of Nitrogen Transformations in Soils

B.Sc Chemical Engineering 2008

The Department of Chemical Engineering, Faculty of Engineering, Ben Gurion University, B'eer Sheva, Israel.

B.Sc Chemistry 2008

The Department of Chemistry, Faculty of Natural Science, Ben Gurion University, B'eer Sheva, Israel.

Postdoctoral Training

Postdoctoral associate 5/2018 - present

The Department of Soil and Crop Science, School of Integrative Plant Science, College of Agriculture and Life

Science, Cornell University, Ithaca, NY, USA.

Advisor: Prof. Ying Sun

Postdoctoral associate 1/2016 - 5/2018

The Department of Environmental, Water, and Agriculture Engineering, Faculty of Civil and Environmental

Engineering, Technion, Israel Institute of Technology, Haifa, Israel

Advisors: Prof. Yael Dubowski

Fellowships

Postdoctoral fellowship 2018-2019

Vaadia-BARD Postdoctoral Fellowship

Ph.D. scholarship 2014-2015

Israel health foundation

Undergraduate scholarship 2005

Excellence in undergraduate studies

Honors and Awards

Curriculum Vitae Dr. Oz Kira

2

Oz Kira | (607)-279-8998 | ok78@cornell.edu

(1) 1st prize for outstanding poster – The 1st Technion-STU Workshop on Recycling of Materials and

Environmental Protection November 2016.

(2) "Vivian Konigsberg Award for Excellence in Teaching" for the spring semester 2014-2015.

(3) 1st prize for outstanding poster - The Dahlia Greidinger International Symposium 2013. March 2013.

(4) "Vivian Konigsberg Award for Excellence in Teaching" for the winter semester 2012-2013.

Teaching Experience (courses)

Teaching survey (Technion, IIT) average score – 4.53 (out of 5).

Lectures: "Introduction to Water and Wastewater Sanitation" (graduate course) 2017-2018

Technion, Israel Institute of Technology, Haifa, Israel

Tutorials: "Chemometrics" (graduate course) 2010-2018

"Introduction to Soil Chemistry" (undergraduate course)

"Introduction to Remote Sensing" (undergraduate course)

"Fundamentals of Environmental Engineering" (undergraduate course)

"Water and Wastewater Treatment" (undergraduate course)

"Water Supply and Wastewater Collection" (undergraduate course)

"Fluid Mechanics" (undergraduate course)

"Laboratory in Air Quality" (undergraduate course)

Technion, Israel Institute of Technology, Haifa, Israel

Publications

Refereed Papers in Professional Journals

(1) Kira, O., Linker, R., Shaviv, A. A Novel Method Combining FTIR-ATR Spectroscopy and Stable Isotopes to

Investigate the Kinetics of Nitrogen Transformations in Soils. Soil Science Society of America Journal. Soil

Science Society of America Journal, 78:54–60 (2014). Impact factor (IF):1.997, Rank (R): 18/35 (Soil

Science), Citation (C):15. * data taken from web of science (IF and R) and google scholar (C))

(2) Kira, O., Linker, R., Gitelson, A. A. New look at non-destructive estimation of foliar chlorophyll and carotenoid

contents. International Journal of Applied Earth Observation & Geoinformation. 38:251-260 (2015). IF: 4.846,

R: 5/30 (Remote Sensing), C: 36.

(3) Kira, O., Dubowski, Y., Linker. R. Reconstruction of passive open-path FTIR ambient spectra using

meteorological measurements and its application for detection of aerosol cloud drift. Optics Express. 23:no.15

(2015). IF: 3.561, R: 20/95 (Optics), C: 8.

(4) Kira, O., Nguy-Robertson, A. L., Arkebauer, T. J., Linker, R., Gitelson, A. A. Informative spectral bands for

remote green LAI estimation in C3 and C4 crops. Agricultural and Forest Meteorology. 218-219 (2016) 243-

249. IF: 4.189, R: 4/89 (Agronomy), C: 22.

(5) Kira, O., Linker, R., Dubowski, Y. Detection and quantification of water-based aerosols using active open-path

FTIR. Scientific Reports. 6, 25110 (2016). IF: 4.011, R: 15/69 (Multidisciplinary Sciences), C: 6.

(6) Kira, O., Linker, R., Dubowski, Y. Estimating pesticide primary drift in orchards using active Open Path FTIR.

Atmospheric Environment. 142: 264-270 (2016). IF: 4.012, R: 15/86 (Atmospheric Sciences), C: 4.

3

Oz Kira | (607)-279-8998 | ok78@cornell.edu

(7) Kira, O., Nguy-Robertson, A. L., Arkebauer, T. J., Linker, R., Gitelson, A. A. Toward Generic Models for

Green LAI Estimation in Maize and Soybean: Satellite Observations. Remote Sensing. 9: 1-16 (2017). IF: 4.118,

R: 7/30 (Remote Sensing), C: 10.

(8) Kira, O., Dubowski, Y., Linker, R. In-situ open path FTIR measurements of the vertical profile of spray drift

from air-assisted sprayers. Biosystems Engineering 169: 32-41 (2018). IF: 2.983, R: 7/56 (Agriculture,

Multidisciplinary), C: 2.

(9) Kira, O., Shaviv, A., Dubowski, Y. Direct Tracing of NH3 and N2O Emissions Associated with Urea

Fertilization Approaches, using Static Incubation Cells. Science of the Total Environment, 661: 75-85 (2019).

IF: 5.589, R: 27/250 (Environmental Sciences), C: 0.

(10) Kira, O., Bareket, M., Sabach, S., Dubowski, Y. VOC emissions from polyurethane mattresses in the sleeping

environmental: comparison under different environmental conditions using chamber experiments.

Environmental Science and Technology (Chosen for press release) 53, 15, 9171-9180 (2019). IF: 7.149, R:

14/250 (Environmental Sciences), C: 0.

(11) Peng, Y., Kira,O., Nguy-Robertson, A., Suyker, A., Arkebauer, T., Sun, Y., Gitelson, A. Towards generic

models for remote estimation of gross primary production in crops. Agronomy Journal 111(6): 1-10 (2019). IF:

1.805, R: 28/89 (Agronomy), C: 0.

In preparation/ submitted/ under review

(1) Kira, O., Shaviv, A., Dubowski, Y. FTIR based advanced direct flow system for lab direct tracing of NH3 and

N2O emission under urea fertilization.

(2) Kira, O., Sun, Y. Extracting Sub-Pixel C3/C4 Emission Sources of Solar-Induced Chlorophyll Fluorescence

(SIF) to Using Artificial Neural Network. ISPRS J. Photogramm. Remote Sens.

Professional Conferences

Oral Platform Presentations

(1) Kira, O., Sun, Y. Solar induced chlorophyll fluorescence pixel un-mixing to emission sources using reflectance

data and artificial neural network. AGU fall meeting, Washington D.C, USA. December 2018.

(2) Kira, O., Dubowski, Y., Raphael Linker., Avi Shaviv., Gitelson. A. Remote sensing for agriculture and the

environment. Ceremony for undergraduate excellent students. Technion IIT, Haifa, Israel. June 2017. Invited

talk.

(3) Kira, O., Dubowski, Y., Raphael Linker. Detection and quantification of water-based aerosols using active open-

path FTIR. The European Aerosol Conference, France, September 2016.

(4) Kira, O., Air pollution monitoring. College of Science Summer School, STUCSS2016, Shantou University,

China. August 2016. Invited talk.

(5) Kira, O., Atmospheric remote sensing. College of Science Summer School, STUCSS2016, Shantou University,

China. August 2016. Invited talk.

(6) Kira, O., Dubowski, Y.,Raphael Linker. Remote sensing of pesticide drift: a tool for estimating and reducing

air pollution in agriculture. The annual conference of the Israeli Society of Agricultural Engineering, July 2016.

(7) Kira, O., Dubowski, Y.,Linker. R. Monitoring Pesticide Drift Using Open-Path FTIR. EPScon, Conference on

research in environmental, earth and planetary sciences. May 2015.

4

Oz Kira | (607)-279-8998 | ok78@cornell.edu

(8) Kira, O., R. Linker., Avi Shaviv. A Novel Method Combining FTIR-ATR Spectroscopy and Stable Isotopes to

Investigate the Kinetics of Nitrogen Transformations in Soils. CARESS, Conference on Active Research by

Environmental Sciences Students. May 2013.

(9) Kira, O., R. Linker., Avi Shaviv. A Novel Method Combining FTIR-ATR Spectroscopy and Stable Isotopes to

Investigate the Kinetics of Nitrogen Transformations in Soils. The joint conference of the Israeli Society of Soil

Science, and the Israeli Society for Clay Minerals Research. December 2012.

Poster Presentations

(1) Kira, O., Zivan, O., Darzi, R., Shaviv, A., Linker, R., and Dubowski, Y. The impact of agrochemicals use on

pollutants emission to the atmosphere. Gordon Research Conference in Atmospheric Chemistry, USA, July

2017.

(2) Kira, O., Dubowski, Y., Linker, R. Remote sensing of pesticide drift: a tool for estimating and reducing air

pollution in agriculture. The 1st Technion-STU Workshop on Recycling of Materials and Environmental

Protection. Israel, November 2016.

(3) Kira, O., Dubowski, Y., Linker, R. Remote sensing of pesticide drift: a tool for estimating and reducing air

pollution in agriculture. The European Aerosol Conference, France, September 2016.

(4) Kira, O., Dubowski, Y., Linker, R. Remote sensing of pesticide drift: a tool for estimating and reducing air

pollution in agriculture. The International Society for Environmental Epidemiology annual conference, Italy,

September 2016.

(5) Kira, O., Dubowski, Y., Linker, R. Remote sensing of pesticide drift using Open Path FTIR. Environmental

Health: New and Noteworthy. April 2016.

(6) Kira, O., Dubowski, Y., Linker, R. Remote sensing of pesticide drift: a tool for estimating and reducing air

pollution in agriculture. The Dahlia Greidinger International Symposium 2016. March 2016.

(7) Kira, O., Nguy-Robertson. A. L., Linker. R., Gitelson. A. Algorithms for estimating green leaf area index using

hyperspectral, MODIS, Landsat TM/ETM+, MERIS, Sentinel MSI/OLCI, and Venµs data. EPScon, Conference

on research in environmental, earth and planetary sciences. May 2015.

(8) Kira, O., Dubowski, Y., Linker, R. Monitoring pesticide drift using passive measurements of open path FTIR.

The 2nd Israeli Graduate Student Symposium on Environmental Health November 2013. Technion IIT.

(9) Kira, O., Dubowski, Y., Linker, R., Shaviv, A. New and Innovative Measuring Method Combining FTIR-ATR

Spectroscopy and Stable Isotopes to Investigate the Kinetics of Nitrogen Transformations in Soils. The

Dahlia Greidinger International Symposium 2013. March 2013.

Service

(1) Designing and executing the building of a satellite reception station – Eumestat. Technion IIT 2017.

(2) Founding the student conference for connecting water engineering student to the local industry. Technion IIT

2016, 2018.

(3) Consultant at the Israel Laboratory Accreditation Authority (ISRAC). 2015-2018.

References

Research (Technion IIT):

(1) Prof. Yael Dubowski, Technion IIT. yaeld@cv.technion.ac.il

(2) Prof. Avi Shaviv, Technion IIT. agshaviv@cv.technion.ac.il

(3) Prof. Raphael Linker, Technion IIT. linkerr@cv.technion.ac.il

5

Oz Kira | (607)-279-8998 | ok78@cornell.edu

(4) Prof. David Broday, Technion IIT. dbroday@cv.technion.ac.il

Research (University of Lincoln Nebraska):

(5) Prof. Anatoly Gitelson, UNL. agitelson2@unl.edu

Research (Cornell University):

(6) Prof. Ying Sun, CU. ys776@cornel.edu

Teaching (Technion IIT):

(7) Prof. Eran Fridler, Technion IIT. eranf@cv.technion.ac.il

Magdalena Masello Souza, DVM

439 Morrison Hall Cel: +1 (646) 330-3355 Cornell University email: mm2648@cornell.edu 14853, Ithaca, NY

CURRENT APPOINTMENT

PhD Candidate – Animal Science (Spring 2016 – present) Cornell University Department of Animal Science Advisor: Dr. Julio Giordano

EDUCATION AND TRAINING

Doctor of Philosophy (2016-2020) Department of Animal Science, Cornell University. GPA: 4.1/4.3 Major and concentrations: Major: Animal Science. Concentrations: Physiology of reproduction, cellular immunology, and population medicine and epidemiology. Mentors: Dr. Julio O. Giordano (Chairperson- Physiology of reproduction), Dr. Daryl Nydam (Population Medicine and Epidemiology), Dr. Jerrie Gavalchin (Cellular immunology), Dr. David Erickson (Biomedical Engineering). Anticipated graduation date: Spring 2020 Doctor of Veterinary Medicine (2008-2014) College of Veterinary Medicine. Universidad de la República (Uruguay). Class Rank: 2nd

WORK AND RESEARCH EXPERIENCE

2015 Visiting Scholar (9 months) at Dr. Giordano’s laboratory, Department of Animal Science, Cornell University.

2010-2014 Co-management of family owned beef farm.

TEACHING AND EXTENSION

2016-2019 Teaching Assistant. Cornell University, Ithaca (NY).

ANSC 3450 Reproductive Physiology and Management of Dairy Cattle ANSC 2500 Dairy Cattle Principles ANSC 3400 Comparative Mammalian Reproduction

ANSC 2650 Equine Biology and Management 2019 Cornell ProDairy Dairy Cattle Reproductive Management Online Course (in

Spanish). Reproductive Management of Dairy Heifers. 2018 Cornell ProDairy Dairy Cattle Reproductive Management Online Course.

Reproductive Management of Dairy Heifers.

https://prodairy.cals.cornell.edu/sites/prodairy.cals.cornell.edu/files/shared/documents/PRO-DAIRY_Flyer.pdf

2017 Cornell ProDairy Wednesday Webinars (in Spanish). Reproductive Physiology

of Dairy Cattle; What is Important to Know for Reproductive Management. https://prodairy.cals.cornell.edu/webinars/spanish-webinars/

MENTORING EXPERIENCE

1. Mentoring Undergraduate and Visiting Students during their research projects in the Dairy and Cattle Biology & Management Laboratory at Cornell University. Students: Jenna Rudolfsky, Juan Manuel Vergara, Tyra Jenkins

2. Mentoring Visiting Scholars in the Dairy and Cattle Biology & Management Laboratory at Cornell University. Froylan Sosa, Matteo Scarbolo, Maria Victoria Schneck, Maria Elisa Cabrera

PEER-REVIEWED PUBLICATIONS:

In Print/accepted

1. Masello, M., Perez, M. M., Granados, G. E., Stangaferro, M. L., Ceglowski, B., Thomas, M. J., and Giordano, J. O. Reproductive performance of replacement dairy heifers submitted to first service with programs that favor insemination at detected estrus, timed artificial insemination, or a combination of both. Journal of dairy science 2019, 102(2), 1671-1681.

2. M. L. Stangaferro, R. Wijma, M. Masello, M. J. Thomas, and J. O. Giordano. Economic performance of lactating dairy cows submitted for first service timed artificial insemination after a voluntary waiting period of 60 or 88 days. Journal of dairy science 2018; 101:7500–7516.

