date prepared: april, 2013 name: peter j. tonellato, ph.d...

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Date Prepared: April, 2013 Name: Peter J. Tonellato, Ph.D. Office Address: Zilber School Of Public Health 234 Lapham Hall Milwaukee, WI 53211 Home Address: 4481 N. Prospect Ave Shorewood, WI 53211 Work Phone: 617-432-7185 Work E-Mail: [email protected] Work FAX: 617-432-3894 Place of Birth: Casablanca, Morocco Education 1978 B.S. Mathematics University of Puget Sound, Tacoma, WA 1980 M.S. Applied Mathematics University of Arizona, Tucson, AZ 1982 Doctorial work, visiting, Mathematics Institute University of Oxford, Oxford, England 1982 Doctorial work, visiting, Mathematical and Life Sciences Hiroshima University, Hiroshima, Japan 1985 Ph.D. Applied Mathematics University of Arizona, Tucson, AZ Faculty Academic Appointments 1985-1992 Assistant Professor, Department of Mathematics, Statistics and Computer Science Marquette University 1987-1999 Adjunct Assistant Professor, Department of Physiology, Medical College of Wisconsin 1993-1999 Associate Professor, Department of Mathematics, Statistics and Computer Science, Marquette University 1993-1994 Visiting Associate Professor, Center for Bioengineering, University of Washington 1999-2005 Senior Scientific Investigator and Assistant Professor, Center for Human and Molecular Genetics and

Department of Physiology, Medical College of Wisconsin 1999-2007 Research Associate Professor, Department of Mathematics, Statistics and Computer Science, Marquette

University 2002-2005 Adjunct Associate Professor, Department of Biomedical Engineering Department Marquette University 2005-2007 Adjunct Research Scientist, Department of Physiology, Computational Biology and Bioinformatics,

Medical College of Wisconsin 2007-2010 Lecturer, Department of Pediatrics, Harvard Medical School Medical School 2009-2010 Adjunct Professor, Chemistry and Biochemistry, University of Wisconsin, Milwaukee WI 2009- Professor, School of Public Health, University of Wisconsin, Milwaukee WI 2009- Professor (Visiting), Department of Pathology, Beth Israel Deaconess Medical Center, 2007- Senior Research Scientist, Center for Biomedical Informatics, Harvard Medical School 2010- Professor, Computer Science, CEAS University of Wisconsin, Milwaukee, WI 2011- Professor, (Courtesy Appointment) College of Health Sciences (Health Informatics), University of

Wisconsin, Milwaukee, WI Appointments at Hospitals/Affiliated Institutions 2007-2010 Senior Research Scientist, Children’s Hospital of Boston, Children’s Hospital Informatics Program Other Professional Positions 2000-2006 Founder, Chief Scientific Officer, Chairman (2004-2006), CEO (2004-2005), POINTONE Systems, LLC 2002-2004 Center Investigator, Great Lakes WATER Institute, University of Wisconsin, Milwaukee 2007-2009 Senior Consultant in Personalized Medicine, Partners HealthCare, Inc. Major Administrative Leadership Positions

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1997-2003 Founder and Director, Bioinformatics Research Center, Medical College of Wisconsin 2001-2004 Founder and Director, Bioinformatics Joint Graduate Program, Medical College of Wisconsin and

Marquette University 2007-2008 Chairman, Chief Executive Officer, President, POINTONE Systems, LLC 2001-2009 Chairman, Chief Scientific Officer, POINTONE Systems, LLC 2011- Founding Director and Member, Biomedical and Health Informatics Research Institute, University of

Wisconsin-Milwaukee. Committee Service University Marquette University 1986-1987 Undergraduate Committee, Department of Mathematics, Statistics, and Computer Science, Marquette

University 1986-1989 Colloquium Coordinator, Department of Mathematics, Statistics, and Computer Science, Marquette

University 1987-1995 Institutional Review Board, Department of Mathematics, Statistics, and Computer Science, Marquette

University 1990-1999 Graduate Committee, Department of Mathematics, Statistics, and Computer Science, Marquette

University 1992-1993 Colloquium Coordinator, Department of Mathematics, Statistics, and Computer Science, Marquette

University 1993-1994 Biomedical Subcommittee of the Institutional Review Board, Department of Mathematics, Statistics, and

Computer Science, Marquette University Medical College of Wisconsin 2000-2006 Web Council, Medical College of Wisconsin 2000-2001 Strategic Issue Group on Information Technology, Medical College of Wisconsin 2001-2004 GCRC Review Committee, Medical College of Wisconsin 2001-2004 Graduate Studies Council, Medical College of Wisconsin 2001-2004 Graduate School Information Day Committee, Medical College of Wisconsin 2002-2004 Strategic Plan for Research Information Systems Committee, Medical College of Wisconsin 2002-2005 Committee on Information Technology, Medical College of Wisconsin 2002-2004 Education Information Technology Committee, Medical College of Wisconsin 2006-2009 Academic Advisory Committee, Program in Biotechnology, Milwaukee Area Technical College 2006-2010 Academic Advisory Board, University of Illinois, Chicago, Bioinformatics Graduate Training Program University of Wisconsin- Milwaukee 2009 SPH Planning Council Committees: School Formation Team and Planning Committee Epidemiology PhD Work Group Public Health Administration and Policy PhD Work Group Master’s of Public Health Work Group Library Resources Committee Research Infrastructure Committee Facilities Advisory Committee 2009- Zilber School of Public Health (ZSPH) Environmental and Occupational Health Program Committee 2009- ZSPH Executive Faculty Committee 2010- ZSPH Epidemiology Search & Screen Committee 2010- ZSPH Biostatistics Search & Screen Committee 2010- ZSPH Impact Institute Committee 2010- Steering Committee, Medical Informatics Program 2010- UWM Research Computing IT Advisory Committee 2010-2011 Special Appointment (Provost), coordinate development of Biomedical and Health Informatics Research

Institute 2010-2012 ZSPH, Biostatistics and Epidemiology, Space Planning Committee 2011- 2012 ZSPH, Dean Search and Screen Committee

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2011- UWM International Council 2011- ZSPH, Academic Planning Committee (Chair, 2012-2013) 2011- ZSPH, Advisor, Masters of Public Health Program 2011- Executive Council, BioMedical Informatics Research Institute, University of Wisconsin, Milwaukee 2012-2013 ZSPH EOH Space Planning Committee 2012-2015 Member, Graduate Committee, UWM 2012-2015 Member, Graduate Fellowship Subcommittee, UWM 2013-2016 Member, Divisional Committee (Natural Sciences) Harvard Medical School 2010- Center of Excellence (COE) Health Disparities Post Graduate Fellowship (HD/PGF) Committee, Harvard

Medical School 2010- HMS Research IT Faculty Advisory Council, Harvard Medical School 2010-2011 CBMI Faculty Search and Screen Committee, Harvard Medical School 2011-2012 Chair, CBMI Faculty Search and Screen Committee, Harvard Medical School 2012-2013 Member, CBMI Faculty Search and Screen Committee, Harvard Medical School National, International 1996 Organizer, USCG Workshop, The Mathematical Association of America, Marquette University,

Milwaukee, Wisconsin 1996-1997 NIH study section: SBIR/STTR program (invited participant) 1997-1999 NIH study section: NCRR Animal Models and Resources (invited participant) 1998-2000 NIH study section: NCRR General Medical Systems 1999 NIH study section: NIH Pharmacogenetics (invited participant) 1999-2002 NIH study section: NCI Innovative Technology Research (invited participant) 2000 Organizer, Physiological Genomics & Rat Models, Cold Spring Harbor Laboratory, Cold Spring Harbor,

NY 2000 Organizer, Bioinformatics: Analysis from Sequence to Disease Symposium, Experimental Biology 2000,

San Diego, CA 2001 NIH study section: NIH/NSF Workshop on Assessing Bioengineering & Bioinformatics Research

Training, Education and Career Development 2002 Organizer and Chair, Techniques & Technology in Physiology Tutorial: Bioinformatics for the

Physiologist, Experimental Biology 2002, New Orleans, LA 2002 Organizer and Chair, Bioinformatics in Physiological Genomics Symposium, Experimental Biology

2002, New Orleans, LA 2002-2005 Chair, International Union of Physiological Sciences (IUPS), 2005 Section on Bioinformatics 2002-2007 Chair, Data Integration and Bioinformatics, World Congress on Chromosome Abnormalities 2002 Organizer and Chair, Satellite Workshop, 14th International Workshop on Genetic Systems in the Rat,

Kyoto, Japan 2002 Member, RCMI Site Visit, Border Biomedical Research Center, El Paso, TX 2003 Member, NIH Genome Study Section, Bethesda, MD 2003 Member, NCI Cancer Center Site Visit, Mayo Clinic, Rochestor, MN 2003 Co-organizer, Intelligent Systems in Bioinformatics, 7th International Conference on Systematics,

Cybernetics, and Informatics, Orlando, FL 2003-2005 Board Member, International Interoperability Biological Consortium (International SNP consortium)

Joint Bioinformatics and Industry Consortium, Tokyo, Japan. 2004 Member, NCRR Genotyping Center Special Emphasis Panel, Bethesda, MD 2004 Member, NCRR, Center for Research Resources Special Emphasis Panel, ZRR1 CR-9 (01), Clinical

Research 2004 Member, NIEHS P30 Site Review Committee, University of Arizona 2004 Member, NCI, Comprehensive Cancer Center Site Review, Duke University 2004 Founding Member, Center for Functional and Environmental Genomics (CFEG). University of

Wisconsin, Milwaukee, Water Research Institute.

