Richard M. Caprioli, Ph.D. Professor of Biochemistry Stanley Cohen Professor of Biochemistry Director Mass Spectrometry Center Professor of Pharmacology Vanderbilt University

Keynote Address: In situ Molecular Profiling and Imaging of Tissues by Mass Spectrometry

Abstract:

Imaging Mass Spectrometry (IMS) is a molecular discovery technology that takes advantage of the methodology and instrumentation of MALDI mass spectrometry.  It can be used to locate specific molecules such as drugs, lipids, peptides and proteins directly from the surface of fresh frozen tissue sections.  Frozen tissues specimens are cut in very thin (~10 m) sections and thaw-mounted on flat metallic target plates.  Matrix can be manually or automatically deposited on the sections.  Molecular profiles recovered upon analysis typically contain over 500 or more distinct signals in the m/z range up to 200,000.  When imaging from a tissue section, matrix is deposited in a homogeneous manner minimizing the lateral dispersion of molecules of interest.  This can be achieved by automatically printing arrays of small droplets.  Each micro spot is then automatically analyzed generating a mass spectrum.  When monitoring the intensity of a signal within the data array, a two-dimensional ion density map (or image) can be reconstructed giving information on the location and relative abundance of a given analyte.  From the analysis of a single section, images at virtually any molecular weight may be obtained. IMS is an effective discovery tool for the qualitative and quantitative analysis of molecular differences unhealthy versus normal tissues and in helping identifying potential protein markers in lesions and in various stages of disease progression.  In this regard, histology directed profiling permits higher sample throughput and reproducibility.  The visual specificity of histology is combined with the positioning accuracy of the robotic micro-dispenser to direct placement of matrix drops onto specific cells with high placement accuracy.  Processing digital images of the spotted plate provides relative locations of each matrix spot.  These coordinates are transferred and registered to the mass spectrometer for automated data acquisition.  Thousands of molecular profiles can now be acquired from large sample sets in very short periods of time, improving analysis statistics.  The margins of lesions can be further imaged to define the extent of the molecular advances in surrounding healthy tissues.  We have applied this technology for the creation of 3-D protein images of substructures of mouse brain.  Finally, we have successfully applied IMS to drug targeting and metabolic studies and the measurement of concomitant protein changes in specific tissues after systemic drug administration.  Identification of statistically significant protein markers can be identified in high throughput mode by mass spectrometry based proteomic approaches.

Biosketch:

Richard M. Caprioli is the Stanley Cohen Professor of Biochemistry and Director of the Mass Spectrometry Research Center at Vanderbilt University School of Medicine.  He is also currently Professor in the Departments of Chemistry and Pharmacology at Vanderbilt University.  Dr. Caprioli received his B.S. in 1965 from Columbia University in New York, N.Y., his Ph.D. in 1969 in Biochemistry, also at Columbia University with Professor David Rittenberg.  He did a one-year postdoctoral fellowship at Purdue University with Professor John H. Beynon.  In 1970, he was appointed as Assistant Professor of Biochemistry at Purdue.  In 1975, Dr. Caprioli moved to the University of Texas Medical School in Houston where he was Professor of Biochemistry and Molecular Biology and Director of the Analytical Chemistry Center until his move to Nashville in early 1998.

Professor Caprioli is interested in the use of mass spectrometry for the analysis of compounds in biological systems.  Current work includes the use of electrospray and laser desorption ionization methods with biological tissues and samples.  Applications have focused on the development of this instrumentation and associated methodologies to achieve ultra-high sensitivity detection of endogenous compounds (e.g., neuropeptides) in live animal systems.  Recent work involves the development of Imaging Mass Spectrometry, a technique whereby molecular images of peptides, proteins, drugs and other compounds are localized in tissue sections with molecular weight specificity.  This method involves molecular mapping of animal tissue through the production of ion images obtained from the analysis of mammalian tissue.  Applications to specific research areas involve questions about certain spatial distributions of molecules within specific tissues, e.g., mapping proteins in cancer tissue.  Specific applications include human glioblastomas, aberrant mouse colon crypts, and mouse prostate tumors

Dr. Caprioli has been a member of the American Society for Mass Spectrometry since 1975; he recently served two years each as President of the Society and Vice-President for Programs.  He is a member of the American Society for Biochemistry and Molecular Biology and the American Association for Cancer Research.  Professor Caprioli has been the Editor-in-Chief of the Journal of Mass Spectrometry since 1990.  He is currently co-editing several volumes of Encyclopedia of Mass Spectrometry.  He has published over 300 scientific papers, including three books.  In 2003, Dr. Caprioli received the Thomson Medal Award from the International Mass Spectrometry Society for "for outstanding achievements in mass spectrometry and for distinguished service to international mass spectrometry."  He received the Field and Franklin Award from the American Chemical Society in April, 2006.

