SPEAKERS

Alex Hartemink
Duke University
Homepage: http://www.cs.duke.edu/~amink/
Lecture: Finding Genes in Genomes (movie)

Dr. Hartemink is the Alexander F. Hehmeyer Associate Professor of Computer Science, Statistical Science, and Biology at Duke University. He is a founding member of Duke's NIH-funded Center for Systems Biology, and his research interests are at the intersection of statistical machine learning (especially Bayesian methods) and cellular and molecular systems biology (especially the interplay between genomics, transcriptional regulation, and cell cycle control). In addition to teaching at the graduate and undergraduate levels in his department, he also participates heavily in Duke's Ph.D. Program in Computational Biology and Bioinformatics. He received B.S. degrees in Mathematics, Physics, and Economics from Duke in 1994, an M.Phil. in Economics from Oxford in 1996, an S.M. in EECS from MIT in 1997, and a Ph.D. in EECS from MIT in 2001. He received an NSF CAREER Award in 2004, an Alfred P. Sloan Research Fellowship in 2005, a David and Janet Vaughn Brooks Distinguished Teaching Award in 2007, and was inducted into the Bass Society of Fellows for Excellence in Teaching and Research in 2009. He took his first sabbatical last year to teach AP Biology and Calculus at Rift Valley Academy in Kenya.

Laurie Heyer
Davidson College
Homepage: http://www.davidson.edu/math/heyer/
Lecture: Designing and Building a Bacterial Computer

Dr. Heyer began research in bioinformatics for her Ph.D. in Applied Mathematics, which she received from the University of Colorado at Boulder in 1998. She was a postdoctoral fellow in the Center for Computational and Experimental Genomics at the University of Southern California. As Associate Professor of Mathematics at Davidson College, Dr. Heyer teaches a cross-listed course in bioinformatics that draws both math and biology majors. Along with A. Malcolm Campbell of the biology department at Davidson, Dr. Heyer is co-author of Discovering Genomics, Proteomics & Bioinformatics. Her current research, in collaboration with Campbell, includes work with interdisciplinary teams of undergraduates in the new field of synthetic biology, with a focus on bacterial computing.

Larry Hunter
University of Colorado
Homepage: http://compbio.ucdenver.edu/hunter/
Lecture: Understanding a Gene List

Dr. Hunter is the Director of the University of Colorado's Computational Bioscience Program and a Professor of Pharmacology (School of Medicine) and Computer Science (Boulder). He received a Ph.D. in computer science from Yale University in 1989, and then joined the National Institutes of Health as a staff scientist, first at the National Library of Medicine and then at the National Cancer Institute, before coming to Colorado in 2000. Dr. Hunter is widely recognized as one of the founders of bioinformatics; he served as the first President of the International Society for Computational Biology, and created several of the most important conferences in the field, including ISMB, PSB and VizBi . Dr. Hunter's research interests span a wide range of areas, from cognitive science to rational drug design. He has published more than 100 scientific papers, holds two patents and has been elected a fellow of both the ISCB and the American College of Medical Informatics. His primary focus recently has been the integration of natural language processing, knowledge representation, machine learning and advanced visualization techniques to address challenges in interpreting data generated by high throughput molecular biology.

Fran Lewitter
Whitehead Institute for Biomedical Research
Homepage: http://jura.wi.mit.edu/bio/
Lecture: Accelerating Biology with Bioinformatics: Collaboration with Lab Scientists

Dr. Lewitter is the Director of Bioinformatics and Research Computing at Whitehead Institute for Biomedical Research. Her group collaborates with biologists in the Institute to provide computational expertise for a wide variety of scientific projects. Currently, her group develops training materials and provides educational opportunities in bioinformatics to biologists in the Institute. In the past, her group offered a successful series of bioinformatics courses for biologists in the Boston area. Dr. Lewitter is a member of the International Society for Computational Biology Board of Directors and the chair of its Education Committee. She is also the Education Editor for PLoS Computational Biology.

