KITP Program: Evolution of Molecular Networks (January 16 - April 13, 2007)
Coordinators: Eric Davidson, Michael Lässig, Tomoko Ohta, Nikolaus Rajewsky, Stephen Small

Evolution of
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Speakers: Please lend your transparencies to the KITP staff members in the front office (Rm 1102) for scanning, or see us about file upload.

Time Speaker Title
1/17, 10:00 a.m. Prof. Michael Lässig
(University of Cologne & KITP)
Prof. Nikolaus Rajewsky
(MDC-Berlin & KITP)
Introduction to the Workshop
1/17, 10:30 a.m. Prof. Doron Lancet
Weizmann Institute & KITP
Life's Origin: What's the Real Question?[Slides][Podcast][Aud][Cam]
1/18, 10:00 a.m. Prof. Jack Szostak
Harvard Medical School
The Origin of Life and the Emergence of Darwinian Evolution[Slides][Podcast][Aud][Cam]
1/18, 3:30 p.m. Dr. Giovanni Murtas
University of Rome & KITP
The Semi-synthetic "Minimal Cell": A Model for Early Living Cells[Slides][Podcast][Aud][Cam]
1/19, 10:00 a.m. Prof. Jeffrey Bada
Prebiotic Synthesis in Planetary Atmospheres[Slides][Podcast][Aud][Cam]
1/19, 3:30 p.m. Prof. Doron Lancet
Weizmann Institute & KITP
Lipid World and Systems Prebiology[Slides][Podcast][Aud][Cam]
1/22, 10:00 a.m. Gerald Joyce
Scripps Research Institute
Recreating the RNA World in the Laboratory[Slides][Podcast][Vid][Aud][Cam]
1/24, 10:00 a.m. Ivan Matic
Necker Medical School, Paris
Evolution of Mutation Rates in Bacteria[Slides][Podcast][Aud][Cam]
1/24, 3:30 p.m. Ivan Matic
Necker Medical School, Paris
Evolution of Mutation Rates in Bacteria, part II[Podcast][Aud]
1/25, 10:00 a.m. Sander Tans
AMOLF, Amsterdam & KITP
Tracing Evolution in Empirical Fitness Landscapes[Podcast][Aud][Cam]
1/25, 2:00 p.m. Hao Li
Yeast Transcriptional Networks- Dynamics and Evolution[Podcast][Aud][Cam]
1/25, 3:30 p.m. Ralf Bundschuh
Ohio State University & KITP
An Evolutionary Hypothesis and Computational Identification of Insertional RNA Editing Sites[Slides][Podcast][Aud][Cam]
1/26, 10:00 a.m. Andrew Murray
What Sets Evolutionary Rates: Experiment and Theory[Podcast][Aud][Cam]
1/26, 2:00 p.m. Andrew Murray
What Sets Evolutionary Rates: Experiment and Theory, part II[Podcast][Aud][Cam]
1/26, 4:00 p.m. Hao Li
Yeast Transcriptional Networks- Dynamics and Evolution, part II[Podcast][Aud][Cam]

Simons Center for Systems Biology / KITP Longevity Meeting
1/29, 10:00 a.m. Stuart Kim
Systems Biology of C. Elegans[Slides][Podcast][Aud][Cam]
1/29, 12:15 p.m. Arnold Levine
Sex, Food, Stress, Longevity: the Connections[Podcast][Aud][Cam]
KITP Blackboard Lunch
1/29, 2:30 p.m. Gurinder Atwal
Genomic Stability, Selection and Longevity[Podcast][Aud][Cam]
1/29, 4:00 p.m. Arnold Levine
Single Nucleotide Polymorphisms in the p53 Pathway: Their Impacts upon Cancer and Fecundity
1/30, 10:30 a.m. Roy Kishony
Drug Interaction and Resistance
1/30, 2:00 p.m. Gyan Bhanot
mtDNA Markers for Longevity in Japan, Selection and Genetic Drift[Podcast][Aud][Cam]
1/30, 3:00 p.m. Todd Riley
The Properties of p53 Transcription Factor Binding Sites[Podcast][Aud][Cam]