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2004 Member, NCRR Special Emphasis Panel, ZRR1 BT-8, NIH RoadMap Exploratory Centers for Interdisciplinary Research

2004-2005 Member, World Congress Local Organizing Committee, Ninth World Congress for Microcirculation, Milwaukee, WI

2005 Member, NCI, Comprehensive Cancer Center Site Review, University of Michigan 2000-2003 Member Steering Committee, International Rat Genome Sequencing Project 2000-2004 GCRC Bioinformatics Conference Steering Committee, NIH, NCRR 2001-2005 Member, Leadership Council, International Human FLcDNA Consortium, Japan Biological Informatics

and Research Center, Tokyo, Japan. 2002 Organizer and Chair, Techniques & Technology in Physiology Tutorial: Bioinformatics for the

Physiologist, Experimental Biology 2002, New Orleans, LA 2002 Organizer and Chair, Bioinformatics in Physiological Genomics Symposium, Experimental Biology

2002, New Orleans, LA 2002-2005 Chair, Data Integration and Bioinformatics, World Congress on Chromosome Abnormalities 2002 Organizer and Chair, Satellite Workshop, 14th International Workshop on Genetic Systems in the Rat,

Kyoto, Japan 2002-2006 Member, Stem Cell Genome Anatomy Projects Scientific Steering Committee, NIH SCGap Program. 2006-2010 Member, NIH, NLM, Biomedical Library and Informatics Review Committee 2009 Member, Fourth Competition of the Ontario Research Fund, Ontario, Canada 2010 Organizing Committee, The International Conference on Bioinformatics (InCoB) of the Asia-

Pacific Bioinformatics Network 2010 Organizing Committee, Genome Era Pathology, Precision Diagnostics and Preemptive Care: A

Stakeholder Summit, Oct, 2010, Banbury, NY 2011 Organizing Committee, The Future of Pathology in Personalized Medicine: A Stakeholder

Summit, May, 2011, Boston, MA 2011 Special Reviewer, CDC and Genetic Alliance Program in Family Health History Patient

Education Toolkit: Health Centers Program Awards RFP 2011 Chair, Exploring Clinical Phenotypes to Enable Translational Bioinformatics Session, AMIA

TRI Summit, San Francisco, CA. March, 2011 2010- Member, American Public Health Association, Genomics Forum 2010-2012 Chair, APHA, Genomics Forum, Health Policy Work Group 2012-2013 Chair, APHA, Genomics Forum Program Committee 2011- Scientific Advisor, Training Residents in Genomics (TRIG) Committee, College of Pathology, Objective

to implement an accredited nation-wide genomics pathology curriculum. 2011-2012 Member Scientific Program Committee for the AMIA Summit on Translational Bioinformatics 2011- Member, Executive Committee, National Center for Systems Biology and the Virtual Rat program 2012- Elected Member-at-large, AMIA Clinical Research Informatics Working Group 2012 Participant, DARPA/Defense Sciences Office. Meeting on Innovations and Emerging Data Science and Mathematical Modeling, Washington D.C., March, 2012 2012 Moderator and Chair, Public Health Response to Personalized Medicine Special Session, 140th APHA Annual Meeting (October 27 - October 31, 2012), San Francisco, CA. Professional Societies 1979- 2004 American Mathematical Society 1979- 2004 Society for Industrial and Applied Mathematics 1982-1995 European Geophysical Society 1985-1998 Sigma Xi 1986- 2004 Society for Mathematical Biology 1989-2006 Microcirculatory Society 1992-2004 Biomedical Engineering Society 1999-2003 Association for Computing Machinery 1999-2004 American Physiological Society

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1999-2003 International Society for Computational Biology 1999-2003 American Association for the Advancement of Science 2001-2004 American Statistical Association 2002-2004 American Society for Human Genetics 2007- American Medical Informatics Association 2010- American Society of Public Health Editorial Activities 1996-2004 Editorial Board, Society for Chaos Therapy in Psychology and Life Sciences 1999-2002 Reviewer, American Journal of Physiology: Heart and Circulatory Physiology 1999-2004 Editorial Member, Physiological Genomics 1998-2006 Reviewer, Nucleic Acids Research 1999-2005 Reviewer, Genome Research 2002-2005 Reviewer, BMC Bioinformatics 2003-2004 Reviewer, Proceedings of the Indian National Academy of Sciences 2002-2005 Physiological Genomics 2004-2006 Editorial Board, Cancer Informatics 2004- Editorial Board, Physiological Genomics, Faculty of Science, PLOS 2010- Reviewer, Proceedings of National Academy of Science 2010 - Reviewer, BMC Medical Informatics and Decision Making 2010 - Reviewer, The Journal of Biological Databases and Curation 2011- Reviewer, BMC Theoretical Biology and Medical Modeling Research 2011- Reviewer, Journal of the American Medical Informatics Association 2011-2012 Special Issue Editor, Future of Medicine: Personalized Medicine, Spring, 2012, Special Issue on Genomic

Pathology. Honors and Prizes 1982 State of Arizona, Summer Graduate Fellowship, University of Oxford 1982 Sigma Xi, Pre-Doctoral Research, University of Oxford 2011 Appointed Member, Dana Farber-Harvard Medical School Cancer Center Faculty (Program Affiliations:

Breast Cancer and Computational Biology), Boston, MA Report on Past and Current Funding 1986 PI Marquette Faculty Research Fund $25,000

Fellowship, Marquette University, Mathematical Analysis of Models of Microvascular Hematocrit Variation

1986-1987 PI Marquette Regular Research Grant $50,000 Numerical Solutions of Microvascular Models

1987-1994 PI NSF Supercomputing Resource Grant, San Diego Supercomputing Center Numerical Solutions of Models in Microvascular Circulation 1990-1993 PI NIH Supercomputing Resource Grant, Pittsburgh Supercomputing Center, Mathematical Analysis of Microvascular Transport Models 1991-1992 PI Medical College of Wisconsin $50,000

Mathematical Modeling of Physiological Phenomena 1992-1994 PI NSF Supercomputing Resource Grant

Modeling in Microvascular Blood Flow, National Center for Supercomputing Applications 1992-1997 Co-PI and Advisory Committee Howard Hughes Medical Institute $250,000

Howard Hughes Medical Institute Marquette University Undergraduate Biological Sciences Education Institution

1992-2003 Co-PI, Director NIH/NHLBI $1.1M Blood Pressure Determinants and Controllers - Core C:Research Services Core (PI A Cowley)

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1993-1994 PI Sun Microsystems Computer Corp., Academic Education and Research Grant 1993-1998 Co-PI Department of Education $300,000

Patricia Roberts Harris Graduate Fellowships in Biomathematics 1994-1995 PI Medical College of Wisconsin $80,000

Mathematical Modeling of Physiological Phenomena 1995-2001 Co-PI NIH/NHLBI $200,000

Genetic Determinants: Rat Mapping Center (PI. H Jacob) 1996-1997 PI, Medical College of Wisconsin Research Grant $80,000

Informatics in Molecular Genetics 1996-2004 Co-PI, Director NIH/NHLBI $.8M

SCOR: Molecular Genetics of Hypertension:Analysis Project and Bioinformatics Core 1997 PI Medical College of Wisconsin $80,000

Bioinformatics in Functional Genomics 1997-1999 Co-PI NSF $250,000

Graduate Research Assistantships in Industrial Mathematics 1997-2002 PI Medical College of Wisconsin $300,000

Construction of a “UNIGEN” Style Rat Map Using Rat RHs 1997-1998 PI Medical College of Wisconsin $100,000

Rat Genomic Informatics 1998-2000 PI Medical College of Wisconsin $160,000

Bioinformatics for Genetic Research 1999-2000 PI Monsanto Corporation $600,000

Genome Comparative Analysis 1999-2004 PI and Co-PI, NIH/NHLBI, The Rat Genome Database $7.3M 2000-2004 Co-PI, Director NIH/NHLBI $1.1M

Programs for Genomic Applications, Physiogenomics of Stressors in Derived Consomic Rats: Bioinformatics (PI.H Jacob)

2000-2004 Co-PI, NIH/NHLBI $100,000 Genetics and Intermittent Myocardial Hypoxia, (PI Jacob)

2001-2002 Co-PI Medical College of Wisconsin $25,000 Cancer Center, Mapping of the Susceptibility Genes for Prostatic Complex Tumors in the Lobund-Wistar Rat (P.I. Datta)

2002-2005 Co-PI, Director NIH/NHGMS $1.6M MCW GCRC Bioinformatics Core (PI Dunn)

2001-2003 PI NIH/NHGRI $200,000 Gene Ontology Consortium (MCW-RGD)

2002-2004 Consultant NIH, SBIR $30,000 Fractal Modeling of Biomedical Time Series in S-PLUS 2002-2005 Co-PI, Director NIH/NHLBI $2.1M

Development of Novel Mass Spectrometry Tools for Individual Cell Proteome Analysis: Bioinformatics (PI A Greene)

2003-2005 Co-PI NIH Innovations in Biomedical Information Science and Technology:Phased Innovation (PI, Wang)

2003-2008 Co-PI NIEHS Marine and Freshwater Biomedical Sciences Center – Zebrafish Research Core 3 - Identification of Genes that Influence Sensitivity to Developmental Toxicants: Utilization of the Zebrafish Genetic Model System (PI Carvan)

2005-2006 PI State of Wisconsin, Department of Commerce Technology Assistance Grant (TAG), Development of Clinical Genetics Research Collaboration

2005-2006 PI State of Wisconsin, Department of Commerce Partnership Matchmaking Service, Personalized Genetic Commercial Partnerships

2005-2006 PI UW-Madison Center for International Business Education and Research (CIBER) and Wisconsin Department of Commerce-International Division, Trade show and Travel grants, Personalized Genetic Commercial Partnerships, BioPartnering, Vancouver, B.C., Canada, 2006.