3. M.L. Stangaferro, R. Wijma, M. Masello, J.O. Giordano. Reproductive performance and herd exit dynamics of lactating dairy cows managed for first service with the Presynch-Ovsynch or Double-Ovsynch protocol and different duration of the voluntary waiting period. Journal of dairy science 2018; 101: 1673-1686

4. R. Wijma, M. M. Pérez, M. Masello, M. L. Stangaferro, and J. O. Giordano. A Resynchronization of Ovulation Program Based on Ovarian Structures Present at Nonpregnancy Diagnosis Reduced Time to Pregnancy in Lactating Dairy Cows. Journal of dairy Science 2018; 101: 1697-1707.

5. M.L. Stangaferro, R.W. Wijma, M. Masello, Mark J. Thomas, J.O. Giordano. Extending the duration of the voluntary waiting period from 60 to 88 days in cows that received timed artificial insemination after the Double-Ovsynch protocol affected the reproductive performance, herd exit dynamics, and lactation performance of dairy cows. Journal of dairy science 2018; 101: 717-735.

6. R. Wijma, M. L. Stangaferro, M. Masello, G. E. Granados, and J. O. Giordano. Resynchronization of Ovulation Protocols for Dairy Cows Including or Not Including GnRH to Induce a New Follicular Wave: Effects on Re-insemination Pattern, Ovarian Responses, and Pregnancy Outcomes. Journal of dairy Science 2017; 100: 7613-7625.

7. R. Wijma, M. L. Stangaferro, M. Masello, M. A. Elmetwally, G. E. Granados, F. Amovilli and J. O. Giordano. Intravaginal instillation of GnRH analogues with an absorption enhancer induced a surge of LH in lactating dairy cows. Journal of dairy Science 2017; 100: 7626-7637.

8. Giordano JO, Thomas MJ, Catucuamba G, Curler MD, Wijma R, Stangaferro ML, and Masello M. Impact of Extending the Interval from Presynch to Initiation of Ovsynch in a Presynch-Ovsynch Protocol on Fertility of Timed Artificial Insemination Services in Lactating Dairy Cows. Journal of Dairy Science 2016; 99:746-57.

9. J. O. Giordano, M. J. Thomas, G. Catucuamba, M. D. Curler, M. Masello, M. L. Stangaferro, and R. Wijma. Reproductive management strategies to improve the fertility of cows with a suboptimal response to resynchronization of ovulation. Journal of dairy science 2016; 99: 2967-2978.

Publications under peer review

1. Masello, M., Ceglowski, B., Thomas M. J., and Giordano, J. O. Reproductive performance of lactating dairy cows managed with a resynchronization strategy aimed at increasing inseminations at detected estrus after non-pregnancy diagnosis. (submitted).

2. Masello, M., Lu, Z., Erickson, D., Giordano, J. O. A lateral flow-based portable platform for determination of reproductive physiological status of lactating dairy cows. (submitted).

3. Masello, M., Scarbolo, M., Schneck, M. V., Perez, M. M., Schillkowsky, E. M., Sitko, E. M., Sosa Hernandez, F., Cabrera, E. M., Rossi, R. M., Giordano, J. O. Intravaginal instillation of prostaglandin-F2α was as effective as intramuscular injection for induction of luteal regression in lactating dairy cows. (submitted).

PRESENTATIONS AT SCIENTIFIC CONFERENCES AND INVITED SEMINARS

1. M. Masello, M. Scarbolo, M.V. Schneck, M.M. Perez, E.M. Schillkowsky, E.M. Sitko, F. Sosa Hernandez, E.M. Cabrera, R.M. Rossi, J.O. Giordano. Efficacy of Intravaginal Administration of PGF2α for induction of Luteal Regression in Lactating Dairy Cows. J. Dairy Sci. 2019; 102. (E-Suppl. 1): 275.

2. M. Masello, E.M. Schillkowsky, Z. Lu, D. Erickson, J. Gavalchin, J.O. Giordano. A Lateral Flow-based Portable Platform for Quantification of Circulating Concentrations of Progesterone. J. Dairy Sci. 2019; 102. (E-Suppl. 1): 345

3. E. M. Sitko, M. M. Pérez, G. E. Granados, M. Masello, F. Dicroce, A. McNeel, D. Weigel, and J. O. Giordano. Genetic merit for fertility and type of reproductive management strategy affected the reproductive performance of primiparous lactating Holstein cows. J. Dairy Sci. 2019; 102. (E-Suppl. 1): 115

4. M. Masello, B. Ceglowski, M. J. Thomas, and J. O. Giordano. Maximazing Inseminations at Detected Estrus for Second and Greater Services in Lactating Dairy Cows. J. Dairy Sci. 2018; 101. (E-Suppl. 2): 84.

5. M. Masello, M. M. Perez, G. E. Granados, M. L. Stangaferro, B. Ceglowski, M. J. Thomas, and J. O. Giordano. Economics of Replacement Dairy Heifers Managed with Reproductive Management Programs that Favor Insemination at Detected Estrus or Timed AI. J. Dairy Sci. 2018; 101. (E-Suppl. 2): 349.

6. M. Masello, M. M. Perez, G. E. Granados, M. L. Stangaferro, B. Ceglowski, M. J. Thomas, and J. O. Giordano. Reproductive Management Strategies for First Service in Replacement Dairy Heifers. J. Dairy Sci. 2017; 100. (E-Suppl. 2): 280.

7. R. Wijma, M. Masello, M. L. Stangaferro, M. M. Pérez, and J. O. Giordano. A resynchronization of ovulation strategy based on the ovarian structures present at non-pregnancy diagnosis reduced time to pregnancy in lactating dairy cows. J. Dairy Sci. 2017; 100, Suppl. 2.

8. M. L. Stangaferro, M. M. Perez, M. Masello, R. Wijma, M. E. Van Amburgh, T. R. Overton, D. Luchini, M. C. Wiltbank, R. D. Shaver, and J. O. Giordano. Effect of supplementing rumen-protected methionine pre- and postpartum on milk yield and components of dairy cows during early lactation. J. Dairy Sci. 2017; 100, Suppl. 2.

9. Wijma R, Stangaferro ML, Masello M, Granados GE, Giordano JO. Resynchronization of ovulation strategies including or not including GnRH treatment before non-pregnancy diagnosis. J. Dairy Sci. 2016 99, E-Suppl. 1.

10. Stangaferro ML, Wijma R, Masello M, Granados GE, Giordano JO. Profitability of Dairy Cows Managed for First Service with the Double-Ovsynch or Presynch-Ovsynch Protocol and Different Duration of the Voluntary Waiting Period. J. Dairy Sci. 2016 99, E-Suppl. 1.

11. Stangaferro ML, Wijma R, Masello M, Giordano JO. Reproductive performance of lactating dairy cows managed for first service with the Double-Ovsynch or Presynch-Ovsynch protocol and different duration of the voluntary waiting period. J. Dairy Sci. 2016 99, E-Suppl. 1.

12. Stangaferro ML, Wijma R, Masello M, Granados GE, Giordano JO. Profitability of Dairy Cows Receiving First Service Timed Artificial Insemination after the Double-

Ovsynch Protocol with a Voluntary Waiting Period of 60 or 88 Days. J. Dairy Sci. 2016 99, E-Suppl. 1.

13. Stangaferro ML, Wijma R, Quinteros C, Medrano MB, Masello M, Giordano JO. Use of a rumination and activity monitoring for the identification of dairy cows with health disorders. J. Dairy Sci. 2015 98, Suppl. 2.

14. Stangaferro ML, Wijma R, Medrano MB, Al Abri MA, Masello M, Giordano JO. Prepartum rumination patterns in dairy cows that develop health disorders in the early postpartum period. J. Dairy Sci. 2015 98, Suppl. 2.

15. Stangaferro ML, Wijma R, Masello M, Bicalho RC, Thomas MJ, Giordano JO. Reproductive performance of lactating dairy cows with an extended duration of the postpartum voluntary waiting period and injectable trace mineral supplementation. J. Dairy Sci. 2015 98, Suppl. 2.

16. Stangaferro ML, Wijma R, Masello M, Thomas MJ, Giordano JO. Effect of extending the duration of the postpartum voluntary waiting period on reproductive performance of lactating dairy cows. J. Dairy Sci. 2015 98, Suppl. 2.

SELECTED SHORT COURSES, SEMINARS, AND CONFERENCES ATTENDED

2019 American Dairy Science Association (ADSA) Annual Meeting. Cincinnati, OH June 23-26, 2019.

2018 American Dairy Science Association (ADSA) Annual Meeting. Knoxville, TN June 24-27, 2018.

2018 Gordon Research Seminar; Bioanalytical Sensors. Salve Regina University, Newport, RI, June 23-24, 2018.

2017 2018 American Dairy Science Association (ADSA) Annual Meeting. Pittsburgh, PA June 25-28, 2017.

Reproductive Physiology/Endocrinology Seminar Series. Spring 2016 - Present. Cornell University. Ithaca, New York.

Reproductive Biotechnology Course in Ruminants. Instituto de Reproducción Animal de Córdoba (IRAC), Argentina, 2013-2014.

Rearing and Early Stages of Productive Life in Cows. Facultad de Veterinaria, Universidad de la República, 2012.

Ultrasonography in Cattle. Facultad de Veterinaria, Universidad de la República, 2012.

HONORS AND AWARDS

2019 Research Innovation Fund of the Cornell Initiative for Digital Agriculture, graduate student summer salary ($9,500).

2018 Cornell University Graduate Student Travel Grant for oral and poster presentation at the American Dairy Science Association (ADSA) Annual Meeting. June 24 – 27, 2018. Knoxville, Tennessee.

2017 Cornell University Graduate Student Travel Grant for oral and poster presentation at the American Dairy Science Association (ADSA) Annual Meeting. June 25 – 28, 2017. Pittsburgh, PA.

2014 Second Best Grade Point Average (Ranked 2). College of Veterinary Medicine,

Universidad de la República, Uruguay.

LANGUAGES

Spanish: Native speaker.

English: Fluent.

Portuguese: Advanced.

PROFESSIONAL MEMBERSHIPS

American Dairy Science Association (ADSA).

Dairy Cattle Reproduction Council (DCRC).

Veterinary Medicine Society (Uruguay).

Society for the Study of Reproduction (SSR).

MaríaKatherineMejíaGuerra,Ph.D.E-mail:mm2842@cornell.edu

SUMMARYOFQUALIFICATIONS

Current postdoctoral researcher working in the application of machine and deep learning approaches (practical knowledge of libraries such as Sklearn, Keras, and TensorFlow) to decipher “grammar-like” rules underlying the architecture of regulatory regions using information derived from functional genomics experiments. I have strong experience leading data analysis process of technologies involving high-throughput sequencing such as CAGE, ATAC-Seq, mRNA-Seq and ChIP-Seq. I am highly skilled in the design, development and configuration of pipelines to investigate biological questions that require integration of information and big data analysis. I have proficiency with several programming languages (Python, Java and R), experience working on cloud type of computational resources (Unix environment), and management of databases (MySQL, SQLite, Monet DB, Neo4J).

EDUCATIONPhD-MolecularCellularandDevelopmentalBiologyTheOhioStateUniversity(Columbus,Ohio,USA)MagisterinBiology,EmphasisinComputationalBiochemistryandMolecularBiologyPontificiaUniversidadJaveriana(BogotáD.C.,Colombia)BSc.,BiologyPontificiaUniversidadJaveriana(BogotáD.C.,Colombia)

RESEARCHEXPERIENCEPostdoctoralResearcher04.2016–toPresentCornellUniversity,BucklerlabforMaizeGeneticsandDiversity. Role: My most current project is to catalog the largest collection of regulatory regionsscored “in-vivo” for any plant (104 transcription factors) to build the gene regulatorynetwork that controls the functionof the leaf tissue inmaize.Data from thisprojectwasusedtotrainartificialintelligencemodelstoallowthescoringofnon-codingvariation,thesemodelsallowtoannotated70%oftheGWAShitsthatexplainkeyagronomictraits(incorn)with data that is orthogonal to genetic information. This research has a vast number ofapplications from basic biology, breeding, and gene editing. As amore general goal,myresearch aims to generate computational approaches and models that integrate severallayers of population genomics information to understand and predict the effects ofsequence variation with a role in gene expression regulation and located at intergenicregions(~90%ofthegenome).Thisprojecthasimplicationsbeyondmaize,asmodelscanbetransferredtootherimportantcropssuchasSorghumandRice.

From a technical stand point, working as a postdoc I have gained practical knowledge of machine learning libraries such as Sklearn, and TensorFlow. As well as developed software development practices such as version control (git), code documentation, and unit testing. CCBL-CAPSComputationalBiologyLaboratoryMember01.2012–12.2015TheOhioStateUniversity,GrotewoldLaboratory.Role: During my time at the CAPS Computational Biology Laboratory I successfullysupervised and trained several visiting scholars and leaded the organization of outreachevents.VisitingScholarDates01.2010–07.2010and01.2009–07.2009TheOhioStateUniversity,GrotewoldLaboratory.Role:DuringthefirstvisitingscholarperiodIfinishedaJAVAapplettodisplaygeneregulatorynetworks. The second period I integrated data from yeast protein-protein interaction andprotein-DNA interactionsand search fornetworkmotifs thatprovidebi-stability.The resultsfromeachvisitwerepartofpeer-reviewpublications(Siegal-Gaskinsetal.,2011,Yilmazetal.,2011).