Steven Walsh, Ph.D. Alfred Black Professor of Entrepreneurship Co-Director of the Technology Management Center University of New Mexico's Anderson School of Management

Talk: Nanotechnology Solutions for Biomedical Applications

Abstract:

Medical nanotechnology is it Science or Science fiction?  More importantly: What is actually being used or contemplated to be used to meet the real medical problems of today?  The author through this presentation seeks to provide some of these answers and to the speed and proliferation of interest in nanotechnology.  Specifically, the author provides a brief discussion of what nanotechnology is and what it is not.  Further he will provide a snapshot of worldwide financial commitments or "bets" that governments and industry have made in nanotechnology around the world.  The author will provide specifically a look at bottom up nanotechnology and when combined with IT and Microsystems technology is forming what many consider a new economic platform a "Schumpeterian" wave.  Enabling or Schumpeterian wave technology provides a base for solutions that can possibly solve problems previously unsolvable, provide a disruptive technology base that has the ability to redefine current medical solutions and form the basis for wealth creation and redistribution.  Moreover, the authors will provide a cascade of current examples of products and companies that seek to garner competitive advantage through a nanomanufacturing, biology and information technology.  Finally, the presenter will borrow heavily from the Micro and Nano Commercialization Education Foundation (MANCEF's) Atomically Precise, Nano bio and Nano-micro fluidics roadmaps.

Biosketch:

Dr. Steven Walsh is the Albert Black Professor of Entrepreneurship, the director of the Technology Entrepreneurship Program, Co-Director of the Management of Technology program and the Co-Director of the Technology Management Center at the University Of New Mexico Anderson Schools of Management.  He is also the Van den Kroonenberg Visiting chair at the University of Twente.  He is an internationally renowned academic and businessman.  He has been a director at a fortune 5-company's division, General Manager and Vice President of a Medium sized businesses and President of Entrepreneurial and Non-Profit companies.  Academically, the International Association of Management of Technology has recently ranked him in the top ten authors in his field worldwide based on quantitative rather than qualitative measures.  Dr. Walsh received his BE, MBA and a Doctorate of Philosophy in Management of Technology, Strategy and Entrepreneurship at RPI where Dr. Joseph Morone and Dr. Daniel Berg served as his co-chairs.  He has moist often worked with startups in Chemical, Micro, Nano, materials, ceramics whom usually focus on rapidly changing technology bases as their source of competitive advantage.  He has consulted for well over 250 firms.  He has helped more than a dozen firms raise capital and others to achieve favorable exit strategies.

Dr. Walsh is one of the world's leading experts on the commercialization of Micro and Nano technologies.  He is the founding President for the MANCEF and Co-chair of the first ever-technological roadmap for MEMS, Top down Nano technologies, bottom up atomically precise manufacturing, RF MEMS and many others.  He is currently chair of the education committee for both MANCEF as well as serving ion the board of the Nano Policy Institute.  He is an expert in competency analysis, disruptive and emerging technology commercialization, and portfolio management.  He is ranked in the top ten (10) researchers in management of technology by the International Association of Management of Technology for the last 5 years and is either on the board of directors or advisors for several firms.  His research has gain acclaimed most recently being awarded a journals best paper of the year.  He is a leading contributor to other academic and professional journals.  Dr. Walsh is the co director of the management of technology center which has recently been ranked in the top 10 programs in North America and a top 20 entrepreneurial program by Princeton review.  In 2006 he was awarded a best paper of the year in the Journal Technological Forecasting and Social Change for their 2005 issues.  He was named as one of 25 technology commercialization all-stars by the state of New Mexico in 2005, and in 2006 he won the lifetime achievement award for commercialization of Micro and Nano firms by the Micro and Nano Commercialization Education Foundation.  He was highlighted in both the Albuquerque the Magazine and The New Mexico Business Weekly for his contribution to Albuquerque and the state of New Mexico.

