Big Data, Genomics and Molecular Networks University of Colorado, Boulder

M a y 2 8 , 2 0 1 4

The BioFrontiers Symposium

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Welcome to the 2014 BioFrontiers Symposium on Big Data, Genomics and Molecular Networks. We are honored today to be showcasing some of the nation’s leading bioscience visionaries in this unique event. These leaders will share with us their stories and vision for transformative research that addresses challenges we now face in scientific research and in the future of medicine. We have designed this symposium so that our speakers can share their knowledge in a setting that is small enough to encourage questions and conversation. Today promises to be an exciting day of ideas. A major focus area of the BioFrontiers Institute is computational biology, big data and genomics, and their applications in personalized medicine. We are thrilled to be hosting many of the leaders in these areas from a variety of institutions. This is our second BioFrontiers Symposium. The 2012 Symposium focused on research to improve human health, with keynote lectures by Harold Varmus, Director of the National Cancer Institute, and Eric Lander, President and Director of the Broad Institute of MIT and Harvard. We expect this series to continue as a biennial event. We host this great event in a great place. The Jennie Smoly Caruthers Biotechnology Building has been our home for two years. It houses many talented, collaborative faculty who are proving that combining different academic disciplines creates opportunities to think in new ways and solve daunting problems. I hope you enjoy this day of discovery. My thanks go to our staff who have organized this special event and to our incredible speakers for taking the time to share their knowledge and insights with us today. Sincerely, Tom Cech Director, BioFrontiers Institute University of Colorado, Boulder

Schedule

The BioFrontiers Symposium on Big Data, Genomics and Molecular Networks

May 28, 2014

University of Colorado, Boulder Jennie Smoly Caruthers Biotechnology Building - Butcher Auditorium

We ask that you please leave all food and drink outside the auditorium.

8:00 – 8:30 a.m. Breakfast and registration 8:30 – 9:50 a.m. Session One Welcome

Tom Cech BioFrontiers Institute, University of Colorado

8:35 – 9:15 a.m. Keynote: “Technologies for reading and writing multicellular systems”

George Church Harvard University

9:20 – 9:45 a.m. “Large-scale cancer genomics”

David Haussler University of California, Santa Cruz

9:50 – 10:20 a.m. Break 10:20 a.m. – 12:10 p.m. Session Two Introduction

Robin Dowell BioFrontiers Institute, University of Colorado

10:30 – 10:55 a.m. “Mapping and interpreting high dimension single cell data”

Dana Pe’er Columbia University

11:00 – 11:25 a.m. “Inferring phenomenological model of regulatory dynamics from data”

Ilya Nemenman Emory University

11:30 a.m. – 12:10 p.m. Panel Discussion: Genomic Research and Privacy

Moderator: Leslie Leinwand – BioFrontiers Institute, University of Colorado Panelists: George Church – Harvard University Paul Ohm – University of Colorado Law School Warren Capell – University of Colorado, Denver Michael Snyder – Stanford University

12:10 – 1:10 p.m. Lunch

Schedule 1:10 – 2:50 p.m. Session Three Introduction

Aaron Clauset BioFrontiers Institute, University of Colorado

1:20 – 1:45 p.m. “Emerging challenges in data intensive genomics”

Mikael Huss Stockholm University

1:50 – 2:15 p.m. “Data-driven approaches for uncovering and understanding biological

networks” Mona Singh Princeton University

2:20 – 2:45 p.m. “Computational genome sequence analysis: the future of deciphering

the past” Sean Eddy Howard Hughes Medical Institute, Janelia Farm

2:50 – 3:20 p.m. Break 3:20 – 5:20 p.m. Session Four 3:20 – 4:00 p.m. Panel Discussion: Open Source vs. Proprietary Software

Moderator: Kate Tallman – University of Colorado Technology Transfer Panelists: George Church – Harvard University Sean Eddy – Howard Hughes Medical Institute, Janelia Farm Mikael Huss – Stockholm University David Haussler – University of California, Santa Cruz Jason Haislmaier – Bryan Cave, LLP

