Speakers

Keynote Speakers

Stan Leibler

Stan Leibler

Professor, Laboratory of Living Matter, Rockefeller University.

Tobias Meyer

Tobias Meyer

Professor of Chemical & Systems Biology, Stanford University.

Bernhard Ø. Palsson

Bernhard Ø. Palsson

Galetti Professor of Bioengineering, University of California, San Diego.

Professor Palsson earned a Ph.D. from the University of Wisconsin in 1984. He held a faculty position at the University of Michigan from 1984 to 1995. He has been with UCSD since 1995. He is the author of over 250 peer reviewed scientific articles. He co-authored the text Tissue Engineering, Prentice Hall in 2004, and Systems Biology, Cambridge University Press in 2006. He sits on the editorial boards of several bioengineering and biotechnology journals.

Professor Palsson current research at UCSD focuses on 1) the reconstruction of genome-scale biochemical reaction networks, 2) the development of mathematical analysis procedures for genome-scale models, and 3) the experimental verification of genome-scale models with current emphasis on cellular metabolism and transcriptional regulation in E. coli and Yeast.

Jonathan Weissman

Jonathan Weissman

Professor of Cellular & Molecular Pharmacology, University of California, San Francisco.

Plenary Speakers

Adam P. Arkin

Adam P. Arkin

Professor of Bioengineering and Chemistry, University of California, Berkeley.

James K. Chen

James K. Chen

Professor of Chemical & Systems Biology, Stanford University.

James K. Chen, Ph.D. is an Assistant Professor of Chemical and Systems Biology at Stanford University. He received a Ph.D. in Chemistry and Chemical Biology from Harvard University in 1999 and completed his postdoctoral studies at the Johns Hopkins School of Medicine in 2003. His laboratory integrates organic chemistry and developmental biology to probe the molecular mechanisms of embryonic patterning, tissue regeneration, and oncogenesis. Dr. Chen's honors include a Kimmel Scholar Award, a March of Dimes Basil O'Connor Award, and an NIH Director's Pioneer Award. He is also the Executive Director of the Stanford High-Throughput Bioscience Center.

Markus W. Covert

Markus W. Covert

Assistant Professor of Bioengineering, Stanford University.

Our focus is on building computational models of complex biological processes, and using these models to guide an experimental program. Such an approach leads to a relatively rapid identification and validation of previously unknown components and interactions. Biological systems of interest include metabolic, regulatory and signaling networks as well as cell-cell interactions. Current research involves the dynamic behavior of NF-κB, an important family of transcription factors whose aberrant activity has been linked to oncogenesis, tumor progression, and resistance to chemotherapy.

Joe DeRisi

Joe DeRisi

Professor of Biochemistry, University of California, San Francisco.

Michael B. Elowitz

Michael B. Elowitz

Assistant Professor of Biology and Applied Physics, California Institute of Technology.

Drew Endy

Drew Endy

Assistant Professor of Bioengineering, Stanford University.

Marcus Feldman

Marcus Feldman

Professor of Biology, Stanford University.

Daniel S. Fisher

Daniel S. Fisher

Professor of Applied Physics, Stanford University.

Klaus Hahn

Klaus Hahn

Professor of Pharmacology, University of North Carolina.

Kerwyn C. Huang

Kerwyn C. Huang

Assistant Professor of Bioengineering, Stanford University.

Our laboratory is interested in the relationships among cell shape detection, determination, and maintenance in bacteria. Cell shape plays a critical role in regulating many physiological functions, yet little is known about how shape is determined and maintained. Inside the cell, many proteins organize, but how they detect and respond to the cellular morphology is also largely mysterious. We are integrating computational physics-based models with evolutionary and synthetic biology approaches to control morphogenesis and cellular organization. Current topics of interest are (i) cell-wall growth, (ii) spatial mechanisms of cell-cycle control, (iii) division, (iv) membrane organization, (v) mechanosensitivity, and (vi) phototaxis.

Grant Jensen

Grant Jensen

Professor of Biology, California Institute of Technology. Howard Hughes Medical Institute.