PUBLICATIONS

Ricci WA, Lu Z, Ji L, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Jordan Rowley M, Corces VG, Zhai J, Scanlon MJ, Buckler ES, Gallavotti A, Springer NM, Schmitz RJ, Zhang X. Widespread Long-range Cis-Regulatory Elements in the Maize Genome. Nature Plants. 2019. (In print) Mejía-Guerra MK, Buckler ES. A k-mer grammar analysis to uncover maize regulatory architecture. BMC Plant Biol. 2019 Mar 15;19(1):103 Washburn JD, Mejía-Guerra MK, Ramstein G, Kremling KA, Valluru R, Buckler ES, Wang H. Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence. Proc Natl Acad Sci U S A. 2019. Mejía-Guerra MK, Li W, Doseff AI, Grotewold E. Genome-Wide TSS Identification in Maize. Methods Mol Biol. 2018; 1830:239-256. Yang F, Li W, Jiang N, Yu H, Morohashi K, Ouma WZ, Morales-Mantilla DE, Gomez-Cano FA, Mukundi E, Prada-Salcedo LD, Velazquez RA, Valentin J, Mejía-Guerra MK, Gray J, Doseff AI, Grotewold E. A Maize Gene Regulatory Network for Phenolic Metabolism. Mol Plant. 2017; 10(3):498-515. (citations 5) Casas MI, Falcone-Ferreyra ML, Jiang N, Mejía-Guerra MK, Rodríguez E, Wilson T,EngelmeierJ,CasatiP,GrotewoldE.IdentificationandCharacterizationofMaizesalmonsilksGenes Involved in Insecticidal Maysin Biosynthesis. Plant Cell. 2016; 28(6):1297-309. (citations12)

Mejia-GuerraMK,LiW,VidalM,GaleanoNF,GrayJ,DoseffAI,GrotewoldE.Corepromoterplasticity between maize tissues and genotypes contrasts with predominance of sharptranscriptioninitiationsites.ThePlantCell.2016;27(12):3309-20.(citations17)GaleanoE,VasconcelosTS,VidalM,Mejia-GuerraMK,CarrerH.Large-scaletranscriptionalprofilingof lignifiedtissuesinTectonagrandis.BMCPlantBiol.2015;15(1):221.(citations16)Ouma WZ,Mejia-Guerra MK, Yilmaz A, Pareja-Tobes P, Li W, Doseff AI, Grotewold E.Important biological information uncovered in previously unaligned reads from chromatinimmunoprecipitationexperiments(ChIP-Seq).SciRep.2015;5:8635.(citations4)BurdoB,GrayJ,Goetting-MineskyMaryP,WittlerB,HuntM,LiT,VelliquetteD,ThomasJ,GentzelI,BritoMichaeldosSantos,Mejia-GuerraMK,ConnollyLN,QaisiD,LiW,CasasMI,Doseff AI and Grotewold E.TheMaize TFome--development of a transcription factor openreadingframecollectionforfunctionalgenomics.PlantJ.2014;80(2):356-366.(citations24)Bolduc N, Yilmaz A,Mejia-Guerra MK, Morohashi K, O’Connor D, Grotewold E, Hake S.UnravelingtheKNOTTED1regulatorynetworkinmaizemeristems.GenesandDevelopment.2012;26(15):1685-1690.(citations156)MorohashiK,CasasMI,Falcone-FerreyraL,Mejia-GuerraMK.PourcelL,YilmazA,FellerA,Carvalho B, Emiliani J, Rodriguez E, Pellegrinet S, McMullenM, Casati P, Grotewold E. Agenome-wideregulatory framework identifiesmaizePericarpColor1 (P1)controlledgenes.ThePlantCell2012;24(7):2745-2764.(citations88)Mejia-Guerra MK, PomeranzM, Morohashi K, Grotewold E. From plant gene regulatorygrids to network dynamics. Biochimica et Biophysica Acta (BBA) – Gene RegulatoryMechanisms.2012;1819(5):454-465.(citations36)Siegal-Gaskins D, Mejia-Guerra MK, Smith GD, Grotewold E. Emergence of switch-likebehavior in a large family of simple biochemical networks. PLoS computational biology.2011;7(5),e1002039.(citations49)Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E. AGRIS: The Arabidopsis Gene Regulatory Information Server, an update. Nucleic Acids Res. 2011; 39 (Database issue): D1118-D1122. (citations 262) Mejia-Guerra MK, Lareo LR. In silico identification of regulatory elements of GRIN1 genes. OMICS. 2005; 9(1): 106-115. (citations 7)

TALKS

BoyceThompsonInstituteSymposia "Integrating-omicsdataforbiologicaldiscovery" Dates09.19.2019Ithaca,NewYork,USATalk"Decodingtheregulatoryarchitectureofthemaizeleaf"MaizeMeeting2019

Dates03.14.2019-03.17.2018St.Louis,Missouri,USATalk"Decodingthetranscriptionalregulatoryatlasofthemaizeleaf"Invited:QTLCloningWorkshop-PAGXXVIDates01.13.2018-01.17.2018SanDiego,California,USATalk"MachineLearningApproachestoTargetNon-CodingFunctionalVariation"Invited:Nationalcenterforresearchinenergyandmaterials(CNPEM)Dates05.2013Campinas,SaoPaulo,BrazilTalk"EmergentPropertiesoftheGreenRegulatoryGrid"Invited: NSF Bioinformatics Workshop at the Samuel Roberts Noble Foundation"Advancingbioinformaticstodecipheringplantgeneregulatorynetworks(GRNs)".Dates04.19.2012-04.21.2012Ardmore,Oklahoma,USATalk"BuildingGeneRegulatoryGrids:ConnectingtheDots"

SERVICEASREVIEWERServedasreviewerforthefollowingprofessionaljournalsandmanuscripts(parenthesis) Frontiers Plant Science (Manuscript ID: 293622) BBA - Gene Regulatory Mechanisms (BBAGRM-16-121R1, BBAGRM-16-100) Bioinformatics (BIOINF-2014-1989) PLoS ONE (PONE-D-11-21620).

WORKSHOPSDates09.19.2019Ithaca,NewYork,USAWorkshop“Anoverviewofmachinelearningprinciplesandtheirapplicationsinbiology”.BoyceThompsonInstituteSymposia"Integrating-omicsdataforbiologicaldiscovery"

AWARDS2010ExcellenceinPlantMolecularBiologyandBiotechnology(PMBB)GraduateFellowshipAwardedbyTheOhioStateUniversity,Columbus,Ohio,USA.

Mi Nguyen, Ph.D.

2647 International Blvd Oakland, CA 94601

(510) 338-8047 mi.nguyentra@gmail.com

BACKGROUND/OBJECTIVE

I am a research group leader with ten years of experience working on environmental issues related to wastewater, fecal sludge, antibiotic resistance genes, and plastic waste. I am seeking an environmental scientist/consultant position. EDUCATION

08/2010-05/2015 University of California at Berkeley Ph.D. in Environmental Engineering 08/2009-05/2010 University of California at Berkeley M.S. in Environmental Engineering

09/2003-05/2008 Ho Chi Minh City University of Technology, Vietnam B.Eng. in Environmental Engineering

WORK EXPERIENCE

10/2019-Present Atkinson-Environmental Defense Fund, Postdoctoral Fellow Ithaca, NY Working on an innovative Side-stream Enhanced Biological Phosphorus Recovery technology (S2EBPR) that removes N and P from manure. This project is a joint program between the Environmental Defense Fund and the Cornell University. 03/2017-09/2019 East Meets West Foundation, Sr Envir. Consultant Hanoi, Vietnam Consulting East Meets West Foundation staff and Vietnamese governmental stakeholders at national and local levels in a fecal sludge management (FSM) project. Activities have included: conducting a network governance study on FSM in Vietnam, supporting and facilitating the first FSM round-table meeting, reviewing Technology Options Report (conducted by Stantec) and Investment Report for the first FSM plant in Vietnam, and developing FSM strategy plans. 10/2017-07/2019 Precious Plastic Saigon, Founder Ho Chi Minh, Vietnam Organized and provided hands-on training courses on plastic waste management with the support of the US Consulate in Ho Chi Minh City, Vietnam. Projects have included: developing and training selected students from local high-schools and universities on plastic waste issues and solutions, partnering with local organizations (non-profit: Fablab Saigon, Upshift; companies: Upcycling Vietnam, Unilever Vietnam; governmental: Department of Natural Resources and Environment) to provide activities to raise public awareness on plastic waste. 02/2017-07/2019 Nguyen Tat Thanh University, Group Leader Ho Chi Minh, Vietnam Conducted research projects on the prevalence of antibiotic resistance genes in fecal sludge and hospital wastewater. Mentored undergraduate and Master students from NTTU and Oregon State University on individual research projects. 05/2015- 06/2017 EAWAG-Inst. for Aquatic Sci. & Tech., Postdoc Duebendorf, Switzerland Conducted research projects on inactivation of E. coli in faecal sludge during anaerobic digestion, network governance of sanitation management in Vietnam, and inactivation and regrowth of pathogens in fecal contaminated water in the Blue Diversion Autarky Toilet. Mentored undergraduate and Master students from ETH Zuerich and Hanoi National University of Civil Engineering. 08/2009- 03/2015 UC Berkeley, Grad. Student Researcher & Instructor Berkeley, CA

Mi Nguyen, Ph.D.

2647 International Blvd Oakland, CA 94601

(510) 338-8047 mi.nguyentra@gmail.com

Developed a model to predict sunlight inactivation rates of fecal indicator bacteria in open-water unit process wetlands and a method to collect and work with indigenous bacteria from wastewater. Led supplementary lectures and laboratory sessions for the Introduction to Environmental Engineering and Control of Water-related Pathogens courses. SELECTED PUBLICATIONS

Wenk J., Nguyen M. T., Nelson K. “Natural Photosensitizers in Constructed Unit Process Wetlands: Photochemical Characterization and Inactivation of Pathogen Indicator Organisms”. Environ. Sci. Technol. 2019 Fischer M., Nguyen M. T., Strande L. “Context matters: horizontal and hierarchical network governance structures in the Vietnamese sanitation sector”. (Accepted & To be published). Ecology and Society. 2019 Schutzius G., Nguyen M. T., Navab-Daneshman T. “Antibiotic resistance in fecal sludge from septic tanks and soil environments in Ho Chi Minh City, Vietnam. (Accepted & To be published). Environmental Science & Pollution Research. 2019 Nguyen M. T., Allemann L., Ziemba C., Larivé O., Morgenroth E. and Julian T. R. “Controlling Bacterial Pathogens in Water for Reuse: Treatment Technologies for Water Recirculation in the Blue Diversion Autarky Toilet”. Front. Environ. Sci. 2017 Bear, S. E., Nguyen, M. T., Jasper, J. T., Nygren, S., Nelson, K. L., Sedlak, D. L. “Removal of Nutrients, Trace Organic Contaminants and Pathogen Indicator Organisms in a Demonstration-Scale Open-Water Unit Process Treatment Wetland”. Ecological Engineering. 2017 Nguyen, M. T., Jasper, J. T., Nelson, K. L. “Sunlight inactivation of fecal indicator bacteria in an open-water natural wastewater treatment system: Modeling endogenous and exogenous inactivation rates in the presence of light-attenuating compounds and photosensitizers”. Water Research. 2015 Hendrickson, T. P., Nguyen, M. T., Sukardi, M., Miot, A., Horvath, A., and Nelson K. L. “Life-Cycle Energy Use and Greenhouse Gas Emissions of a Building-Scale Wastewater Treatment and Nonpotable Reuse System”. Environ. Sci. Technol. 2015 Nguyen, M. T., Silverman, I. A., Nelson, K. L. “Sunlight inactivation of MS2 coliphage in the absence of photosensitizers: Modeling the endogenous inactivation rate using a photoaction spectrum”. Environ. Sci. Technol. 2014

ACADEMIC HONORS

2019 Lower Mekong Initiative Women’s Leadership Forum Participant 2018 Lower Mekong Initiative Young Scientists Fellow 2018 Recipient of the U.S. Department of State – Federal Assistance Award, awarded of $10,000 to conduct a community project on plastic waste issues 2016 EPFL Seed Money Grant, awarded $10,000 to conduct an individual research project on fecal sludge inactivation in Hanoi, Vietnam 2015 Schlumberger Faculty for the Future Fellowship 2009 Vietnam Education Foundation Fellowship Reviewer for Environment, Development and Sustainability; J. Water Supply: Research and Technology; and J. Environment International

CURRICULUM VITAE

NAME Donny Harry Persaud, MA, Hon.B.Sc. ADDRESS 10 Cashman Crescent Toronto, ON M6N 4M7 Tel: (914) 338-2714 Email: dhp75@cornell.edu EDUCATION Aug 2019 – Present PhD Student in Science and Technology Studies Cornell University, Ithaca, NY Sept 2015 – Oct 2018 Master of Arts

Geography Memorial University of Newfoundland, St. John’s, NL

Sept 2010 – June 2014 Honours Bachelors of Science

Physical and Environmental Geography University of Toronto, Toronto, ON

PUBLICATIONS Persaud, D., Lepawsky, J., and M. Liboiron (forthcoming). Viscous objects. Techniques and

Culture 72. Lepawsky, J., Davis, J.-M., Akese, G., & D. Persaud (2019). Cooking with Controversies: How

Geographers Might Use Controversy Mapping as a Research Tool. The Professional Geographer, 71(3), 437–448.

Persaud, D. (2018). Behind breakdown: The case of the MV Veteran. Master’s Thesis. Reports: Fang, T., Sapeha, H., Neil, K., Jaunty-Aidamenbor, O., Persaud, D., Kocourek, P., and T.

Osmond (2018). Retention and Integration of Refugees in Newfoundland and Labrador. St. John’s, NL: Leslie Harris Centre For Regional Development and Policy.

Lepawsky, J., Davis J. M., Persaud D., Akese G., and L. Chen (2017). Transboundary

Movements of Electronic Waste: mapping a controversy. Retrieved from United Nations University - Solving the E-waste Problem (StEP) Initiative: http://scalar.usc.edu/works/transboundary-e-waste/index

Other Writing: Persaud, D. (2019, April 11). Linking North York: a case for extending the Finch West LRT.

Downsview Advocate. Retrieved from https://www.downsviewadvocate.ca/2019/04/linking-north-york-case-extending-finch-west-lrt/

Persaud, D. (2019, March 13). On the 36: the Split Finch West bus. Downsview Advocate.

Retrieved from https://www.downsviewadvocate.ca/2019/03/36-split-finch-west-bus/ Persaud, D. (2019, February 14). ‘I still use tokens’: Switch to Presto monthly passes reveals

fare accessibility issues for residents. Downsview Advocate. Retrieved from https://www.downsviewadvocate.ca/2019/02/still-use-tokens-switch-presto-monthly-passes-reveals-fare-accessibility-issues-residents/

Persaud, D. (2018, November 26). Swapping Metropasses for Presto passes: TTC discontinuing

Metropasses this December. Downsview Advocate. Retrieved from https://www.downsviewadvocate.ca/2018/11/swapping-metropasses-presto-passes-ttc-discontinuing-metropasses-december/

CONFERENCE PRESENTATIONS Refereed Papers and Presentations: Persaud, D., Lepawsky, J. & M. Liboiron ‘The Viscosity of Objects: Warranty Work and the

Maintenance and Repair of a Maritime Ferry in Newfoundland, Canada’. Meeting presentation at Techniques and Culture 72: En cas de panne [In case of breakdown]. Centre de la Vieille Charité: Marseille, France. January 2019.