4:00 – 4:25 p.m. “Emerging principles of genome regulation with application to human

health” Jason Lieb Princeton University

4:30 – 4:55 p.m. “Personalized medicine: Personal omics profiling for healthy and

disease states” Michael Snyder Stanford University

5:00 – 5:20 p.m. Closing Remarks

Rob Knight BioFrontiers Institute, University of Colorado

5:20 – 6:00 p.m. Reception

Speaker Biographies

Warren Capell Assistant Professor of Medicine, University of Colorado Director, Colorado Multiple Institutional Review Board Dr. Capell joined the faculty in the Department of Medicine in the Division of Endocrinology in 2005, with a research focus in lipidology. Prior to that, he received his undergraduate education at Pomona College in Claremont, CA where he received a Bachelor of Arts in 1992. He then attended the University of Washington in Seattle, WA where he received his medical degree in 1996. He went on to do his internship and residency in Internal Medicine at the University of Colorado Health Sciences Center in Denver, Colorado from 1996 to 1999. He remained at the University of Colorado Health Sciences Center for a fellowship in Endocrinology, which he completed in 2003. Dr. Capell was on staff at Denver Health Medical Center in Denver, Colorado from 2005 – 2012 as a clinical Endocrinologist. He also served as a co-chair of the Colorado Multiple Institutional Review Board (COMIRB) for four years before becoming the Director of COMIRB, a position he has held since 2011.

Tom Cech Distinguished Professor, Department of Chemistry and Biochemistry Director, BioFrontiers Institute, University of Colorado Investigator, Howard Hughes Medical Institute After his Ph.D. in chemistry from the University of California, Berkeley and postdoctoral research at the Massachusetts Institute of Technology, Dr. Cech joined the faculty of the University of Colorado, Boulder in 1978. In 1982 Dr. Cech and his research group discovered self-splicing RNA in Tetrahymena, providing the first exception to the long-held belief that biological reactions are always catalyzed by proteins. Because RNA can be both an information-carrying molecule and a catalyst, perhaps a primordial self-reproducing system consisted of RNA alone. Dr. Cech became a Howard Hughes Medical Institute investigator in 1988 and Distinguished Professor of Chemistry and Biochemistry in 1990. From 2000-2009, he served as president of the Howard Hughes Medical Institute, the largest private biomedical research organization in the U.S.A. He has now returned to full-time research and teaching at the University of Colorado, Boulder. Dr. Cech’s work has been recognized by many national and international awards and prizes, including election to the U.S. National Academy of Sciences (1987), the Heineken Prize of the Royal Netherlands Academy of Sciences (1988), the Albert Lasker Basic Medical Research Award (1988), the Nobel Prize in Chemistry (1989), and the National Medal of Science (1995).

George Church Robert Winthrop Professor of Genetics Harvard Medical School MIT Health Sciences and Technology George Church is Professor of Genetics at Harvard Medical School, Director of PersonalGenomes.org, providing the world's only open-access information on human Genomic, Environmental and Trait data (GET). His 1984 Harvard Ph.D. included the first methods for direct genome sequencing, molecular multiplexing and barcoding. These led to the first commercial genome sequence (pathogen, Helicobacter pylori) in 1994. His innovations in essentially all of the "next generation" genome sequencing (CGI, Life, Illumina, nanopore) methods and companies and oligo synthesis plus cell/tissue engineering resulted in founding additional application-based companies spanning fields of medical diagnostics (Knome, Alacris, AbVitro, Pathogenica) and synthetic biology/therapeutics (Joule, Gen9, Editas, Egenesis, enEvolv, WarpDrive) as well as new privacy, biosafety and biosecurity policies. He is director of the NIH Center for Excellence in Genomic Science. His honors include election to NAS and NAE and Franklin Bower Laureate for Achievement in Science. He has coauthored 330 papers, 60 patents and one book (Regenesis).