1/31, 10:00 a.m. Michael Elowitz
Noise Driven Transient Differentiation System
1/31, 2:00 p.m. Stuart Kim
Genome-wide View of Aging Gene Networks[Slides][Podcast][Aud][Cam]
1/31, 4:00 p.m. Harlan Robins
Fred Hutchinson Cancer Research Center
Isochores: the Origins are at the Ends[Podcast][Aud][Cam]
2/01, 10:00 a.m. Susi Remold
University of Louisville
Genetic Context Dependence Diversifies Evolving Microbial Populations[Slides][Podcast][Aud][Cam]
2/01, 1:30 p.m. Michael Krasnitz
Influenza Virus with a Low Mutation Rate, but Surprisingly Great Longevity
2/01, 2:15 p.m. Raul Rabadan
Influenza Virus, High Mutation Rate and Ubiquitous Chromosome Changes Lead to Great Longevity
2/01, 3:00 p.m. Jiri Vanicek
Herpes Virus and Persistence/Latency over a Lifetime in Humans

Focus Week: Genome Expansion and Population Genetics
2/05, 10:00 a.m. Tomoko Ohta
National Inst. Genetics
Population Genetics of Gene Regulation and Gene Duplication[Slides][Podcast][Aud][Cam]
2/05, 3:30 p.m. Michael Lässig
University of Cologne & KITP
Genomic Fitness Landscapes and Seascapes[Slides][Podcast][Aud][Cam]
2/06, 10:00 a.m. Austin Hughes
University of South Carolina
Gene Duplication and the Evolution of Novel Protein Functions[Podcast][Aud][Cam]
2/06, 11:00 a.m. Wen-Hsiung Li
University of Chicago
Gene Conversion and Codon Usage Bias in the Evolution of Yeast Duplicate Genes[Slides][Podcast][Aud][Cam]
2/07, 10:00 a.m. Hideki Innan
SOKEN, Kanagawa
Comparative Genomics, Duplication, and Coevolution of Duplicates[Slides][Podcast][Vid][Aud][Cam]
2/07, 11:00 a.m. Manyuan Long
University of Chicago
New Genes behind Males: The Patterns and Phenotypes of Gene Duplicates[Podcast][Aud][Cam]
2/08, 10:00 a.m. Dominic Grün
University of Köln & KITP
Genome Evolution by Repeat Duplication[Slides][Podcast][Aud][Cam]
2/08, 11:00 a.m. Gerton Lunter
University of Oxford & KITP
Adaptive Evolution in Dark Genomic Matter? Evidence for Positive Selection in Human Non-coding DNA[Podcast][Aud][Cam]
2/08, 3:30 p.m. Michael Desai
How Asexual Populations Adapt[Slides][Podcast][Aud][Cam]
2/09, 10:00 a.m. Sergey Gavrilets
University of Tennessee
Fitness Landscapes, Gene Duplication, and Speciation

2/12, 10:30 a.m. Eric Davidson
Principles of Developmental Gene Regulation[Podcast][Aud][Cam]
2/12, 4:00 p.m. Stephen Small
Tutorial: Manipulating Genes in Drosophila[Podcast][Aud][Cam]
2/13, 10:00 a.m. Eric Davidson
The Sea Urchin Endomesoderm Gene Regulatory Network as an Explanation of Developmental Phenomenology[Podcast][Aud][Cam]
2/13, 3:00 p.m. Mihaela Zavolan
University of Basel & KITP
Computational Methods for Studying mRNA Diversity[Slides][Podcast][Aud][Cam]
2/14, 10:00 a.m. Stephen Small
Gradients, Networks, and Evolution in Insects[Podcast][Aud][Cam]
2/14, 3:30 p.m. Stephen Small
Gradients, Networks, and Evolution in Insects, cont'd[Podcast][Aud][Cam]
2/15, 10:00 a.m. Martin Kreitman
University of Chicago
Variation and Evolution of Segmentation in Drosophila[Slides][Podcast][Aud][Cam]
2/15, 3:30 p.m. Terry Hwa