Persaud, D. ‘Configuring repair: The case of the MV Veteran.’ Annual Meeting of the Society

for Social Studies of Science: Boston, MA. August 2017. Non-Refereed Talks: Persaud, D. ‘The case of the MV Veteran: Re-scripting repair in outport Newfoundland.’ Cornell

University: Ithaca, NY. August 2018. Persaud, D. ‘Geographies of Infrastructural Breakdown: The Case of the MV Veteran.’ Canadian

Association of Geographers Annual Meeting: Toronto, ON. May 2017. Persaud, D. ‘Behind Breakdown: The case of the MV Veteran.’ Blue Box Seminar Series,

Memorial University of Newfoundland: St. John’s, NL. March 2017. Non-Refereed Posters:

Persaud, D. ‘Behind Breakdown: The Case of the MV Veteran.’ Canadian Association of

Geographers Annual Meeting: Halifax, NS. May 2016. Conference Participation: Participant, ‘The Ends of Repair’ workshop at Memorial University of Newfoundland: St,

John’s, NL. September 2016. AWARDS Aug 2017 Society for Social Studies of Science Travel Grant $380.00 USD 4S Travel Grants Committee June 2013 Dr. Stanley Ho Scholarship $1500.00 CAD University of Toronto ACADEMIC WORK EXPERIENCE Research Experience: May 2017 – Aug 2017 Research Assistant, ‘Syrian Refugee Arrival, Resettlement and

Integration in Newfoundland and Labrador’ Department of Economics, Memorial University of Newfoundland Supervisor: Dr. Tony Fang

Nov 2015 – Apr 2017 Research Assistant, ‘Mapping the International Trade and Traffic of

Electronic Waste’ Department of Geography, Memorial University of Newfoundland Supervisor: Dr. Josh Lepawsky

Teaching Assistant Positions: Sept – Dec 2017 GEOG 3405: Canada

Memorial University of Newfoundland Jan – Apr 2017 GEOG 3701: Urban Geography

Memorial University of Newfoundland Sept – Dec 2016 GEOG 3620: Migration and Colonization Memorial University of Newfoundland Jan – Apr 2016 GEOG 3510: Geography of the Seas

Memorial University of Newfoundland Sept – Dec 2015 GEOG 3800: Political Geography

Memorial University of Newfoundland Guest Lectures: Nov 2017 Topic: Demographic Change in the 21st Century GEOG 3405: Canada Nov 2017 Topic: Parks, Nature, and Environmentalism GEOG 3405: Canada Mar 2017 Topic: Academic Writing Workshop GEOG 3701: Urban Geography Oct 2016 Topic: Securitization and Biopolitics GEOG 3620: Migration and Colonization Sept 2016 Topic: Research Skill Development GEOG 3620: Migration and Colonization COMMUNITY INVOLVEMENT Apr 2017 Featured Reader: St. John’s Spoken Word St. John’s, NL. Oct 2016 – Oct 2017 Co-Chairperson: Geography Graduate Student Association Department of Geography, Memorial University of Newfoundland Oct 2016 Public Forum: Social License to Operate (SLO) Volunteer PROFESSIONAL DEVELOPMENT Affiliations: May 2017 – Present Society for Social Studies of Science Mar 2017 – Present Canadian Association of Geographers Sept 2015 – Oct 2018 Waste and Science, Technology & Environment (WaSTE) Hub Certifications: Mar 2016 Ethical Conduct for Research Involving Humans, TCPS-2 CORE Mar 2015 Teaching English as a Foreign Language (TEFL) Certificate

EDUCATIONAL BACKGROUND June 2012 – Sept. 2017 Doctoral studies in the Plant Breeding and Plant Genetics program with a minor in Statistics, at the

department of Agronomy of the University of Wisconsin – Madison, under the supervision of Michael D. Casler: Inference of candidate causal variants and assessment of genomic prediction for bioenergy traits in switchgrass (Panicum virgatum L.)

Sept. 2010 – March 2011 Specialization in agronomy and plant genetics in AgroParisTech, France’s top post-graduate engineering school for life sciences

Sept. 2007 – Oct. 2011 Licence and Master’s studies in Montpellier SupAgro – International University Centre for Advanced Studies in Agricultural Sciences and Rural Development

PROFESSIONAL EXPERIENCE Oct. 2017 – Present Postdoctoral research associate at the Institute of Biotechnology in Cornell University,

under the supervision of Edward S. Buckler: computational biology and quantitative genomics for dissecting the basis of agronomic traits in maize and sorghum; bioinformatics and genomic prediction in a sorghum breeding program (collaboration with Gael Pressoir, Chibas)

Nov. 2011 – May 2012 Fixed-term contract in Arvalis (Paris, France) for the study of genotype-by-environment interactions in wheat: development of predictive models accounting for sensitivities of cultivars to different types of abiotic stress

March 2011 – Sept. 2011 Internship in Syngenta (Delft, The Netherlands) for studying the resistance of sweet pepper to Fusarium fruit rot: identification of resistant lines, identification of plant and fruit traits involved in the resistance, and guidelines to breeders

April 2010 – Sept. 2010 Internship at the National Museum of Natural History of Paris (France): reviewing the taxonomy of Arthroclianthus and Nephrodesmus (genera of legumes of New Caledonia); involvement in the making of a scientific publication

Sept. 2009 – March 2010 Internship in ICRISAT (Consultative group for international agricultural research; Hyderabad, India): genotyping at molecular markers, within a marker-assisted recurrent selection (MARS) program for drought tolerance in chickpea; physiology project for the study of transpiration efficiency, in sorgho and millet

June 2009 – August 2009 Internship at the University of Wisconsin – Madison (USA): mapping of a gene involved in mitochondrion sorting in cucumber

ACHIEVEMENTS Scientific publications

Washburn, J. D., Mejia-Guerra, M. K., Ramstein, G.P., Kremling, K. A., Valluru, R., Buckler, E. S., & Wang, H. (2019). Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence. Proceedings of the National Academy of Sciences, 116(12), 5542-5549.

Ramstein, G.P. and Casler, M.D., 2019. Extensions of BLUP models for genomic prediction in heterogeneous populations: Application in a diverse switchgrass sample. G3: Genes, Genomes, Genetics, pp.g3-200969.

Ramstein, G.P., Jensen, S.E. and Buckler, E.S., 2018. Breaking the curse of dimensionality to identify causal variants in Breeding 4. Theoretical and Applied Genetics, pp.1-9.

Ramstein, G.P., Evans, J., Nandety, A., Saha, M.C., Brummer, E.C., Kaeppler, S.M., Buell, C.R. and Casler, M.D., 2018. Candidate Variants for Additive and Interactive Effects on Bioenergy Traits in Switchgrass (Panicum virgatum L.) Identified by Genome-Wide Association Analyses. The Plant Genome.

Taylor, M.S., Tornqvist, C.E., Zhao, X., Grabowski, P., Doerge, R., Ma, J., Volenec, J., Evans, J., Ramstein, G., Sanciangco, M. and Buell, C.R., 2018. Genome-Wide Association Study in Pseudo-F2 Populations of Switchgrass Identifies Genetic Loci Affecting Heading and Anthesis Dates. Frontiers in plant science, 9, p.1250.

Guillaume Ramstein Born 21st March 1987 gr226@cornell.edu +1 608 395 8564 www.maizegenetics.net/guillaumeramstein

Scientific publications (cont’d)

Jabbour, F., Gaudeul, M., Lambourdière, J., Ramstein, G., Hassanin, A., Labat, J.N. and Sarthou, C., 2018. Phylogeny, biogeography and character evolution in the tribe Desmodieae (Fabaceae: Papilionoideae), with special emphasis on the New Caledonian endemic genera. Molecular phylogenetics and evolution, 118, pp.108-121.

Casler, M.D. and Ramstein, G.P., 2018. Breeding for biomass yield in switchgrass using surrogate measures of yield. BioEnergy Research, 11(1), pp.1-12.

Grabowski, P.P., Evans, J., Daum, C., Deshpande, S., Barry, K.W., Kennedy, M., Ramstein, G.P., Kaeppler, S.M., Buell, C.R., Jiang, Y. and M.D. Casler, 2017. Genome‐wide associations with flowering time in switchgrass using exome‐capture sequencing data. New Phytologist, 213(1), pp.154-169.

Ramstein, G.P., Evans, J., Kaeppler, S. M., Mitchell, R.B., Vogel, K. P., Buell, C.R., and M.D. Casler, 2016. Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium. G3: Genes| Genomes| Genetics, 6(4), 1049-1062.

Ramstein, G.P., Lipka, A.E., Lu, F., Costich, D.E., Cherney, J.H., Buckler, E.S., and M.D. Casler, 2015. Genome-wide association study based on multiple imputation with low-depth sequencing data: application to biofuel traits in reed canarygrass. G3: Genes| Genomes| Genetics, 5(5), 891-909.

Invited presentations Ramstein G. P. (January 2016). Accuracy of genomic prediction in switchgrass improved by accounting for linkage disequilibrium. In Plant and Animal Genome XXIV Conference.

Ramstein G. P. (May 2015). Genomic selection for biofuel traits in switchgrass: Evaluation of procedures. In 2015 GLBRC Annual Science Meeting.

Ramstein G. P. (January 2015). Genome-Wide Association Study Based on Multiple Imputation with Low-Depth Sequencing Data: Application to Biofuel Traits in Reed Canarygrass. In Plant and Animal Genome XXIII Conference.

Ramstein G. P. (May 2014). Genome-wide association studies in bioenergy grasses for biofuel quality traits. In 2014 GLBRC Annual Science Meeting.

Awards & Honors 2016: Henry Steenbock Academic Merit Award (UW-Madison, College of Agricultural and Life Sciences)

2016: Fellowship for participation in the 5th International Conference on Quantitative Genetics (USDA, National Institute of Food and Agriculture)

2015: Royce Bringhurst Memorial Scholarship (UW-Madison, College of Agricultural and Life Sciences)

2015: O. N. Allen Scholarship (UW-Madison, Department of Agronomy)

2014 - 2016: Gabelman-Shippo Distinguished Graduate Fellowship (UW-Madison, Plant Breeding and Plant Genetics program)

Teaching experience Mentorship of undergraduate student (Spring 2018) and graduate student (July 2019) Spring 2017: Teaching assistantship in a graduate-level class in applied statistics at the UW-Madison (Agronomy 771 - Experimental designs)

Fall 2015: Teaching assistantship in a graduate-level class in quantitative genetics at the UW-Madison (Agronomy/Horticulture 811 - Biometrical Procedures in Plant Breeding)

Extracurricular activities 2015: Member of the Plant Sciences Graduate Student Council (PSGSC; association of graduate students in the departments of Agronomy, Horticulture and Plant Pathology at the UW-Madison): promotion of graduate student social interactions and organization of the 5th Annual Plant Sciences symposium at the UW-Madison (campus-wide scientific symposium)

2015: Journal Club chair for the departments of Agronomy, Horticulture and Plant Pathology at the UW-Madison: supervision of weekly discussions about scientific articles

Services to the profession Reviews: Heredity (Spring 2018), Molecular Breeding (Spring 2016), Crop Science (Fall 2015, Fall 2017, Fall 2018), Theoretical and Applied Genetics (Spring 2018), PLoS One (Spring 2019, Summer 2019)

SKILLS Languages English: C1 Level (bilingual), TOEFL : 101/120 (Internet-based test)

Spanish: B2 Level (spoken, read and written)

Computer skills Programming/scripting languages: R (solid bases); Python, Bash and SAS (good notions)

Bioinformatics tools: vcftools, bcftools, BEAGLE, TASSEL, GCTA, GEMMA (solid bases); bwa, samtools, GATK, PicardTools, plink (good notions)

Candice J. Reeves canjreeves@gmail.com (personal); cr558@cornell.edu (academic) (631) 943-8370 | Ithaca, New York

EXPERIENCE

Livepeer, NYC Consultant in Operations | March 2019—August 2019 ● Worked as a consultant in operations, advising on financial, strategic, and people operations projects

YouNow, Inc., NYC VP Operations | April 2018—February 2019 ● Oversaw all operations for the company, including but not limited to OKR management and alignment, strategic

initiatives to execute on company mission, budgeting across departments, and increasing productivity company-wide ● Lead people operations across company, helping to motivate teams and facilitate feedback loops between management

and staff ● Liaison with legal compliance of all mobile apps, also leading trust & safety and customer service departments

VP Community Operations | January 2016—April 2018 ● Developed and lead the community department within the company, working to improve engagement with our user

base, and create a method of communication between users and internal teams ● Led trust & safety, fraud prevention, and customer service departments

Director, Trust & Safety | July 2013—January 2016 ● Built processes for trust & safety and fraud prevention teams from the ground up

Content Manager | October 2012—July 2013 ● Managed relations with Internet influencers to grow YouNow’s user base

EDUCATION

Cornell University Ithaca, New York | Current student, graduation expected 2020 Master of Professional Studies (MPS), Natural Resources State University of New York at Geneseo Geneseo, New York | September 2008—December 2011 Bachelor of Arts: English Literature and Environmental Studies

SPEAKING ENGAGEMENTS VidCon, Anaheim, CA | June 2017 ● Ideated and moderated a panel called, “Protecting Yourself Online,” featuring three Internet influencers

Social Computing Symposium, Microsoft Research, NYC | January 2016 ● Spoke on panel with other trust & safety professionals

TechWeek, NYC | October 2015 ● Spoke on a panel entitled, “Moderating Online Content for Quality vs. Freedom of Speech”

SPECIAL PROJECTS/SKILLS

● Member: Union Square Ventures Women’s Executive Leadership Program ● Organizer and Gardener: Geneseo Food Project and Community Supported Market (CSM), 2008—2011

YUE REN

C O N T A C T

Cornell, Ithaca,USA

yr233@cornell.edu

(607) 697 3742

renyue402

C O R N E L L

U N I V E R S I T Y Ph.D. Student in MAE

K O R E A A D V A N C E D

I N S T I T U T E O F

S C I E N C E A N D

T E C H N O L O G Y

Bachelor of Science 2012–2016

GPA: 3.92/4.3

Major GPA: 4.11/4.3

Awarded Dean’s list 2014 Fall

（Top3%）

S E L E C T E D S K I L L S

Programming ★★★★★

Embedded Systems ★★★★★

PCB Design ★★★★★

3D printing ★★★★★

Molding ★★★★★

Wireless ★★★★★

Data Analysis ★★★★★

IOS app dev ★★★★★

P R O G T A M M I N G

L A N G U A G E S

Python ★★★★★

Java ★★★★★

MATLAB ★★★★★

C/C++ ★★★★★

Java Script ★★★★★

Swift ★★★★★

E X P E R I E N C E Graduate research assistant, Integrated Micro & Nano Fluidic Systems Lab,

Cornell University Oct 2016 – now MOSQUITONET

Design UAV for automatically image capturing and navigation in a tasked area.

Collect data from neighborhood in NY city and studying the relationship

between water, waste and mosquito larva. Using neural networks to analysis the

image taken to help increase the efficiency of integrated mosquito

management.

TIDBIT II

Design and build a compact, Bluetooth integrated platform for lateral flow strip

automatic analysis. This device takes image with Raspberry Pi 3 under UV light

and automatically extract the line intensity, substrate the background light of

the strips with python, and communicate the result through Bluetooth with

customized iOS app developed through Xcode.

E-SYNCH

Develop an intravaginal drug delivery platform to automate and optimize cattle

reproductive management. This device composed of 3D printing of solid and

flexible materials, molding for protection and water sealing, peristaltic pump for

drug delivery, customized PCB for controlling, sensing and RF communication

with optimized power consumption.

Undergraduate research assistant, Nano Integrated Circuits Expertise lab,

KAIST Sep 2014 – 2015 VOLTAGE FEEDBACK CONTROL

Designed feedback control of output voltage given data acquired from data-

acquisition using Labview

AUTOMATIC CHARGER

Designed a Modular Li-Ion Battery charger for automated test and evaluation

of entropy based algorithm of charging and discharging patterns using

dynamic current to prevent decay and improve safety. Development of

algorithm and power PCB handling 8 batteries with feedback control of current.

SMART CHARGING ALGORITHM

Characterized optimal charging patterns for the different electrolytic phases of

Li-Ion batteries.

S K I L L S Software Development

C, C++, Python, Java, MATLAB, Cypress PSoC Designer, Digital Signal

Processing, Feedback Control, Machine Learning, Data acquisition, iOS app

development, FPGA

Hardware Development

VSM/AMS simulation and PCB design, Verilog HDL on ModelSim, Drone

development, 3D printing, molding

Known Hardware:

Arduino, raspberry Pi, BeagleBone (ARM/Linux), CC13X0, CYKIT8-BLE (Cypress

PSoC/PRoC), PixHawk, NI USB-6000 (IO DAQ), DE1-SoC

S E L E C T E D L E C T U R E P R O J E C T FPGA Convolution Neural Network Accelerator

• Implemented the picture features extraction through running CNN on FPGA.

