One of the best reasons to attend the O'Reilly Bioinformatics Technology Conference is the unprecedented gathering of top-notch presenters, leaders, and experts. Core developers, unique users, and visionaries share their knowledge with you to help you solve your computing or programming challenges. You won't find a gathering like this at any other conference.
Our speaker list is growing daily. Please check back regularly to see who we have lined up for you.R. Mark Adams
R. Mark Adams trained in biology and computer science, receiving an A.B. from Oberlin College, and a Ph.D. from Baylor College of Medicine. His postdoctoral fellowship was spent with Dr. Temple Smith at the BioMolecular Engineering Research Center. Adams is currently an editor of the journal Briefings in Bioinformatics.
Click here for more info.J. W. Bizzaro
Jeff Bizzaro is the founder and president of Bioinformatics.Org. He is a Ph.D. student in biochemistry at the University of Massachusetts in Lowell, and his interests include structural and evolutionary bioinformatics, data visualization, user interfaces, and advocating freedom and openness in science. He holds an M.Sc. in biochemistry from Boston College.
Click here for more info.Alvis Brazma
Alvis Brazma is the Microarray Informatics Group leader at the European Bioinformatics Institute. He is in charge of establishing ArrayExpress, a public repository for microarray gene expression data. Brazma is one of the founders and the president of the Microarray Gene Expression Data (MGED) Society, an international organization for facilitating sharing and standardization of microarray data. His research interests include gene expression data analysis and reverse engineering of gene networks from gene expression data. He received his Ph.D. in Computer Science from Moscow State University in 1987.
Click here for more info.Jesus Castagnetto
Jesus Castagnetto, a physical-organic chemist by training and a computational chemist and net-head by inclination, works in The Scripps Research Institute’s Metalloprotein Structure and Design Group. He developed the Metalloprotein Database and Browser (MDB), a bioinformatics resource with both a user interface and a set of APIs (web services).
Click here for more info.Michael Caudy, Ph.D.
Michael Caudy received a Ph.D. in Biophysics from U.C. Berkeley and postdoctoral training at U.C. San Francisco. He was at Cornell University Medical College from 1990 to 1999, studying the cellular, molecular and genetic mechanisms that control neuronal development. In 1999 he moved to Burke Medical Research Institute, an affiliate of Cornell.
Click here for more info.Maciej Ceglowski
Maciej Ceglowski is lead developer at the Vermont-based National Institute for Technology and Liberal Education, where he helps to create advanced open source search engines and runs the NITLE Blog Census (http://www.blogcensus.net). He is an avid Perl programmer and the author of several CPAN modules, including Search::ContextGraph, WWW::Blog::Identify, and AI::General. He keeps a weblog at www.idleworlds.com.
Click here for more info.Susan Chacko
Susan Chacko used to be a protein crystallographer before she moved to bioinformatics. She is a scientist in the Helix Systems group at the National Institutes of Health, which runs high-performance systems for the intramural NIH scientific community.
Click here for more info.Doris Chen, Ph.D.
Dr. Doris Chen is a staff engineer/Technology Evangelist at Sun Microsystems. As a Technology Evangelist, Chen's expertise includes web services, J2EE® technologies, JSP® technology and Servlets, Java® technology performance tuning, J2ME® platform wireless programming and web-based distributed computing. She has also made presentations on these topics at conferences around the world.
Before coming to Sun, Chen developed medical image compression applications and web-based network management products. She received her Ph.D. from the University of California at Los Angeles (UCLA) in computer engineering, specializing in medical informatics.
Click here for more info.Tim Clark
Speaker biography coming soon.
Click here for more info.Damian Conway
Damian has been a vi addict for quarter of a century. His h, j, k, and l keys are polished blank with overuse. He's noremapped his space and tab keys to more useful functions. His .vimrc is over 600 lines long, about 90% of it scripting code. VIM is his second favorite programming language and his only IDE.
Click here for more info.Sophie Coon
Sophie Coon received her M.S. in Computer Science Applied to Biology from the University of Paris 6, France in 1999. She joined Dr. Arthur Olson's group at The Scripps Research Institute’s Molecular Graphics Laboratory in May 1999 as an intern, and is now a Research Programmer. She is the main programmer for the Python-based Molecular Viewing environment (PMV). Her responsibilities involve developing new tools for PMV, writing documentation, developing a Python-based tool to distribute the components developed at MGL through the Web, and giving PMV tutorials.
Click here for more info.Peter Cooper
Peter Cooper is a Staff Scientist with the National Library of Medicine. He has been conducting training courses on the use of NCBI tools and databases for over four years. Cooper’s diverse biological background includes biochemistry, entomology, marine biology, and molecular biology.
Click here for more info.Peter Covitz
Peter Covitz manages the development of integrated biomedical informatics infrastructure for the National Cancer Institute. Before joining the NCI, he was VP of Professional Services at InforMax, Inc. Earlier in his career, Covitz worked as a research scientist and manager at Incyte Pharmaceuticals and Molecular Applications Group.