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2008- 2009 PI Siemens-Partners Council for Clinical Research Award $150,000 Predictive Risk of Breast Cancer Use Case

2008-2009 PI Siemens-Partners Council for Clinical Research Award $125,000 Computational Algorithms for Clinical Genetics. Partners Healthcare Inc.

2008-2010 PI, Amazon, Inc, Academic AWS Service Credit Program $65,000 Translational Science on the Cloud.

2009-2012 PI NIH/NLM EUREKA (R01) $400,000 20% Effort Method for Prediction of Efficacy of Genetic-Based Prediction Models of Personalized Medicine with Clinical Avatars

2010-2014 CI NIH/NINDS R01MH090611 (Wall) $100,000 10% Effort RNA Expression Patterns in Autism

2010-2011 PI NIH/NLM EUREKA Supplement (R01) $100,000 2.5% Effort Supplement to: Method for Prediction of Efficacy of Genetic-Based Prediction Models of Personalized Medicine with Clinical Avatars

2010-2011 PI NIH/NLM EUREKA Supplement (R01) $100,000 2.5% Effort Supplement to: Method for Prediction of Efficacy of Genetic-Based Prediction Models of Personalized Medicine with Clinical Avatars

2010-2011 CI NIH/NLM Training Program Supplement (T15) $200,000 5.0% Effort Supplement to: Boston Informatics Research Training Program. 2011-2013 PI Amazon Inc. Academic Program Grant $100,000

Modeling and Simulation of Genomics Medicine 2011-2016 CI NIH 1R01GM095476-01A1 $1,500,000 (H Yu) 2.5% Effort Exploring Natural Language Processing, Image Processing, Machine Learning, and User

Interfacing for Intelligent Biomedical Figure Search 2011-2012 PI Complete Genomics, Inc. Program in Clinical Genomics $100,000 (est) 2.5% Effort Uncovering Clinical Insight into Triple-Negative Breast Cancer 2012-2013 PI University of Wisconsin, System, Research Grant Initiative $135,000, 12.5% Effort 2012-2015 CI NIH/NIEHS, Children’s Environmental Health Sciences Core Center, Bioinformatics Core (Director) 20% Effort 2012-2013 PI NIH/NIEHS, Pilot Project Computational Pipeline for Next Generation Sequencing Information from Zebrafish $54,000, 10% Effort

CI NIH Fogerty Program Exploratory Planning for a Proposed GEOHealth Hub in the Alto Mayo Region of Peru, (P North)

Submitted and Pending 2012-2013 PI UWM, SURF, “Biomarkers of Reproduction Staging of Sturgeon” summer support for Mr. Eric Johnson, Junior, Mathematical Sciences, UWM

CI Aurora Health Care, Aurora Cardiac Research Award 2012 (M Michalwiscek, PI) AHC’s peripheral arterial disease (PAD) patient heterogeneity and new EMR approach to identify risks, clarify diagnosis and improve treatment of PAD. CI NIH, Early Life Gut Microbiome Exposure to Biocides and their Environmental Metabolites (T Miller)

Submitted Not Funded 2012-2013 PI NSF, In Silico Pharmacogenetic Clinical Trial Design, Simulation, and Predicted Outcomes

PI (Supplement) NIEHS, Children’s Environmental Health Sciences Core Center Supplement for Zebrafish Model of Human Gene-Environment Interaction Multi-PI UW Research Foundation, Predicting Clinical Validity of Bladder Cancer Nomograms CI NIH, Mechanism by which dioxin impairs hematopoiesis across multiple generations (M Laiosa, PI)

In preparation 2013 CI Lalla Salma Foundation for the Prevention and Treatment of Cancer, Moroccan Female Breast Cancer Risk

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CI NIEHS, Developmental MeHg Exposure Alters Adult Behavior via DNA Methylation Modification, M Carvan (PI) PI Population Clinical Avatars, A Novel approach to Public Health Genetics Impace - in silico

Teaching of Students in Courses 1983-1985 Calculus, Algebra, Trigonometry, Teaching Assistant, University of Arizona 1986-1993 Developed and taught undergraduate and graduate applied mathematics courses:Mathematical Biology,

Modeling in Physiology, Computational Models, Informatics Systems: Analysis and Design, Partial and Ordinary Differential Equations, Calculus, Scientific Visualization, High Performance Computing, Parallel Processing, Bioinformatics. Average of four courses per year. Undergraduate courses average twenty students.

1993-2005 Founded joint Graduate Program in Biomathematics Marquette University and Medical College of Wisconsin. Developed and taught graduate courses in bioinformatics, physiological genomics, and computational biology. Graduate courses average ten students. Bioinformatics I - BIIN 200 Designed to aid students in the application of knowledge gained through previous course work in informatics, information systems, mathematics, medical and/or biological research to the design, development, implementation and evaluation of information systems and analysis methods applied to biomedical data. Prereq: BIOL 4 and CHEM 24 which may be taken concurrently and COSC 66 Bioinformatics II - BIIN 201 Designed to aid students in the application of knowledge gained through previous course work in informatics, information systems, mathematics, medical and/or biological research to the design, development, implementation and evaluation of information systems and analysis methods applied to biomedical data. Prereq: BIIN 200 and cons. of dept. ch. Bioinformatics Seminar - BIIN 17250. The course consists of a series of seminars focused on state-of-the-art methodologies and current research subjects in bioinformatics and computational biology. Each seminar is given by a leader in the field invited from institutions throughout the country. Discussion sessions are arranged around each seminar to allow extensive interactions between students and invited speakers. Prior completion of graduate-level courses in biology and quantitative sciences is recommended. Bioinformatics Research Practicum - BIIN 17294. Provides students, who are enrolled in the Bioinformatics program, with an opportunity to participate in the practice of research and/or development in the area of bioinformatics. Prereq: BIIN 200 and consent of department chair.

1999-2003 Annual Seminar on Physiological Genomics (bioinformatics) for Medical College of Wisconsin, average ten students.

2009 Founder and Director, Clouded Translational Science. Harvard Medical School, Seminar and Project training program for undergrads, graduates and post-doctorial fellows (56 participants) Feb-June, 2009

2009 Co-Director, Methods of Translational Science. Harvard Medical School, Seminar and Project training program for undergrads, graduates and post-doctorial fellows(38 participants) Sept-Dec, 2009

2010- Director, PH 939 Seminar on Environmental and Public Health Informatics and Research, Zilber School of Public Health, University of Wisconsin, Milwaukee

2011- Track Director, MMSc in Biomedical Informatics, Harvard Medical School 2011- Founder, Medical Informatics: Public Health Informatics Track, University of Wisconsin, Milwaukee 2011- Director, BMI 714 Introduction to Biomedical Informatics: Next Generation Sequencing, Technology,

Analysis and Applications, Harvard Medical School 2012- Director, PH 709, Introduction to Public Health Informatics, Zilber School of Public Health, University of

Wisconsin, Milwaukee 2012- Director, PH 709, Introduction to Public Health Informatics and Genomics, ZSPH, UWM 2013- Director, PH 7XX (proposed), Data Science – Basic Science, Biomedical Translation, and Public Health,

Zilber School of Public Health, University of Wisconsin, Milwaukee Formally Supervised Trainees

Trainee name Type Degree Supervised

Institution YR Current Position

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38 Master Thesis Students

Pre-doctoral M.S., Biomathematics

Marquette University

1985-2005

7 Students Pre-doctoral M.S., Biomedical Engineering


1985-2005

30 Students Pre-doctoral M.S. Bioinformatics

Medical College of Wisconsin – Marquette University

1999-2005

Ondine Harris Doctoral Ph.D. (Biomathematics advisor)


1992

Mark Rieder Doctoral Ph.D. (Bioinformatics Advisor)

Medical College of Wisconsin

1996 Associate Professor, Molecular Genetics, U.of Washington

Christina Kendziorski

Doctoral Ph.D. Mathematics


1998 Associate Professor, University of Wisconsin

Elizabeth Nora

Doctoral M.D. -Ph.D. Physiology (Bioinformatics Advisor)

Medical College of Wisconsin

1998 Private Practice, WI

Roumyana Kirova

Doctoral Ph.D., Mathematics


2005 Research Scientist, Oak Ridge Labs

Manuel Torres

Doctoral Ph.D., (Bioinformatics Advisor)

University of California, Davis

2005 Fellow, CDC

Nancy Sobczak

Doctoral Ph.D., Electrical and Computer Engineering


2008

Deceased

Peter Kos Doctoral PhD Medical Informatics

University of Wisconsin, Milwaukee

2010- Pre Doctoral Research Assistant

Vince Fusaro Post Doctoral PhD Harvard Medical School

2009- NIH NLM Post Doctoral Fellow

Kristina Demas

CTSC Catalyst pre doctoral Research Fellow

MD Harvard Medical School

2009 George Washington University Medical School, Susan G. Komen, Medical Rotation Award

Chih-Lin Chi Post Doctoral PhD Harvard Medical School

2009- Post Doctoral Fellow

Sheida Nabavi

Post Doctoral PhD Harvard Medical School

2010- NIH NLM Post Doctoral Fellow

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Kourosh Raavatz

Doctoral PhD University of Wisconsin, Milwaukee


Mary Shimoyama

Doctoral PhD (Advisory Committee)

UWM Medical Informatics

2010-2011 Bioinformatics Faculty, Medical College of Wisconsin

Jessica Plati Post Doctoral PhD Harvard Medical School


Zhengqiu Cai Post Doctoral PhD Harvard Medical School and Beth Israel Deaconess Medical Center

2011- Post Doctoral Fellow, Bioinformatics Research Scientist

Michiyo Yamada

Post Doctoral PhD Harvard Medical School


Pushkar Phadke

MD, Pathology Resident


2011 Pathology Resident, Harvard Medical School

Qing Liu Doctoral (Bioinformatics advisor)