• Designed and built Verilog system in DE1-Soc and implemented convolution

layer calculation which improves algorithm performance by 12% compared to

calculation on HPS in C++

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Dr. Nisha Singh Post-Doctoral Scientist Institute of Genomic Diversity, Cornell University 175 Biotechnology Building Ithaca, New York, USA 14853 Mob: +1-607-216-7363, +91-9650908143

E-Mail ID: singh.nisha88@gmail.com, ns868@cornell.edu https://www.maizegenetics.net/nishasingh https://scholar.google.co.in/citations?user=occkhqAAAAAJ&hl=en https://www.researchgate.net/profile/Nisha_Singh18/publications?sorting=newest&page=2

SUMMARY

• Post-Doctoral Scientist (Buckler’s Lab) at Institute of genomic diversity, Cornell University Ithaca

New York, USA (February2019-Till).

• Ph.D. (Biotechnology) thesis entitled “DEVELOPMENT AND APPLICATIONS OF GENOME WIDE

HIGH-DENSITY SNP GENOTYPING ASSAYS FOR THE CHARACTERIZATION OF INDIAN

WILD RICE GERMPLASM”, (April, 2018), completed under the guidance of Dr. Sukhjeet Kaur (HOD

Biotechnology) & Dr. N. K. Singh (ICAR, National Professor in plant Genomics) from National

Research Centre on Plant Biotechnology, New Delhi India .

• M.Sc. (Bioinformatics) from Orissa University of Agriculture and Technology, Bhubaneswar, Orissa.

• Proficiency in Genomics, Comparative Genomics, Evolutionary Genetics, Bioinformatics tools, scripting

with R and perl, NGS Data analysis, Proteomics techniques and data analysis (2-D, MALDI TOF-TOF),

Protein modelling, Molecular Biology techniques, and Plant tissue culture.

• Experience in genome sequencing, Repeats finding, synteny analysis, gene annotations, GWAS, gene

identifications, Marker developments (SSR and SNP), assay design, QTL mapping and identifications,

diversity analysis, populations stratifications, gene based haplotypes identification and analysis and tools

development

• Teaching experience ranges from large lectures to undergraduate students to practicing professionals from

local and international academic institutions

FIELD OF SPECIALIZATION - (Genomics, Proteomics, NGS Big data analysis, structural Biology,

Molecular biology and Bioinformatics)

• Genomics, Evolutionary Genetics, GWAS, Proteomics, Transcriptomics, NGS Big Data analysis, gene

identification, Marker development (SSR and SNP), assay design, QTL mapping and identification,

diversity analysis, population stratification, gene based haplotypes identification and analysis, BI tool

development, Protein modeling, Molecular Biology, scripting in R and PERL.

ABSTRACT OF PhD. RESEARCH WORK

• Developed first (Genic, rice genomic resource) 50K “OsSNPnks” single copy gene based SNP

genotyping chip for genetics and molecular breeding applications in rice. The chip incorporates 50,051

high qualities, non-redundant SNPs from 18,980 different genes spanning 12 rice chromosomes, including

2

3,710 single-copy (SC) genes conserved between wheat and rice, 14,959 SC genes unique to rice, 194

agronomically important cloned rice genes and 117 multi-copy rice genes. The novelty of this high-

density 50K genic rice SNP chip it has 96% SNPs from SC genes. Rice is native to India is the verdict

through this chip published in “Nature Scientific Reports”, (Singh et al., 2015) have effectively

proved that the rice varieties grown in India have actually originated in India. Chip is already finding use

and the popular Pusa Basmati-1 variety has recently been made resistant to a damaging disease called 'rice

blast' and to develop this new resistant variant the chip was deployed. The chip is also being used to

develop varieties of rice that can tolerate long durations of flooding. Modern molecular breeding can help

bridge this yield gap and the chip will be helpful.

• Genome wide 48-plex GoldenGate SNP assay was also designed for the characterization and population

structure analysis of total 418 Indian wild rice accessions of Oryza nivara/ Oryza rufipogon complex

collected from nine different eco-geographical regions of India published in Frontier in plant Sciences

(Singh et al., 2018).

• Haplotypes based analysis was done on pericarp color (Rc), hull color (Bh4), grain size (GS3) and ten

different starch synthase genes (GBSSI, SSSI, SBE3, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, SSIVb and ISA2)

to infer the mystery of rice evolution and domestication, published in “Frontiers in plant sciences”,

(Singh et al., 2017).

• Study the convergent and divergent evolution of rice using 50K genic rice chip.

AREA OF RESEARCH WORK

• Currently working on NGS Phase-2 of Cassava at Cornell University, USA.

• Whole Genome Sequencing, Annotation and comparative analysis-Pigeonpea, Jute, Mango.

• Affymetrix genic SNP Chip designing- Rice 50K (OsSNPnks), Pigeonpea- 62K (CcSNPnks) and mango

82K (MiSNPnks)

• Genome wide Association mapping (GWAS) -Rice and Mango.

• High throughput SNPs genotyping of (Oryza sativa) using GOLDENGATE assay technology and

Affymetrix SNP array.

• Designed 48-plex GoldenGate Assay for wild rice population stratification.

• Designed 6K Infinum Assay for rice genotyping.

• Phylogenetic and evolutionary study of Indian wild rice germplasm.

• Population structure analysis - Rice, Wheat, Pigeonpea and Mango.

• Phylogenetic and evolutionary studies in Mango.

• Gene based haplotype analysis -Rice, Mango and pigeonpea

• Proficient in microarray data analysis

• Proteomics & Pathway analysis of Pigeonpea.

• Developed promoter prediction tool for sandfly.

• Identified cloned agronomically important Pigeonpea genes in the development of 60K Single-copy

genes based SNP chip of Pigeonpea.

• Proficient in handling Big data from Different NGS Platforms like Affymetrix, Illumina and Aglient

3

• Experience in integrating and analysing whole-genome resequencing and comparative genomics data sets.

• Expertise in writing Scripts in R and Perl.

EDUCATION QUALIFICATIONS

• Ph.D. (Life Science-Biotechnology) thesis en ti t led “Development and applications of

genome wide high-density SNP genotyping assays for the characterization of Indian

wild rice germplasm”, (2018), completed under the guidance of Dr. Sukhjeet Kaur

(HOD Biotechnology) & Dr. N. K. Singh (ICAR, National Professor in plant

Genomics) from National Research Centre on Plant Biotechnology, New Delhi India .

• Orissa University of Agriculture and Technology, Bhubaneswar, September 2010, Master of Science in

Bioinformatics, 78.10% (2nd University topper).

Thesis enti t led “Computational Drug Designing against KALAZAR targeting Chitinase enzyme of

Phlebotomus Papatasi (Sand Fly Vector)”

• Ranchi University, (Ranchi Women’s College), Jharkhand, June 2008, Bachelor of Science in

Biotechnology, 72.08% (Gold Medalist).

Thesis enti t led “in vitro Callus Induction, Multiplication and Organogenesis in Schleichera oleosa

(Kusum)”

• Kendriya Vidyalaya, Namkum, Ranchi, (CBSE Board), May 2005, Intermediate of Science (10+2) 71.9%.

• Kendriya Vidyalaya, Namkum, Ranchi, (CBSE Board), May 2003 SSC (10th) 63%.

CERTIFICATION COURSE • Certification course in Linux and Python.

• Diploma in Computer application March 2005-June2006.

• Six-month certification course in C, C++ and JAVA.

AWARDS & HONOURS - 8

• DST-Inspire Faculty award 2019 February.

• Young Biotechnologist award, JNU, New Delhi, April 2018.

• Young Scientist award, International Conference on Global Research Initiatives for Sustainable

Agriculture & Allied Sciences (GRISAAS), Udaipur, Rajasthan, December 2017.

• First prize in Oral Presentation (Rs. 10,000/-) in 5th Rajasthan Science Congress, Jaipur Rajasthan,

October 2017.

• Scientific Associate Award, ICASS, Hyderabad, December 2016.

• ARS NET Qualified (Agriculture Biotechnology) with 89.9% May 2014.

• Bioinformatics National Certification Examination Qualified 2013.

• GATE Qualified 89 percentile (Biotechnology) 2011.

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PROFESSIONAL EXPERIENCE

• Post-Doctoral Scientist (Buckler’s Lab) at Institute of genomic diversity, Cornell University Ithaca

New York, USA February 2019 onwards .

• Research Associate 1 July 2018- January 2019 National Research Centre on Plant

Biotechnology, LBS Building, IARI, New Delhi.

• Assistant Professor, Department of Computat ional Sciences (Bioinformatics), Central

University of Punjab, Bathinda, February 2018-June 2018.

• Senior Research Fellow, Rice Genome, National Research Centre on Plant Biotechnology, LBS Building,

IARI, New Delhi from 26 July 2011-February 2018. In project entitled “Allele Mining for Abiotic Stress

tolerance genes in wild rice and landraces germplasm growing in hot spot regions of India” Supervisor-

Dr. Nagandra Kumar Singh (ICAR-National Professor).

• 7-month, Traineeship (1/01/201111 to 25/07/2011), on “In silico structural and mutational analysis of

Lactoferrin protein within Camelus, Bovine and Human” Supervisor-Dr. J.K. Kaushik, Senior Scientist

at Animal Biotechnology Centre (ABTC) National Dairy Research Institute (NDRI), Karnal-132001

(Haryana).

TEACHING ASSIGNMENTS

M.Sc. (Life Science specialization in Bioinformatics)

• System Biology, Course Code-LB1.621 (Credits: 4)

• Molecular Evolution, Course Code-LB1.622 (Credits: 4)

• Sequence Analysis, Course Code-LB1.522 (Credits: 3)

STUDENT GUIDED- 3 MSc Bioinformatics thesis, 1 MPhil. Biotechnology

RESEARCH PATENT AND PUBLICATIONS Patent - “Design and validation of a single-copy gene based 50K SNP chip for association mapping and molecular

breeding in rice” Nisha Singh, T. R. Sharma & N.K. Singh Application number 2280/DEL/2014 11.8.2014.

RESEARCH PAPERS total-22, citations-232 impact factor papers-50.23, patent-50, Total IF=100.23 h

index-8.

1. Nisha Singh, Pawan Kumar Jayaswal, Kabita Panda, Paritra Mandal, Vinod Kumar, Balwant Singh,

Shefali Mishra, Yashi Singh, Renu Singh, Vandna Rai, Anita Gupta, Tilak Raj Sharma & Nagendra

Kumar Singh Single-copy gene based 50K SNP chip for genetic studies and molecular breeding in rice

(2015) “Nature Scientific Reports” 5:11600 | DOI: 10.1038/srep11600. IF-5.56 citations-52

2. Nisha Singh, Neha Jain, Ram Kumar, Ajay Jain, Nagendra K Singh, Vandna Rai. A comparative method

for protein extraction and 2-D gel electrophoresis from different tissues of Cajanus cajan (2015).

“Frontiers in Plant Science” 6, 606 DOI: 10.3389/fpls.2015.00606. IF-4.29 citations-10

3. Nisha Singh, Balwant Singh, Vandna Rai, Sukhjeet Sidhu, A. K. Singh, and N. K. Singh. “Evolutionary

Insights Based on SNP Haplotypes of Red Pericarp, Grain Size and Starch Synthase Genes in Wild and

Cultivated Rice” (2017), Frontiers in Plant Science, DOI: 10.3389/fpls.2017.00972. I. F. 4.29

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4. Renu Singh, Yashi Singh, Suchit Xalaxo, S. Verulkar, Neera Yadav, Shweta Singh, Nisha Singh, K.S.N.

Prasad K et al., From QTL to variety- harnessing the benefits of QTLs for drought, flood and salt tolerance

in mega rice varieties of India through a multi-institutional network (2015). “Plant Sciences” DOI:

10.1016/j.plantsci.2015.08.008. IF-3.9 citations-39

5. Bikram Pratap Singh, Pawan Kumar Jayaswal, Balwant Singh, Pankaj Kumar Singh , Vinod Kumar,

Shefali Mishra, Nisha Singh, Kabita Panda, Nagendra Kumar Singh Natural allelic diversity in

OsDREB1F gene in the Indian wild rice germplasm led to ascertain its association with drought tolerance

(2015) Plant Cell Rep. DOI 10.1007/s00299-015-1760-6. IF-2.9 citations-20

6. Sonia Goel, Nisha Singh, Sapna Grewal, Shilpa D’souza, Ajay Mahato, N. K. Singh. Single nucleotide

polymorphism in wheat triticin gene (Tri 1) among diverse wild wheat species. “Australian Journal of

Crop Science” 9(12):1131-1138 (2015). IF-1.9

7. Ram Kumar, Nisha Singh, Neha Jain, Nagendra K Singh, Vandna Rai. Phenomics approach in drought

tolerant and sensitive cultivars of rice International journal of tropical agriculture 33, 2, 1559-1564 (2015).

8. Shefali Mishra, Balwant Singh, Kabita Panda, Nisha Singh, Bikram Pratap Singh, Pragati Misra, Vandna

Rai, Nagendra Kumar Singh “Association of SNP Haplotypes of HKT Family Genes with Salt Tolerance

in Indian Wild Rice Germplasm” (2015). “Rice” (2016) 9:15 DOI 10.1186/s12284-016-0083-8. IF-3.9

citations-10

9. Nagendra K. Singh, Ajay K. Mahato, Pawan K. Jayaswal, Akshay Singh, Sangeeta Singh, Nisha Singh,

Vandna Rai et al., Origin, Diversity and Genome Sequence of Mango (Mangifera indica L.) (2016).

Indian Journal of History of Science, 51.2.2

10. Nisha Singh, Balwant Singh, Vandna Rai, Sukhjeet Kaur and Nagendra Kumar Singh. “Haplotype based

phylogenetic analysis of black hull (Bh4) gene in wild and cultivated rice”, (2016), Progressive Research

- An International Journal, Volume 11 (Special-VII): 5082-5084. citations-1

11. Nagendra Kumar Singh, Balwant Singh, Shefali Mishra, Nisha Singh, Kabita Panda and Vandna Rai.

“Indian wild rice: diversity, population structure, trait value and relation with cultivated rice”, (2016),

Indian J. Plant Genet. Resour. 29(3): 366-368 DOI 10.5958/0976-1926.2016.00072.3. citations-2

12. Debabrata Sarkar, A. K. Mahato, Pratik Satya, Avijit Kundu, Sangeeta Singh, Nisha Singh, Pawan K

Jaswal et al., “The draft genome of Corchorus olitorius cv. JRO-524 (Navin)”, (2017), Genomics Data,

DOI: 10.1016/j.gdata.2017.05.007.

13. Balwant Singh, Nisha Singh, Vandna Rai, Shefali Mishra, Kabita Panda, A. K. Singh, and N. K. Singh.

“Morphological and molecular variations delineate species and population structure of Indian wild rice

Oryza rufipogon Griff. species complex” (2018), 9, 123 Frontiers in Plant Science, DOI:

10.3389/fpls.2018.00123. I. F. 4.29.