Covitz describes what drew him to bioinformatics: “My entry into bioinformatics began while I was still a bench scientist. I was working on an organism with fascinating symbiotic biology, but for which many of the standard molecular genetic techniques had not yet been worked out. I decided that the high-throughput sequencing approach would be a great way to move things forward. Once the data started pouring in, I had to learn how to automate many of the tasks that one does manually with smaller data sets, and also how to publish the data electronically. That led me to computer programming, databases, and bioinformatics. So, it was a desire to move my biological research forward more rapidly that led me to bioinformatics.”
Click here for more info.Matthew E. Crawford, Ph.D.
Matt Crawford is the Senior Curation Technology Manager at Incyte-Proteome. He holds a Ph.D. in Biology from the University of New Mexico. At Incyte, he is responsible for the design and execution of the various curation paradigms and data structures used to curate the information in the BioKnowledge Library.
Click here for more info.John Cuadrado
John Cuadrado is an independent consultant with extensive experience designing and building artificial intelligence systems for several government agencies. He holds a doctorate in mathematics from the University of Illinois, and has an eclectic range of interests, including data mining, image processing, and distributed computing. He has been working with National Institute for Technology and Liberal Education to make advanced search technologies accessible to users who may not have a programming background.
Click here for more info.Chris Dagdigian
As a founding partner of the independent consulting firm BioTeam Inc., Dagdigian specializes in research computing and infrastructure technology issues in the life sciences. A supporter of free software and open standards for life science research he is a founding member of the Bioperl Project, co-founder of the Bioclusters mailing list, and serves on the board of directors as Treasurer of the Open Bioinformatics Foundation.
Click here for more info.Bill Day
Bill Day is a Staff Engineer and Technology Evangelist at Sun Microsystems.
Day created the J2ME Archive to help developers build applications and services using Java technology. He manages jGuru's J2ME and Java Media FAQs. Day writes frequently about software development and has contributed feature articles to many sites and publications including CNN.com, ServerWorld, JavaWorld, Dr. Dobb's Journal Software Careers, Gamasutra, and Sun's site.
Day serves as an Association for Computing Machinery Distinguished Lecturer and speaks frequently on wireless technology, system security, and multimedia. He has presented keynotes, technical sessions, and courses at major industry conferences including SIGGRAPH and JavaOne and teaches Java and Wireless development as an extension instructor for the University of California Berkeley. Bill is also a Sun Certified Programmer for Java 2 Platform and Sun Certified System Administrator for Solaris 8 Operating Environment.
Prior to joining Sun, Day was a software engineer at Silicon Graphics. He held fellowships with the Honeywell Technology Center, Edinburgh Parallel Computing Centre, and Lawrence Livermore National Laboratory. Day earned a BS in Aerospace Engineering from the University of Oklahoma and completed one year of graduate studies in Scientific Computation while a National Science Foundation Graduate Research Fellow at the University of Minnesota.
More information is available from: www.billday.com
Click here for more info.Michel Dumontier
Dumontier is pursuing his Ph.D. (Biochemistry) at the University of Toronto. His research activities are directed towards exploiting differences that exist for organisms living in the most extreme environments, and applying knowledge to protein folding and protein engineering. His approach includes a combination of proteomics, bioinformatics, and statistical data analysis. Dumontier enjoys consulting, traveling, and dominating multiplayer online games.
How did Dumontier discover bioinformatics? “The focus of my initial Ph.D. work was to investigate the mechanism by which proteins from the thermophilic organism M. jannaschii were not only able to withstand high temperatures but also were optimized to work at those temperatures. At that time, I used conventional molecular biology and biochemistry laboratory techniques to experiment with such proteins as well as use bioinformatics tools to find sequence homologues and examine 3D structures in the hopes of finding a significant pattern. However, with 100 completely sequenced genomes (including human and mouse) and over 200 ongoing sequencing projects from an amazing variety of organisms (including thermophiles, halophiles, acidophiles, etc), I could now try to identify other forms of adaptation based only on sequence information and extended to structure computation via homology modelling. Clearly, this required some more rigorous tools for computation... and that is how I discovered bioinformatics.”
Click here for more info.Christopher Dwan
Christopher Dwan is a bioinformatics programmer at the University of Minnesota's Center for Computational Genomics and Bioinformatics. He helps life scientists apply high-performance computational resources to their research.
How did Dwan get into bioinformatics? “I have always been fascinated by the mechanisms of life. Many members of my nuclear family are physicians. I've always wanted to explore biochemistry and ‘how life works,’ but my aptitudes are stronger for computers than with people. My prior work was in vision processing and pattern recognition. One of my colleagues had taken his Ph.D. in biochemistry, and we would frequently talk about the potential for applying machine learning and information sciences to biological problems. I would also chat with my family about how their research/work might be a bit more productive if we could combine our disciplines. Thus, when the opportunity came for me to work with a bioinformatics and genomics research group, I jumped at it.”