Stuart Kim

Stuart Kim

Professor of Genetics, Stanford University.

Karla Kirkegaard

Karla Kirkegaard

Professor of Microbiology & Immunology, Stanford University.

Daphne Koller

Daphne Koller

Professor of Computer Science, Stanford University.

Daphne Koller is a Professor of Computer Science at Stanford University. Her main research focus is in developing and using statistical learning methods to understand complex systems. She is the author of numerous publications, in venues that include Science, Nature Genetics, and Cell. She has the Sloan Foundation Faculty Fellowship (1996), the ONR Young Investigator Award (1998), the Presidential Early Career Award for Scientists and Engineers (1999), the IJCAI Computers and Thought Award (2001), the Cox Medal for excellence in fostering undergraduate research (2003), the MacArthur Foundation Fellowship (2004) and the first-ever ACM/Infosys award (2008).

Galit Lahav

Galit Lahav

Assistant Professor of Systems Biology, Harvard University.

Galit Lahav received her PhD in 2001 from the Department of Biology in the Technion, Israel Institute of Technology. Between the years 2001-2003, she completed her postdoctoral fellowship at the Weizmann Institute of Science in Israel. She then spent a year at Harvard's Bauer Center for Genomics Research and in the fall of 2004 was appointed as an Assistant Professor in the Department of Systems Biology at Harvard Medical School. Her lab combines experimental and theoretical approaches to study the dynamics of signaling networks in human cells as well as to understand cellular decision-making in individual cells.

Kong-Joo Lee

Kong-Joo Lee

Professor, Center for Cell Signaling amp;& Drug Discovery Research, College of Pharmacy & Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea 120-750.

Kong-Joo Lee received her Ph.D in 1986 from the Department of Chemistry at the Stanford University, USA. She worked as a post-doctoral fellow in Cancer Biology Program at Stanford Medical School, 1987-88, returned to Korea and worked as senior scientists in Korea Research Institute of Standards and Sciences (KRISS) 1989-1994, then as a professor in Ewha Womans University, College of Pharmacy, 1994-present. Now she is a director of National Core Research Center, “Center for Cell Signaling and Drug Discovery Research”, which is a program grant funded by KOSEF. Her lab combines biological, proteomic and informatic tools to understand signaling processes in stress- and metastasis-related, especially to understand the relationship between protein modifications and cellular processes.

Wendell Lim

Wendell Lim

Professor of Department of Cellular and Molecular Pharmacology, University of California, San Francisco.

Gene Myers

Gene Myers

Group Leader, Janelia Farm Research Campus, Howard Hughes Medical Institute.

Dr. Eugene W. Myers is a Group Leader at the new Janelia Farms Research Campus of the Howard Hughes Medical Institute. He was one of the first computer scientist to enter the field of computational molecular biology in the early 80's, and was a key developer of BLAST. In 1995 he and Jim Weber proposed the whole genome shotgun sequencing of the human genome, and from 1998-2001 at Celera his team produced reconstructions of the Drosophila, Human, Mouse, and Anopheles genomes. In 2003 he was elected to the National Academy of Engineering. His current interest is developing algorithms and software for the automatic interpretation of images produced by light and electron microscopy of stained samples with a particular emphasis on building 3D and 4D “atlases” of brains, developing organisms, and cellular processes.

Daniel S. Rokhsar

Daniel S. Rokhsar

Professor of Genetics, Genomics and Development, University of California, Berkeley.

Jeong-Sun Seo

Jeong-Sun Seo

Professor of Biochemistry, Seoul National University.

Kevan Shokat

Kevan Shokat

Professor of Cellular and Molecular Pharmacology, University of California, San Francisco.

Michael Snyder

Michael Snyder

Stanford Ascherman Professor and Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine, Stanford University.

