Below are the planned events listed in chronological order. Introductory talks are indicated in bold face. Audio/video recording of the talks together with the respective viewgraphs can be accessed by clicking the talk titles when they become available.
Summary |
Introduction (section leader: T. Hwa)
date |
time |
event |
speaker |
Jan 16 (Tues) |
2pm |
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Jan 17 (Wed) |
10 am |
||
|
2pm |
" | |
Jan 18 (Thur) |
10am |
'' |
|
2pm |
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Jan 19 (Fri) |
10am |
'' |
Sequence Analysis (section leader: R. Bundschuh)
date |
time |
event |
speaker |
Jan 22 (Mon) |
2:30pm |
S. Altschul (NCBI, NIH) |
|
Jan 23 (Tue) |
10am |
Sequence comparisons using position-specific scoring systems |
'' |
Jan 24 (Wed) |
10am |
Tutorial: Sequence alignment, directed polymers, and the asymmetric exclusion process |
|
2pm |
|||
Jan 25 (Thur) |
10:30am |
Sequence and Structure Matching: Applications of Probability Theory |
|
Jan 26 (Fri) |
10am |
Y.-K. Yu (physics, Florida Atlantic Univ.) |
|
Jan 29 (Mon) |
10 am |
M. Gribskov (UCSD and SDSC) |
|
Jan 30 (Tues) |
10 am |
||
2 pm |
R. Ramaswamy (physics, New Delhi) |
RNA folding (section leader: R. Bundschuh)
date |
time |
event |
Speaker |
Jan 31 (Wed) |
10am |
||
2 pm |
L. Tang (physics, HKBU), |
||
Feb 1 (Thur) |
10am |
D. Moroz (physics, UCSD), |
|
Feb 2 (Fri) |
10 am |
Screening of a Charged Particle by Mutivalent Counterions in Salty Water: Giant Charge Inversion |
B. Shklovskii (physics, Minnesota) |
2 pm |
H. Orland (physics, Saclay) |
||
Feb 5 (Mon) |
2 pm |
G. Stormo (biology, WUSTL) |
|
Feb 6 (Tues) |
10 am |
P. Schuster (Vienna) |
|
Feb 7 (Wed) |
10 am |
I. Tinoco (Berkeley) |
|
2 pm |
D. Lubensky (physics, Harvard), |
||
Feb 8 (Thur) |
10 am |
S. Woodson (biophysics, Johns Hopkins) |
|
2 pm |
H. Isambert (Strassbourg) |
||
Feb 9 (Fri) |
10 am |
P. Schuster (Vienna) |
|
|
2 pm |
S. Woodson (biophysics, Johns Hopkins) | |
3 pm |
Bioengr Colloquium |
S. Leibler (Princeton) |
Protein Folding I: kinetics (section leader: H. Orland)
date |
time |
event |
speaker |
Feb 12 (Mon) |
10 am |
||
Feb 13 (Tue) |
10 am |
||
Feb 14 (Wed) |
10 am |
Exploringng the Energy Landscape for Folding: Connecting Theory and Experiments |
Onuchic (physics, UCSD) |
Feb 15 (Thurs) |
10 am |
Thinking Big: From the Folding of Small Proteins to the Assembly of Large Molecular Complexes |
|
2:30 pm |
Discussion: Aspects of Cold Unfolding, Loop Entropies of Compact Polymers |
K. Sneppen (physics, NORDIDA) |
|
Feb 16 (Fri) |
10 am |
1. Tutorial on Proteins |
|
3 pm |
Bioengr Colloquium |
K. Dill (UCSF) |
Protein Folding II: structure and design (section leader: H. Orland)
date |
time |
event |
speaker |
Feb 19 (Mon) |
2pm |
||
Feb 20 (Tue) |
10am |
Seeing Is Believing: Transition States and Intermediates in Realistic Folding Models |
E. Shakhnovich (chemistry, Harvard) |
2 pm |
|||
Feb 21 (Wed) |
10am |
Prediction and Design of Protein Structures and Folding Mechanisms |
|
Feb 22 (Thurs) |
10am |
||
2 pm |
Discussion on Design: Designability of Protein structures: on and off Lattice, Functional Protein Design |
C. Tang (NEC) |
|
Feb 23 (Fri) |
10am |
Protein Folding III: prediction & structural genomics (section leader: H. Orland)
date |
time |
event |
speaker |
Feb 26 (Mon) |
2 pm |
||
2:30pm |
N. Buchler |
||
Feb 27 (Tue) |
10 am |
Physical, Biological and Algorithmic Approaches to Protein Folding |
|
2 pm |
|||
Feb 28 (Wed) |
10 am |