Click here for more info.Iddo Friedberg
Iddo Friedberg recently completed his Ph.D. in the field of Structural Bioinformatics at The Hebrew University, Jerusalem at the Margalit lab. Friedberg is active in the biopython project, and is the author of the PeCoP online analysis tool, hosted by Bioinformatics.Org. Currently, Friedberg is postdoc’ing at the Godzik lab at The Burnham Institute in La Jolla, California.
Friedberg discusses his entry into bionformatics: “Sometime in the beginning of graduate school I got interested in protein structure. At the time, William R. Pearson (of FastA fame) gave a talk on distant evolutionary relationships among proteins. The ‘talk’ was given as part of an online computational biology course, on a MOO (remember those?) called BioMOO. The transcript of the talk is still available.
“As you can see from my questions, I was pretty much the newbie. However, the subject of distant evolutionary relationships among proteins fascinated me. Reason: protein structure is determined by its sequence. If completely different sequences provide us with similar structures, where do we find those elusive structural determinants? At that point, I decided to do my doctorate looking at structurally similar, sequence dissimilar proteins.
“Bioinformatics is constantly producing new subfields, which in many cases stem from novel high throughput technology, and associated computational tools. Examples: high throughput sequencing, brought us genomics, followed by proteomics. High troughput structure determination brings us structural genomics. Pretty soon, we will be hearing a lot more about glycomics: protein-carbohydrate interactions. To fully realize the potential of each subfield, people from different disciplines, with different backgrounds, vocabularies, and aptitudes have to work together. I find this interaction fascinating, on many levels.”
Click here for more info.William Gleason
Bill Gleason does research and teaches in the Department of Laboratory Medicine & Pathology at the University of Minnesota Medical School. He is also a fellow of the Minnesota Supercomputer Institute. One current research interest is the use of parallel computing, especially on Linux clusters, for practical applications in computational biology and medicine. Bill was co-developer of an early protein analysis package (PAP) and continues to take a "tools approach" in his research related to biological structure.
Click here for more info.Alan Goates
Alan Goates is Director of the Bioinformatics Department at Isis Pharmaceuticals. He currently leads multiple internal software development efforts at Isis, including the support of the antisense database pipeline and applications for the GeneTrove target validation program. He has also set up Oracle databases and Unix servers, translated chemical information into database structure and provided user support for internal software. As a graduate student, he performed research in a neurobiology lab at the University of California, San Diego developing a retro-viral expression system for ribozymes (catalytic anti-sense RNA constructs) targeted to specific sub-units of nicotinic acetylcholine receptors. Prior to graduate school, he spent five years as an independent computer programmer and consultant on a variety of applications such as multimedia teaching tools and cross-platform compatibility utilities. Mr. Goates has a Master's degree in Biology from his work at the University of California, San Diego, and two bachelor's degrees from the University of Utah, one in Computer Science and one in Biology.
Click here for more info.Martin Gollery
Martin Gollery is the Associate Director of Bioinformatics at the University of Nevada at Reno, the Chief Scientific Officer of Infoceutics, and the CEO of Tahoe Informatics. He has been the Director of Research at TimeLogic, a high school science teacher, an aerospace engineer, a photographer, and a wedding singer.
Click here for more info.Nathan Goodman
Dr. Nathan Goodman, a computer scientist by training, has been working in bioinformatics for more than a decade. He is presently a Senior Research Scientist at the Institute for Systems Biology in Seattle, Washington and an Affiliate Professor of Bioinformatics at the Arctic Region Supercomputing Center at the University of Alaska in Fairbanks. Previously, he was a founding member of the Whitehead Institute / MIT Center for Genome Research, one of the nation’s first and most illustrious genome centers, and ran the center’s bioinformatics group from 1991-1996. He subsequently ran his own bioinformatics research group at The Jackson Laboratory in Bar Harbor, Maine where he worked on information systems for large scale biological laboratories and mining of large biological datasets. He has also worked in the bioinformatics industry, heading a technical marketing group at Compaq Computer Corporation focused on bioinformatics applications in the pharmaceutical industry, and serving as a bioinformatics consultant.
Outside of life sciences, Dr. Goodman has more than twenty-five years experience in computer industry and academia. He was Chief Computer Scientist and founder of Kendall Square Research Corporation, a manufacturer of multiprocessor supercomputers for transaction processing and scientific applications. He was a professor of computer science at Harvard University and Boston University. He spent many years at Computer Corporation of America working on distributed and object oriented database systems. He worked at Encore Computer Corporation and Sequoia Systems, Inc., two start-up companies that developed shared memory multi-processor computers. He was President of Marble Associates, Inc., a consulting firm specializing in object-oriented, client/server business information systems, Senior Vice President of Codd and Date, a leading consulting firm in the relational database field, and also worked as an independent consultant specializing in object oriented, distributed, and multiprocessor databases. Early in his career, in the laboratory of Prof. Seymour Papert at MIT, he was a member of the team that developed the LOGO computer language for children.