Ran Libeskind-Hadas
Harvey Mudd College
Homepage: http://www.cs.hmc.edu/~hadas/
Lecture:
Bioinformatics Education at Harvey Mudd
Flowers, Bees, and Algorithms: Adventures in Cophylogenetics

Dr. Ran "RON" Libeskind-Hadas received the A.B. in applied mathematics from Harvard University and the M.S. and Ph.D. in computer science from the University of Illinois Urbana-Champaign. He has been a member of the computer science faculty at Harvey Mudd College since 1993. His research interests are in algorithms and computational biology. He is also interested in curriculum development and, with colleagues at Harvey Mudd, has developed a new course that integrates introductory biology and computer science.

Florian Markovetz
CRUK Cambridge Research Institute
Homepage: http://www.markowetzlab.org/
Lecture: Joining the Dots: Network Analysis of Gene Perturbation Screens

Dr. Markowetz holds degrees in Mathematics and Philosophy from the University of Heidelberg (2002) and a PhD in Computational Biology from Free University Berlin (2006). He was affiliated with the German Cancer Research Center (DKFZ) in Heidelberg and the Max Planck Institute for Molecular Genetics in Berlin. His Ph.D. thesis on Probabilistic Models for Gene Silencing Data was honored with an Otto-Hahn medal by the Max Planck Society. From 2006 to 2008, he pursued post-doctoral research in the Lewis-Sigler Institute for Integrative Genomics at Princeton University. Since 2009 he has served as a Junior Groupleader at Cancer Research UK's Cambridge Research Institute. Dr Markowetz is an associate editor of BMC Cancer and serves on the program committee of several bioinformatics and statistics conferences including ISMB, ECCB and AISTATS. He has been invited to give lectures and tutorials at several international summer schools and conferences. In particular, he taught tutorials on gene perturbation screens at ISMB 2009 and 2010.

Bernard Moret
École Polytechnique Fédérale de Lausanne
Homepage: http://people.epfl.ch/bernard.moret
Lecture: How Can We Compare and Summarize Trees?

Dr. Moret is Professor of Computer Science, holding the chair of Bioinformatics at the Swiss Federal Institute of Technology (EPFL) in Lausanne, Switzerland. He received his Ph.D. in 1980 from the University of Tennessee and was on the faculty of the Department of Computer Science at the University of New Mexico until 2006, serving as chair from 1991 to 1993. His research interests are in the area of algorithms and applications, particularly in computational molecular biology. He founded the ACM Journal of Experimental Algorithmics in 1995, serving as its editor-in-chief for seven years. Since 2000, he has focused on the development of models and algorithms for evolutionary genomics, publishing around 80 peer-reviewed articles in the area and founding, in 2001, the annual Workshop on Algorithms in Bioinformatics (WABI).

Pavel Pevzner
University of California, San Diego
Homepage: http://cseweb.ucsd.edu/~ppevzner/

Dr. Pevzner is the Ronald R. Taylor Chair Professor of Computer Science and Director of the Center for Algorithmic and Systems Biology at University of California, San Diego. He holds a Ph.D. (1988) from the Moscow Institute of Physics and Technology, Russia. He is the author of the graduate textbook Computational Molecular Biology: An Algorithmic Approach, 2000 and the undergraduate textbook (with Neil Jones) Introduction to Bioinformatics Algorithms, 2004. He was named Howard Hughes Medical Institute Professor in 2006. Dr. Pevzner is the director of the Interdisciplinary Bioinformatics Program at UCSD.

Tal Pupko
Tel Aviv University
Homepage: http://www.tau.ac.il/~talp/
Lecture: Phylogenetic Trees and the Parsimony Criterion

Dr. Pupko is a faculty member at the Department of Cell Research and Immunology, the Faculty of Life Science, Tel-Aviv University. He holds two bachelor's degrees, one in biology and another in mathematics, an experimental master's degree in lipid biochemistry, and a Ph.D. in molecular evolution, which focused on improving probabilistic evolutionary models to study sequence evolution. His broad interests are to understand how genes and genomes evolve and to use this information for biological function prediction. More specifically, his research in molecular evolution and bioinformatics covers: probabilistic models of sequence evolution, machine learning approaches to detect pathogenicity determinants, methods for lateral gene transfer detection, operon structure evolution, and viral evolution. He teaches a course in molecular evolution at Tel Aviv University, as well as an introductory course in bioinformatics that is compulsory for over 250 undergraduate students enrolled in the Faculty of Life Sciences.