Speaker Biographies

Aaron Clauset Assistant Professor, Department of Computer Science BioFrontiers Institute, University of Colorado Aaron Clauset is an Assistant Professor in the Department of Computer Science and the BioFrontiers Institute at the University of Colorado, Boulder, and is External Faculty at the Santa Fe Institute. He received a Ph.D. in Computer Science, with distinction, from the University of New Mexico, a B.S. in Physics, with honors, from Haverford College, and was an Omidyar Fellow at the prestigious Santa Fe Institute. He is an internationally recognized expert on network science, data science, and machine learning for complex systems. His work has appeared in prestigious scientific venues like Nature, Science, PNAS, JACM, ICML, STOC, SIAM Review and Physical Review Letters, and has been covered in the popular press by the Wall Street Journal, The Economist, Discover Magazine, New Scientist, Wired, Miller-McCune, the Boston Globe and The Guardian.

Robin Dowell Assistant Professor, Department of Molecular, Cellular and Developmental Biology BioFrontiers Institute, University of Colorado Robin Dowell is an Assistant Professor in Molecular, Cellular and Developmental Biology at the University of Colorado in Boulder. Using a combination of machine learning and systems biology techniques, the Dowell laboratory compares closely related individuals to understand how genomic changes, from single nucleotide polymorphisms to whole chromosome aneuploidy, influence transcription and adaptation. Robin received her D.Sc. in Biomedical Engineering from Washington University in St. Louis studying algorithms for RNA secondary structure. She also holds a M.S. in Computer Science, a B.S. in Genetics, and a second B.S. in Computer Engineering.

Sean R. Eddy Group Leader, Howard Hughes Medical Institute, Janelia Farm Sean Eddy is a group leader at the Howard Hughes Medical Institute's Janelia Farm Research Campus near Washington D.C. He is interested in deciphering the evolutionary history of life by comparison of genomic DNA sequences. His expertise is in the development of computational algorithms and software tools for biological sequence analysis. He is the author of several computational tools for sequence analysis including the HMMER and Infernal software suites. He is a coauthor of the book Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (Cambridge University Press, 1998). He received a bachelor’s degree from Caltech, a Ph.D. from the University of Colorado, Boulder, and was a postdoctoral fellow at NeXagen in Boulder and at the MRC Laboratory of Molecular Biology in Cambridge, England. He was a faculty member in Genetics at Washington University in Saint Louis for eleven years before moving to Janelia Farm. He serves as an advisor to several foundations and U.S. and U.K. science agencies, including the National Institutes of Health, the National Academy of Sciences and the U.K.'s Wellcome Trust, often on matters of large-scale computation and data analysis in biology.

Jason Haislmaier Partner, Bryan Cave LLP Jason Haislmaier is a Partner in the Boulder, Colorado office of Bryan Cave LLP (www.bryancave.com). He also serves as an Adjunct Professor and a member of the board of the Silicon Flatirons Center for Law and Technology at the University of Colorado School of Law. Jason assists emerging and established companies in structuring, negotiating and closing technology and intellectual property transactions. He has developed a specialty advising clients in the area of free and open source software. Jason helps clients throughout the world develop and implement open source compliance strategies, contend with open source enforcement actions and leverage open source software within their businesses. In addition to open source software, Jason has lectured internationally on topics including data privacy and security, data ownership, cloud computing, outsourcing, and technology issues in mergers and acquisitions.