Dr. Goodman writes a monthly column for Genome Technology magazine and has authored more than 80 technical articles and 25 abstracts on bioinformatics, database management, and advanced information systems. He is coauthor of the textbook, Concurrency Control and Recovery in Database Systems.
Nathan Goodman received the Bachelor of Science degree in Mathematics from the Massachusetts Institute of Technology (MIT) in 1972, the Master of Science degree in Computer Science from MIT in 1976, and the PhD in Applied Mathematics from Harvard University in 1980. Dr. Goodman's Ph.D. thesis, Power of Semijoins in Distributed Database Query Processing, studies practical and theoretical aspects of query optimization for distributed, relational database systems.
Click here for more info.James Gosling
James Gosling is a VP & Fellow at Sun Microsystems. He has built satellite data acquisition systems, a multiprocessor version of Unix, several compilers, mail systems ,and window managers. He has also built a WYSIWYG text editor, a constraint-based drawing editor, and a text editor called "Emacs" for Unix systems.
At Sun, his early activity was as lead engineer of the NeWS window system. He did the original design of the Java programming language and implemented its original compiler and virtual machine. He has recently been a contributor to the Real-Time Specification for Java.
Gosling received a B.Sc. in Computer Science from the University of Calgary, Canada in 1977. He received a Ph.D. in Computer Science from Carnegie-Mellon University in 1983. The title of his thesis was "The Algebraic Manipulation of Constraints."
Click here for more info.Robert Grossman
Robert Grossman is the Director of the Laboratory for Advanced Computing at the University of Illinois at Chicago and the spokesperson for the Data Mining Group, an industry consortium developing for the Predictive Model Markup Language (PMML). He is also the President of the Two Cultures Group, which provides consulting and outsourced services focused on data. He has published over seventy five papers.
Click here for more info.Jeff Hasty
Speaker biography coming soon.
Click here for more info.Tom Hudson
Tom Hudson looks for better user interfaces for computational biologists as part of the Bioinformatics Research Group at the University of North Carolina at Wilmington and teaches in the Department of Computer Science there. His previous research, at UNC Chapel Hill, was in collaborative, distributed interfaces for Atomic Force Microscopy.
Click here for more info.Per Jambeck
Per Jambeck is a Ph.D. student in the Bioengineering department at the University of California, San Diego. He is the coauthor of Developing Bioinformatics Computer Skills (O'Reilly), and he does research on machine learning applications in structural bioinformatics.
Click here for more info.Eric A. Johnson
Speaker biography coming soon.
Click here for more info.Jurgen Kaljuvee
Jurgen Kaljuvee is a freelance programmer living in New York and his language of choice is Java, in which he has been programming over five years. He is particularly interested in Java-based open-source extreme programming tools, open-source application frameworks, and applications of Java to bioinformatics. He is co-authoring two books on these topics to be published next spring.
Kaljuvee earned a bachelor’s degree from Harvard University where he studied molecular biology, computer science, and applied mathematics. He is a Sun Certified Enterprise Architect for Java and Sun Certified Java Programmer.
Click here for more info.Jill Kaufman
Jill Kaufman is Program Director, Life Sciences Standards at IBM Life Sciences. Kaufman participates in five standards organizations including I3C, HL7, GGF, DICOM, and OMG-LSR. Additionally, she directs IBM's overall standards work in Life Sciences.
At I3C, Kaufman is co-chair of Tech Ops Committee and Chair of Outreach Working Group. At HL7, she is chair of the Clinical Genomics Special Interest Group. Kaufman has twenty years of technical and marketing expertise in high tech industries including telecommunications, computers, and e-commerce. Previous standards work was in telecommunications where she was a Working Group chair and on the Board of Directors and Vice President of The ATM Forum (asynchronous transfer mode.)
Kaufman has a Ph.D. in Management from the University of Kent in Canterbury, England. She has a Masters in Telecommunications from PACE University and a B.S. in Computer Science from North Carolina State University.
Click here for more info.Jim Kent
William James Kent, who goes by Jim, is a research scientist at the University of California Santa Cruz. He is best known for producing the first assembly of the human genome and the human genome browser at UCSC. He studied math and art in college, and went on to a career making paint and animation programs for computers. These include the award winning Aegis Animator on the Amiga, Cyber Paint on the Atari ST, and Autodesk Animator on the PC.