||
Mar 1 (Thurs) |
10 am |
||
Mar 2 (Fri) |
9:30 am |
Protein Folding - What's the Question? |
Genomics I: Gene and DNA motif finding (section leader: H. Li)
date |
time |
event |
speaker |
Mar5 (Mon) |
10am |
||
Mar 6 (Tue) |
10am |
Building a Dictionary for DNA: Decoding the Regulatory Regions of a Genome |
|
Mar 7 (Wed) |
10 am |
DNA-protein interactions: experiments, models and pattern discovery algorithms |
G. Stormo (biology, WUSTL) |
Mar 8 (Thurs) |
10am |
V. Bafna (Celera) |
|
2pm |
'' |
||
Mar 9 (Fri) |
10am |
||
2 pm |
A stochastic extension of the dictionary model for motif finding |
'' |
Genomics II: Large-scale genomic organization (section leader: H. Li)
date |
time |
event |
speaker |
Mar 12 (Mon) |
10am |
||
3:30 pm |
|||
Mar 13 (Tue) |
10 am |
'' |
|
2 pm |
|||
Mar 14 (Wed) |
10 am |
E. Domany (physics, Weizmann) |
|
4 pm |
MRL seminar: Algorithmic Self-Assembly of DNA |
E. Winfree (CalTech) |
|
Mar 15 (Thur) |
10 am |
||
2 pm |
Natural genetic engineering -- the toolbox for evolution: prokaryotes |
'' |
|
Mar 16 (Fri) |
10 am |
Natural genetic engineering -- the toolbox for evolution: eukaryotes |
'' |
3 pm |
Bioengineering Colloquim: DNA-Protein Interactions at the Single Molecule Level |
D. Bensimon (ENS, Paris) |
Genomics III: protein-DNA/RNA interaction (section leader: H. Li)
date |
time |
event |
speaker |
Mar 19 (Mon) |
10 am |
||
2pm |
Discussion: Regulatory motif finding via comparative genomics |
N. Rajewsky (biophysics, Rockefeller); |
|
Mar 20 (Tue) |
10am |
Helicase mechanisms and the `coupling' of regulatory components within macromolecular machines |
|
3:30pm |
Salt-effects on DNA-histone stability |
R. Netz, Max-Planck Inst. |
|
Mar 21 (Wed) |
11 am |
A. Lapedes, LANL |
|
1 pm |
|||
Mar 22 (Thurs) |
10 am |
Olfaction: from genome mining to molecular recognition statistics |
|
2 pm |
New surprises for an old enzyme: structure and function of a bacterial ribonuclease P |
||
3:30pm |
S. Brenner, UC Berkeley |
||
Mar 23 (Fri) |
10am |
||
2 pm |
Thermodynamics of tertiary RNA folding: metal ions, urea and a thermophilic ribozyme |
Network I: Gene expression analysis (section leader: Kim Sneppen)
date |
time | event | speaker |
Mar 26 (Mon) | 10am | DNA Microarrays: Yeast, Parasites, Viruses, and People | J. DeRisi (biology, UCSF) |
3:30pm | Discussion: Clustering analysis | N. Socci (biophysics, Rockefeller) | |
Mar 27 (Tue) | 10am | Challenges in gene expression analysis | R. Stoughton (Rosetta) |
2 pm | Discussion: Clustering analysis | G. Getz (physics, Weizmann) R. Sasik (physics, UCSD) |
|
Mar 28 (Wed) | 10 am | From microarrays and DNA sequence features to gene network inference and verification | B. Wold (biology, CalTech) |
Mar 29 (Thurs) | 10am | Reverse-engineering the flagella gene circuit based on accurate expression kinetics | U. Alon (biology, Weizmann) |
2 pm | Tutorial on E. Coli chemotaxis; robustness of the chemotaxis circuit | '' | |
Mar 30 (Fri) | 10am | Expression analysis of colorectal cancer: opportunities and pitfalls | D. Notterman (biology, Princeton) |
2pm | Discussion: Clustering analysis | Y. Tu (physical science, IBM Watson) |
Network II: Overview of biological networks (section leader: Kim Sneppen)
date |
time | event | speaker |
April 2 (Mon) | 10am | TBA | R. Brent (Molecular Science Inst., Berkeley) |
April 3 (Tue) | 10am | Regulated Recruitment: Transcription and Otherwise | M.Ptashne (Sloan Kettering) |
April 4 (Wed) | 10 am | Molecular evolution | A. Libchaber (Rockefeller U.) |