Ben Raphael
Brown University
Homepage: http://www.cs.brown.edu/people/faculty/braphael.html
Lecture: Finding Mutations that Cause Cancer

Dr. Raphael is an Assistant Professor in the Department of Computer Science and Center for Computational Molecular Biology at Brown University. His research focuses on the design of combinatorial and statistical algorithms for the interpretation of genomes. Particular areas of emphasis include somatic structural rearrangements in cancer genomes; analysis of genetic structural variation in human populations; and comparative genomics. Dr. Raphael received an S.B. in Mathematics from MIT, a Ph.D. in Mathematics from the University of California, San Diego (UCSD), and completed postdoctoral training in Bioinformatics and Computer Science at UCSD. He is the recipient of a Career Award at the Scientific Interface from the Burroughs Wellcome Fund, an Alfred P. Sloan Research Fellowship, and an NSF CAREER award.

Ron Shamir
Tel Aviv University
Homepage: http://www.cs.tau.ac.il/~rshamir/

Dr. Shamir is Professor of Computer Science and holds the Raymond and Beverly Sackler Chair in Bioinformatics at Tel Aviv University (TAU). He has a BSc in mathematics and physics from Hebrew University and a Ph.D. in operations research from UC Berkeley. Dr. Shamir founded the bioinformatics undergraduate degree program at TAU and heads the Edmond J. Safra Bioinformatics Program at TAU. He specializes in design and analysis of algorithms, and since 1990 has focused on computational biology. His research interests include gene expression analysis, comparative genomics, gene regulation, systems biology and medical genetics. He serves on the editorial board of ten leading journals and series in theoretical computer science and computational biology, and was on the steering committee of RECOMB for 13 years. He has over 200 scientific publications.

Beth Simon
University of California, San Diego
Homepage: http://cseweb.ucsd.edu/~bsimon/
Lecture: Best Practices in Teaching Introductory Programming

Dr. Simon is a computer science education researcher in the Computer Science and Engineering Department at the University of California, San Diego as well as a former Science Teaching and Learning Fellow at the Carl Wieman Science Education Initiative. She combines her extensive teaching experience in introductory computing with efforts to define and assess best practices in teaching computing, both to computing majors and to the university student body at large. Beth is a strong proponent of pedagogies based in constructivist learning theory, including Peer Instruction(aka "clickers"), various peer-review frameworks (link), legitimate peripheral participation, and authentic learning. Finally, Dr. Simon finds it important to focus on identifying appropriate learning goals for introductory computing courses, and often starts with an assessment of how our exams and assignments do or do not reflect the goals we have for students (link).

Terry Speed
University of California, Berkeley
Homepage: http://www.stat.berkeley.edu/~terry/
Lecture: Normalizing and Removing Unwanted Variation from Microarray Data

Dr. Speed is a statistician.  He has been teaching theoretical and applied statistics for over 40 years. These days most of his teaching concerns the application of statistics to genetics and molecular biology, his major research interest for the last 25 years. He is head of the Bioinformatics Division of the Walter &Eliza Hall Institute of Medical Research in Melbourne, Australia, and an active emeritus professor in the Department of Statistics at UC Berkeley.

Jens Stoye
Bielefeld University
Homepage: http://www.techfak.uni-bielefeld.de/~stoye/
Lecture: Multiple Sequence Alignment: NP-Hardness and How to Deal with It

Jens Stoye studied Informatics in the Natural Sciences at Bielefeld University, Germany, where he received the PhD degree in 1997 on a topic related to multiple sequence alignment. After postdoctoral positions at the University of California at Davis and the German Cancer Research Center in Heidelberg, he became the head of the Algorithmic Bioinformatics Group at the Max Planck Institute of Molecular Genetics, Berlin. Since 2002, he has been a professor of genome informatics at Bielefeld University, where he is involved in the undergraduate and graduate programs Bioinformatics and Genome Research, from the outset an interdisciplinary curriculum featuring computer science and molecular biology at equal amounts.