Michael Snyder is the Stanford Ascherman Professor and Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine. Dr. Snyder received his Ph.D. training at the California Institute of Technology and carried out postdoctoral training at Stanford University. He is a leader in the field of functional genomics and proteomics. His laboratory study was the first to perform a large-scale functional genomics project in any organism, and currently carries out a variety of projects in the areas of genomics and proteomics both in yeast and humans. These include the large-scale analysis of proteins using protein microarrays and the global mapping of the binding sites of chromosomal proteins. His laboratory built the first proteome chip for any organism and the first high resolution tiling array for the entire human genome.

Peter K. Sorger

Peter K. Sorger

Professor of Systems Biology, Harvard University.

Ernst H. K. Stelzer

Ernst H. K. Stelzer

Professor of Biophysics, European Molecular Biology Laboratory (EMBL), Heidelberg.

Ernst Stelzer started working on confocal fluorescence microscopy in 1983, developed the 4Pi microscope during 1990-1992 and since 1993 worked on various orthogonal and multi-lens detection schemes (e.g. confocal theta fluorescence microscopy). Recently, he invented and applied the novel azimuthally arranged light-sheet-based fluorescence mi-croscopes (SPIM, DSLM). Dr. Stelzer authored and co-authored about 200 papers and three books. Several of his patents secure commercially available instruments, most promi-nently the Carl Zeiss LSM series. Other contributions include the optical tweezers based Photonic Force Microscope, commercialized by JPK (Berlin, Germany) and novel ap-proaches to laser cutting devices. In his talks he currently discusses: a) the importance of actively addressing “Three-dimensional Cell Biology and Biophysics” and b) light sheet based fluorescence microscopy (LSFM) and its applications in the life sciences. Ernst Stelzer is the scientific group leader for Light Microscopy in EMBL's Cell Biology and Biophysics Unit in Heidelberg, a principal investigator at the CEF in Frankfurt am Main and a Professor for Biophysics at Frankfurt's Goethe University.

Alexander van Oudenaarden

Alexander van Oudenaarden

Professor of Physics, Massachusetts Institute of Technology.

Tom Wandless

Tom Wandless

Associate Professor of Chemical & Systems Biology, Stanford University.

Robert Waterson

Robert Waterson

Professor and Chair of Genome Sciences, University of Washington.

Breakout Speakers

Alan A. Aderem

Alan A. Aderem

Co-founder and Director, Institute for Systems Biology.

Alan Aderem has studied the interface between the innate and adaptive immune system for more than twenty five years. He obtained his Ph.D. at the University of Cape Town and completed a postdoctoral fellowship at The Rockefeller University. Dr. Aderem rose through the ranks at The Rockefeller University, becoming head of the Laboratory of Signal Transduction in 1991. In 1996, he accepted a position as Professor of Immunology and Medicine at the University of Washington in Seattle. In 2000, Dr. Aderem co-founded the Institute for Systems Biology (ISB) with Drs. Leroy Hood and Ruedi Aebersold. The ISB is an interdisciplinary institute that focuses on the biology of complex systems including the immune system.

David Bartel

David Bartel

Professor of Biology, Massachusetts Institute of Technology.

Philippe Bastiaens

Philippe Bastiaens

Professor of Systemic Cell Biologie, Max Planck Institute of Molecular Physiology.

Mark D. Biggin

Mark D. Biggin

Department Head, Genome Sciences Department, Lawrence Berkeley National Laboratory.

Charles Boone

Charles Boone

Professor of Cellular and Biomolecular Research, University of Toronto.

Arup K. Chakraborty

Arup K. Chakraborty

Professor of Chemical Engineering, Chemistry, & Biological Engineering, Massachusetts Institute of Technology.

Francis J. Doyle

Francis J. Doyle

Professor of Chemical Engineering, University of California, Santa Barbara.