14. Pragya Mishra, Nisha Singh, Ajay Jain, Neha Jain, Vagish Mishra, Pushplatha G, Kiran P. Sandhya,

Nagendra Kumar Singh, Vandna Rai “Co-expression gene interaction networks and common cis-

regulatory elements for salinity and drought stress tolerance in rice” (2018) Bioinformation 14(3): 123-

131.

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15. PoojaArchana Sahani1, Megha Ujinwal1, Sangeeta Singh2, Nisha Singh1* “Genome wide insilico

characterization of dirigent protein family in flax (Linumu sitatissmum L)” (2018), Plant Archevies 18,

61-68, NAS IF-4.9.

16. Kabita Tripathy, Balwant Singh, Nisha Singh, Vandna Rai, Gouri Mishra, Nagendra Singh “A database

of Oryza rufipogon species complex wild rice germplasm collected from different agro-climatic zones of

India” (2018), Oxford Database, bay058 I.F. 3.9. doi: 10.1093/database/bay058 IF 3.9.

17. Mishra Pragya, Jain Ajay, Takabe Teruhiro, Tanaka Yoshito, Negi Manisha, Singh Nisha, Jain Neha,

Mishra Vagish, Waditee-Sirisattha, Rungaroon Maniraj, R Krishanmurthy, S Sreevathsa, Rohini, Singh

Nagendra, Rai Vandna. “Heterologous Expression of Serine Hydroxymethyltransferase-3 From Rice

Confers Tolerance to Salinity Stress in E. coli and Arabidopsis”. (2019) 10, 217

https://doi.org/10.3389/fpls.2019.00217 IF 3.6

18. Megha Ujinwal, Pooja Archana Sahani and Nisha Singh* “Comparative sequence and structural analysis

of lectin protein in chickpea (Cicer crietinumn L.) and their relationship with fabaceae family”. accepted

in International Journal of Proteomics and Bioinformatics (2019) IF 1.2.

19. Sangeeta Singh , Ajay Mahato, Pawan Jayaswal , Nisha Singh , Meenakshi Dheer , Preeti Goel, Ranjeet

Raje, Jeshima Khan Yasin, Rohini Sreevathsa, Vandna Rai, Kishor Gaikwad, N. K. Singh. “A 62K genic-

SNP chip for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.)” 2019

accepted in Scientific Reports IF 4.4.

20. Aditi Bhandari, Pawan Jayaswal, Neera Yadav, Renu Singh, Yashi Singh, Balwant Singh, Nisha Singh,

Sangeeta Singh, Amitha Sevanthi, Vandna Rai, Satish Verulkar “Genomics-assisted backcross breeding

for infusing climate resilience in high-yielding green revolution varieties of rice” Indian J. Genet., 79(1)

Suppl. 160-170 (2019) doi: 10.31742/IJGPB.79S.1.5. IF 1.2.

21. Sufia Farhat, Neha Jain, Nisha Singh, Sandeep Yadav, Pramod Kumar, Rohini Sreevathsa, Prasanta

Dash, Rhitu Rai, Ananda K Sarkar, Vandna Rai, Ajay Jain, Nagendra Kumar Singh “CRISPR-cas 9

directed genome engineering for enhancing salt stress tolerance in rice”. 2019 Seminars in Cell and

Developmental Biology https://doi.org/10.1016/j.semcdb.2019.05.003. IF 6.9

22. Wang, Hai; Cimen, Emre; Singh, Nisha; Buckler, Edward S “Deep Learning for Plant Genomics and

Crop Improvement” accepted in Current Opinion in Plant Biology IF 7.8.

BOOK CHAPTERS-3

1. Nisha Singh “Advances of NGS technologies to enhanced the Biofortifications in crops” Springer,

Nature, Singapore 2019.

2. Nisha Singh “Genetic diversity, population structure and Genome wide association studies (GWAS) in

crop plant”, “CAFT- NGS applications in crop sciences”, published by ICAR- National research centre

on plant Biotechnology, New Delhi, India, 2017.

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3. Nisha Singh “Applications of SNP genotyping using SNP chips”, “CAFT- NGS applications in crop

sciences”, published by ICAR- National research centre on plant Biotechnology, New Delhi, India,

2017.

4. Ram Kumar, Neha Jain, Vagish Mishra, Nisha Singh, Pragya Mishra, Sajad Majeed Zargar, Ajay Jain,

Nagendra Kumar Singh, and Vandna Rai. Potentialities of Proteomics for Generating Abiotic Stress

Tolerant Crop Species. “Plant OMICS and Crop Breeding” Apple Academic Press. USA, 2017.

INVITED TALKS-2

1. Delivered a lecture on “Development and applications of genic SNP genotyping chip for molecular

breeding in rice”, 5th Rajasthan Science Congress, 13-15 Oct 2017, Amity Jaipur Rajasthan.

2. Delivered a lecture on “Development of a 48- plex SNP genotyping GOLDENGATE assay for molecular

characterization of Indian wild rice germplasm”, National Conference on Innovative and Current

Advances in Agriculture and Allied Sciences (ICAAAS-2016), 10-11 December 2016, Hyderabad.

TRAINING DELIVERED- 21 days training program on “Next Generation Sequencing and its

Applications in crop Sciences” from 1-21 December, 2017, under the aegis of ICAR sponsored centre

for advanced faculty training in plant Biotechnology at ICAR-NRCPB, New Delhi, India.

POSTER & PAPERS PRESENTED AT CONFERENCES-12

1. Nisha Singh, Balwant Singh, Vandna Rai, Sukhjeet Sidhu and Nagendra Kumar Singh. P0768-

“Evolutionary Insights Based on Haplotype and Phylogenetic Analysis of Red Pericarp, Grain Size and

Starch Synthase Genes in Wild and Cultivated Rice”, Plant and Animal Genomics, January 13 - 18,

2017, San Diego, CA, USA.

2. Nisha Singh, Vandna Rai, Sukhjeet Sidhu and Nagendra Kumar Singh. “Applications of Genome Wide

Association Studies (GWAS) for Crop Improvement”, International Conference on Global Research

Initiatives for Sustainable Agriculture & Allied Sciences (GRISAAS), Udaipur, Rajasthan, December 2-

4, 2017.

3. Nisha Singh, Balwant Singh, Vandna Rai, Anita Gupta and Nagendra Kumar Singh. Genetic diversity

and phylogenetic analysis of Indian wild rice germplasm based on 50K genotyping chip. 6th World

Congress on Biotechnology October 05-07, 2015 New Delhi, India. J Biotechnol Biomater. 2015, 5:6

http://dx.doi.org/10.4172/2155-952X.C1.044.

4. N. Singh, P. Jayaswal, V. Rai, T.R. Sharma1, A. Gupta, N.K. Singh. Design and validation of a single-

copy gene based 50K SNP chip for association mapping and molecular breeding in rice “4 International

Rice Congress”, 27 Oct-1 Nov 2014, Bangkok Thailand.

5. Nisha Singh, Vandna Rai, Anita Gupta & Nagendra Kumar Singh. Analysis of background recovery

in backcross derived submergence tolerant rice varieties using 50K (OsSNPnks) chip “Emerging

challenges and Opportunities in Biotic and Abiotic Stress management (ECOBASM-2014)” 13th and 14th

December, 2014 at Directorate of Rice Research, Rajendranagar, Hyderabad

8

6. Singh Nisha, Singh Balwant, Mishra Shefali, Panda Kabita, Singh Renu, Rai Vandna, Singh N. K.

Designing and validation of a 48-plex GoldenGate SNP assay for determining the population structure

in wild rice. “National Conference on Science of Omics for Agricultural Productivity: Future

Perspectives”, March 4-6, 2014. Uttarakhand, India.

7. Singh N, Jaiswal P, Panda K, Mandal P, Mishra S, Singh B, Singh R, Sharma TR, Gupta A, Singh NK.

Development and validation of a 50K SNP genotyping chip based on conserved single copy and

domestication related rice genes. “International Symposium of Rice Functional Genomics Sustaining

Food & Nutritional Security”, Nov. 20 – 23, 2013, New Delhi, India

8. Singh Balwant, Mishra Shefali, Singh Nisha, Panda Kabita, Singh B. P., RaiVandna, Bhawmick P. K.,

Singh A. K., Singh N. K. Morphological and genetic characterization of wild rice germplasm collected

from different state of India. “International Symposium of Rice Functional Genomics Sustaining Food &

Nutritional Security”, Nov. 20 – 23, 2013, New Delhi, India

9. Mishra S, Singh B, Panda K, Singh N, Rai V,Singh AK, Singh NK. Allele mining of high affinity

potassium transporter genes in Indian wild rice germplasm (O. nivara and O. rufipogon) accessions. .

“International Symposium of Rice Functional Genomics Sustaining Food & Nutritional Security”, Nov.

20-23, 2013, New Delhi, India

10. Kabita Panda, Balwant Singh, Nisha Singh, Shefali Mishra, VandanaRai, Tilak R Sharma Nagendra K

Singh. A web enabled database of wild rice germplasm collected from different geographical niches of

India. “International Symposium of Rice Functional Genomics Sustaining Food & Nutritional Security”,

Nov. 20 – 23, 2013, New Delhi, India

11. Singh Balwant, Mishra Shefali, Singh Nisha, Panda Kabita, Singh B. P., Singh Dipika, Rai Vandna,

Bhawmick P. K., Singh A. K., Singh N. K. Short interspersed elements (p-SINE) markers based

categorization of Indian wild rice. “National Conference on Science of Omics for Agricultural

Productivity: Future Perspectives”, March 4-6, 2014, Uttarakhand, India

12. Singh B P, Jayaswal P K, Singh Balwant, Mishra Shefali, Panda Kabita, Singh Nisha, Singh A K and

Singh N K. Diversity analysis of registered rice varieties and wild rice germplasm using molecular

markers. International Conference on Plant Biotechnology for Food Security: New Frontiers, 20-23

February, 2012. New Delhi, India.

INTERVIEWS/ POPULAR MEDIA-3

• Indian scientists' new DNA chip for speeding up rice breeding Read more at: //economictimes.indiatimes.com/articleshow/47944320.cms?utm_source=contentofinterest&utm_medium=text&utm_campaign=cppst. July 5, 2015.

• No match for mango's diversity, http://www.thehindu.com/sci-tech/science/No-match-for-mangos-diversity/article14494261.ece. July 17, 2016.

9

• Genome sequencing can spin disease-free jute, soon. http://www.thehindubusinessline.com/economy/agri-business/genome-sequencing-can-spin-diseasefree-jute-soon/article9686799.ece. May 8, 2017.

BIOINFORMATICS SKILLS Bioinformatics Tools : ORF Analysis, MEGA, Modeller, BioEdit, RASMOL, CN3D,

ClusterW, ClusterX2.0.1win, Swiss PDB viewer eLnemo, Genome Studio, Yashra, GOLD, SILVER,

Chemsketch, GTC, PLINK, TASSEL, GAPIT, FigTree, PowerMarker, DNAsp, Darwin, QTL cartographer,

Joinmap, Genalex, Image master 2D platinum, Decider, PopGene, Affymetrix power tool, STRUCTURE,

DESTRUCT, Fast Structure, Network, and CLC Genomic.

Statically software : SPSS and SAS.

COMPUTER SKILLS:

Operating Systems : MS-DOS, Win 95/98/2000/XP, Linux (Red hat), Ubuntu.

Programming Languages : C, C++, Data structure, Java, Perl and R language.

Databases : MS-Access, FoxPro, Oracle (10 g), mySQL.

PROJECTS EXPERIENCE

M.Sc. (Bioinformatics)

PROJECTS #1

Organization : Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna

Period : Feb 15/2010-June16/2010

Project Title : Computational Drug Designing against KALAZAR targeting Chitinase

enzyme of Phlebotomus Papatasi (Sand Fly Vector)

Key Learning Area :

Work on Software : Discovery Studio 2.0, GOLD 2.1, AUTO Dock, Flex X, Yasara, FoldX,

Preflex, Genespring gx and Chemskech.

PROJECT #2 • Mini project on the “Analysis and Prediction of Secondary Structure of Myosin Protein by using GOR 4,

nn Predict and PHD Server” under the guidance of Suchrita Balabant Roy from Orissa University of

Agriculture and Technology, Bhubaneswar.

B.Sc. (Biotech) PROJECT AND TRAINING

PROJECT

• Six months project work on “in vitro callus induction, Multiplication and Organogenesis in Schleichera

oleosa (Kusum)” under the guidance of Dr. Dipnarayan Saha from Dept. of Biotechnology, Indian

Institute of Natural Resins & Gums (ICAR), Namkum, Ranchi, Jharkhand.

WORKSHOPS & CONFERENCE ATTEND - 11

• Computational Biology Workshop, 12-14 March 2018, NABI, Mohali, Punjab

• International Conference on Global Research Initiatives for Sustainable Agriculture & Allied Sciences

(GRISAAS-2017), 02-04 December 2017 at MPUAT, Udaipur, Rajasthan.

• 5th Rajasthan Science Congress, October 13-15, 2015 Jaipur Rajasthan.

10

• National Conference on ICAAAS-2016 at PJTSAU Hyderabad on date 10-11 December 2016.

• 6th World Congress on Biotechnology October 05-07, 2015 New Delhi, India.

• 4th International Rice Congress”, 27 Oct-1 Nov 2014 Bangkok, Thailand.

• ECOBASM-2014 13th and 14th December, 2014 at Directorate of Rice Research, Rajendranagar,

Hyderabad.

• International Symposium of Rice Functional Genomics Sustaining Food & Nutritional Security”, Nov. 20

– 23, 2013, New Delhi, India

• National Conference on Science of Omics for Agricultural Productivity: Future Perspectives”, March 4-

6, 2014. Uttarakhand, India.

• International Conference on Plant Biotechnology for Food Security: New Frontiers”, 20-23 February,

2012. New Delhi, India.

• Participated in “National conference on recent advances in environment biotechnology” for Forest

biodiversity management, organized by Ranchi women’s college, Ranchi- 2007

TRAININGS - 4

• 3rd national training-cum workshop on “Bioinformatics & its Significant” in Agricultural research,

BTIS net DBT Project organized by OUAT, Bhubaneswar 2010.

• Participated in training cum-workshop on “Bioinformatics & Information Management in Aqua

culture” organized by DBT CIFA (Central institute of fresh water Aquaculture.) Bhubaneswar, 2009.

• 20 days training in Vaccine Production, ELISA Test, Seed Analysis and Disease Diagnosis Dept. Of

Animal Husbandry, Institute of Animal; Health Production, Kanke, Ranchi (Jharkhand).

• 15 days training in Pathological Test from Dept. of Pathology, Rajendra Institute of Medical

Sciences, Ranchi (Jharkhand).

MEMBERSHIP

Life Member of Society for Scientific development in Agriculture and Technology (SSDAT).