Speaker Biographies

David Haussler Investigator, Howard Hughes Medical Institute Distinguished Professor, Biomolecular Engineering Director, Center for Biomolecular Science and Engineering Director, UCSC Cancer Genomics Hub Scientific Co-Director, California Institute for Quantitative Biosciences (QB3) Cofounder, Genome 10K Project University of California, Santa Cruz David Haussler develops new statistical and algorithmic methods to explore the molecular function, evolution and disease process in the human genome, integrating comparative and high-throughput genomics data to study gene structure, function and regulation. He is credited with pioneering the use in genomics of hidden Markov models (HMMs), stochastic context-free grammars, and discriminative kernel methods, the latter first applied to gene expression in cancer in 1999. As a collaborator on the international Human Genome Project, his team posted the first publicly available computational assembly of the human genome sequence on the Internet on July 7, 2000. His team subsequently developed the UCSC Genome Browser, a web-based tool that is used extensively in biomedical research and serves, along with the Ensembl platform, virtually all large-scale vertebrate genomics projects, including NHGRI’s ENCODE project, the 1000 Genomes Project and NCI’s TCGA. He built the CGHub database to hold NCI’s cancer genome data. His group’s informatics work on cancer genomics provides a complete analysis pipeline from raw DNA reads through the detection and interpretation of mutations and altered gene expression in tumor samples. He collaborates with the Stand Up To Cancer “Dream Teams” and TCGA to discover molecular causes of cancer and pioneer a new personalized, genomics-based approach to cancer treatment. He is an organizing member of a new global alliance of the top research, health care, and disease advocacy organizations that have taken the first steps to standardize and enable secure sharing of genomic and clinical data, co-leading the data working group. Haussler received his Ph.D. in computer science from the University of Colorado, Boulder. He is a member of the National Academy of Sciences and the American Academy of Arts and Sciences and a fellow of AAAS and AAAI. He has won a number of awards, including the 2011 Weldon Memorial Prize for application of mathematics and statistics to biology; 2009 ASHG Curt Stern Award in Human Genetics; the 2008 Senior Scientist Accomplishment Award from the International Society for Computational Biology; the 2006 Dickson Prize for Science from Carnegie Mellon University and the 2003 ACM/AAAI Allen Newell Award in Artificial Intelligence.

Mikael Huss Bioinformatics Scientist, Science for Life Laboratory Stockholm University Mikael Huss works as an “embedded bioinformatician” at SciLifeLab in Stockholm, Sweden, as part of a national infrastructure for providing project-oriented bioinformatics analysis support. He has over a decade’s experience in computational biology ranging from genomics to computational neuroscience, and blogs about things like big data, machine learning, genomics, personalized health and crowdsourcing at http://followthedata.wordpress.com. He obtained his Ph.D. from the Royal Institute of Technology in Stockholm, Sweden in 2007, and subsequently moved to the Genome Institute of Singapore to work on next-generation sequencing bioinformatics with an emphasis on epigenomics and stem cell biology. Since 2010, he has been a senior researcher at Stockholm University/Science for Life Laboratory. He has published some 30 scientific articles. He currently focuses on challenges in analyzing data from RNA sequencing experiments. He has recently co-written a book on the subject which will appear in September 2014.

Speaker Biographies

Rob Knight Professor, Departments of Chemistry and Biochemistry and Computer Science BioFrontiers Institute, University of Colorado Rob Knight is a Professor at the BioFrontiers Institute at the University of Colorado, Boulder, in the Departments of Chemistry and Biochemistry and Computer Science. He did his undergraduate work at the University of Otago in his native New Zealand, then his Ph.D. at Princeton University. His lab primarily works on microbial community ecology including the human microbiome. He is a Howard Hughes Medical Institute Early Career Scientist, an AAAS Fellow, a Kavli Fellow, a member of the American Gastroenterology Association Science Advisory Board, co-founder of Biota, Inc., and co-founder of the Earth Microbiome Project and the American Gut Project.

Jason Lieb Professor of Molecular Biology and Lewis-Siglar Institute for Integrative Genomics Princeton University Jason Lieb is a Professor of Molecular Biology at the Lewis-Sigler Institute for Integrative Genomics at Princeton University. Prior to coming to Princeton, Lieb was the Beverley W. Long Chapin Distinguished Professor of Biology in the UNC College of Arts and Sciences, and the Director of the Carolina Center for Genome Sciences. Research projects in the Lieb lab are united by the scientific goal of understanding relationships between chromatin, transcription factor targeting and gene expression. In particular, Lieb studies how information is encoded and dynamically utilized in living eukaryotic genomes, focusing on those areas of the genome that serve to regulate chromosomal functions, including transcription, DNA replication and repair, recombination and chromosome segregation. Lieb came to UNC in 2002 after completing a postdoctoral fellowship at Stanford University. He earned his undergraduate degree in biology at the University of North Carolina at Chapel Hill and his Ph.D. in genetics at the University of California at Berkeley. He is a winner of the Phillip and Ruth Hettleman Prize for Artistic and Scholarly Achievement at UNC Chapel Hill and has received a number of additional awards and honors.