One day, when the Microsoft Windows 95 developer's platform arrived on 12 CD-ROMs, Kent freaked out at the complexity of software development. Reasoning that the human genome could fit on one CD-ROM and didn't change every three months, he decided to change careers to bioinformatics. After a year studying basic biology and chemistry at community college and another year studying more advanced biology at the University of California Extension, he entered the Molecular, Cell, and Developmental biology PhD program at UC Santa Cruz. As a graduate student, he built a browser for the C. elegans genome.
As fate would have it, Kent was at the right place at the right time with the right tools to quickly develop a program that could assemble the public sequence of the human genome just days before Celera assembled their private sequence of the human genome.
Kent went on to write a browser for the human genome that is used by many thousands of biomedical researchers every day. His main focus these days is to understand the genome, particularly the elaborate control systems that turn genes on and off in a coordinated fashion. These control systems are key to understanding how an entire human body can develop from a single egg cell.
Click here for more info.Brian King
Brian King is a software developer and consultant with 12 years of development experience. He specializes in Java and web technologies for life science informatics. His most recent work was designing XML and visualization tools as a Senior Software Architect for DoubleTwist, Inc., and developing specifications for the Interoperable Informatics Infrastructure Consortium (I3C). He is co-author of the AGAVE Open Source XML format for genomic annotation.
Click here for more info.Timothy Kunau
Timothy M. Kunau is on academic staff at the University of Minnesota, where he designs information systems for genomics and computational biology. Tim has worked in high performance computing and research for over fifteen years, holds an MS in Software Engineering, and is now pursuing a Ph.D. Scientific Computation.
Click here for more info.Christopher Lee
Christopher Lee is a member of the UCLA Bioinformatics team. His research interest is the bioinformatics of the proteome, focusing on whole genome analysis in three areas: identification and characterization of Single Nucleotide Polymorphisms (SNPs), detecting alternative splicing across the entire human genome, and protein functional analysis.
Click here for more info.Steven Lembark
Steven Lembark is a sysadmin, and has been a Perl addict for ten years -- gluing code for fun and profit. He authored the CPAN modules Schedule::Depend and Schedule::Parallel, and currently maintains Quantum::Superpositions.
Two things attracted Lembark to bioinformatics: “Reading Science News for 30+ years, I've been able to watch the field grow, and working in the data warehousing industry gave me a feeling for the amount of work involved. The combination of watching what these people had accomplished from the outside and understanding how much work it was from the inside made bioinformatics interesting to me.”
Click here for more info.Maury Leysens
Maury Leysens, a graduate of the University of Iowa, has been involved in software development for fifteen years, and working in bioinformatics for eleven years. During that time, he has worked in both academic and industrial settings, managing development groups made up of people at all educational levels, and has lead numerous projects.
Click here for more info.Jian Lu
Jian Lu is currently working at Bioinformatics Reseach Center of Medical College of Wisconsin as a lead Bioinformatics Specialist. He has solid experience in biological information management system design, development and implementation, complex biological database design, management, migration and integration, complex biological data processing and exchange, and software development and project management for web applications.
Click here for more info.Aaron Mackey
Aaron Mackey is a graduate student under Dr. William Pearson at the University of Virginia, and has significant experience designing databases for scientific and commercial use. His graduate research focuses on observing evolutionary patterns of mutation indicative of positive selection for change, both within single-gene families and between entire bacterial genomes. He holds an M.S. in Immunology (1998) from Washington University in St. Louis.
How did Mackey discover bioinformatics? “During the second year of my Ph.D. program in Immunology at Washington University in St. Louis, I had one credit of coursework left to take before I could become ‘ABD’ (All But Dissertation); not wanting to take ‘Yet Another Molecular Biology Course,’ I instead took Computational Molecular Biology, which at that time (1997) was taught by David States, Sean Eddy, Warren Gish, and Michael Zuker, with guest lectures by Stephen Altschul. Of course, back then I had little idea who these people were, coming from an Immunology background, but needless to say, it was an outstanding class and showed me that it was possible to combine an aptitude for mathematics and computer science with non-theoretical biological research. I was hooked. Later, when I found myself transferring to the U. of Virginia, it was only natural that I should find my way into William Pearson's laboratory to finish my Ph.D.”
Mackey recently published Relational Modeling of Biological Data: Trees and Graphs on O'Reilly Network.
Click here for more info.Ayesha Malik
Ayesha Malik is a Senior Consultant at Object Machines, a software engineering firm providing Java and XML solutions to businesses. Malik has worked extensively on large XML and messaging systems for companies such as Deutsche Bank and American International Group (AIG). Most recently, she has been researching new ways to make schemas extensible and object-oriented. She also serves on the Architecture Working Group of FpML (Financial Products Markup Language), a data-interchange standard set forth by ISDA (International Swaps and Derivatives Association).
Malik holds a B.A. with honors from Harvard University and an M.S. from Columbia University, where she studied operations research, applied mathematics, and computer science. She also worked on computational genomics projects as a graduate student and is currently taking classes in bioinformatics at Stanford University. You can contact Malik at firstname.lastname@example.org.