PERSONAL DETAILS

Date of Birth : 2nd Jan 1988

Marital Status : Married

Nationality : Indian

Gender : Female

Father’s Name : Late. M. M. Singh

Mother’s Name : Mrs. Kiran Devi

Husband’s Name : Manish Kumar

Residential Address (India) : Nisha Singh, WZ- 256, F/4, IInd floor, Opposite to Goel

medicos Inderpuri, New Delhi-110012 (India)

Residential Address (USA) : 2314, Hasbrouck Apartments, 121 Pleasant Grove Rd, Ithaca,

NY,14850

11

STRENGTH

• Self Confidence, Sincere, Disciplined, Committed, Hardworking, Determined, Dedicated, Punctuality, Honest, Energetic, Friendly & always strive to give the best.

DECLARATION: • I hereby declare that the above information is true to the best of my knowledge. PLACE: - Ithaca, New York (USA) _______________ SIGNATURE

GenevieveSullivangbs55@cornell.edu cell:(607)229-0268 EDUCATIONCornellUniversity,CollegeofAgricultureandLifeSciences,Ithaca,NY DoctorofPhilosophyinFoodScience,GPA:3.5 August2016–PresentCornellUniversity,CollegeofAgricultureandLifeSciences,Ithaca,NY BachelorofScienceinFoodScience,withDistinctioninResearch,GPA:3.7 May2016NationalUniversityofSingapore,FacultyofScience,SingaporeExchangeStudent Spring2015KEYFACTS4Publications3IndustryInternships6FoodSafetyCertifications11ProfessionalOralPresentations

11Awards30FoodFacilityConsultations8STEMStudentOutreachEvents3IndustryWorkshopsOrganizedandDelivered

FOODSAFETYRESEARCHDr.MartinWiedmann Ithaca,NYFoodSafetyLab,CornellUniversity August2016-Present• CurrentprojectinvolvesdevelopingListeriacontrolstrategiesforprocessingfacilitiesnationwidebydesigning,implementing,andevaluatingListeriapathogenenvironmentalmonitoring(PEM)andseekanddestroyprograms.Evaluationoftheseprogramsisaidedbydatafromwholegenomesequencing(WGS)andhqSNPanalyses.

• Completedprojectthatevaluatedclassicalandmolecularmethodsfortheirabilitytodetectfoodbornepathogensinchallengingmatrices,usingSalmonellaindarkchocolateandpetfoodasmodelsystems.

• ServesastheCornellliaisontotheCDCNewYorkIntegratedFoodSafetyCenterofExcellence.Coordinate,moderate,anddelivertrainingsrelatedtowholegenomesequencingandmolecularepidemiology.

Dr.RenataIvanek Ithaca,NYEpidemiologyofFoodborneDiseasesComputerLab,CornellUniversity January2019-Present• CurrentprojectinvolvesusingamodelingandcomputationalapproachtosimulateandevaluatescenariosofListeriacontaminationandspreadinproduceoperationstooptimizesampling,correctiveactionstrategies,andoverallcontrolprograms.

Dr.CarmenMoraru Ithaca,NYFoodSafetyEngineeringLab,CornellUniversity January2013-July2016• Project1(2015-2016):Honorsthesisinvestigatedphysicochemicalpropertiesoffoodpackagingsurfacesandtheeffectonbacterialattachment.Received2ndplaceforposterandoralpresentationatIFT16UndergraduateResearchCompetition.

• Project2(2013-2015):IndependentresearchfocusedontheeffectivenessofpulsedlighttreatmentusedassingletreatmentandinahurdlestrategyontheinactivationofListeriainnocuaonprocessedcheese.Optimizedtheexperimentaldesign,independentlyexecutedthework,processedtheexperimentaldataandformulatedtheconclusionsofthework.Refinedproblemsolvingskillsinadynamicenvironment.

• Project3(2013):Contributedtoagraduatestudentprojectonexperimentinvolvingappleciderfiltration.Independentlyusedandmaintainedmembranesystems.

FOODSAFETYTRAINING/CERTIFICATIONSFSPCAPreventiveControlsQualifiedIndividualforHumanFoods(PCQI),Epi-ReadyTeamTrainingFoodborneIllnessResponse,GeneralHACCP,SeafoodHACCP,ImplementingSQFSystems(Post-FarmGate),GoodManufacturingPractices(GMP)

INDUSTRYEXPERIENCEIBM SanJose,CaliforniaResearchIntern Summer2019• MemberoftheIndustrialandAppliedGenomicsGroup,whichusesgenomicsandmetagenomicsforappliedgoalssuchasadvancingfoodsafety,throughadvancedsoftwareandsystemstogetherwithrigorousscience.

• Projectfocusedonevaluatingtheeffectivenessofwell-knownandnewbioinformaticsmethodsincomparingbacterialgenomes,usingcomputationalexperimentsbasedontestcasesderivedfrompublicandproprietarygenomicdata,usingapowerfulcomputingplatformforbioinformatics.Communicatedfindingstorelevantstakeholders,includingcomputerscientistsandfoodindustrycollaborators.

• Servedasafoodsafetysubject-matter-expertinarangeofdiscussionsandeffortsinvolvinggenomics,metagenomics,softwaresystems,andfoodsafety.

WegmansFoodMarkets,Inc. Rochester,NewYorkFoodSafetyIntern Summer2015• ProvidedleadershipandguidanceonimplementationofFoodSafetyModernizationActwithspecializationonforeignsupplierverificationprogramsandsanitarytransportation.

• Collaboratedwithseniorleadership,quality,manufacturinganddistributionteamstoexplainimplications,conductgapanalysisandcoordinateactionsforexecution.

• Retainedasremoteconsultantduringschoolyear.

MondelēzInternational EastHanover,NewJerseyRD&QIntern Summer2014• ManagedprojectonbelVita,200milliondollarbrandwithprojected19%growthrate.• Leveragedanalyticalmethodstoscopeformulaoptionsandscreennewingredients.• Partneredwithcrossfunctionalgroupssuchassensory,marketingandresearch.Ledpilotplanttrials.• Developedorganizationalagility,problemsolving,technicalwritingandstrongpresentationskills.• Participatedinworkshops,lecturesandmeetingstobetterunderstandallaspectsofbusiness.

SELECTEDORALPRESENTATIONS • Sullivan,G.,Strawn,L.(2019,October).ControllingListeriainproducefacilitiesandpackinghouses:awebinarseries.

Nationwidewebinarwith255liveattendees.https://www.youtube.com/watch?v=IHLjOk_LlCs • Sullivan,G.(2019,July).DetectionandprevalenceofListeriainproducepackingandfresh-cutoperations.

PresentationattheInternationalAssociationforFoodProtectionMeeting.Louisville,KY.• Sullivan,G.,Wiedmann,M.(2019,June).The3C'sofListeria:Characteristics,Contamination,andControl.Nationwide

webinarwith156liveparticipants.175YouTubeviewsasof7/30/2019.https://www.youtube.com/watch?v=I8NSscc-B2o&feature=youtu.be

• Sullivan,G.(2019,March).Listeria:PersistenceandSourceIdentificationinPackinghouses.PresentationattheNorthwestHorticultureCouncilMeeting.Yakima,WA.113registeredattendeesfromWashington,Oregon,andIdaho.

• Sullivan,G.(2018,December).EnvironmentalAssessmentStrategiesintheAgeofWholeGenomeSequencing.PresentationattheFDARapidResponseTeamsMeeting.Austin,TX.The208attendeesrepresentedvariousresponsepartnersfromfood/feedregulatory/environmentalhealth,epidemiology,laboratory,academia,FederalBureauofInvestigations(FBI),FDA,CDC,andUSDA/FSIS.

• Sullivan,G.(2018,July).EstablishingabaselineforListeriamonocytogenesandListeriaspeciesprevalence3-4hoursintoproductioninspecialtycropfacilities.PresentationattheInternationalAssociationforFoodProtectionMeeting.SaltLakeCity,UT.

• Sullivan,G.(2017,September).ThisYear’sTopFoodborneOutbreaks:CausesandKeyLearnings.PresentationattheNewYorkStateAssociationforFoodProtectionConference.Syracuse,NY.

• Sullivan,G.(2017,July).ExtendedEnrichmentProceduresCanbeUsedtoDefineFalseNegativeRateforCulturalGoldStandardMethodsforSalmonellaDetectionFacilitatingComparisonsbetweenGoldStandardandAlternativeMethods.PresentationattheInternationalAssociationforFoodProtectionMeeting.Tampa,FL.

PUBLICATIONS• Sullivan,G.,X.Guo,J.Tokman,S.Roof,A.Trmcic,R.Baker,S.Tang,P.Markwell,M.WiedmannAndJ.Kovac.2019.ExtendedenrichmentprocedurescanbeusedtodefinefalsenegativeprobabilitiesforculturalgoldstandardmethodsforSalmonelladetection,facilitatingcomparisonsbetweengoldstandardandalternativemethods.J.FoodProt.SubmittedJFP-19-422.

• Estrada,E.,Hamilton,A.M.,Sullivan,G.B.,Wiedmann,M.,Critzer,F.J.,andStrawn,L.K.2019.Prevalence,PersistenceandDiversityofListeriamonocytogenesandListeriaspeciesinProducePackinghousesinThreeU.S.States.J.FoodProt.SubmittedJFP-19-411.

• Carroll,L.,Gaballa,A.,Guldimann,C.,Sullivan,G.,Henderson,L.,Wiedmann,M.2019.IdentificationofNovelMobilizedColistinResistanceGenemcr-9inaMultidrug-Resistant,Colistin-SusceptibleSalmonellaentericaSerotypeTyphimuriumIsolate.mBio10(3)e00853-19;DOI:10.1128/mBio.00853-19

• ProulxJ.,AgustinM.,SullivanG.,VanWeesS.,JianJ.,HiltonS.T.,andMoraruC.I.2017.ShortCommunication:InfluenceofPulsedLighttreatmentonthequalityandsensorycharacteristicsofcheddarcheese.JournalofDairyScience100(2):1004-1008

• ProulxJ.,SullivanG.,MarosteganL.F.,VanWeesS.,HsuL.C.,andMoraruC.I.2017.PulsedLightandantimicrobialcombinationtreatmentsforsurfacedecontaminationofcheese:favorableandantagonisticeffects.JournalofDairyScienceDOI:10.3168/jds.2016-11582

• Proulx,J.,Hsu,L.C.,Miller,B.M.,Sullivan,G.,Paradis,K.,andMoraru,C.I.2015.Pulsedlightinactivationofpathogenicandspoilagebacteriaoncheesesurface.JournalofDairyScience98(9):5890–5898

SELECTCOMPUTATIONALSKILLS• LinuxBashScripting–foranalysisofwholegenomesequencingdata

• R–forgeneralstatisticalanalysisanddatavisualization

• NetLogo–fordevelopmentofagent-basedmodelsoffoodproductionenvironments

• Python–fordatavisualizationandtosupplementothercodingendeavors

SELECTAWARDSANDACHIEVEMENTSResearchAwards• CenterforProduceSafety

TravelScholarship• NSFGRFPHonorableMention• GoyaFoodsPrize• 2ndPlace,UndergradResearch

Competition,IFTAnnualMeeting

• PaulSchreursMemorialAwardforExcellenceinUndergradResearch

IndustryAwards• UnileverU.S.Undergraduate

Award• EasternFrostedFoods

AssociationUndergraduateAward

• TICGumsUndergraduateAwardinFoodChemistryandFunctionality

GeneralScholarships• DoctorC.AnnHollingsworth

StudentLeadershipScholarship(IFT)

• WesternNewYorkIFTGraduateScholarship

• CornellFoodScienceAdvisoryCouncilScholarship

• PMAFoundationPackScholar

Hannah Thomas

785-214-8300 | hrt38@cornell.edu

Education

Doctorate of Philosophy Candidate in Plant Biology

Title: Understanding the Role of Intercellular Communication in Vegetable Crop Grafting

Thesis Advisor: Margaret Frank

Cornell University, Ithaca, NY

Bachelor of Science in Biology July 2017

Pittsburg State University, Pittsburg, KS

Minor: Chemistry | Emphasis: Molecular plant biology and plant physiology

GPA: 3.98 | Credits: 156

Research Experience

Undergraduate Research Assistant 1/2016-7/2017 Dr. Virginia Rider, Department of Biology, Pittsburg State University

The spatial expression of the T cell homing receptor, CCR7 and T cells marker, FoxP3 are differentially regulated by

progesterone and estradiol in the rat uterus

Undergraduate Research Assistant (NSF REU) 5/2016-8/2016

Dr. Blake Meyers, Donald Danforth Plant Science Center, St. Louis, MO

Functional analysis of phasiRNA in soybean anthers

PhD Intern 8/2017-12/2017

Dr. James Giovanonni, USDA, Boyce Thompson Institute, Ithaca, NY

Gene expression in Coffea arabica fruit development

PhD Intern 1/2018-6/2018

Dr. Joyce Van Eck, Boyce Thompson Institute, Ithaca, NY

Formal training on Solanaceous plant transformation and tissue culture

Teaching and Mentoring Experience

Biology Tutor 8/2014-1/2017

Department of Biology, Pittsburg State University

Teaching Assistant 8/2015-05/2017

Department of Biology, Pittsburg State University

General Chemistry I, General Chemistry II, Principles of Biology I, and Principles of Biology II

Substitute Teacher 8/2016-5/2017

Department of Biology, Pittsburg State University

Principles of Biology II, Invasive Species Management, and Taxonomy of Vascular Land Plants

Graduate Teaching Assistant 8/2018-Current

CALS | Cornell University

Field Crop Systems, Plant Physiology, Introduction to Plant Diversity and Evolution

Undergraduate Mentor 01/2019-Current

Cornell University Undergraduates (4), REU summer intern (1)

Honors and Awards

Member of the Pittsburg State University Honors College Association

Named a K-INBRE, Kansas IDeA Network of Biomedical Research Excellence, Scholar in 2016

Member of Phi Eta Sigma Honor Society and National Society of Leadership and Success

Recipient of the Young Botanist Award by the Botanical Society of America (2017)

Cornell Plant Biology First Year Fellowship (2017)

ASPB Conviron Scholar (2018)

Awarded summer funding from The Cornell Institute for Digital Agriculture Research Innovation Fund (2019)

Volunteer Work and Enrichment

Graduate:

Weekly volunteer at the Free Science Workshop. The FSW is a free, open door workshop for minority and low-income

kids in the Ithaca area (2018-2019)

Alliance for Science Volunteer; gave demonstrations and led a DNA extraction lab with visiting Training Team from

Africa and Asia (2018)

Cultural Exchange Volunteer for Tokyo University of Agriculture and Technology at Cornell University (2017 &

2018)

Event Coordinator for international science communication workshop at Cornell University (2018)

Selected to attend CommSciCon-Cornell (Science Communication Workshop), where students from various schools

were tasked to create original written pieces and met with NPR, RadioLab etc.

Volunteer for the Cornell Diversity Preview Weekend, designed to promote diversity and inclusion in the incoming

graduate program applicants (2018)

Volunteer for the Plant Biology graduate student recruitment program at Cornell University (2018-current)

Treasurer for the Plant Biology Graduate Student Association (2018-2019)

Volunteer for Expanding Your Horizons, all-day young women in science workshop at Cornell University (2018)

Member of Careers Beyond Academia/BEST at Cornell Univesrity (2017-current)

Member of the Graduate Women in Science (GWIS) organization (2017-current)

Member of Cornell Graduate and Professional Women’s Network (2017-current)

Undergraduate:

Pittsburg State University Biology Club (2013-2017); Participated in local community services, including: judging

local science fairs and community clean-up projects

Founded the Pittsburg State University Natural History Collection Curation Club (2015-2017); Works on the PSU

campus to maintain as well as spread awareness about the natural history collections, including: cataloging,

fundraising, and geo-referencing specimens; Worked in the T.M. Sperry Herbarium mounting and cataloging

specimens

Skills

Competent in R, imageJ, C, and python

Trained in bioinformatic analysis

Trained in molecular laboratory, with emphasis on immunohistochemistry, histology and section preparation, library

construction, and plant transformation.