Dr. FRANCIS J. DOYLE III is the Associate Dean for Research in the College of Engineering at UC, Santa Barbara and he is the Associate Director of the Army Institute for Collaborative Biotechnologies. He holds the Duncan and Suzanne Mellichamp Chair in Process Control in the Department of Chemical Engineering, as well as appointments in the Electrical Engineering Department, and the Biomolecular Science and Engineering Program. He received his B.S.E. from Princeton (1985), C.P.G.S. from Cambridge (1986), and Ph.D. from Caltech (1991), all in Chemical Engineering. He is currently the editor-in-chief of the IEEE Transactions on Control Systems Technology, and holds Associate Editor positions with the Journal of Process Control, the SIAM Journal on Applied Dynamical Systems, and Royal Society's Interface. In 2005, he was awarded the Computing in Chemical Engineering Award from the American Institute of Chemical Engineers for his innovative work in systems biology. In 2008 he was appointed as a Fellow in IEEE, and in 2009, as a Fellow in IFAC. His research interests are in systems biology, network science, modeling and analysis of circadian rhythms, drug delivery for diabetes, model-based control, and control of particulate processes.

Jay C. Dunlap

Jay C. Dunlap

Professor and Chairman of Genetics, Dartmouth University.

Jay Dunlap started working on circadian clocks and Neurospora genetics sometime in the Pleistocene and found them so interesting he never got around to working on much else. The lab cloned the clock gene frequency, and demonstrated via transgene manipulations the essential role of transcriptional/translational negative feedback in the core circadian oscillator. Subsequent analysis of oscillator regulation uncovered molecular bases for most classical circadian properties including period length, entrainment by light and temperature steps, persistence, and temperature compensation. In the past decade we also launched high throughput functional genomics focused on the ~10,000 genes in the filamentous fungal genome.

Josh Elias

Josh Elias

Assistant Professor of Chemical & Systems Biology, Stanford University.

Jim Ferrell

Jim Ferrell

Professor and Chairman of Chemical & Systems Biology, Stanford University.

Trey Ideker

Trey Ideker

Associate Professor of Bioengineering, University of California, San Diego.

Rustem F. Ismagilov

Rustem F. Ismagilov

Professor of Chemistry, University of Chicago.

Marc W. Kirschner

Marc W. Kirschner

Professor and Chair of Systems Biology, Harvard Medical School.

Mark Krasnow

Mark Krasnow

Professor and Chair of Biochemistry, Stanford University.

Michael Laub

Michael Laub

Assistant Professor of Biology, Massachusetts Institute of Technology.

Dave Morgan

Dave Morgan

Professor of Physiology, University of California, San Francisco.

Garry Nolan

Garry Nolan

Professor of Microbiology & Immunology, Stanford University.

Dr. Nolan's laboratory at the Stanford University School of Medicine focuses on the analysis of biological events at the single cell level using novel genetic and FACS-based approaches at the intersection of immunology, autoimmunity, biochemistry, and cancer. The laboratory studies phospho-protein immune cell and cancer signaling, and other metabolic parameters by analysis of biochemical functions at the single cell level in primary cell populations. This includes interrogation of cancer (Cell, 2004) and immune signaling networks in complex cell populations (Science, 2005), and using multiparameter data to stratify signaling maps from patient samples, (Cancer Cell, 2008). Other major interest areas of the laboratory include mapping of signaling networks within complex populations of immune cells, developing systems biology approaches to develop an atlas of immune cell differentiation, the development of mechanism-based diagnostics for use in clinical trial studies.

Shayn Peirce-Cottler

Shayn Peirce-Cottler

Assistant Professor of Biomedical Engineering, University of Virginia.

Rob Phillips

Rob Phillips

Professor of Applied Physics and Mechanical Engineering, California Institute of Technology.

Peter Pryciak

Peter Pryciak

Professor of Molecular Genetics and Microbiology, University of Massachussetts.

Stephen R. Quake

Stephen R. Quake

Professor of Bioengineering, Stanford University.

Stephen R. Quake received a B.S. in physics and an M.S. in mathematics from Stanford University and a D.Phil. in physics from Oxford University. He is Professor of Bioengineering at Stanford University. He has won the NIH Director’s Pioneer Award and been named a Packard Fellow.

Sharad Ramanathan

Sharad Ramanathan

Assistant Professor, Molecular and Cellular Biology, Harvard University.

Ingmar Riedel-Kruse

Ingmar Riedel-Kruse

Postdoctoral Fellow, California Institute of Technology.

