Infobio - Daily Schedule

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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.

Introduction

Sequence Analysis

RNA Folding

Protein Folding

Genomics

Molecular Networks

Molecular Evolution

Molecular Phylogeny

Population Genetics

Summary


Introduction (section leader: T. Hwa)

date

time

event

speaker

Jan 16 (Tues)

2pm

Introduction and overview

T. Hwa (physics, UCSD)

Jan 17 (Wed)

10 am

Intro to molecular biology I

G. Stormo (biology, WUSTL)

 

2pm

Intro to molecular biology II

"

Jan 18 (Thur)

10am 

Intro to molecular biology III

''

 

2pm

Evolution, Phylogeny, and Population Biology I 

C. Wills (biology, UCSD)

Jan 19 (Fri)

10am

Evolution, Phylogeny, and Population Biology II

''

Sequence Analysis (section leader: R. Bundschuh)

date

time

event

speaker

Jan 22 (Mon)

2:30pm

Statistics of local sequence alignment 

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 

R. Bundschuh (physics, UCSD)

 

2pm

Significance of probabilistic sequence alignments 

M. Lässig (physics, Universität zu Köln)

Jan 25 (Thur)

10:30am

Sequence and Structure Matching: Applications of Probability Theory 

A. Dembo (statistics & math, Stanford)

Jan 26 (Fri)

10am

Probabilistic alignment and hidden Markov models 

Y.-K. Yu (physics, Florida Atlantic Univ.)

Jan 29 (Mon)

10 am

Multiple alignemnt and profiles

M. Gribskov (UCSD and SDSC)

Jan 30 (Tues)

10 am

DNA Markov Models for Gene Identification

M. Borodovsky (biology & math, Georgia Tech)

 

2 pm

Discussion: Statistical analysis of prokaryote genomes

R. Ramaswamy (physics, New Delhi) 
B. Hao (physics, Beijing)

RNA folding (section leader: R. Bundschuh)

date

time

event

Speaker

Jan 31 (Wed)

10am

Tutorial: RNA folding: structure, energy, and statistics

R. Bundschuh (physics, UCSD)

 

2 pm

Discussion: Effects of sequence disorders on DNA and RNA

L. Tang (physics, HKBU), 
R. Bundschuh (physics, UCSD)

Feb 1 (Thur)

10am

Discussion: Excluded-volume effect on DNA and RNA

D. Moroz (physics, UCSD), 
D. Mukamel (physics, TelAviv) 
H. Orland (physics, Saclay)

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

Tutorial: Intorduction to protein folding

H. Orland (physics, Saclay)

Feb 5 (Mon)

2 pm

RNA structure prediction using phylogenetic  information

G. Stormo (biology, WUSTL)

Feb 6 (Tues)

10 am

RNA Structure and Molecular Evolution

P. Schuster (Vienna)

Feb 7 (Wed)

10 am 

Unfolding single RNA molecules by force

I. Tinoco (Berkeley)

 

2 pm

Discussion: Unfolding of DNA and RNA

D. Lubensky (physics, Harvard), 
M. Mezard (physics, Orsay) 
U. Gerland (physics, UCSD)

Feb 8 (Thur)

10 am 

Experimental approaches for probing RNA folding pathways

S. Woodson (biophysics, Johns Hopkins)

 

2 pm

Modeling RNA folding paths

H. Isambert (Strassbourg)

Feb 9 (Fri)

10 am

RNA Evolution and the theory of neutral networks

P. Schuster (Vienna)

 

2 pm

Tutorial on RNA Tertiary Interaction

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

Simple Statistical Mechanical Models of Protein Folding

K. Dill (biophysics, UCSF)

Feb 13 (Tue)

10 am

Fast Kinetics and Mechanisms in Protein Folding

W. Eaton (NIH)

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

S. Jackson (chemistry, Cambridge)

 

2:30 pm

Discussion: Aspects of Cold Unfolding, Loop Entropies of Compact Polymers

K. Sneppen (physics, NORDIDA) 
J. Kondev (physics, Brandeis)

Feb 16 (Fri)

10 am 

1. Tutorial on Proteins
2. Protein Folding Rate and Protein Folding Nucleus

A. Finkelstein (IPR, RAS)

 

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

Sequence Determinants of Protein Folding  and Evolution

R. Sauer (biology, MIT)

Feb 20 (Tue)

10am

Seeing Is Believing: Transition States and Intermediates in Realistic Folding Models

E. Shakhnovich (chemistry, Harvard)

 

2 pm

Understanding Proteins in their Evolutionary Context

R. Goldstein (Biophys, Michigan)

Feb 21 (Wed)

10am

Prediction and Design of Protein Structures and Folding Mechanisms

D. Baker (biochem, U of Washington)

Feb 22 (Thurs)

10am

RNA folding and protein misfolding

S. Doniach (physics, Stanford)

 