Aspects of Bacterial Gene Regulation and Evolution[Slides][Podcast][Aud][Cam]
2/16, 10:00 a.m. Curt Callan
Princeton & KITP
A Likeli(hood) Story: Precise Modeling of Transcription Factor-DNA Interaction from High-Throughput Binding Assays[Slides][Podcast][Aud][Cam]
2/16, 11:00 a.m. Ville Mustonen
Univ. Koeln & KITP
Fitness Landscapes of Transcription Factor Binding Sites[Podcast][Aud][Cam]
2/16, 3:00 p.m. Marko Djordjevic
Ohio State University & KITP
Using in Vitro Selection to Infer Transcription Regulatory Networks[Podcast][Aud][Cam]
2/20, 10:00 a.m. Eric Davidson
Animal Evolution[Podcast][Aud][Cam]
2/20, 10:00 a.m. Eric Davidson
Animal Evolution, cont'd[Podcast][Aud][Cam]
2/21, 10:00 a.m. Stephen Small
Insect Evolution[Podcast][Aud][Cam]
2/21, 4:00 p.m. Gary Ruvkun
Massachusetts General Hospital
Worlds within the Tiny RNA World[Podcast][Aud][Cam]
2/22, 10:00 a.m. Erik van Nimwegen
University of Basel & KITP
Computational Annotation of Regulatory Sites[Slides][Podcast][Aud][Cam]
2/23, 10:00 a.m. Uwe Ohler
Duke University & KITP
Variation and Evolution of Core Promoters[Slides][Podcast][Aud][Cam]
2/26, 10:00 a.m. Mike Levine
UC Berkeley
Gene Networks for Fly Gastrulation and Sea Squirt Cardiogenesis[Podcast][Aud][Cam]
2/26, 12:15 p.m. Michael Lässig
University of Cologne & KITP
The Arrow of Time in Biology[Podcast][Aud][Cam]
KITP Blackboard Lunch
2/26, 3:00 p.m. Eric Siggia
Evolution of Antibiotic Resistance in S. Aureus[Podcast][Aud][Cam]
2/27, 10:00 a.m. Marie-Anne Felix
Institut Jacques Monod
Robustness and Evolution of the Caenorhabditis Vulva Signaling Network[Slides][Podcast][Aud][Cam]
2/27, 3:00 p.m. Ulrich Gerland
Ludwig Max. Univ. & KITP
Evolutionary Selection between Alternative Modes of Gene Regulation[Slides][Podcast][Aud][Cam]
2/28, 10:00 a.m. David Arnosti
Michigan State University
Deciphering a Cis-regulatory Transcriptional Grammar: a Bottom-up Approach[Podcast][Aud][Cam]
2/28, 4:00 p.m. Angela Stathopoulos
Dorsoventral Patterning of the Drosophila Early Embryo
3/01, 4:00 p.m. Kim Sneppen
Nordita & KITP
Transcription Regulation in Temperate Phages: Mechanisms, Functions, and Evolution[Podcast][Aud][Cam]
3/02, 10:00 a.m. Joel Rothman
Networks for Cell Fate Specification and Reprogramming in C. elegans Embryos[Podcast][Aud][Cam]
3/05, 10:00 a.m. Eugene Koonin
National Inst. of Health
Origin and Evolution of Eukaryotes: the Role and Fate of Introns[Slides][Podcast][Aud][Cam]
3/05, 2:00 p.m. Erik van Nimwegen
Univ. Basel & KITP
Inferring Protein-Protein Interactions from Aminoacid Sequences: Application to Two-component Systems[Slides][Podcast][Aud][Cam]
3/05, 3:30 p.m. Shamil Sunyaev
Harvard Medical School & KITP
Functional Importance and Selective Constraints in Human Non-coding DNA[Slides][Podcast][Aud][Cam]
3/06, 10:00 a.m. Andreas Wagner
University of Zurich
Is There a Network Biology?[Podcast][Aud][Cam]
3/06, 11:15 a.m. Eugene Koonin
National Inst. of Health
The Cosmological Model of Eternal Inflation and the Transition from Chance to Biological Evolution in the History of Life[Slides][Podcast][Aud][Cam]