Ingmar obtained his Diplom in theoretical solid-state physics. For his PhD he joined Jonathon Howard (Max Planck Institute Cell Biology / Genetics, Dresden) to study collective phenomena of molecular motors and cells, i.e., how sperm tails work. Then he did two postdocs: One in developmental biology with Andrew Oates (also Max Planck) on synchronized genetic oscillators and one in systems neuroscience with Gilles Laurent (Caltech) on insect olfaction. He will start his own lab this fall.

Lucy Shapiro

Lucy Shapiro

Professor of Developmental Biology, Stanford University.

Jan M. Skotheim

Jan M. Skotheim

Assistant Professor of Biology, Stanford University.

Dr. Jan M. Skotheim is an assistant professor in the Stanford Biology Department and by courtesy in the Chemical and Systems Biology Department. His research focuses on fundamental aspects of cell cycle control and principles underlying genetic regulatory networks in general. In particular, he has published on the dynamics of cell cycle transitions and cell size control.

Christina D. Smolke

Christina D. Smolke

Professor of Bioengineering, Stanford University.

Julie A. Theriot

Julie A. Theriot

Associate Professor of Biochemistry and of Microbiology and Immunology, Stanford University.

Masaru Tomita

Masaru Tomita

Professor and the Director of Institute for Advanced Biosciences, Keio University.

Masaru Tomita is a Professor and the Director General of the Institute for Advanced Biosciences, Keio University. He received Ph.D. in Computer Science from Carnegie Mellon University (1985), Ph.D. in Electrical Engineering from Kyoto University (1994) and Ph.D. in Molecular Biology from Keio University (1998). He is a recipient of Presidential Young Investigators Award from National Science Foundation of USA (1988) and various other awards. His current research field includes Systems Biology, Metabolomics, and Computational Biology.

Claire Tomlin

Claire Tomlin

Professor of Electrical Engineering & Computer Science, University of California, Berkeley.

Hiroki R. Ueda

Hiroki R. Ueda

Team Leader, Laboratory for Systems Biology and Functional Genomics Unit, Center for Developmental Biology, RIKEN, Japan.

Dr. Hiroki R. Ueda graduated from Medicine school in University of Tokyo in 2000, and obtained Ph.D there in 2004. While a graduate student, he was appointed as laboratory head at the CDB from 2003 and appointed as a manager of Functional Genomics Unit at the CDB from 2004. He also became a visiting professor in Tohoku University in 2005-2006, and Tokushima University from 2005, and an invited professor (biology) in Osaka University from 2006, and an invited professor (mathematics) in Kyoto University from 2009. His research interests include system-level understanding of biological time, space and information, and systems-based medicine on human disease.

Christopher A. Voigt

Christopher A. Voigt

Assistant Professor of Pharmaceutical Chemistry, University of California, San Francisco.

Andreas Wagner

Andreas Wagner

Professor of Biochemistry, University of Zürich.

Sunney Xie

Sunney Xie

Professor of Chemistry and Chemical Biology, Harvard University.

Xiaoliang Sunney Xie is the Mallinckrodt Professor of Chemistry and Chemical Biology at Harvard University. Xie was among the first to conduct fluorescence studies of single molecules at room temperature in early 1990s. His group has since contributed to the emergence of the now vital field of single-molecule science and its application to biology. His work focuses on single-molecule enzymology and biosphysics, and gene expression in living cells. Xie's team also has pioneered coherent Raman scattering microscopy, a highly sensitive imaging technique for living cells and organisms, which does not rely on fluorophores, but on vibrational contrast with molecular selectivity.

Lingchong You

Lingchong You

Assistant Professor of Biomedical Engineering, Duke University.

Lingchong You is an Assistant Professor of Biomedical Engineering at the Duke University. He obtained his PhD from the University of Wisconsin-Madison in 2002. He then did postdoctoral research at the California Institute of Technology before moving to Duke in 2004. Combining modeling and experiments, his laboratory explores design features of natural biological networks and builds synthetic gene circuits for applications in computation and medicine. He received a David and Lucile Packard Fellowship in 2006 and a DuPont Young Professor Award in 2008. He serves on the editorial boards of Synthetic Biology and Systems and Synthetic Biology.