Stephen Kingsmore, M.B., Ch.B., B.A.O. President & CEO National Center for Genome Resources

Talk: Emerging Proteomic Technologies in Medicine

Abstract:

Measurement proteomics - measurement of the abundance of many proteins precisely and simultaneously in experimental samples - is an important, recent advance for static and dynamical, descriptive and predictive biological research.  The value of multiplexed protein measurement is becoming established in applications such as comprehensive proteomic surveys, studies of protein networks and pathways, validation of genomics discoveries, and clinical biomarker development.  Since standards do not yet exist that bridge this continuum, a recommended best practice for validation of results is an iterative study design and integration of data from several measurement technologies.  This talk will discuss recent developments in measurement proteomic technologies and applications of these technologies to biomarker development, drug clinical trials and multiplexed diagnostic tests.

Biosketch:

Dr. Kingsmore is a physician-scientist with significant experience in senior leadership roles in the biotechnology industry.  Dr. Kingsmore's previous roles included Chief Operating Officer of Molecular Staging Inc. and Vice President of Research of CuraGen Corporation, both of New Haven, CT.  Prior to that, he was Assistant Professor at the University of Florida in Gainesville, where he positionally cloned 5 disease genes and published over 70 peer-reviewed research papers.  Dr. Kingsmore received a B.Sc. in medical microbiology with first class honors and graduated in medicine (M.B., Ch.B., B.A.O.) from the Queen's University of Belfast, Northern Ireland.  He completed internship and residency in Internal Medicine, and a fellowship in Rheumatology, at Duke University Medical Center, Durham, NC.

Brian Haab, Ph.D. Scientific Investigator Van Andel Research Intitute

Talk: Novel Formats and Applications of Antibody Arrays

Abstract:

Cancer induces a variety of alterations to the protein composition of blood.  Increased cell breakdown in the tumor environment, oxidative stress, inflammation, new blood vessel formation, secretions from tumors, and immune responses against tumors all may contribute to changes in the composition of the blood.  Measurements of these various alterations may be useful to understand the roles of secreted and circulating proteins in cancer progression and to develop improved blood tests for cancer diagnosis and management.  We have developed several array-based protein analysis methods to look at different aspects of proteins, including protein abundance, protein glycosylation, protein-protein interactions, and protein immunoreactivity (1-5).  This talk will present these methods and their application to characterizing protein changes that are prevalent in the blood of cancer patients.  The utility of these results for cancer diagnostics and functional studies also will be discussed.

Biosketch:

Dr. Brian Haab is a Scientific Investigator and director of the Laboratory of Cancer Immunodiagnostics at the Van Andel Research Institute in Grand Rapids, Michigan.  Prior to joining the Van Andel Research Institute in May of 2000, Dr. Haab performed post-doctoral research in the laboratory of Dr. Patrick O. Brown at Stanford University.  He received his Ph.D. in Chemistry from the University of California at Berkeley in 1998, and his B.S. in Chemistry from the University of Michigan in Ann Arbor in 1992.  His research focuses on the development of array-based protein analysis methods and their application to the study of cancer-associated alterations to secreted proteins.

Jean-Loup Faulon, Ph.D. Sandia National Laboratory

Talk: Shotgun Protein Sequencing and Analysis

Abstract:

Current proteomics techniques that use mass spectrometry rely on genomic sequence data for protein identification.  This approach has serious drawbacks because (1) 30-50% of the genome annotations for bacterial species are incorrect; (2) 40-60% of human genes have alternative splice forms; and (3) genes contain no information on post-translational modifications.  De novo protein sequencing using MS/MS can overcome the pitfalls of protein identification but is limited to short sequences.

In the first part of this talk, I will present a novel computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from overlapping peptides.  The de novo sequencing problem is tackled as an inverse design problem, the proposed solution consists of computing molecular descriptors for the collected peptides and then reverse engineer the possible sequences matching the descriptors.  This approach, analogous to shotgun sequencing of DNA, is to be used to correct and complete erroneous genome annotations, to identify in vivo and in vitro (sample preparation) post-translational modifications, and to sequence alternative splices and genetically engineered proteins.

In the second part of the talk, I will present applications of molecular descriptors in proteome analyses.  In particular I will show how machine learning kernels can be constructed from molecular descriptors and be used in a variety of applications: protein functional classification, protein thermal stability predictions, and protein-protein and protein-metabolites interactions.

