Plenary Talks - June 3-5, 2008
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Laura Landweber
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Curriculum VitaeLAURA LANDWEBER is an Associate Professor in the Department of Ecology & Evolutionary Biology at Princeton University. She received her A.B. from Princeton in 1989 and her Ph.D. from Harvard in 1993. Before returning to Princeton as faculty in 1994, she was a Junior Fellow of the Harvard Society of Fellows. She has served on several panels, working groups, and advisory committees for the NSF, NIH, NHGRI, and NASA and co-chaired the NHGRI Comparative Genome Evolution Working Group from 2003-2007. She is an author of over 100 publications in molecular and evolutionary biology and editor of 3 books, ranging from genetics to DNA-Based Computers II. She is currently Co-Editor-in-Chief of Biology Direct (biology-direct.com), a new journal experimenting with open, signed peer review. She is also an associate editor of Journal of Molecular Evolution, on the advisory board for Genome Biology, and a member of Faculty of 1000. She has organized more than ten workshops and conferences at Princeton and abroad. A recipient of Burroughs-Wellcome Fund (1994) and Sigma Xi (1999) young investigator awards, she was elected a 2005 Fellow of AAAS for probing the diversity of genetic systems in microbial eukaryotes, including scrambled genes, RNA editing, variant genetic codes, and comparative genomics in protists. | |
RNA-guided, Epigenetic Programming and Re-programming of Genomic Information in CiliatesGlobal DNA rearrangements occur in many cells but are most exaggerated in ciliated protozoa. For example, during development of the somatic nucleus, Oxytricha destroys 95% of its germline genome, severely fragmenting its chromosomes, and then sorts and reorders hundreds of thousands of remaining pieces during the process of "gene unscrambling". Understanding how the information is encoded to reorder all these pieces has been the subject of both modeling and experiments. We have found that maternal RNAs provide both an organizing scaffold for DNA rearrangements and a template that can transfer point substitutions that arise during somatic growth (Nowacki et al. 2008 Nature 451:153-8). This unveiled a new influence of RNA, normally thought of as a passive message or intermediate in gene expression. As an example of inheritance beyond the conventional DNA genome, we demonstrate that a complete RNA cache of the parental somatic genome may be present during a limited period of development and that these non-coding RNAs can epigenetically transfer information across generations, hinting at the power of RNA molecules to sculpt the information in our genomes and to help execute difficult cellular computations. The evolutionary consequences of a viable mechanism in ciliates to transmit acquired characters may contribute to their cosmopolitan success, as well as high substitution rates in evolutionary sequence comparisons. | |
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Niles Pierce
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Curriculum VitaeNiles Pierce is an Associate Professor of Applied & Computational Mathematics and Bioengineering at Caltech. His research group focuses on programming biomolecular function: developing computational algorithms for the analysis and design of nucleic acid systems, designing and constructing molecular mechanisms for detection, transduction, amplification, and locomotion, and engineering molecular technologies for applications in biosensing, bioimaging and therapeutics. Pierce grew up in rural Fallbrook, California, graduating from Princeton University in 1993, with a BSE in Mechanical & Aerospace Engineering. He attended Oxford University on a Rhodes Scholarship, receiving a DPhil in Applied Mathematics in 1997 for research in computational fluid dynamics. Switching fields, Pierce arrived at Caltech as a senior postdoctoral scholar in computational molecular biology. He joined the Caltech faculty in 2000 and now serves as Executive Officer for Bioengineering. Outside the lab, he has been an avid trumpet and soccer player, performing with a variety of Princeton and Caltech orchestras, wind ensembles and jazz bands, and twice winning the Football Cup while at Oxford. | |
Molecular Choreography - Programming Nucleic Acid Self-Assembly and Disassembly Pathways. | |
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Ming Li
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Curriculum VitaeMing Li is a Canada Research Chair in Bioinformatics and professor of Computer Science at the University of Waterloo. He is a fellow of Royal Society of Canada, ACM, and IEEE. He is a recipient of Canada's E.W.R. Steacie Fellowship Award in 1996, and the 2001 Killam Fellowship. Together with Paul Vitanyi they have pioneered the applications of Kolmogorov complexity and co-authored the book "An Introduction to Kolmogorov Complexity and Its Applications". His main research focus recently is protein structure prediction. | |
Modern Homology SearchHomology search, finding similar parts between two sequences, is the most fundamental and popular task in bioinformatics. Traditional homology search technology is a heuristic science. The search is either too slow or too insensitive. When it does return something, the results are simply some non-specific fragments of alignments. We introduce new ideas, including a new mathematical theory of optimized spaced seeds, that allow modern homology search achieve high sensitivity, high specificity, and high speed simultaneously. The spaced seed methodology is now implemented in most modern homology search software serving thousands of queries daily. Joint work with Bin Ma, John Tromp, X.F. Cui, B. Brejova, T. Vinar, D. Shasha | |
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Luca Cardelli
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Curriculum VitaeLuca Cardelli was born in Montecatini Terme, Italy, studied at the University of Pisa (until 1978), and has a Ph.D. in computer science from the University of Edinburgh (1982). He worked at Bell Labs, Murray Hill, from 1982 to 1985, and at Digital Equipment Corporation, Systems Research Center in Palo Alto, from 1985 to 1997, before assuming a position in 1997 at Microsoft Research, in Cambridge UK, where he is currently Principal Researcher and head of the Programming Principles and Tools and Security groups. His main interests are in type theory and operational semantics, mostly for applications to language design, semantics, and implementation. He implemented the first compiler for ML (the most popular typed functional language), was a member of the Modula-3 design committee, and has designed a few experimental languages, of which the latest are Obliq: a distributed higher-order scripting language, and Polyphonic C#, a distributed extension of C#. His more protracted research activity has been in establishing the semantic and type-theoretic foundations of object-oriented languages, resulting in the 1996 book "A Theory of Objects" with Martin Abadi. More recently he has focused on modeling global and mobile computation, via the Ambient Calculus and on Spatial Logics, which indirectly led to a current interest in Systems Biology. He has published over 70 papers, 1 technical monograph and 2 proceedings as chair/editor (POPL'98 and ECOOP'03). He has served as editor of Foundations and Trends in Theoretical Computer Science (Models and Systems) (Now Publishers 2005+), Transactions on Computational Systems Biology (Springer 2004+), Mathematical Structures in Computer Science (CUP 2001+), Science of Computer Programming (North Holland 1999+), Journal of Functional Programming (CUP 1995-2004), and Theory and Practice of Object Systems (Wiley 1994-1999). He is a Fellow of the Royal Society, an ACM Fellow, an Elected Member of the Academia Europaea and of AITO, and a member of EATCS.
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Molecules as AutomataChemical and biochemical systems are described as collectives of interacting stochastic automata: each automaton represents a molecule that undergoes state transitions. This framework constitutes an artificial biochemistry, where automata interact by the equivalent of the law of mass action. We analyze systems and networks, both by stochastic simulation and by ordinary differential equations, and relate the two approaches. | |