Haiyuan Yu

Haiyuan Yu

Research Fellow in Genetics, Dana Farber Cancer Instititute, Harvard University.

Entrepreneurship in Systems Biology Panelists

Malek Faham

Malek Faham

Chief Scientific Officer, MLC Dx

Dr. Faham developed a SNP discovery technology during his postdoctoral research in Ron Davis lab at Stanford Genome Technology Center. He went on to co-found ParAllele Biosciences in 2001 as Director of Research. ParAllele's technologies were adopted by many customers and used for polymorphism detection and genotyping by multiple pharmaceutical and academic partners, including the HapMap project. The company was acquired by Affymetrix for $120M in 2005, and Dr. Faham transitioned into VP Research, Oncology Technology where he remained until 2008. During that time he spearheaded the development of multiple genomic technologies that combined different methods for specific highly multiplexed amplifications with array readouts. These were applied to analysis of copy number from formalin fixed samples, high resolution promoter methylation, and high throughput high accuracy array resequencing. He recently co-founded and obtained funding for a new company (MLC Dx) in the molecular diagnostics space where he is currently CSO. Dr. Faham obtained a Ph.D. in human genetics and an MD (board eligible in Psychiatry) from the University of California San Francisco. He has published more than 25 articles and is an inventor on more than 15 patents.

Bernhard Ø. Palsson

Bernhard Ø. Palsson

Galetti Professor of Bioengineering, University of California, San Diego.

Professor Palsson earned a Ph.D. from the University of Wisconsin in 1984. He held a faculty position at the University of Michigan from 1984 to 1995. He has been with UCSD since 1995. He is the author of over 250 peer reviewed scientific articles. He co-authored the text Tissue Engineering, Prentice Hall in 2004, and Systems Biology, Cambridge University Press in 2006. He sits on the editorial boards of several bioengineering and biotechnology journals.

Professor Palsson current research at UCSD focuses on 1) the reconstruction of genome-scale biochemical reaction networks, 2) the development of mathematical analysis procedures for genome-scale models, and 3) the experimental verification of genome-scale models with current emphasis on cellular metabolism and transcriptional regulation in E. coli and Yeast.

Stephen R. Quake

Stephen R. Quake

Professor of Bioengineering, Stanford University.

Stephen R. Quake received a B.S. in physics and an M.S. in mathematics from Stanford University and a D.Phil. in physics from Oxford University. He is Professor of Bioengineering at Stanford University. He has won the NIH Director’s Pioneer Award and been named a Packard Fellow.

Eric Schadt

Eric Schadt

Chief Scientific Office, Pacific Biosciences, Founder, Sage Bionetworks

Dr. Schadt joined Pacific Biosciences as Chief Scientific Officer in June 2009 to oversee the scientific strategy for the company, including creating the vision for next-generation sequencing applications of the company's technology. Dr. Schadt is also a founding member of Sage Bionetworks, an open access genomics initiative designed to build and support databases and an accessible platform for creating innovative, dynamic models of disease. Dr. Schadt's current efforts were motivated by the genomics and systems biology research he carried out at Merck to elucidate common human diseases and drug response using novel integrative genomics approaches based on genetic and molecular profiling data. His research helped revolutionize a field in statistical genetics (the genetics of gene expression), has energized the systems biology field, and has led to a number of discoveries relating to the causes of common human diseases. As of earlier this year, greater than 50% of all new drug discovery programs at Merck in the metabolic space were derived from Dr. Schadt's work. Dr. Schadt also holds an affiliate professor position in the Departments of Medical Genetics and Biostatistics at the University of Washington in Seattle, and he was recently appointed as Fellow to the Institute of Systems and Synthetic Biology, Imperial College London. Dr. Schadt received his B.S. in applied mathematics/computer science from California Polytechnic State University, his M.A. in pure mathematics from UCD, and his Ph.D. in bio-mathematics from UCLA (requiring Ph.D. candidacy in molecular biology and mathematics).