Biosketch:

Jean-Loup Faulon (http://www.cs.sandia.gov/~jfaulon) is currently a Distinguished Member of the Computational Bioscience Department at Sandia National Laboratories.  He graduated from the University of Dijon, France in 1982 with a degree in Physics and Chemistry, received a MS degree in 1986 in Computer Science from the University of Paris VI, France, and a Ph.D. in 1991 in Computational Chemistry from Ecole des Mines, Paris, France.  Faulon's expertise is in cheminformatics and bioinformatics.  Faulon has developed algorithms to infer and predict properties and activities of chemicals and biological sequences.  To this end he has designed molecular descriptors that can be used for both chemicals and biological sequences.  He has written more than 60 papers related to the structure elucidation of natural compounds, quantitative structure activity for drug design, protein classification, and protein-protein and protein-chemical interaction predictions.

Srinivas Iyer, Ph.D. Technical Staff Member Bioscience Division Los Alamos National Laboratory

Talk: Biological mass spectrometry: Current approaches and future prospects

Abstract:

Mass spectrometry (MS) as an analytical chemistry technique has been around for decades.  While several applications are served by this versatile technique, it is perhaps safe to say that MS-based biomolecule analysis has now become extremely significant and widespread.  In particular, the proteomics revolution would not have been possible without advances in MS and separations technology.  I will begin with a quick introduction to some standard proteomics approaches and their dependence on bioinformatics.  The applications of these approaches will be illustrated using examples of projects in our laboratory including one on the study of bacterial iron acquisition.  This project led to the development of some novel approaches involving nanoscale LDI-MS platforms that demonstrate the potential of MS in a variety of biomolecular analyses.  I propose to spend the final segment of this talk discussing current efforts in micro- and nanoscale separations upstream of MS and the challenges faced in integrating MS based protein/peptide analysis with these technologies.

Biosketch:

Srinivas Iyer is a Technical Staff Member (read Staff Scientist) in the Bioscience Division of the Los Alamos National Laboratory (LANL).  His interests lie in MS based biomolecule analysis and the integration of biology with the physical sciences.  Srinivas completed his Ph.D. in Biochemistry from the University of Houston and postdoc'ed at UNM Albuquerque and LANL before assuming his current position.  He is the co-founder of (and chairs) the Biotechnology track of the Nanotech Conference organized by NSTI.

Kimberly K. Leslie, M.D. University of New Mexico

Talk: Endometrial Cancer and Proteomic Screening

Biosketch:

I received my degree of M.D. at the University of Texas, Southwestern Medical School, in 1981.  I completed my fellowship in Maternal-Fetal Medicine at Georgetown University in 1987.  My present academic appointment is Professor with Tenure in the Departments of Obstetrics and Gynecology (primary appointment) and Biochemistry and Molecular Biology (secondary appointment) at the University of New Mexico, Chief of Obstetrics for the Department of Obstetrics and Gynecology and Director of the Division of Maternal-Fetal Medicine, as well as Director for the Maternal-Fetal Medicine Fellowship Program at the University of New Mexico.  I am also the principal investigator at the Reproductive Molecular Biology Laboratory and Co-director of the Women's and Hormone Dependent Cancer Research Program at the University of New Mexico Cancer Research and Treatment Center.  I was awarded the AGOS Charles Hunter Prize Thesis Award for "Molecular Tools to Re-establish Progestin Control of Endometrial Cancer Cell Proliferation" in 2000, and awarded the American Biographical Institute, Outstanding Female Executive in the Field of Medical Sciences in 2002, along with numerous honors, abstracts and publications.  I currently hold membership in the Endocrine Society since 1997, Clinical Affairs Committee since 2000, the Society for Molecular and Analytical Morphology since 1999, Uterine Corpus Committee of the Gynecologic Oncology Group since 2000, Program committee in the Society for Gynecologic Investigation since 2003, and the Committee for Experimental Medicine of the Gynecologic Oncology Group since 2004.