PhD University of Wisconsin, Milwaukee


Theopolis Hill CTSC Catalyst pre doctoral Research Fellow


2011 MD Student, Howard University, Awardee, Donor Scholar.

Ali Dashti Doctoral PhD UWM, Computer Science

2011- Doctoral Student

Uma Saxena Doctoral (advisory Committee)

PhD University of Massachusetts


Rui Du Doctoral PhD UWM-ZSPH, EOH


Qing Zhang Doctoral (Bioinformatics Advisor)

PhD UWM-ZSPH, EOH


Emmanual Owusu Asante-Asamani

Doctoral PhD UWM-Mathematics


Zeinab Salari Far

Master Degree MS UWM-College of Health Sciences

2011- MS Student

Local Invited Presentations

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2000 Bioinformatic Approaches in the Study of Physiological Genomics of the Rat. US-Astra Research Center Boston Inc, Boston, MA 2002 The Impact of HPTC and Bioinformatics on Disease Focused Comparative Genomics. Whitehead Institute – 21st

Century Life Science Technology Revolution, Cambridge, MA 2007 Genetics Applied: Biomedical Informatics Facilitates Best Practice Personalized Medicine, Center for

Biomedical Informatics, Harvard medical School, Boston, MA 2009 Personalized Medicine Clinical Algorithms for Whole Genome Data, Siemens Research Council, Boston, MA 2010 Genome Reduction to Actionable Health Information, Combined Pathology Ground Rounds, Harvard Medical

School, Boston, MA 2011 Translational Bioinformatics, Clinical Avatars and Predictions of Personalized Genomic Medicine.

Boston MA, VA Seminar Series, July, 2011, 2011 Genomic Pathology, Executive Committee, Beth Israel Deaconess Medical Center, Executive Committee, Oct, 2011 Translation to Genomics Medicine, Cancer Center, Beth Israel Deaconess Medical Center, Nov, 2011.

Report of Regional, National and International Invited Teaching and Presentations 1986 Modeling and Analysis of Microvascular Blood Flows. Marquette University, Milwaukee, WI 1987 Critical Behavior of an Ignition Model in Chemical Combustion. SIAM Meeting on Numerical Methods in

Combustion, San Francisco, CA 1988 Transport Mechanisms in Microcirculation. Marquette University, Milwaukee, WI 1989 Mathematical Modeling of Oxygen Transport in the Microvascular System. Department of Physiology,

Medical College of Wisconsin, Milwaukee, WI 1992 Modeling, Mathematics, and the Microvascular. Marquette University, Milwaukee, WI 1997 Informatics in Science and Business. Information Technology Symposium, Milwaukee County Board,

Milwaukee, WI 1998 The Microcirculation Physiome Project. FASEB, San Francisco, CA

Physiological Genomics: Building a Physiological Map with Bioinformatics. Department of Mathematics, Marquette University, Milwaukee, WI

1999 Bioinformatics Of Genomic Tools and Database. GeneticFX, Austin, TX Bioinformatics in Clinical Research. General Clinical Research Centers: Bioinformatics Workshop, San Antonio, TX The Rat Genome Database. Physiology Genomics and Rat Models, Genome Sequence and Biology, Cold Spring Harbor, NY

2000 Physiological Genomics: Tools and Knowledge Development. Medical College of Wisconsin, Milwaukee, WI Bioinformatics in Physiological Genomics. Per Bio, Inc., Milwaukee, WI Careers in Bioinformatics. Whitefish Bay High School, Milwaukee, WI Whole Genome Comparison Mapping. Monsanto, St. Louis, MO Bioinformatics in Clinical Research. Clinical Scholars Training Program, Milwaukee, WI Bioinformatics and the MCW General Clinical Research Center: Strategy, Development and Progress. GCRC

Bioinformatics Conference, New Orleans, LA Bioinformatics: A New Professional Field. Carthage College, Whitefish Bay, WI 2001 Bioinformatics and the Medical College of Wisconsin: Mathematics, Statistics, and Computer Science.

Marquette University, Milwaukee, WI Functional Genomics for Drug Discovery. Celera Genomics, Rockville, MD

Microarray Science: Technical, Experimental, Design and Analysis. Wake Forest University, Greensboro, NC Microarray and Physiological Profiling and Analysis, Experimental Biology 2001, Orlando, FL Rat Genome Database. Rat Genome Sequencing Consortium Meeting, Houston,TX

A Disease-Centric Proposal for Rat Genome Sequencing, Analysis and Annotation. Department of Physiology, Medical College of Wisconsin, Milwaukee, WI Physiological Profiling: A New Approach to Complex Physiological Genomics. Wisconsin Symposium II: The Analysis of Human Biology – Genes, Genomes, and Molecules, Madison, WI Managing and Accessing Large Complex Scientific Data Sets, Informatics Approaches to Neuroscience and Sleep Research, Bethesda, MD

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Statistical Methodology and Tools in Clinical Genetics Informatics. ASA Joint Statistical Meeting, Atlanta, GA The Rat Genome Database 2.0. Rat Genome Database Workshop, Medical College of Wisconsin, Milwaukee, WI Bioinformatics: Approaches and Tools for Discovery. Physiological Genomics: From Phenotype to Genotype and Back Again, Cold Spring Harbor, NY Identification of Prostate Cancer Susceptibility Genes Through Cross-Species Bioinformatics.Wisconsin Symposium II: The Analysis of Human Biology – Genes, Genomes and Molecules, Madison, WI

2002 Research Strategies and Bioinformatics: Concepts, Structure, Design and Implementation.GCRC Research, Imaging and Bioinformatics Workshop, Medical College of Wisconsin, Milwaukee, WI Research Strategies and Bioinformatics: Concepts, Strategies, Design and Implementation. Bioinformatic Approaches to Neuroimaging in Clinical Research, Seattle, WA Disease Research, The Rat Genome and Bioinformatics. University of Wisconsin Milwaukee, Milwaukee, WI Bioinformatics, Comparative Genomics, and Disease Oriented Research, 26th Annual Great Lakes Biomedical Conference – Genomics and Beyond: The Engineering and Business of Biotechnology, Racine, WI

Disease Oriented Rat Research. Experimental Biology 2002, New Orleans, LA RGD – Mapping Disease onto the Genome. Genome Sequencing & Biology Meeting, Cold Spring Harbor, NY Bioinformatics, Comparative Genomics, and Disease-Oriented Research. ATS 2002 – 98th International Conference, Atlanta, GA Future Direction in Bioinformatics. Department of Physiology, Medical College of Wisconsin, Milwaukee, WI Identifying and Annotating Disease Specific Rat Genome Sequences: A Case Study in Prostate Cancer,.American Association for Cancer Research 93rd Annual Meeting, San Francisco, CA Rat Genome Database: A Comparative Genomics Platform for Rat, Mouse and Human. NCRR Resource Directors Meeting, San Antonio, TX Comparative Genomics and Disease Analysis, The International Mammalian Genome Society, San Antonio, TX The NIH/NIAID/Wellcome Trust Workshop on Model Organism Databases, National Human Genome Research Institute, Bethesda, Md.

2003 Bioinformatics, Genomics and Clinical Genetics. University of Wisconsin-Parkside, Department of Biological Sciences, Kenosha, WI

Medical Knowledge in the Genetic Era. Marshfield Clinic Research Foundation, Marshfield, WI Mechanistic Mining of Rat Disease Genes. FASEB, 2003, San Diego, California Future Directions in Bioinformatics, Biostatistics, University of Wisconsin, Madison, WI Bioinformatics and the Future of Life Science, Medical College of Wisconsin, Milwaukee, WI Bioinformatics, Physiological Genomics and (moving towards a) Phenome, APS, Physiological

Genomics, Augusta, Georgia Rat Genome Database Complex Disease Research, FASEB, San Diego, CA The Bioinformatics of Complex Disease Research, FASEB, San Diego, CA 2004 Personalized Medicine through Bioinformatics, Medical College of Wisconsin, Milwaukee, WI

The Bioinformatics of Complex Disease Research, Plant Genetics Institute and Bioinformatics Center, Iowa State University, Ames, Iowa Using Informatics to Deliver Personalized Genetically Based Patient Care, Great Lakes Biomedical Conf., Milwaukee, WI Bioinformatics support of Clinical Registries for Community Health Initiatives, World Congress for Chromosomal Abnormalities, San Antonio, TX Bioinformatics and Translational Research, Division of Biomedical Sciences, Univeristy of Parkside, Parkside, WI Mathematical Impact on Clinical Genetics, Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI

2005 Bioinformatic’s Impact on Clinical Genetics, Bioinformatics and Medical Informatics: Tools for Mining & Applying Genetic Information in Patient Care, Biomedical Technology Alliance, Milwaukee, WI

2006 Post Human Genome Project, The NIH “Roadmap”, and Impact on Best Practice Medicine, American Medical Group Association (AMGA) 2006 Annual Meeting, San Antonio, TX Bioinformatics and Translational Medicine. Center for Functional Genomics, University of Wisconsin, Milwaukee, WI

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The Human Genome Project and Clinical Translation to Best Practice Medicine, The Division of Biomedical Informatics, Cincinnati Children’s Health Medical Center and Research Foundation, Cincinnati, OH Genetic “Bench to Bedside”, Challenges are Opportunities for Biomedical Informatics, School of Mathematics Sciences, University of Wisconsin, Milwaukee, WI Personalized Medicine. The Synergy between Drugs and Devices, G.E. Healthcare and Wisconsin Biotechnology and Medical Device Association, 8th Annual WMBDA meeting, Milwaukee, WI The Promise, Status, and Future of Personalized Medicine at the Point of Care, Wisconsin Technology Pavilion, BIO 2006, Chicago, IL

2007 The Case for Personalized Medicine, BioBit, School of Engineering, University of Illinois, Chicago, IL Gender Specific Considerations: Warfarin, CME program hosted by the Alexian Brothers Hospital Network, Early Detection and Disease Prevention: A Case Based Approach to Personalized Medicine, Chicago, IL The Wisconsin Warfarin Collaboration: Clinical Decision Support for Pharmacogenomics Guided Warfarin Dosing, Office of the Secretary, Priority in Personal Health Care, Department of Health and Human Services, Washington, DC Early Detection and Disease Prevention: A Case Based Approach to Personalized Medicine, CME accredited event, Chicago Illinois.