Leslie Leinwand Professor, Department of Molecular, Cellular and Developmental Biology Chief Scientific Officer, BioFrontiers Institute, University of Colorado Dr. Leinwand is a Molecular, Cellular, and Developmental Biology (MCDB) Professor and the Chief Scientific Officer of the BioFrontiers Institute at the University of Colorado, Boulder. She was recruited to be Chair of MCDB in 1995. She received her Bachelor’s degree from Cornell University, her Ph.D. from Yale University and did post-doctoral training at Rockefeller University. She joined the faculty at Albert Einstein College of Medicine in New York in 1981 and remained there until moving to Colorado. While at Albert Einstein she became a Full Professor and was Director of the Cardiovascular Research Center. Once she moved to Colorado she, along with Michael Bristow, founded the intercampus University of Colorado Cardiovascular Institute, which promotes research and training in cardiovascular disease. They, along with Eric Olson at the University of Texas, Southwestern Medical Center, founded Myogen, Inc., which was sold to Gilead Pharmaceuticals. More recently, she was a co-founder of Hiberna, Inc., a biotechnology company using pythons and hibernating ground squirrels to develop novel pharmaceuticals. She also recently co-founded MyoKardia, Inc. a company founded to develop therapeutics for inherited cardiomyopathies. Her work as a cardiac biologist is of importance to both basic scientists and clinicians.

Speaker Biographies

Ilya Nemenman Associate Professor of Physics and Biology Emory University After receiving his Ph.D. in theoretical physics from Princeton University, Dr. Nemenman completed additional postdoctoral training at the Kavli Institute for Theoretical Physics at UC Santa Barbara, and at the Columbia University Medical Center. He was then a Staff Scientist at Los Alamos National Laboratory, where he was one of the founding organizers of The q-bio Conference and Summer School, now some of the leading events in the field of quantitative studies of cellular regulation. In 2009, he moved to Emory University, Departments of Physics and Biology, as an Associate Professor. His laboratory focuses on building coarse-grained models of information processing phenomena in diverse biological systems, from cellular networks, to brains, and to adapting populations. In 2013, he was elected to the Chair line of the Division of Biological Physics of the American Physical Society.

Paul Ohm Associate Professor, University of Colorado Law School Paul Ohm is an Associate Professor at the University of Colorado Law School. He specializes in information privacy, computer crime law, intellectual property, and criminal procedure. He teaches courses in all of these topics and more, and in 2010 he was awarded the prize for Excellence in Teaching by the students of Colorado Law. In his work, Professor Ohm tries to build new interdisciplinary bridges between law and computer science. Much of his scholarship focuses on how evolving technology disrupts individual privacy. His article Broken Promises of Privacy: Responding to the Surprising Failure of Anonymization, 57 UCLA Law Review 1701, has sparked an international debate about the need to reshape dramatically the way we regulate privacy. He is commonly cited and quoted by news organizations including the New York Times, Wall Street Journal, and NPR. From 2012 to 2013, Professor Ohm served as Senior Policy Advisor to the Federal Trade Commission. Prior to joining the academy, he served as an Honors Program trial attorney in the U.S. Department of Justice's Computer Crime and Intellectual Property Section. Before that, he clerked for Judge Betty Fletcher of the United States Court of Appeals for the Ninth Circuit and Judge Mariana Pfaelzer of the United States District Court for the Central District of California. He is a graduate of the UCLA School of Law. Before attending law school, Professor Ohm worked for several years as a computer programmer and network systems administrator after earning undergraduate degrees in computer science and electrical engineering from Yale University. Today he continues to write thousands of lines of Python and Perl code each year. Professor Ohm blogs at freedom-to-tinker.com.