2 pm

Discussion on Design: Designability of Protein structures: on and  off Lattice, Functional Protein Design

C. Tang (NEC) 
C. Zeng (Physics, GWU) 
L. Lai (Chemistry, PKU)

Feb 23 (Fri)

10am

Computational and Experimental Aspects of Protein Design

S. Mayo (biology, Cal Tech)

Protein Folding III: prediction & structural genomics (section leader: H. Orland)

date

time

event

speaker

Feb 26 (Mon)

2 pm 

Pairwise Contact Potentials Can Not Fold Proteins

E. Domany (Physics, Weizmann)

 

2:30pm

Protein Structure Designability and Alphabet

N. Buchler

Feb 27 (Tue)

10 am

Physical, Biological and Algorithmic Approaches to Protein Folding

M. Levitt (biology, Stanford)

 

2 pm

Chaperonin Mediated Protein Folding

D. Thirumalai (Chemistry, Maryland)

Feb 28 (Wed)

10 am

Integrative Genomics: Surveys of a Finite Parts List

M. Gerstein (biophys & biochem, Yale)

Mar 1 (Thurs)

10 am

Theory and Applications of Protein Threading

S. Bryant (NCBI)

Mar 2 (Fri)

9:30 am 

Protein Folding - What's the Question?

G. Rose (biophys & biophys chem, JHU)

Genomics I: Gene and DNA motif finding (section leader: H. Li)

date

time

event

speaker

Mar5 (Mon)

10am 

Introduction to genome harvesting

D. Lancet (genome center, Weizmann)

Mar 6 (Tue)

10am

Building a Dictionary for DNA: Decoding the Regulatory Regions of a Genome

H. Li (biophysics, UCSF)

Mar 7 (Wed)

10 am

DNA-protein interactions: experiments, models and pattern discovery algorithms

G. Stormo (biology, WUSTL)

Mar 8 (Thurs)

10am

Detecting non-adjoining correlations within signals in DNA

V. Bafna (Celera)

 

2pm

The Conserved Exon Method for Gene Finding

''

Mar 9 (Fri)

10am 

Tutorial: Gibbs sampler and MCMC mehods

J. Liu (Statistics, Harvard)

 

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

Finding Genes and Finding Introns in Eukaryotic Genomes

C. Burge (biology, MIT)

 

3:30 pm 

On finding the 'parts lists' for worms and humans

P. Green (CS and biology, U. Washington)

Mar 13 (Tue)

10 am

Genome sequencing and assembly

''

 

2 pm

Cool things about RNA

C. Burge (biology, MIT)

Mar 14 (Wed)

10 am

Clustering analysis of DNA microarray data

E. Domany (physics, Weizmann)

 

4 pm 

MRL seminar: Algorithmic Self-Assembly of DNA

E. Winfree (CalTech)

Mar 15 (Thur)

10 am

Thinking about genome system architecture

J. Shapiro (biology, Chicago)

 

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

Molecular mechanisms of transcription control

P. von Hippel (biology, U. Oregon)

 

2pm 

Discussion: Regulatory motif finding via comparative genomics

N. Rajewsky (biophysics, Rockefeller); 
W. Krivan (Karolinska Inst, Sweden, & ZymoGenetics Inc, Seattle)

Mar 20 (Tue)

10am

Helicase mechanisms and the `coupling' of regulatory components within macromolecular machines

P. von Hippel (biology, U. Oregon)

 

3:30pm

Salt-effects on DNA-histone stability

R. Netz, Max-Planck Inst.

Mar 21 (Wed)

11 am

Analysing Interactions Among Amino Acids, Genes, etc

A. Lapedes, LANL

 

1 pm

Chromatin structure and transcriptional regulation

J. Kadonaga (biology, UCSD)

Mar 22 (Thurs)

10 am 

Olfaction: from genome mining to molecular recognition statistics

D. Lancet (genome center, Weizmann)

 

2 pm

New surprises for an old enzyme: structure and function of a bacterial ribonuclease P

T. Pan (biology, Chicago)

 

3:30pm

Genome Annotation and Protein Structure

S. Brenner, UC Berkeley

Mar 23 (Fri)

10am 

Exploring and Exploiting RNA-Ligand Interactions

Y. Tor (biochemistry, UCSD)

 

2 pm

Thermodynamics of tertiary RNA folding: metal ions, urea and a thermophilic ribozyme

T. Pan (biology, Chicago)

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

M  Savageau (biology, Michigan)

April 17(Tue)

 

10am 

Engeneering synthetic networks/P53 network

M. Elowitz (biophysics, Rockefeller)

 

2pm

Tutorial and stat mec of the lambda phage switch

K. Sneppen (physics, NORDITA)

April  18(Wed)

10 am

Modelling  bacteriophage T7 development

D. Endy  (Mol. Sci. Insti.)

April  19(Thurs)