2008 Incrementing the Medical Enterprise for Discovery: Dissolving the Barriers between Clinical Care and Research, AMIA Translational Bioinformatics Summit, San Francisco, CA

Biomedical Informatics Translated to Best Practice Personalized Medicine, Center for Translational Research in Cancer, West Virginia University, Morgantown, WV

2009 Clouded Clinical and Translational Science, Morgridge Institute for Research, University of Wisconsin, Mad, WI Translational Science on the Cloud, Outside Expert Seminar Series, Amazon, Inc., Seattle, WA Pharmocogenetics, Clinical Avatars and Predictions of Personalized Medicine, Director’s Seminar, NLM, National Institute of Health, Bethesda, MD A Methodology for Translational Science, School of Public Health, University of Wisconsin, Milwaukee, WI

2010 Pharmocogenetics, Predictions of Personalized Medicine, and the Role of Bioinformatics in Addressing Health Inequities, Health in the New Era: The Role of Technology in Addressing Health Inequities in the Midwest, Univeristy of Chicago, Chicago, Illinois Genomic Reduction to Clinical Action, American Association for the Advancement of Science Symposium on Personalized Medicine in the Clinic: Policy, Legal, and Ethical Implications, Phoenix, AZ National Library of Medicine, Special Topics in the EUREKA program, 2010, “Method for Prediction of Efficacy of Genetic-Based Prediction Models of Personalized Medicine with Clinical Avatars”

2011 IHT2 Health Summit , Aug, 2011, Seattle, WA, “Bioinformatics Essentials for a Personalized Genomic Medicine Era” Outside Expert Seminar Series, Amazon, Inc., Seattle, WA, Aug, 2011. “Translational Medicine: Cloudy with Chance of Rain” EDUCAUSE 2011, Oct, 2011, Philadelphia, PA, “Transforming Research in the Cloud: A Harvard Medical School Case Study”

2012 Molecular Biology Graduate Students at the University of Colorado School of Medicine, Keynote Speaker, Mini-symposium, Personalized Medicine: Translating the Genome into Health Care, April 19-20, 2012

Advances in Personalized Breast Cancer Treatment, SU2C/PI3K Dream Team Meeting, Boston, MA Sept, 2012 If you are able, we will be having a session on biomarkers and retrospective analysis on Monday afternoon. Yuker Wang

will be presenting during that afternoon block and we thought you would like to participate. I will send follow-up information to you, if you are able to attend. 2013 International Invited Presentations 2000 Physiological Profiling: Methods for Biomedical Data Mining. Max-Planck Institute for Molecular Genetics,

Berlin, Germany

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Multivariable Analysis of Physiological and Microarry Expression. Institut fur Pharmakologie, Christian-Albrechts-Universitat Kiel, Kiel, Germany

2001 Introduction: Multivariable Analysis: New Approaches to Modeling and Analysis of Physiological Genomics. XXXIV International Congress of Physiological Sciences, Christchurch, New Zealand

Disease Centric Rat Gene Initiative. Japan Biological Information Research Center, Koutou-ku, Tokyo 2002 NLP and Disease Oriented Data Mining and Knowledge Retrieval. Workshop on Natural Language Processing

and Ontology Building in Biology, Tokyo Garden Palace Hotel, Tokyo Japan Comparative Genomics in Disease Oriented Research. Life Sciences School, Fudan University, Shanghai China The Rat Genome Database and Sequencing Project and Human Disease. Second Information of the Waterfront Symposium of Human Genome Science (WASH), Odaiba, Tokyo, Japan The Rat Genome Database Disease-Centric Initiative. Impact of Genomics on Medicine: Linking Functional Genomics and Proteomics Approaches for Drug Development, Munich, Germany Bioinformatics and the Study of Complex Disease Genetics, Department of Physiology, University of Kiel,Kiel, Germany The Impact of HPTC and Bioinformatics on Disease Focused Comparative Genomics.Bioscience Asia 2002, Taipei, Taiwan ASAP: The Automated Sequence Analysis Pipeline For Assembly & Annotation, Genome Informatics, Wellcome Trust Campus, Bioinformatics Lecture Series, UK The Rat Genome Database and Sequencing Project and Human Disease. Second Information of the Waterfront Symposium of Human Genome Science (WASH), Odaiba, Tokyo

2003 Medical Knowledge in the Genetic Era, The 2nd Annual Biology Exposition Japan Conference, Tokyo, Japan. From Genomic Discovery to Clinical Application, National Cancer Institute, Tokyo, Japan Rat Genome Database (RGD) and Complex Disease Research, Utrecht Graduate School of Developmental Biology, Utrecht, Netherlands The Bioinformatics of Complex Disease Research, Institute of Genomics and Integrated Biology, New Delhi, India Clinical Translation of Genomic Discoveries, Institute of Genomics and Integrated Biology, New Delhi, India From Genomic Discovery to Clinical Application, Institute of Genomics and Integrated Biology, New Delhi, India

2004 The Health Care Impact of Personalized (Genetic) Medicine, Annual Meeting of the Joint Bioinformatics and Industrial Consortium, Tokyo, Japan

The Health Care Impact of Personalized (Genetic) Medicine, National Cancer Institute , Tokyo, Japan The Health Care Impact of Personalized (Genetic) Medicine, IBM, Bi-Annual Life Science Asia Meeting, Amagi, Japan

2009 Molecular Medicine at the Point of Care. Tokyo Medical and Dental University, 1st Symposium on Genome Medical Informatics, Tokyo, Japan Biomedical Informatics and Mechanical Turks, Tokyo Medical and Dental University, Tokyo, Japan

2010 Translational Science – A Paradigm Shift to Preventive Medicine, Symposium of Translational Medicine, Yokohama City University Medical Center, Yokohama, Japan

US-Japan Translational Collaboration, Symposium of Translational Medicine, Yokohama City University Medical Center, Yokohama, Japan

A NGS Whole Genome reduced to Actionable Health Care Information, 4th Omic’s Symposium on Translational Medicine, Yokohama, Japan

Workshop on Biomedical Informatics in Translational Medicine, (4 lecctures). American University of Beirut, Lebanon. Cloud Computing Workshop, Nile University, Dec, 2010.

Lecture 1: “Clouded Pharmocogenetics, Clinical Avatars and Predictions of Personalized Medicine” Lecture 2: “Whole Genome Based Personalized Medicine”

2011 Personalized Medicine World Conference, Feb 2011, Silicon Valley, CA. How Current Genomic Technologies Deployed in Personalized Medicine to Improve Clinical Care 10th Annual Bio-IT World Conference & Expo on April 12-14, 2011, Boston Ma, “Genome Era Medicine and HealthCare Disruptive Technology” OECD-NSF Workshop: Building a Smarter Health and Wellness Future – 15-16 February 2011, Washington D.C., “: Bioinformatics Essentials for a Personalized Genomic Medicine Era

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2012 Personalized Medicine with Biomedical Informatics, Workshops (2) and lectures (2) in Morocco, January, 2012 3rd Annual Personalized Diagnostics Conference, Feb, 2012, San Francisco, CA, “Clinical Whole Genome Analysis: Experience and Recommendations For Genomic Pathology”

2013 International conference on Predictive, Preventive and Personalized Medicine & Molecular Diagnostics" (Personalized Medicine-2013), August 05-07, 2013, Chicago, IL, “An optimized Whole Genome Analysis System with Clinical annotation.” Report of Technological and Other Scientific Innovations 01/07/2005 Physiological Profiling (U.S. Patent Application 11/031,322) 01/01/2013 Software to conduct Whole Genome Analysis (Registered with Office of Technology Development), Harvard Medical School Report of Education of Patients and Service to the Community 2009- Mentor and Participant, Harvard Catalyst Visiting Research Internship Program (VRIP), Harvard Medical School 2009- Mentor and Participant, Project Success, Summer Diversity Student Internship Program, Harvard Medical School 2009- Mentor and Participant, Biomedical Informatics Co-Op program, Northeastern University, Boston, MA 2009- Mentor, American Medical Informatics Association Mentorship Program 2010- Participant, Health Disparities Post Graduate Fellowship Program, Harvard Medical School, Boston, MA 2010- Participant, Reviewer, New England Science Symposium, Harvard Medical School, Boston, Ma 2010- Participant, Mentor, The Biomedical Science Careers Program, Harvard Medical School Medical School, Boston,

MA 2010 Chair, Reflections on H1N1: What have we learned about responding to a pandemic, Annual Urban Initiatives

Conference on Public Health, Milwaukee, WI June, 2010. 2010 Participant and Speaker, Pathology Education Summit, Developing and Implementing a nation-wide Curriculum

in genomics and personalized medicine for pathology residents, Harvard Medical School and Beth Israel Deaconess Medical School, Boston, MA Aug, 2010

Report of Scholarship 1. Lomen DO, Tonellato PJ, Warrick AW. Salt and water transport in unsaturated soil for non-conservative systems.