Click here for more info.Sean Martin
Sean Martin is a Senior Technical Staff Member in IBM's Advanced Internet Technology Group in Cambridge, MA. He leads a team of developers working on the I3C's LSID reference implementation as well as a number of other IBM Life Science projects. Previously, Martin was one of the inventors and implementers of the Sash weblication client technology and before that architected and assembled much of the infrastructure technology behind IBM's high volume web sites including the Atlanta Olympics, Wimbledon, the US Open and the Kasparov Chess matches. He was the inventor of IBM's prototype Web Object Manager (WOM) web application and content management server and has written a number of patents.
Click here for more info.John McNeil
John McNeil has over 14 years experience modeling, designing, building, and deploying instrumentation, robotics, and software systems. He is responsible for all computer systems and for developing a research-wide software toolkit, including the GeneTrove database, at Isis Pharmaceuticals. He also co-developed sequence comparison and RNA structure prediction algorithms.
Click here for more info.Loralyn Mears, Ph. D.
Loralyn completed a Ph.D. in molecular biology at Case Western Reserve University, a M.Sc. in physiology at the University of Toronto and an Honours B.Sc. at Queen's University in Canada. She previously worked for a then start-up software company, NetGenics in a variety of roles and later moved onto Sun Microsystems where she is currently employed as the Life Science Segment Head of Market Development setting the strategy for ISV initiatives and how to grow the industry for Sun.
Click here for more info.Krista Miller
Krista Miller is the Director of Software Development at INCOGEN, Inc. She has been with the company for three years. She serves as a co-chair of the Technical Architecture working group in the I3C and is also a member of the Technical Operations Committee. Miller graduated from Clemson University in 1999 with a BS in computer engineering and a minor in mathematics.
Click here for more info.Ron Neyland
Ron Neyland is responsible for leading RLX’s efforts to create and deliver cluster solutions based on RLX’s ServerBlade architecture. He joined RLX in January of 2001, with an initial responsibility of building a team to deliver Microsoft Windows support for RLX systems. He later took on the challenge of delivering cluster systems. Prior to joining RLX Technologies, Neyland spent ten years at Compaq Computer where he held several engineering and management positions. Key responsibilities were leading in the delivery of deployment and management products including SmartStart, Compaq Insight Manager, Server Manager/R, and support for third party management products such as HP OpenView, Tivoli TME, and CA Unicenter. Neyland also led engineering teams responsible for the development and testing of Internet products for Compaq’s Consumer Products Division. These included the Internet keyboard, Presario Internet services, and MP3 players. Neyland holds seven patents for his work on management products at Compaq. Prior to joining Compaq, he spent ten years as an Engineering Manager and Systems Engineer with Johnson Controls. Neyland holds a B.S. in Electrical Engineering from Texas Tech University.
Click here for more info.Ian Ollmann
Ian Ollmann is in Apple's Vector and Numerics Group, where he works on code optimization and optimization strategies for Apple's vector processing initiatives. He joined Apple from the biotech industry, where he worked on active transport based approaches for enhanced pharmaceutical bioavailability. Ian received his Ph.D. in Chemistry from the Scripps Research Institute with Post Doctoral Studies at Caltech.
Click here for more info.Glen Otero
Glen Otero received his Ph.D. in Microbiology and Immunology from UCLA in 1995. Otero is the founder and principal at Linux Prophet, a bioinformatics consultancy specializing in the implementation, design, and deployment of Linux Beowulf clusters in the life sciences.
Click here for more info.Francis Ouellette
Francis Ouellette is Associate Professor at the University of British Columbia's Biotechnology Laboratory, and Director of the UBC Bioinformatics Centre, in Vancouver, Canada. He is also Director of the Canadian Genetic Diseases Network (CGDN) bioinformatics core facility where he coordinates the Canadian Bioinformatics Workshops that have trained more than 400 students in the past three years. Formerly at the NCBI, he now leads a research group interested in gene identification and genome annotation.
Click here for more info.Gregory Quinn
Greg Quinn is currently working as lead software architect on the Encyclopedia of Life (EOL) project at the San Diego Supercomputer Center. Greg received his academic training at Leeds University, UK, where he majored in biochemistry and physiology, and at Southampton University, UK, where molecular biology and computational sequence analysis were the major components of his Ph.D. work. His postdoctoral training includes time spent at the University of South Florida in Tampa Bay, Florida and the Burnham Institute in La Jolla, California. In his free time he annoys the neighbors by playing blues guitar, and has (likely unrealistic) aspirations as a screenwriter.
Click here for more info.Darrell Ricke
Darrell Ricke spends most of his time developing new bioinformatics algorithms/software and discovering genes in multiple genomes. A sample of some of his work is presented for the rice genome in Science, Vol. 296, 5 April 2002. Previously, he worked on the human genome project at the Los Alamos National Laboratory Center for Human Genome Studies.