Dana Pe’er Associate Professor, Department of Biological Sciences and Systems Biology Columbia University Dana Pe’er is an Associate Professor in the Departments of Biological Sciences and Systems Biology. Her team develops computational methods that integrate diverse high-throughput data to provide a holistic, systems-level view of molecular networks. Currently she has two key focuses: developing computational methods to interpret single cell data and understand cellular heterogeneity; Modeling how genetic and epigenetic variation alters regulatory network function and subsequently phenotype in health and disease. This path has led her to explore how systems biology approaches can be used to personalize cancer care. Dana is recipient of the Burroughs Wellcome Fund Career Award, NIH Directors New Innovator Award, NSF CAREER award, Stand Up To Cancer Innovative Research Grant and a Packard Fellow in Science and Engineering.

Speaker Biographies

Mona Singh Professor, Department of Computer Science and Lewis-Sigler Institute for Integrative Genomics Princeton University Mona Singh is on the faculty at Princeton University, where she is a Professor in the Department of Computer Science and in the Lewis-Sigler Institute for Integrative Genomics. She received her Ph.D. in computer science from the Massachusetts Institute of Technology (MIT), and did postdoctoral work at the Whitehead Institute for Biomedical Research. Her group develops computational methods for analyzing cellular networks, predicting specificity in protein interactions, and functionally characterizing proteins using sequence, structure and network approaches.

Michael Snyder Stanford Ascherman Professor Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine Stanford University Michael Snyder is the Stanford Ascherman Professor, Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine. He received his Ph.D. from the California Institute of Technology and postdoctoral training at Stanford University. He is a leader in the field of functional genomics and proteomics, and one of the major participants of the ENCODE project. His laboratory study was the first to perform a large-scale functional genomics project in any organism, and has launched many technologies in genomics and proteomics. These including the development of proteome chips, high resolution tiling arrays for the entire human genome, methods for global mapping of transcription factor binding sites (ChIP-chip now replaced by ChIP-seq), paired end sequencing for mapping of structural variation in eukaryotes, de novo genome sequencing of genomes using high throughput technologies and RNA-Seq. These technologies have been used for characterizing genomes, proteomes and regulatory networks. Seminal findings from the Snyder laboratory include; the discovery that much more of the human genome is transcribed and contains regulatory information than was previously appreciated, and a high diversity of transcription factor binding occurs both between and within species. He has also combined different state-of–the-art omics technologies to perform the first longitudinal detailed integrative personal omics profile (iPOP) of person and used this to assess disease risk and monitor disease states for personalized medicine. He is a co-founder of several biotechnology companies including; Protometrix (now part of Life Technologies), Affomix (now part of Illumina), Excelix, and Personalis, and he presently serves on the board of a number of companies.

Kate Tallman Interim Associate Vice President University of Colorado Technology Transfer Office Kate Tallman was appointed Interim Associate Vice President for Technology Transfer in July 2013. As AVP she has responsibility for intellectual property and technology licensing matters across CU’s four campuses. Kate directed tech transfer operations for CU’s Boulder and Colorado Springs campuses since 2007, and was appointed a Senior Director in 2012. She joined TTO in 2002 as a member of the Boulder licensing group specializing in software licensing. Kate has served as an instructor in the Association of University Technology Managers software licensing course. Previously, Kate was a co-founder and Director of Marketing at Roving Planet, a venture-backed Colorado software company that developed wireless LAN technology. She earned her MBA from CU-Boulder’s Leeds College of Business, where she focused on marketing. She previously spent four years as a research analyst, performing market and financial analysis of health care companies.

Acknowledgements

We wish to thank the following people for their work on the 2014 BioFrontiers Symposium: Event Coordinator: Lisa Van Goor BioFrontiers Staff: Cynthia Clifford, Stefanie Coltrain, Emilia Costales, Sandy Duff, Janice Jones, Kim Kelley, Laura Konyha, Kim Little, Lindsay Reeves, Lee Silbert, Megill Stewart, Andrea Stith, Meagan Taylor, Jana Watson-Capps, Jessica Wright BioFrontiers Audio/Visual and IT Services: Jeff DeReus, Matt Hynes-Grace, Ryan Krumpeck, Dan Timmons Jennie Smoly Caruthers Biotechnology Building Staff: Maryellen Ancell, Angela Janacek, Laura Vogler, Steve Najera All of our volunteers, and the researchers, students and staff who make their home in the Jennie Smoly Caruthers Biotechnology Building