Patrick A. Anquetil, Ph.D. BioInstrumentation Laboratory Department of Mechanical Engineering Massachusetts Institute of Technology

Talk: Emerging NanoBioIT Markets and Applications

Abstract:

Nanotechnology, which is the multidisciplinary, rational design, fabrication and manipulation of material properties and functions at a scale less than 100 nanometers, has the potential to lead to a large range of innovative technologies across major industries.  Supported by multi-billion dollars government and industry funding world wide, it promises to have a tremendous impact on our economy.  Revenues of products incorporating these emerging nanotechnologies are expected to reach a trillion US Dollars by 2015.  Yet, to date the commercial impact of nanotechnology has been more difficult to discern.  To Wall Street it has been largely a disappointment from an investment perspective.  Arguably some of the most exciting technologies though are coming out of venture-backed start-ups such as Konarka, Molecular Imprints, or Cambrios.  This talk will present an overview of the emerging nanotechnology markets and applications in particular in the NanoBioIT space.  Unusual applications made possible by nanotechnology and created at MIT will also be discussed.

Biosketch:

Dr. Patrick A. Anquetil is the head of conducting polymer devices and technologies of the Bioinstrumentation Laboratory at the Massachusetts Institute of Technology (MIT), directed by Ian Hunter.  His academic career has spanned across three continents.  Prior to receiving his Ph.D. in Mechanical Engineering from MIT, he earned a Master's Degree from the Swiss Federal Institute of Technology in Zurich (ETH Zurich) and also carried post-masters research activities at the University of Tokyo in the field of nanotechnology.  Patrick has a passion for bringing technologies from the laboratory to the market place.  Over the past five years has been involved with several startups in the greater Boston entrepreneurial community.  From 2004 to 2006 he was the nanotechnology expert at investment firm Susquehanna International Group (SIG), advising clients on investments in this area.  His work has appeared in peer-reviewed publications as well as mainstream media such as Technology Review, Wired Magazine, PBS and CNBC.

Jim Huntley, Ph.D. National Center for Genome Resources

Workshops: 1) Introduction to Bioinformatic Tools and Resources for Protein Research; 2) Protein Structure Visualization Tools

Abstract:

The study of proteins using bioinformatic and computational approaches is an increasingly successful, but often intimidating, aspect of molecular structure and function projects.  A quick search of the World Wide Web results in literally hundreds of freely-available protein databases and analysis tools, each with their own advantages and disadvantages.  Unfortunately, comparative protein analyses can sometimes be dauntingly complex, even to the seasoned experimentalist.  Nonetheless, the use of bioinformatic tools, resources and strategies for cursory protein analysis and visualization of protein structure can be performed by any experimentalist with access to a computer and the internet.  In this two-part workshop, we will introduce a variety of easy-to-use bioinformatics resources and databases that can be used to conduct cursory protein sequence/structure analyses.

In part 2, we will focus on a number of molecular visualization tools to display, manipulate and annotate protein structures, and to learn to produce quality representations of protein structures suitable for presentation or publication.

Biosketch:

Jim Huntley is a Senior Research Scientist at The National Center for Genome Resources developing computational models to study the role of protein dynamics in protein function.  His research is diverse, ranging from studies of peanut allergens and enzymes involved in antibiotic resistance to cell cycle proteins that serve as targets for cancer therapy.  Prior to joining NCGR, he served as an Assistant Professor of Biochemistry at New Mexico Highlands University and the Program Director of NMHU's Research Infrastructure in Minority Institutions initiative.  He received a Ph.D. in Biochemistry from Arizona State University, a M.S. in Medical Physics from the University of Colorado Health Science Center, and a B.A. in Physics from the University of Colorado, Boulder.

Gary Siuzdak, Ph.D Senior Director, Center for Mass Spectrometry Associate Professor, Molecular Biology Scripps Center for Mass Spectrometry

Workshop: Mass Spectrometry in Biotechnology

Abstract:

Mass spectrometry is an established technology in protein and drug analysis and is now expanding into endogenous metabolite research.  Its utility derives from its wide dynamic range, reproducible quantitative analysis, and the ability to analyze biofluids with extreme molecular complexity.  The aims of our further developing mass spectrometry for proteomics and metabolomics range from understanding basic biochemistry to biomarker discovery and the structural characterization of physiologically important metabolites.  In this presentation I will discuss our evolution in mass-based approaches for proteomics and endogenous metabolite analysis toward biomarker discovery and understanding fundamental biochemistry.

Biosketch:

Gary Siuzdak, B.S. in Chemistry and B.A. in Mathematics, Rhode Island College; Ph.D. in Physical Chemistry, Dartmouth College.  Gary is currently the Senior Director of the Center for Mass Spectrometry and Associate Professor of Molecular Biology at The Scripps Research Institute in La Jolla, California (http://masspec.scripps.edu/).