What drew Ricke to bioinformatics? "As a computer scientist, I believe that to be able to solve a problem, I must understand it first. When I became interested in the Human Genome Project, I went back to college to study genetics and molecular biology. My hope was to be able to someday discover the gene for a human disease. While I was at the Los Alamos National Laboratory, Center for Human Genome Studies (LANL CHGS), I correctly identified the gene for Familial Mediterranean Fever [Cell 90:797-807, 1997] from fragments of two exons analyzed with a novel bioinformatics tool that I had developed (SCAN). SCAN is useful for high throughput sequence analysis and annotation. SCAN integrates the similarity results from BLASTN, TBLASTN, TBLASTX, and FASTA with gene prediction results from GRAIL. I used it to annotate 12 finished megabases of the human genome at LANL. In addition to my interests in bioinformatics and gene discovery, I am personally interested in the basics of which missense mutations are deleterious in human diseases [Hum. Mutat. 7:202-13, 1996].
"Bioinformatics is a very young field. While many basic bioinformatics applications exist, a lot of the needs of scientists are still unmet. New solutions that include data integration and integration of analysis and visualization interfaces are needed. The development of integrated bioinformatics data warehouses and associated N-tier software will be an important focus area for the next five years. New techniques are enabling the high throughput capture and integration of genomic, expression, proteomic, and metabolomic data from biological samples. These techniques will enable systems biology and systems modeling to become reality."
Click here for more info.Alan Robinson
Alan Robinson moved to the European Bioinformatics Institute in 1996 as part of the newly created "Industry Programme," to work on issues of visualisation and data mining in bioinformatics. He became coordinator of the EBI's Industry Programme in 1998, focusing on R&D in IT infrastructure and open standards for bioinformatics, genome analysis, visualization, and data mining. Robinson currently coordinates EBI's role in the EPSRC's myGrid project, and is a visitor to the Department of Genetics, University of Cambridge.
Click here for more info.Michel Sanner, Ph.D.
Michel Sanner is an assistant professor in the Molecular Biology department of The Scripps Research Institute. He is the author of the program MSMS, which enables the efficient and accurate calculation of molecular surfaces and has been distributed to more than 950 laboratories around the world. Sanner obtained his Ph.D. in Computer Science in 1992 from the University of Haute-Alsace in France for his work on the modelization of molecular surfaces. This research was carried out while working in the molecular modelling group of the pharmaceutical company Sandoz in Basel, Switzerland. In 1993, Sanner accepted a post-doctoral position in the Molecular Graphics Laboratory of The Scripps Research Institute. He has worked in collaboration with Boris Reva and Alexei Finkelstein on the determination of phenomenological residue pair-wise interaction potentials. More recently, he has lead the development of a Python-based scripting environment enabling the rapid development of customized applications to view, manipulate, and analyze molecular data. His involvment with the Python community goes back to 1997.
Click here for more info.Michael A. Schulman
Michael Schulman is the product line manager of graphics APIs and media libraries at Sun Microsystems. He is responsible for Sun's strategy in the graphics software area and for determining future real time collaboration products. Previously he was Silicon Graphics, Inc. He received a Bachelors of Science Degree in Civil/Structural engineering from Cornell University, and a Masters of Science Degree from Cornell University in computer graphics.
Click here for more info.Lincoln D. Stein
Lincoln Stein was a hospital pathologist until he saw the light and joined the bioinformatics revolution. He learned the tricks of the trade in Eric Lander's lab at the MIT Genome Center, before striking off on his own at Cold Spring Harbor Laboratory. He is now an associate professor at CSHL and runs a lab, the main interest of which is in integrative databases for biological sciences.
Click here for more info.Jason Stewart
Jason Stewart is the founder of Open Informatics, a bioinformatics software consulting and contracting firm that specializes in Open Source solutions.
Why did Stewart get into bioinformatics? "I was a biologist setting up a high-throughput DNA sequencing facility, and became far more interested in building infrastructure for data communication than actually doing the biology, so I switched fields from Biology to Computer Science."
Click here for more info.James Tisdall
James Tisdall was Member of Technical Staff at Bell Laboratories in Murray Hill, New Jersey, where he worked in the Information Principles Research Laboratory as a programmer and researcher. He began using Perl in bioinformatics in 1991. In 1992 he released the first version of DNA Workbench, a client/server, multi-platform (PC, Mac, Unix) and parallel processing bioinformatics toolkit written entirely in Perl and served from fifteen Sun servers in the Human Genome Project to hundreds of laboratories worldwide, featuring regular expression search of all of Genbank in 30 seconds. After leaving the Human Genome Project, he led the scientific computing effort at Mercator Genetics; and he led the Bioinformatics Group at Fox Chase Cancer Center. He currently consults for Biocomputing Associates. He is the author of Beginning Perl for Bioinformatics and the upcoming Mastering Perl for Bioinformatics, both from O'Reilly & Associates, as well as several articles and papers in scientific journals. He holds a B.A. in mathematics from City College of New York, an M.S. in computer science from Columbia University, and has held university and dean's fellowships at the University of Pennsylvania and the University of Michigan.