April 5 (Thurs) | 10am | Single molecule nano-bioscience | T. Yanagida (Osaka U. School of Medicine) |
April 6 (Fri) | 10am | Architecture of genomic regulatory systems: how gene control programs are encoded in DNA | E. Davidson (biology, Caltech) |
Network III: Protein circuits, signal transduction, chemotaxis (section leader: K. Sneppen)
date |
time | event | speaker |
April 9 (Mon) | 10am | Putting the horse before the chart: Phenomenology, Robustness, and Evolvability | A. Murray (Genome Center, Harvard) |
April 10 (Tue) | 10am | Tutorial on immune network | J.-M. Le Doussal & D. Lancet |
2 pm | Tutorial on signal transduction pathways | A. Murray (Genome Center, Harvard) | |
April 11 (Wed) | 10 am | Robustnes in model genetic networks and its implications | B. Shraiman (physics, Bell Lab) |
3:30pm | Tutorial on Ca-signaling and chemotactic response of Dictyostelium | H. Levine (physics, UCSD) | |
April 12 (Thurs) | 10am | Robustnes of signal transduction networks | J. Doyle (Engr, Caltech) |
April 13 (Fri) | 10am | TBA | S. Subramanianm (Bioengr, UCSD) |
Network IV: Gene regulation and gene circuits (section leader: K. Sneppen)
date |
time |
event |
speaker |
April 16 (Mon) |
10am |
Function design and evolution of cell and molecular networks |
|
April 17(Tue)
|
10am |
M. Elowitz (biophysics, Rockefeller) |
|
2pm |
|||
April 18(Wed) |
10 am |
||
April 19(Thurs) |
10am |
S. Liang (physics, NASA Ames) |
|
3 pm |
Carsten Peterson (Lund) |
||
April 20(Fri) |
10am |
Round table discussion on statistical physics and molecular biology |
everyone welcomed ! |
3 pm |
Bioengineering seminar: Effects of Mechanical Forces on Signal Transduction and Gene Expression |
S. Chien (Bioengr, UCSD) |
Molecular Evolution I: Prebiotic and directed evolution (section leader: P. Higgs)
date |
time | event | speaker |
April 23 (Mon) | 10am | Introduction to molecular evolution | W. Fitch (biology, UC Irvine) |
April 24 (Tue) | 10am | Origin of Life without Biopolymers | D. Lancet (genome ctr, Weizmann) |
2pm | Topology of RNA Shape Space and Evolutionary Dynamics of RNA | W. Fontana (Santa Fe Institute) | |
April 25 (Wed) | 10 am | Molecular Ecology Studies with Nucleic Acids | P. Ordoukhanian (biochemistry, Scripps) |
3.30 pm | Discussion | All previous speakers | |
April 26 (Thurs) | 10am | Opportunities with Aptamers: Ready for Prime Time | L. Gold (SomaLogic Inc) |
2 pm | Computing with RNA | L. Landweber (biology, Princeton) | |
April 27 (Fri) | 10 am | Molecular Evolution and Design - Practical Aspects | D. Estell (Genencor Int'l) |
Molecular Evolution II: RNA world, genetic code, and genomic evolution (section leader: P. Higgs)
Phylogeny I:Protein evolution; introduction to phylogenetic trees (section leader: R. Goldstein)
date |
time |
Event |
speaker |
May 7 (Mon) |
10 am |
P. Higgs (Biology, U. Manchester) |
|
2 pm |
S. Holmes (Statistics, Stanford) |
||
May 8 (Tue) |
10 am |
D. Hillis (Zoology, U. Texas Austin) |
|
2 pm |
D. Hillis (Zoology, U. Texas Austin) |
||
May 9 (Wed) |
10 am |
A. Wagner (Biology, U. New Mexico) |
|
3:30 pm |
ITP Picnic |
All welcome ! |
|
May 10 (Thurs) |
10 am |
Modular evolution in the basic helix-loop-helix family of transcriptional regulators |
W. Atchley (Genetics, NC State) |
2:00 pm |
Discussion |
|
|
May 11 (Fri) |
10 am |
Genomic biodiversity: Molecular evolution meets functional genomics |
D. Pollock (Biology, LSU) |
11 am |
The origin and significance of amino acid associations in proteins |