10am

Discussion: Gene expression modeling & analysis

S. Liang (physics, NASA Ames) 
J. Hertz (physics, NORDITA)

 

3 pm

Analysis of Microarray Data for the Clinic

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)

date

time Event speaker
April  30  (Mon) 10am  RNA-Catalyzed Chemistry: The Winding Road to RNA Replication P. Unrau (biology, Simon Fraser)
  2pm Phenomenological Theory of Survival and Non-Darwinian Evolution M. Azbel (physics, Tel-Aviv)
May 1 (Tue) 10am  Consensus of Amino-Acid Chronology and Evolution of the Genetic Code E. Trifonov (biophysics, Weizmann)
  11am Quantitative and Experimental Tests of the Origin and Evolution of the Genetic Code L. Landweber (biology, Princeton)
  2 pm Discussion on the Genetic Code M. DiGiulio, E. Trifonov, and L. Landweber
May 2 (Wed) 10 am Nature's Anomolies: Molecular Evolution of Scrambled Genes and RNA Editing L. Landweber (biology, Princeton)
May 3 (Thurs) 10am Mutational Patterns and Evolution of Genome Size D. Petrov (biology, Stanford)
  3.30pm Molecular Evolution and Statistical Mechanics L. Peliti and U. Gerland
May 4 (Fri) 10 am Mutational Patterns and Evolution of GC Content in Eukaryotes D. Petrov (biology, Stanford)
  2:30pm Modeling Correlated Sequence Mutations P. Arndt (physics, UCSD)

Phylogeny I:Protein evolution; introduction to phylogenetic trees (section leader: R. Goldstein)

date

time

Event

speaker

May 7 (Mon)

10 am 

Introduction to phylogenetics methods

P. Higgs (Biology, U. Manchester)

 

2 pm

The geometry of the space of phylogenetic trees

S. Holmes (Statistics, Stanford)

May 8 (Tue)

10 am 

How do we know if phylogenetic inference works?

D. Hillis (Zoology, U. Texas Austin)

 

2 pm

Computational approaches to big phylogenetic problems

D. Hillis (Zoology, U. Texas Austin)

May 9 (Wed)

10 am

Robustness and redundancy in large genetic networks

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 

RNA structure, evolution, and phylogenetics

P. Higgs (Biology, U. Manchester) 

 

3:30 pm

Modeling evolution at the amino acid level

R. Goldstein (Biophysics, U. Michigan)

May 16 (Wed)

10 am

Parsimony in phylogenetic inference

A. Kluge (Biology, U. Michigan)

 

3:30 pm

Discussion

 

May 17 (Thurs)

10 am

Phylogenetics based on gene order

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

Models and tests for gene order evolution

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 

Predicting future evolution in influenza virus

W. Fitch (Biology, UC Irvine)

 

3:30 pm

Discussion

 

May 22 (Tue)

10 am 

Directed Discussion:   Neutrality and selection in evolution

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

Memes and the evolution of imitation

P. Higgs (Biology, U. Manchester) 

May 25 (Fri)

10 am

Comparative genomics at the joint genome institute: Molecular evolution at 20 million nucleotides per day

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

Phylogenomics of Protein Domains

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

Evolution Over Adaptive Landscapes in the RNA Virus Phi6

L. Chao (biology, UCSD)

 

3:30 pm

Discussion

 

June 1 (Fri)

10:00 am

Tutorial: Theories of Speciation

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

Economics in nature and the theory of evolutionary games

P. Hammerstein (theoretical biology, Berlin)

 

3:30 pm

Discussion

 

June 5 (Tues)

10:00 am

Models of sympatric speciation

A. Kondrashov (NCBI, NIH)

 

3:30 pm

Difference, distance and speciation

M. Rost (physics, Köln)

June 6 (Wed)

10:00 am

Near neutrality and its implications for evolution

T. Ohta (Mishima)

 

3:30 pm

Deleterious mutation as an evolutionary force

A. Kondrashov (NCBI, NIH)

June 7 (Thu)

10:00 am

The Generation and Fixation of Genetic Diversity

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

The Predictive Power of Simple Population Models

Roger Nisbet (UC Santa Barbara)

June 12 (Tues)

10:00 am

Evolutionary Dynamics of Multispecies Communities

Alan McKane (Manchester)

 

11:00 am

Dynamics and Topology of Species Networks

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

Matrix Field Theorists try to fold RNA

Antony Zee (ITP)

June 14 (Thu)

10:00 am

To Ecologists, Species Diversity is Like Gravity

Michael Rosenzweig (University of Arizona)

 

3:30 pm

discussion

 

June 15 (Fri)

10 am

Perspectives at the Interface of Biology and Statistical Physics
(provisory link to overheads of the talk)

Mehran Kardar (MIT)