Agricultural Water Management 1984, 8:397-409. 2. Greene AS, Tonellato PJ, Lui J, Lombard J, Cowley AW Jr. Microvascular rarefaction and tissue vascular resistance

in hypertension. Am J Physiol 1989, 256: H126-H131. 3. Newton-Nash DK, Tonellato PJ, Swiersz M, Abramoff P. Assessment of chemokinetic behavior of inflammatory

lung macrophages in a linear under-agarose assay. J Leukocyte Biol 1990, 48:297-305. 4. Tonellato PJ, Greene AS. Oxygen distribution in the microvascular system. Pixel 1991, 2(1):14-20. 5. Tonellato PJ. Critical behavior of an ignition model in chemical combustion. Quarterly Appl Math 1991, 4:795-812. 6. Greene AS, Tonellato PJ, Zhang Z, Lombard J, Cowley AW Jr. Effect of microvascular rarefaction to tissue oxygen

delivery in hypertension. Am J Physiol 1992, 262: H1486- H1493. 7. Rieder MJ, O'Drobinak DM, Tonellato PJ, Greene AS. Mathematical analysis of type-I and type-IIb muscle fiber

force generation in renal hypertension. Annals of Biomedical Engineering 1996, 24: 489-499. 8. Cowley AW Jr, Tonellato PJ. The Physiome: Tool for Physiological Genomics. Proceedings of “On Designing the

Physiome Project” Petrodvoret, July 5-8, 1997, St. Petersburg ,Russia [on-line article nsr.bioeng.washington.edu/NSR/physiome/files/Petrodvoret.1997].

9. Popel AS, Greene AS, Ellis CG, Ley KF, Skalak TC, Tonellato PJ. The Microcirculation Physiome Project. Annals of Biomedical Engineering 1998, 26(6):911- 913.

10. Kendziorski CM, Bassingthwaighte JB, Tonellato PJ. Evaluating maximum likelihood estimation methods to determine the Hurst coefficient. Physica A 1999, 273:439-451.

11. Lu J, Kwitek-Black A, Jacob HJ, Tonellato PJ. A web-based rat radiation hybrid map server. Rat Genome 1999, 5(2):77.

12. Steen RG, Kwitek-Black A, Glenn C, Gullings-Handley J, Van Etten W, Atkinson OS, Appel D, Twigger S, Muir M, Mull T, Granados M, Kissebah M, Russo K, Crane R, Popp M, Peden M, Matise T, Brown DM, Lu J, Kingsmore S, Tonellato PJ, Rozen S, Slonim D, Young P, Knoblauch M, Provoost A, Ganten D, Coleman S, Rothberg J, Lander

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ES, Jacob HJ. A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat. Genome Res 1999, 9:AP1-8.

13. Gosele C, Hong L, Kreitler T, Rossmann M, Hieke B, Grob W, Kramer M, Himmelbauer H, Bihoreau MT, Kwitek-Black A, Twigger S, Tonellato PJ, Jacob HJ, Schalkwyk LC, Lindpaintner K, Ganten D, Lehrach H, Knoblauch M. High-throughput scanning of the rat genome using interspersed repetitive sequence-PCR markers. Genomics 2000, 69:287-294.

14. Cowley AW Jr, Stoll M, Greene AS, Kaldunski ML, Roman RJ, Tonellato PJ, Schork NJ, Dumas P, Jacob HJ. Genetically defined risk of salt sensitivity in an intercross of Brown Norway and Dahl S rats. Physiology Genomics 2000, 2(3):107-115.

15. Kwitek AE, Tonellato PJ, Chen D, Gullings-Handley J, Cheng YS, Twigger S, Scheetz TE, Casavant TL, Stoll M, Nobrega MA, Shiozawa M, Soares MB, Sheffield VC, Jacob HJ. Automated construction of high-density comparative maps between rat, human, and mouse. Genome Res 2001, 11:1935-1943.

16. Stoll M, Cowley AW Jr, Tonellato PJ, Greene AS, Kaldunski ML, Roman RJ, Dumas P, Schork NJ, Wang Z, Jacob HJ. A genomic-systems biology map for cardiovascular function. Science 2001, 294:1723-1726.

17. Nora E, Tonellato PJ, Greene AS. Quantification of the contribution of Type 1 and Type 2 angiotensin II receptors to the net tissue specific effect of angiotensin II. Annals of Biomedical Engineering 2002, 28(6):653-664.

18. Lombard JH, Frisbee JC, Greene AS, Hudetz AG, Roman RJ, Tonellato PJ. Microvascular flow and tissue PO(2) in skeletal muscle of chronic reduced renal mass hypertensive rats. Am J Physiol 2002, 279:H2295-H2302.

19. Twigger S, Lu J, Shimoyama M, Chen D, Pasko D, Long H, Ginster J, Chen CF, Nigam R, Kwitek-Black A, Eppig J, Maltais L, Maglott D, Schuler G, Jacob H, Tonellato PJ. Rat Genome Database (RGD) – mapping disease onto the genome. Nucleic Acids Research 2002, 30(1):125-128.

20. Kendziorski CM, Cowley AW Jr, Greene AS, Salgado HC, Jacob HJ, Tonellato PJ. Mapping baroreceptor function to genome: a mathematical modeling approach. Genetics 2002, 160:1687-1695.

21. Roman RJ, Cowley AW Jr, Greene A, Kwitek AE, Tonellato PJ, Jacob HJ., Consomic rats for the identification of genes and pathways underlying cardiovascular disease. Cold Spring Harb Symp Quant Biol. 2002, 67:309-15.

22. Kotchen TA, Broeckel U, Grim CE, Hamet P, Jacob H, Kaldunski ML, Kotchen JM, Schork NJ,Tonellato PJ, Cowley AW Jr., Identification of hypertension-related QTLs in African American sib pairs. Hypertension. 2002 Nov; 40(5):634-9.

23. Thomas MA, Chen CF, Jensen-Seaman, Tonellato PJ, Twigger SN. Phylogenetics of rat inbred strains.Mamm Genome. 2003 Jan; 14(1): 61-4.

24. Thomas MA, Weston B, Joseph M, Wu W, Nekrutenko A, Tonellato PJ. Evolutionary Dynamics of Oncogenes and Tumor Suppressor Genes: Higher Intensities of Purifying Selection than Other Genes. Mol Biol Evol. 2003 Jun; 20(6): 964-8.

25. Tatay JW, Feng X, Sobczak N, Jiang H, Chen C, Kirova R, Struble C, Wang N, Tonellato PJ. Multiple Approaches to Data-Mining of Proteomic Data based on Statistical and Pattern Classification Methods. Proteomics. Special Issue: Mining MALDI-TOF Data . Issue Edited by Michael J. Campa, Michael J. Fitzgerald, Edward F. Patz Jr.. Sept. 2003, 3(9):1704-1709.

26. Ghosh K, Nie J, Chen D, Nie, J., Tonellato PJ. A Problem Solving Environment for Gene Analysis.Sixth International Conference on Computational Intelligence and Natural Computing, Sept 2003, (6): 1621-1624.

27. Wang X, Jiang N, Feng X, Xie Y, Tonellato, PJ, Ghosh S, Hessner, MJ. A novel approach for high-quality microarray processing using third-dye array visualization technology. Transactions on Nanobioscience, Dec 2003, 2(4):193-201.

28. Moreno C, Dumas P, Kaldunski ML, Tonellato PJ, Greene AS, Roman RJ, Cheng Q, Wang Z, Jacob HJ, Cowley AW Jr. Genomic map of cardiovascular phenotypes of hypertension in female Dahl S rats. Physiological Genomics. 2003 Nov 11; 15(3): 243-5.

29. Postlethwait J, Ruotti V, Carvan MJ, Tonellato PJ. Automated analysis of conserved syntenies for the zebrafish genome. Methods Cell Biol. 2004;77:255-71.

30. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato PJ, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004 Jan 1; 32(1): D258-61.

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31. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Alba M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hubner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, Lopez-Otin C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F; Rat Genome Sequencing Project Consortium. The Rat Genome Project Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521.

32. Kwitek AE, Gullings-Handley J, Yu J, Carlos DC, Orlebeke K, Nie J, Eckert J, Lemke A, Andrae JW, Bromberg S, Pasko D, Chen D, Scheetz TE, Casavant TL, Soares MB, Sheffield VC, Tonellato PJ, Jacob HJ. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Genome Res. 2004 Apr;14(4):750-7.

33. Twigger SN, Nie J, Ruotti V, Yu J, Chen D, Li D, Mathis J, Narayanasamy V, Gopinath GR, Pasko D, Shimoyama M, De La Cruz N, Bromberg S, Kwitek AE, Jacob HJ, Tonellato PJ. Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data. Genome Res. 2004 Apr;14(4):651-60.

34. Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Md Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, R Gopinath G, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato PJ, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2004 Jun;2(6):E162.

35. Halligan BD, Dratz EA, Feng X, Twigger SN. Tonellato, PJ. Greene AS. Peptide Identification Using Peptide Amino Acid Attribute Vectors. J. of Proteome Research 2004. 3(4): 813 -820.

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36. Zhou G, Wen X, Liu H, Schlicht MJ, Hessner MJ, Tonellato PJ, Datta MW. B.E.A.R. GeneInfo: a tool for identifying gene-related biomedical publications through user modifiable queries. BMC Bioinformatics. 2004 Apr 29;5(1):46

37. Etim A, Zhou G, Wen X, Liu H, Ruotti V, Twigger S, Jin W, Matysiak B, Mathis J, Tonellato PJ, Datta MW. ChromSorter PC: a database of chromosomal regions associated with human prostate cancer. BMC Genomics. 2004 Apr 28;5(1):27.