His research includes the development of nanostructure-initiated desorption/ionization, intact viral analysis, preparative mass spectrometry, mass-based inhibitor-enzyme screening and, most recently, novel approaches to metabolomics.  He has over 130 peer-reviewed publications and three books, the latest being The Expanding Role of Mass Spectrometry in Biotechnology, 2nd Edition 2006.

Gary has been a member of ASMS since 1991, the ACS since 1990, and is founder of the San Diego Mass Analysis Network.  He participates as a reviewer for the NIH and several journals including PNAS, Nature Methods, JACS, Analytical Chemistry, Journal of Proteome Research and JASMS.  He also organized and chaired the ASMS Asilomar conference on Metabolomics, organized ASMS scientific sessions and has taught numerous courses including those offered at the ASMS annual conference.  Gary also established and maintains a website dedicated to the history of mass spectrometry (http://masspec.scripps.edu/MSHistory/mshisto.php).

Bruce Paul Gaber, Ph.D. Vision Rising, LLC

Workshop: Molecular Visualization

Abstract:

The old phrase, "I'll believe it when we see it", truly expresses why molecular visualization is so very critical to the bio-sciences.  We can't "see" proteins, DNA, and lipids, but we can visualize them and thus "believing" we manipulate their structures and properties.  We will explore the vocabulary of molecular visualization using the freeware program Visual Molecular Dynamics and the rich structural data resources of the Protein Data Bank.

In this hands-on workshop you will learn to:

• Use basic molecular modeling tools to produce visual models in a variety of graphic representations.
• Turn ordinary molecular graphics into effective illustrations for journals presentations, commercial displays, and advertisements.
• Chose the most appropriate tools your graphics project.

Biosketch:

During his long career at the Naval Research Laboratory, Bruce Paul Gaber established a firm reputation as one of the pioneers of nanobiotechnology.  His innovative areas of research include: liposome encapsulated hemoglobin; controlled release from mineral microstructures; molecular machining; template-directed molecular imprinting; and molecular motor-driven "Nano Assembly Lines".

In his second career as a scientific illustrator and animator Dr. Gaber has achieved worldwide recognition as a visual interpreter of the "small world" of nanotechnology.  His work has appeared in books, journals, and juried exhibitions worldwide.  Dr. Gaber is also an award-winning photographer.  In addition to teaching at the University of Washington, where he is an Affiliate Professor of Bioengineering, he has taught numerous workshops on computer illustration, visual esthetics, and photography.  His studio, Vision Rising LLC, counts among their clients: Baxter Health Care, Bristol Meyers Squibb, Scientific American, Foley & Lardner, and the Encylopaedia Britannica.

Michael Smoot, Ph.D. Cytoscape Core Architect UC San Diego

Workshop: Visualization and Analysis of Biological Interaction Networks using Cytoscape

Abstract:

Cytoscape, is an open-source, cross-platform network visualization and analysis application.  Cytoscape has it's roots in Systems Biology and is therefore well suited for analyzing data from high-throughput experimentation as well as other molecular state information.  The central organizing metaphor of Cytoscape is a network (graph), with genes, proteins, and molecules represented as nodes and interactions represented as edges between nodes.  The Cytoscape application acts as an extensible framework by providing core functionality to handle common tasks and software interfaces that allow easy extension to support unique needs.  The core functionality includes the visualization, layout, and manipulation of networks in addition to data handling services needed for importing, exporting, and managing network data.  Cytoscape's raison d'etre is its ability to integrate data and map it onto visual attributes of the networks.  This functionality allows for rich visualizations that can provide insight into otherwise complicated data.  In addition to the core functionality we have an ever growing library of plugins that extend and enhance Cytoscape's abilities.  Cytoscape is a collaborative effort of the University of California San Diego, the Institute for Systems Biology, Memorial Sloan-Kettering Cancer Center, Agilent Technologies, Unilever, the Pasteur Institute, and the University of Toronto.  See http://cytoscape.org for downloads and more detail

Biosketch:

Ph.D. in Systems Engineering (with concentration in bioinformatics) from U. Va. in 2005.  Now head programmer in the Ideker Lab.  Project lead for Cytoscape (http://cytoscape.org), Pathblast (http://pathblast.org), and NCT (http://chianti.ucsd.edu/nct).