Trained in botanical collection, identification, and preservation for herbaria

Beginner in spoken and written Mandarin Chinese. Course work ongoing at Cornell University.

Publications

Thomas, H. R., & Frank, M. H. (2019). Connecting the pieces: uncovering the molecular basis for long-distance

communication through plant grafting. New Phytologist. https://doi.org/10.1111/nph.15772

Conference Presentations

Oral Presentations Thomas, H., Teng, C. Meyers, B. Functional analysis of phasiRNA in soybean and maize (2016, August). REU

Research Symposium, Donald Danforth Plant Science Center, St. Louis, Missouri. (2017, February). Michigan State

University Fellowship Committee, East Lansing, Michigan.

Thomas, H., Frank, M. Pepmato: a potential model for graft incompatibility (April 2019). Plant Biology, Cornell

University, Ithaca, New York.

Poster Presentations Thomas, H. Arruda, J. (2015, February). Preliminary Key to Aquatic Snails in Kansas. Pittsburg State Research

Colloquium, Pittsburg, Kansas.

Thomas, H., Teng, C. Meyers, B. Functional analysis of anther phasiRNA in soybean. (2017, January). Plant and

Animal Genome Conference, San Diego, California (2017, February). Pittsburg State Research Colloquium 2017,

Pittsburg, Kansas.

Thomas, H. Rider, V. The spatial expression of the T cell homing receptor, CCR7, is differentially regulated by

progesterone and estradiol in the rat uterus. (2017, February). Capitol Research Summit, Topeka, Kansas. (2017, April)

Endocrine 2017, Orlando, Florida. (2017, April). Pittsburg State Research Colloquium 2017, Pittsburg, Kansas.

Thomas, H., Frank, M. Pepmato: a potential model for graft incompatibility (June 2019). Plant Vascular Biology

Meeting, Asilomar, California

References

Margaret Frank, PhD | Assistant Professor of Plant Biology

Cornell University

(607) 255-1734

mhf47@cornell.edu

Joyce Van Eck, PhD | Adjunct Professor of Plant Breeding and Genetics, Direction of BTI Transformation Facility

Boyce Thompson Institute

(607)-254-1686

jv27@cornell.edu

Blake Meyers, PhD | Professor of Plant Sciences, University of Missouri

Donald Danforth Plant Science Center

(314) 587-1422

bmeyers@danforthcenter.org

Neil Snow, PhD | Professor of Botany, Director of T.M. Sperry Herbarium

Pittsburg State University

(620) 235-4424

nsnow@pittstate.edu

Virginia Rider, PhD | Professor of Biology

Pittsburg State University

(620) 235-4739

vrider@pittstate.edu

Zijian Wang Tel: (+86) 158-2228-3502 or (+1) 626-314-9447 Email: wangzijian@tju.edu.cn

Website: http://zijianwatertech.com/.

EDUCATION

School of Environmental Science and Engineering (ESE), Tianjin University, Tianjin Sep 2015-Jun 2019

➢ Bachelor of Engineering in Environmental Engineering, Overall GPA: 3.696/4.0, 89.085/100 (Top 4/56)

➢ Oversea research experiences: undergraduate researcher in Rice University under supervision of Prof. Pedro J.

Alvarez; research intern in Cornell University under supervision of Prof. April Z. Gu.

➢ Honors & Awards: Tianjin University Sang De Scholarship (top 5%, Dec 2017) Excellent Undergraduate Researcher

(top 2%, Dec 2017 & 2018) Excellent Student Leader& Excellent Undergraduate (top 5%, Dec 2017 & 2018) Excellent

Bachelor’s Thesis (top 1%, Jun 2019)

PUBLICATIONS

➢ Wang Z.J.; Sun P.Z.*; et. al. •NO Mediated Degradation of Estrogenic Disrupting Chemicals (EDCs) by

Biochar/Monochloramine in Buffered Water and Synthetic Hydrolyzed Urine. Environ. Sci. Technol. Just Accept

DOI: doi.org/10.1021/acs.est.9b04704

➢ Li Y.X.; Zhang R.C.; Wang Z.J.; Sun P.Z.*; et. al. Removal of Sulfamethoxazole and Metabolite in Synthetic

Hydrolyzed Urine by Biochar/Peroxydisulfate. Water Res. Submitted.

➢ Zhang B.; Wang Z.J.; Yu P.F.*; Pedro J. Alvarez*. Dose-Response Relationship of Dual Species Biofilm and

Bacteriophage: A Computational and Experimental Study. Environ. Sci. Technol. Submitted.

➢ Sun P.Z.*; Wang Z.J.; et. al. How spatial heterogeneity impacts on the antibiotic resistant bacteria (ARB) and antibiotic

resistant gene (ARG) abundance in natural environment. Proc. Natl. Acad. Sci. U.S.A. Under Writing.

➢ Wang D.Q.; He P.S.; Li G.Y.; Najed; Wang Z.J.; April Gu*. Application of Single Cell Raman Micro-Spectroscopy

Technology for Biological Studies. Invited Review. Curr. Opin. Biotechnol. Under Writing.

➢ Yu P. F.*; Wang Z. J.; Pedro J. Alvarez* et. al. Bottom-Up Biofilm Eradication Using Bacteriophage-Loaded Magnetic

Nanocomposites: A Computational and Experimental Study. Environ. Sci. Nano DOI: doi.org/10.1039/C9EN00827F

➢ Sun P.Z.*; Meng T.; Wang Z.J.; et. al. Degradation of Organic Micro-pollutants in UV/NH2Cl Advanced Oxidation

Process. Environ. Sci. Technol. DOI: doi.org/10.1021/acs.est.9b00749

➢ Chao C.F.; Zhao Y.X.; J. Keskar; Ji M.; Wang Z.J.; Li X. Simultaneous removal of COD, nitrogen and phosphorous

and the tridimensional microbial response in a sequencing batch biofilm reactor with varying C/N/P ratios. Biochem.

Eng. J. DOI:doi.org/10.1016/j.bej.2019.04.017

➢ Zhao Y.X.; Chao C.F.; Zhai S.Y.; Wang Z.J.; Ji M. Treatment of Rural Wastewater Using a Spiral Fiber Based Salinity-

Persistent Sequencing Batch Biofilm Reactor. Water. DOI: doi.org/10.3390/w9120970

➢ Chao C.F.; Zhao Y.X.; Song Q.; Ji M.; Wang Z.J. Rock Based Ceramsite Adsorbent for Highly Selective Fluoride

Removal: Function Optimization and Mechanism. J. Chem. Technol. Biotechnol. DOI: doi.org/10.1002/jctb.6014

➢ Zhao Y.X.; Wang Z.J.; Chao C.F. Intellectual Controlling of SBBR. (Patent, Written in Chinese) 201910056737.8

➢ Participant of Book ‘Biochar-Based Technology for Source-Separated Urine Treatment.’ (Written in Chinese)

➢ Wang Z.J.; Gu April* et. al. High Throughput Phenotyping and Identification of Plant-Relevant Soil Microorganisms

via Single Cell Raman Spectroscopy. In Prep.

SELECTED RESEARCH EXPERIENCES

Research Assistant, School of CEE, Cornell University (with Prof. April Z. Gu). Jul 2019–Present

High Throughput Phenotyping and Identification of Plant-Relevant Soil Microorganisms via Single Cell Raman

Spectroscopy and Machine Learning Tools.

➢ Established Raman database of 50 plant-relevant soil strains for bacterial phenotyping and identification.

➢ Developed and applied different machine learning algorithm to analyze environmental soil samples.

Research Assistant, School of CEE, Rice University (with Prof. Pedro J. Alvarez). May 2018–Present

Bottom-Up Biofilm Eradication Using Bacteriophage-Loaded Magnetic Nanocomposites: A Computational and

Experimental Study

➢ Established individual-based stochastic model to simulate the interactions of phages-nanocomposite conjugates (PNC)

and bacteria in biofilms under weak magnetic field.

➢ Elucidated the enhanced biofilm removal efficiency mechanism: PNCs targeted dominant species at the bottom of

biofilm and promoted the removal; small PNCs were distributed more uniformly and resulted in complete removal.

➢ Provided novel and potential methods for biofilm removal in water treatment plants, pipelines, human diseases, etc.

Dose-Response Relationship of Dual Species Biofilm and Bacteriophage: A Computational and Experimental Study

➢ Established a 3-dimensional biofilm growing computational model and analyzed the interaction of matured 3D biofilm and

polyvalent bacteriophages from both biofilm structural perspective and gene expression perspective.

➢ Discovered dosage-response relationship of dual species biofilm and bacteriophage: high dosage of phage inhibited the

bacteria growth, while low dosage of phage promoted the biofilm growth.

Research Assistant, School of ESE, Tianjin University (with Prof. Peizhe Sun). Sep 2017–Present

Reactive Nitrogen Species Mediated Degradation of Estrogenic Disrupting Chemicals by Biochar/Monochloramine

in Buffered Water and Synthetic Hydrolyzed Urine

➢ Established a biochar/monochloramine degradation system, analyzed the removal of EDCs, developed UV/nitrite

system, measured linear sweep voltammetry, and analyzed dependence of biochar characteristics and EDC removal.

➢ Elucidated novel reaction pathways and catalytic mechanism: reactive nitrogen species •NO as dominant contributor

for EDCs removal; nitrogen/silicon dopants and annealing temperature to enhance catalytic activity.

➢ Analyzed the effects of components in hydrolyzed urine, analyzed the endocrine disrupting effects of transformative

products by recombined yeast bioassay, and elucidated potential application for onsite source-separated urine treatment.

How spatial heterogeneity impacts on the antibiotic resistant gene (ARG) abundance in natural environment

➢ Established an individual-based stochastic model to elucidate the dynamics of ARG and horizontal gene transfer in

heterogeneous soil and elucidated the implication towards agricultural practice (i.e. irrigation, manure fertilization).

➢ Developed the stochastic and probabilistic Poisson model to analyze the effects of soil heterogeneity on horizontal gene

transfer and the possible influences on human-relevant pathogenic bacteria.

Research Assistant, School of ESE, Tianjin University (with Prof. Yingxin Zhao). May 2017–Jun 2018

Simultaneous Removal of COD, N, P and Tridimensional Microbial Response in Sequencing Batch Biofilm Reactor

(SBBR) with Varying C/N/P Ratios Equipped with Intelligent Control System for Rural Wastewater Treatment.

➢ Conducted experiments and cultivated SBBR to elucidate how various C/N/P ratios affected the microbial composition.

➢ Analyzed the relationship between the microbial composition and N, P removal efficiency in various C/N/P ratios by

high-throughput DNA sequencing, and decreased the energy consumption by controlling amount of dissolved oxygen.

➢ Provided guideline for future application of SBBR: ideal C/N/P ratios for simultaneously enhanced removal of N & P.

CONFERENCES AND SKILLS

➢ ACS Fall 2019 National Meeting and Exposition in San Diego, CA. Aug 25-Aug 29, 2019

Abstracts: Going viral: Emerging opportunities for phage-based bacterial control in water treatment and reuse

➢ Volunteer of the 1st International Symposium on BioEnergy and Environment July 2017

➢ President of College Music Society & College Host Union, Tianjin University Aug 2017-Sep 2018

➢ Computer Skills: Python, MATLAB, C++, SQLite, MySQL, Latex, AutoCAD, Adobe Photoshop, ECOSAR.

➢ TOEFL: 102 (R28, L24, S23, W27); GRE: Verbal-152, Quantity-165, Writing-3.0

SIYU ZHU

sz393@cornell.edu Tel. (612) 839-0201 224 Olin Hall, Cornell University, Ithaca, NY, 14853

EDUCATION

Cornell University Chemical Engineering Ph.D. (3.71/4.00) Aug. 2014 – Present

University of Minnesota-Twin Cities Chem. Eng. (Top 10) B.Ch.E. (3.60/4.00) Jan. 2011 – May. 2014

PROFESSIONAL EXPERIENCE

Graduate Research Assistant, Cornell University, Ithaca, NY Aug. 2014 – Present

• Optimized the design for a drought stress sensing microfluidic device, and reduced its response time by 60-fold.

• Designed an osmotic probing technique for sensor tuning, and expanded the application scope of the drought

stress sensor from single-media to multi-media.

• Initiated an embedding technique to interface the drought stress sensor with the plant tissue.

• Demonstrated unprecedented accuracy of drought stress monitoring in apple trees for up to 60 days.

• Performed statistical analysis on the 60-day big data sets to discover data trends, patterns and relationships.

• Developed mathematical models to validate the observed 60-day dynamics in apple trees, and to predict the

plant behavior based on the weather forecast.

• Designing a model-predictive-control system for precise irrigation scheduling on potted apple trees. • Presented research achievements at 10 conferences, and established collaboration with 5 research groups who

have common interests and complementary expertise.

Ph.D. Intern, Dow Chemical Company, Midland, MI Aug. 2018 – Dec. 2018

• Proposed and refined mathematical models for a key reaction process of one of Dow’s largest business units.

• Hosted weekly stakeholder meetings to coordinate feedback and determine implementation strategies for greater

productivity.

Teaching Assistant, Cornell University, Ithaca, NY Spring 2017

• Led group discussions and review sessions for CHEME 6400 Polymeric Materials.

Undergraduate Research Assistant, University of Minnesota, Minneapolis, MN May 2012 – May 2014

• Studied the mechanisms that inhibit the transfer of antibiotic resistance among bacterial cells.

SKILLS

Computer Skills Expert Computer Skills Intermediate Other Technical Skills Non-Technical Skills

MATLAB Python Big Data Analytics Complex Problem-Solving

Microsoft PowerPoint C++ Mathematical Modeling Adaptability

Microsoft Excel 3D CAD: SOLIDWORKS Internet of Things (IoT) Communication

Microsoft Word Adobe Photoshop Project Management Leadership

Adobe Illustrator Micro-Fabrication Teamwork

Packaging Design Creativity

AWARDS

Best Poster Award, Cornell Nanoscale Facility 40th Anniversary Celebration and Annual Meeting 2017

Best Poster Award, Graduate Research Symposium (Cornell) 2017

Lisa Walker Travel Award, Department of Chemical and Biomolecular Engineering (Cornell) 2016

Undergraduate Research Opportunities Program Award, University of Minnesota Twin Cities 2013

ACTIVITIES

Mentor for 4 Undergraduate Students and 3 Graduate Students (Cornell) May 2016 – Present

Colman Graduate Leadership Program (Cornell) Jan. 2018

Welcome Week Leader (University of Minnesota – Twin Cities) Aug. 2012

PERSONAL INTERESTS

Traveling: Visited 10 countries, 15+ cities and areas in the U.S., and 20+ cities and areas in China.

Sports: Competitive player in badminton and table tennis.