38. Schlicht MJ, Matysiak B, Brodzeller T, Wen X, Liu H, Zhou G, Dhir R, Hessner MJ, Tonellato PJ, Suckow M, Pollard M, Datta MW. Cross-Species Global and Subset Gene Expression Profiling Identifies Genes Involved in Prostate Cancer Response to Selenium. BMC Genomics. 2004 Aug 20;5(1):58.

39. de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, Chen J, Fan C, Harris G, Jin W, Mathis J, Nenasheva N, Nie J, Nigam R, Petri V, Wang W, Wu W, Zhao L, Kwitek A, Tonellato PJ, Jacob H, The Rat Genome Database (RGD): Developments towards a Phenome Database, Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D485-91.

40. Hamet P, Merlo E, Seda O, Broekel U, Trembley J, Kaldunski M, Gaudet D, Bouchard, G, Deslauriers B, Gagnon F, Antoniol G, Pausova Z, Labuda M, Jamphe M, Gossard F, Kirova R, Tonellato PJ, Orlov S, Pintos J, Platfo J, Hudson T, Riousx J, Kotchen T, Cowley A. Qualitative Founder-Effect Analysis of French Canadian Families Identifies Specific Loci Contributing to Metabolic Phenotypes of Hypertension. Am J Hum Genet. 2005 May; 76(5): 815-832.

41. Twigger SN, Pasko D, Nie J, Shimoyama M, Bromberg S, Campbell D, Chen J, dela Cruz N, Fan C, Foote C, Harris G, Hickmann B, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nigam R, Petri V, Reilly D, Ruotti V, Schauberger E, Seiler K, Slyper R, Smith J, Wang W, Wu W, Zhao L, Zuniga-Meyer A, Tonellato PJ, Kwitek AE, Jacob HJ. Tools and strategies for physiological genomics: the Rat Genome Database. Physiol Genomics. 2005 Oct 17;23(2):246-56.

42. Indap AR, Marth GT, Struble CA, Tonellato PJ, Olivier M. Analysis of concordance of different haplotype block partitioning algorithms. BMC Bioinformatics. 2005 Dec 15;6:303.

43. Ghosh K, Wade B, and Tonellato PJ, Optimization of a Gene Analysis Application, Computing Letters 2006, 2 (1-2), pp. 81-88.

44. Kwitek AE, Jacob H, Baker J, Dwinell M, Forster H, Greene A, Kunert M, Lombard J, Mattson D, Pritchard K, Roman R, Tonellato PJ, and Cowley AW. BN phenome: detailed characterization of the cardiovascular, renal, and pulmonary systems of the sequenced rat. Physiol Genomics. 2006 Apr 13;25 (2):303-13.

45. Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, TaniyaT, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, BarreroRA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB,Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo M, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato PJ, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares M, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, and Gojobori T. Genome Information Integration Project and H-Invitational 2* (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research36 (Database Issue) 2008: D793-D799.

46. Haspel, RL, Arnaout, R, Briere, L, Kantarci, S, Marchand, K, Tonellato, PJ, Connolly, C, Boguski, MS,.Saffitz,JE, A Call to Action: Training Pathology Residents in Genomics and Personalized Medicine, Am J Clin Pathol. 2010 Jun;133(6):832-4.

47. Wall, DP, Kudtarkar, P, Fusaro, V, Pivovarov, R, Patil, P and Tonellato, PJ. Cloud Computing for Comparative Genomics. BMC Bioinformatics. 2010 May 18;11:259.

48. Chi, C-L, Kos, PJ, Fusaro, VA, Pivovarov, R, Patil, P, and Tonellato, PJ. Mining Personalized Medicine Algorithms with Surrogate Algorithm Tags. In Proceedings of the 1st ACM International Informatics Symposium (IHI '10), Tiffany Veinot (Ed.). ACM, New York, NY, USA, 474-478.

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49. Wall, D.P., Pivovarov, R., Tong, M., Jung, JY., Fusaro, V., DeLuca, T., & Tonellato, P.J., Genotator: A disease-agnostic tool for genetic annotation of disease. BMC Medical Genomics 2010 3:50.

50. Kudtarkar, P., DeLuca, T., Fusaro, V., Tonellato P.J., and Wall, D.P. Evolutionary Bioinformatics 2010:6 197-203 51. Dumontier M, Andersson B, Batchelor C, Denney C, Domarew C, Jentzsch A, Luciano J, Pichler E, Prud'hommeaux

E, Whetzel P, Bodenreider P, Clark T, Harland L, Kashyap V, Kos P, Kozlovsky J, McGurk J, Ogbuji C, Samwald M, Schriml L, Tonellato PJ, Zhao J, Stephens S. The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench Proceedings of the 13th ISMB'2010 SIG meeting "Bio-ontologies" 2010:120-123.

52. Tonellato PJ, Crawford JM, Boguski MS, Saffitz JE. A national agenda for the future of pathology in personalized medicine. Am J Clin Pathol. 2011 May;135(5):668-72.

53. Fusaro VA, Patil P, Gafni E, Wall DP, Tonellato PJ. Biomedical cloud computing with Amazon web services, PLoS Comput Biol. 2011 Aug;7(8).

54. Wall, DP, Tonellato PJ. The future of genomics in pathology, F1000 Medicine Reports 2012:4:14. 55. Wall, DP, Tonellato PJ. Deriving clinical action from whole-genomic analysis. Personalized Medicine, (Accepted for

publication in the May, 2012 'Genomic Pathology' special focus issue) 56. Suzuki, S, Takai-Igarashi, T, Fukuoka, Y, Wall, DP, Tanaka, H, and Tonellato, PJ. Systems Analysis of Inflammatory

Bowel Disease Based on Comprehensive Gene Information. BMC Med Genet. 2012 Apr 5;13:25 57. Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L,

Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M. The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. J Biomed Semantics. 2011 May 17;2

58. Chi CL, Fusaro VA, Patil P, Crawford MA, Content CF, Tonellato PJ. A simulation platform to examine heterogeneity influence on treatment. AMIA Summits Transl Sci Proc. 2012;2012:19-24.

59. El-Kalioby M, Abouelhoda M, Krüger J, Giegerich R, Sczyrba A, Wall DP, Tonellato P., Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package. BMC Bioinformatics. 2012;13 Suppl 17:S22. doi: 10.1186/1471-2105-13-S17-S22. Epub 2012 Dec 13.

60. Fusaro VA, Patil P, Chi CL, Contant CF, Tonellato PJ, A systems approach to designing effective clinical trials using simulations. Circulation. 2013 Jan 29;127(4):517-26.

61. Liu Q, Basu N, Goetz G, Jiang N, Hutz RJ, Tonellato PJ, Carvan MJ 3rd. Differential gene expression associated with dietary methylmercury (MeHg) exposure in rainbow trout (Oncorhynchus mykiss) and zebrafish (Danio rerio). Ecotoxicology. 2013 May; 22 (4):740-51.

62. Przybytkowski E, Aguilar-Mahecha A, Nabavi S, Tonellato PJ, Basik M., Ultradense array CGH and discovery of micro-copy number alterations and gene fusions in the cancer genome. Methods Mol Biol. 2013;973:15-38.

Proceedings of Meetings and Technical Reports 1. Warrick AW, Lomen DO, Tonellato PJ. Soil and moisture flow for point and line sources - computer programs for

linearized solutions. Technical Report 81-82, Agricultural Engineering and Soil Science, Dept of Soils, Water Engineering, University of Arizona Press, 1983.

2. Feng X, Jiang H, Dong X, Tonellato PJ. A New Self-Organizing Map and Fuzzy Logic Based Data Mining Approach for Genetic and Phenotypic Analysis of Rat Strains. Faramarz Valafar, Homayoun Valafar (Eds.): Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Scienes, June 23 - 26, 2003, Las Vegas, Nevada, USA pp.54-59 CSREA Press 2003.

3. Ghosh K and Tonellato PJ. A Novel Algorithm using Context Free Grammer for Promotor Prediction in Genomic Sequencing. Proceeding of 7th World Multiconference on Systemics, Cybernetics and Informatics,Volume 8, pp 335-339, Orlando, July, 2003.

4. Dong X, Jiang H, Feng X, and Tonellato PJ. Identifying Correlated Phenotypes using Kohonen Competitive Learning Neural Network. Proceeding of 7th World Multiconference on Systemics,Cybernetics and Informatics,Volume 8, pp 233-236, Orlando, July, 2003.

5. Sobzek, N.L., Corliss, G.F., Seitz, M.A., Tonellato, PJ. Cluster Methodology Defines Archetype Sentinel Consomic Rats, Proceedings of the 2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, pp 54-58, Honolulu, April, 2007.

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6. Tonellato, PJ, Kos, P, Patil, P, Gainer, VS. Patient Discovery with Clinical Specialty Ontologies. Proceedings of the 2009 AMIA Summit on Translational Bioinformatics, San Francisco, CA, March, 2009.[pdf available on request]

7. Suzuki, S, Takai-Igarashi, T, Fukuoka, Y, Tanaka H, Fusaro, V, Pivovarov, R, Tonellato,PJ. Clinical gene network analysis on Inflammatory Bowels Disease, Omics’10, Yokohama, Japan, February, 2010

8. Prasad, P and Tonellato, PJ. Individual Whole Genome Mapping: From NGS Reads to Clinical Variants, Proceedings of the 2010 AMIA Summit on Clinical Research Informatics, San Francisco, CA, March, 2010.[pdf available on request]

9. Fusaro, VA, Kos, P, Tector, M, Patil,P, Tonellato, PJ, Electronic Medical Record Analysis Using Cloud Computing, . Proceedings of the 2010 AMIA Summit on Clinical Research Informatics, San Francisco, CA, March, 2010.[pdf available on request]

10. Tonellato, PJ, Reede, J, Kos, P, Demas, K, Personalized Medicine and the Potential for Health Inequity. 2010 Annual Wisconsin Public health Association, Madison, WI, June, 2010

11. Kantarci S, Al-Gazali L, Tonellato P, Boguski M, Bissar-Tadmouri N, An exome strategy to identify the genetic basis of nonsyndromic mental retardation in large consanguineous Arab families. (2010, Nov) American Society of Human Genetics (ASHG), Vancouver, CA.