W. Atchley (Genetics, NC State) |
Phylogeny II: Multiple alignment, tree building, and tree statistics (section leader: R. Goldstein)
date |
time |
Event |
speaker |
May 14 (Mon) |
10 am |
Accounting for phylogenetic uncertainty in comparative studies: MCMC and MCMCMC approaches |
M. Pagel (Zoology, U. Reading) |
3:30 pm |
Discussion |
|
|
May 15 (Tue) |
10 am |
P. Higgs (Biology, U. Manchester) |
|
3:30 pm |
R. Goldstein (Biophysics, U. Michigan) |
||
May 16 (Wed) |
10 am |
A. Kluge (Biology, U. Michigan) |
|
3:30 pm |
Discussion |
|
|
May 17 (Thurs) |
10 am |
D. Sankoff (Mathematiques et Statistique, U. Montréal) |
|
2:00 pm |
Panel Discussion on the Origin of Life |
F. Dyson (IAS, Princeton) |
|
May 18 (Fri) |
10 am |
D. Sankoff (Mathematiques et Statistique, U. Montréal) |
Phylogeny III: Beyond trees: Horizontal transfer and evolution networks (section leader: R. Goldstein)
date |
time |
Event |
speaker |
May 21 (Mon) |
10 am |
W. Fitch (Biology, UC Irvine) |
|
3:30 pm |
Discussion |
|
|
May 22 (Tue) |
10 am |
L. Peliti (Fisiche, Università di Napoli) and D. Pollock (Biology, LSU) |
|
May 23 (Wed) |
10 am |
Repetitions in genealogical trees: predictions of a simple model |
B. Derrida (Physique, Ecole Normale Supérieure) |
3:30 pm |
Discussion |
|
|
May 24 (Thurs) |
10 am |
Use of high-density arrays in the analysis of human chromosome 21 sequences |
K. Frazer (Perlegen) |
3:30 pm |
P. Higgs (Biology, U. Manchester) |
||
May 25 (Fri) |
10 am |
J. Boore (DOE Joint Genome Institute) |
Population Genetics I: Microbial evolution (section leader: M. Lassig)
date |
time |
Event |
speaker |
May 28 (Mon) |
---- |
Memorial Day Holiday |
---- |
May 29 (Tues) |
3:30 pm |
E. Koonin (NCBI, NIH) |
|
May 30 (Wed) |
10 am |
Laboratory-scale Darwinian Evolution -- Where is the physics ? |
H. Levine (physics, UCSD) |
May 31 (Thur) |
10 am |
L. Chao (biology, UCSD) |
|
3:30 pm |
Discussion |
|
|
June 1 (Fri) |
10:00 am |
B. Drossel (physics, Tel-Aviv) |
Population Genetics II: Theory and Model approaches (section leader: M. Lassig)
date |
time |
Event |
speaker |
June 4 (Mon) |
10:00 am |
P. Hammerstein (theoretical biology, Berlin) |
|
3:30 pm |
Discussion |
|
|
June 5 (Tues) |
10:00 am |
A. Kondrashov (NCBI, NIH) |
|
3:30 pm |
M. Rost (physics, Köln) |
||
June 6 (Wed) |
10:00 am |
T. Ohta (Mishima) |
|
3:30 pm |
A. Kondrashov (NCBI, NIH) |
||
June 7 (Thu) |
10:00 am |
D. Thaler (Rockefeller U) |
|
3:30 pm |
Evolution beyond landscapes: Robustness of gene regulation and the speed of speciation |
S. Bornholdt (Kiel) |
|
4:15 pm |
Spontaneous Speciation and Survival in extremely harsh stochastic environments |
S. Solomon (Jerusalem) |
|
June 8 (Fri) |
10 am |
Bridging the gap between phenotypic and genetic models of evolutionary adaptation |
P. Hammerstein (theoretical biology, Berlin) |
2:00 pm |
Discussion |
|
Population Genetics III: Ecology and Coevolution (section leader: M. Lassig)
date |
time |
Event |
speaker |
June 11 (Mon) |
10:00 am |
Roger Nisbet (UC Santa Barbara) |
|
June 12 (Tues) |
10:00 am |
Alan McKane (Manchester) |
|
11:00 am |
M. Lassig (physics, Köln) |
||
June 13 (Wed) |
10:00 am |
Scaling in the Spatial and Abundance Distribution of Species |
Annette Ostling (UC Berkeley) |
3:30 pm |
Antony Zee (ITP) |
||
June 14 (Thu) |
10:00 am |
Michael Rosenzweig (University of Arizona) |
|
3:30 pm |
discussion |
|
|
June 15 (Fri) |
10 am |
Perspectives at the Interface of Biology and Statistical Physics |
Mehran Kardar (MIT) |