Click here for more info.Helge Weissig, Ph.D.
Helge Weissig obtained his Ph.D. in Molecular Biology from the Albert-Ludwigs University in Freiburg, Germany. He currently is a Project Leader for Bioinformatics at ActivX Biosciences, a technology driven proteomics company. Prior to joining ActivX in summer of 2002 he worked at the San Diego Supercomputer Center where he developed the underlying database infrastructure and query interfaces for the Protein Data Bank WWW site and ftp archive. Helge Weissig has been teaching bioinformatics and structural bioinformatics for several years at UCSD extension. where he participated in the establishment of a professional certificate for bioinformatics. He has recently co-edited the first text book in Structural Bioinformatics to be published in early spring of this year.
Click here for more info.Philip Werner
As Vice President of Product Management at AVAKI, Philip Werner is responsible for managing product lifecycles, product definition, and go-to-market planning for AVAKI's grid software. A software industry veteran with more than 15 years of experience in product management, software development, and enterprise systems integration, Werner has held management positions at Art Technology Group, Vermeer Technologies, Epesi Technologies, InConcert, and Interleaf over the course of his career.
Considered an industry expert on web services, middleware, enterprise application integration, content management, and search technologies, Werner is currently extremely active in the definition of open standards for secure, wide-area data integration in the life sciences. He is a member of the Technical Architecture Group of the I3C (Interoperable Informatics Infrastructure Consortium) and co-author of the Life Science Identifier (LSID) standard draft. In addition, Werner is widely published within the neuroscience, computational linguistics, and computer science industries.
Werner received his undergraduate degree from Carnegie Mellon University and holds an MSc in Cognitive Science from the University of Edinburgh in Scotland.
Click here for more info.Joseph White
Joseph White has a B.S. in Biochemistry from Centre College (KY), and a Ph.D. in Genetics from NCSU. In the laboratory, White has studied oxygen radical biology in plants, ethylene biosynthesis in tomatoes, and energy metabolism in rats. White currently develops software and database methods for managing microarray data.
Click here for more info.Ken Williams
Ken Williams is a Perl consultant, instructor, and the author of several CPAN modules, including AI::Categorizer, Class::Container, Module::Build, Apache::Filter, and others. Williams is also one of the current developers of HTML::Mason and co-authored the recent O'Reilly book Embedding Perl in HTML with Mason with Dave Rolsky. He also co-authored the Fall 1999 Perl Journal article, "Genetic Algorithms in Perl," with Brad Murray. Williams co-founded the "Ask Dr. Math" service at the Math Forum, which provides lots of questions and answers that need categorization. He is pursuing graduate studies in computer science in Sydney, Australia.
Adds Williams, "My background is in Machine Learning applied to Automatic Text Categorization, and many of the Machine Learning techniques are also applied to problems in Bioinformatics. I have collaborated with some Bioinformatics people on tools common to both fields."
Click here for more info.Stephen Wolfram
Stephen Wolfram published his first scientific paper at the age of 15, and received his Ph.D. in theoretical physics from Caltech by the age of 20. Wolfram's early scientific work was mainly in high-energy physics, quantum field theory, and cosmology. Wolfram became a leader in the emerging field of scientific computing, and in 1979 he began the construction of SMP, the first modern computer algebra system, which he released commercially in 1981, the same year he became the youngest recipient of a MacArthur Prize Fellowship.
He then set out to understand the origins of complexity in nature, which led to a wide range of applications, and provided the main scientific foundations for such initiatives as complexity theory and artificial life. Wolfram himself used his ideas to develop a new randomness generation system and a new approach to computational fluid dynamics.
After a highly successful career in academia, Wolfram launched Wolfram Research, Inc., and began the development of Mathematica in late 1986. Mathematica was released in 1988 and was immediately hailed as a major advance in computing.
Following the release of Mathematica Version 2 in 1991, Wolfram began to divide his time between Mathematica development and scientific research. By the mid-1990s, his discoveries led him to develop a fundamentally new conceptual framework, which he then spent the remainder of the 1990s applying, not only to new kinds of questions, but also to many existing foundational problems in physics, biology, computer science, mathematics, and several other fields.
Wolfram described his achievements in his 1200-page book A New Kind of Science. Released on May 14, 2002, the book was widely acclaimed and immediately became a bestseller. Its publication has been seen as initiating a paradigm shift of historic importance in science. Wolfram is now developing a series of research and educational initiatives in the science he has created.
Click here for more info.
oreilly.com Home | O'Reilly Bookstores | How to Order | O'Reilly Contacts
© 2002, O'Reilly Media, Inc.