12. Chi, C.-L., Fusaro, V.A., Patil, P., Crawford, M.A., Contant, C.F. & Tonellato, P.J. An approach to optimal individualized warfarin treatment through clinical trial simulations. Proceedings of IEEE Cairo International Biomedical Engineering Conference (CIBEC’10). Cairo, Egypt, accepted.

13. Chi, C.-L., Patil, P., Fusaro, V.A., Kos, P.J., Pivovarov, R., Contant, C.F. & Tonellato, P.J. Simulated Comparison of Warfarin Treatment Protocols. Proceedings of the 2010 American Medical Informatics Association Annual Symposium, Washington, DC, November 2010, accepted.

14. Patil P, Heus H, Arnaout R, Tonellato PJ. Refining a method for processing an individual’s whole genome to clinical utility. CSHL Personal Genomes, Cold Spring Harbor, NY. Sept. 2010.

15. Boguski, M., Arnaout, R., Haspel, R., Briere,L., Kantarci,S., Marchand, K., Connolly, A, Saffitz, J., Tonellato, P.J., The Pathologist’s Post-Genome Practice, CSHL Personal Genomes, Cold Spring Harbor, NY Sept. 2010.

16. Kos, P., Fusaro, V, Tector, M.,Tonellato, P.J. , Electronics health records, knowledge management, informatics and the potential to differentiate health disparities, 138 Annual APHA, Denver Co, Oct, 2010

17. Chi, C.-L., Kos, P.J., Fusaro, V.A., Pivovarov, R., Patil, P., & Tonellato, P.J. Mining personalized medicine algorithms with surrogate algorithm tags. Proceedings of the First ACM International Health Informatics Symposium, pages 474-478, Arlington, VA, November 2010.

18. Chi, C.-L., Fusaro, V.A., Patil, P., Crawford, M.A., Contant, C.F., Tonellato, P.J. An approach to optimal individualized warfarin treatment through clinical trial simulations. Proceedings of the 5th IEEE Cairo International Biomedical Engineering Conference (CIBEC’10), page 16-18, Cairo, Egypt, December 2010.

19. Chi, C.-L., Patil, P., Fusaro, V.A., Kos, P.J., Pivovarov, R., Contant, C.F., & Tonellato, P.J. Simulated Comparison of Warfarin Treatment Protocols. Pro¬ceedings of the 2010 American Medical Informatics Association Annual Symposium, page 1009, Washington, DC, Nov 2010 (peer-reviewed poster paper).

20. Tonellato P, Payne PR, Gastonguay M. 2011. Synthetic Patients Use in Clinical Research. In: AMIA Clinical Research Informatics Summit Proc. San Francisco, CA.

21. Fusaro, V.A., Patil, P., Chi, C.-L., Contant, C.F., & Tonellato, P.J. Modeling complex warfarin pharmacogenetic protocols in clinical trial simulations. AMIA CRI Summit Proceedings, San Francisco, CA, March 2011

22. Fusaro, V.A., Chi, C.-L., Contant, C.F., & Tonellato, P.J. , Designing Effective Clinical Trials Using Simulations. AMIA TRI Summit Proceedings, San Francisco, CA. March, 2011

23. Chi, C, Fusaro V, Patil, P, Tonellato P.J.,Using Modeling and Simulation on Personalzied Medical Decision Support, INFORMS Healthcare, Montreal, CA, July, 2011.

24. Nabavi S, Cai, X., Tonellato, P.J., Comparative analysis of copy number variation detection methods using next generation sequencing. 12th International Meeting On Human Genome Variation and Complex Genome Analysis, San Fran, CA, Aug, 2011

25. Chi, C., Fusaro, V.A., Patil, P., Crawford, M., Content, C.F., Tonellato, P.J., A Simulation Platform to Examine Heterogeneity Influence on Treatment. AMIA CRI Summit Proceedings, San Francisco, CA. March, 2012 (accepted).

Reviews, Book Chapters, Editorials

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1. Committee on New and Emerging Models in Biomedical and Behavioral Research, Institute for Laboratory Animal Research, Commission on Life Sciences, National Research Council. Biomedical Models and Resources: Current Needs and Future Opportunities, The National Academes Press, 1998 (Contributor)

2. Constantine WLB,, Percival DB, Bassingthwaighte JB, Reinhall, PG, Tonellato, PJ. S+FRACTAL, Version 1.0. , Insightful Corporation, Oct. 2002.

3. Postlethwait J, Ruotti V, Carvan M, Tonellato PJ. Automated Analysis of Conserved Syntenies for the Zebrafish Genome, in The Zebrafish: Genetics, Genomics and Informatics (Methods in Cell Biology) by William H., III Detrich, Leonard I. Zon, Monte Westerfield, , Academic Press, 2nd edition (November 22, 2004) ISBN: 0125641729

4. Przybytkowski E, Aguilar-Mahecha A, Nabavi S, Tonellato PJ, Basik M., Ultradense array CGH and discovery of micro-copy number alterations and gene fusions in the cancer genome. Methods Mol Biol. 2013;973:15-38.

PhD Thesis Critical Behavior of an Ignition Model in Chemical Combustion, 1985, Program in Applied mathematics, University of Arizona Narrative Report

My career started in a mathematics department (Marquette University) and since I have founded and directed a research center of bioinformatics at the Medical College of Wisconsin (1997-2004), founded and ran a private healthcare informatics company (PointOne, 2001-2008). And more recently, returned to academic research sharing half-time appointments at Harvard Medical School and University of Wisconsin-Milwaukee, Zilber School of Public Health. My new research focus is three fold: (1) Development and applications of methods of biomedical informatics, mathematical modeling and simulations to characterize and predict the use of genetics in medical practice and in particular pathology. (2) Extension of those methods and analysis to predict the implication, outcome and efficacy of the use of genetics when applied to large mixed populations such as large urban centers in the United States or large but more homogeneous populations such as those found in Asia or the Middle East or in certain zip-code bound regions in the United States. And (3) Apply and test the use of high-throughput genetic technologies such as microarrays and next generation sequencers in the discovery and applications of genetics to complex diseases and environmental-gene development pathways.

My early research (at Marquette and the Medical College of Wisconsin) emerged from formal mathematics training applied to biomedical problems in collaboration with basic and clinical scientists working to quantify and illuminate the genetic basis of human disease using animal models and genome-wide association studies. This effort rapidly evolved into large data collection, integration and analysis of rat genome resources and the creation of the Rat Genome Database, the first disease-centric repository of phenotype and genetic data and the Program in Genomic Applications (pga.mcw.edu) data mining system for a heterogeneous collection of phenotypes, microarray expression and genetic data. The genome efforts expanded to homology analysis between rat, zebrafish, mouse and human and a broader effort to characterize human disease mechanisms derived from individual’s genetic differences. Eventually this led to my focus on research and development of systems that processed human genetic data for clinical use.

My interest in applications of genetics to human health emerged from this research and discovery applications and In 2001, I founded and was Chairman of POINTONE Systems, LLC, the first personalized medicine software company that provided genetic enabled ‘best practice’ decision support system to hospitals and health care facilities. I headed the company fulltime for four years (2003-2007) before returning to academia.

In 2007, I joined the faculty of the Center for Biomedical Informatics (CBMI) at Harvard Medical School, recently founded by Isaac Kohane and Alexa McRay. I am now split my time evenly between my joint position in Boston at the CBMI, Harvard Medical School and Department of Pathology, Beth Israel Deaconess Medical Center and my appointment at the Zilber School of Public Health, University of Wisconsin-Milwaukee. My labs (lpm.hms.harvard.edu and uwm.edu/publichealth/research/lphig) develop strategies, methods, bioinformatic tools, simulations and

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analyses to study, test and predict the accuracy and clinical efficacy of genetic discoveries and accelerate their translation to practical clinical use (Harvard Medical School) and their application to public health and health disparities (Wisconsin). In 2009, I was awarded an NIH EUREKA grant to create ‘clinical avatars’ used to simulate realistic patient populations, provide a collection of electronic medical records used to test the efficacy of genetic data, to quantify the accuracy of predictive algorithms and to conduct clinical trial simulations using sophisticated translational software systems such as i2b2. The lab was one of the first to establish all computational systems and services ‘on the cloud’ implemented on Amazon’s AWS environment.

Since 2009, I have established collaborative relationships with premier hospital systems (Partners HeathCare, Beth Israel Deaconess Medical Center, Yokohama City University Medical Center, and Tokyo Medical and Dental University) to test the migration and general use of genetics in the hospital, clinical and public health settings. These studies will explore the use of specific genetics tests and estimate the likely value of the tests in typical clinical care. In addition, we are pursuing the use of the same modeling framework to test the efficacy of genetic-based personalized medicine and public health. These collaborations provide access to over 10 million de-identified medical record patient or cohort study participant data. Together, we have launched programs in pharamcogenetics funded by the EUREKA grant (2009-2012 and supplement 2010-2011), pharmacovigilance (U01 proposal submitted Oct, 2011), breast cancer risk prediction (DOD and NIH submitted Oct, 2011) and autism disease genetics (R01 – Wall, funded May 2010-2014) and health disparity research (unfunded). Most recently, we are directing this research, new educational programs, and an ‘outsource’ model of next generation sequencing and analysis to establish a ‘preventive’ pathology initiative testing the use of genetics and molecular tests in predictive pathology practice.

date prepared: april, 2013 name: peter j. tonellato, ph.d...

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