3/07, 10:00 a.m. Fabio Piano
Early Embryogenesis in C. elegans and Related Nematodes[Podcast][Aud][Cam]
3/07, 2:00 p.m. Kris Gunsalus
Functional Genomics in C. Elegans: Genome-Scale Approaches in an Animal Reference Species[Podcast][Aud][Cam]
3/08, 10:00 a.m. Kris Gunsalus
Molecular Machines and Networks in C. Elegans Early Development[Podcast][Aud][Cam]
3/08, 4:00 p.m. Lisa Stubbs
Rapidly Evolving Transcription Factors and Selection for Change in Vertebrate Regulatory Networks[Podcast][Aud][Cam]
3/09, 10:00 a.m. Mihaela Zavolan
Univ. of Basel & KITP
(micro)RNomics: Identification and Expression Analysis of Small Regulatory RNAs[Slides][Podcast][Aud][Cam]
3/09, 11:30 a.m. Eugene Koonin
National Inst. of Health
The Origin of Viruses and Cells: a 'Virus-first' Concept[Slides][Podcast][Aud][Cam]
3/12, 10:00 a.m. Giuseppe Macino
Univ. Roma
RNA Directed Post Trancriptional Silencing[Podcast][Aud][Cam]
3/12, 2:00 p.m. Oliver Hobert
Decoding the Regulatory Architecture of Cell Type Specification in C.elegans[Podcast][Aud][Cam]
3/13, 10:30 a.m. Nikolaus Rajewsky
MDC-Berlin & KITP
microRNA Targets[Podcast][Aud][Cam]
3/13, 2:00 p.m. Fabio Piano
3' UTRomics in C. elegans[Podcast][Aud][Cam]
3/14, 10:00 a.m. Shamil Sunyaev
Harvard Medical & KITP
Functional Importance and Selective Constraints in Human Non-coding DNA, Continued[Podcast][Aud][Cam]
3/14, 11:15 a.m. Peter Arndt
Max Planck & KITP
The Evolutionary Processes Shaping the Human Genome[Podcast][Aud][Cam]
3/14, 4:00 p.m. Artemis Hatzigeorgiou
University of Penn & KITP
Identification and Editing of microRNAs[Slides][Podcast][Aud][Cam]
3/15, 10:00 a.m. Giuseppe Macino
Univ. Roma
What is the Natural Function of Gene Silencing?[Podcast][Aud][Cam]
3/15, 2:00 p.m. Massimo Vergassola
Institute Pasteur & KITP
Small non-coding RNAs in Bacteria[Slides][Podcast][Aud][Cam]
3/19, 10:00 a.m. Pamela Green
University of Delaware
Elucidating the Small RNA Profile of the Transcriptome[Podcast][Aud][Cam]
3/19, 2:00 p.m. Herve Isambert
Institut Curie & KITP
(1) Gene Regulation by RNA Switches and Knots (2) A Duplication-divergence Model for Network Evolution[Slides][Podcast][Aud][Cam]
3/20, 10:00 p.m. Kevin Chen
Macro- and Micro Evolution of Gene Regulation Mediated by MicroRNAs[Podcast][Aud][Cam]
3/21, 10:00 a.m. Scott Tenenbaum
SUNY, Albany
Using RNA Binding Proteins and MicroRNAs Targeting to Identify cis Regulatory Elements in RNA[Podcast][Aud][Cam]
3/26, 10:00 a.m. Sergei Maslov
Brookhaven Natl. Lab & KITP
Protein Binding Networks: from Topology to Kinetics[Slides][Podcast][Aud][Cam]
3/27, 10:00 a.m. Sarah Teichmann
MRC Laboratory of Molecular Biology
Evolvability and Protein Divergence in Homo Sapiens[Slides][Podcast][Aud][Cam]
3/27, 3:30 p.m. Johannes Berg
University of Cologne & KITP
Clusters, Motifs, and Cross-species Correlations in Biological Networks[Slides][Podcast][Aud][Cam]
3/28, 10:00 a.m. Jin Wang
SUNY Stony Brook & KITP
Robustness and Potential Landscapes of Cellular Networks[Podcast][Aud][Cam]
3/28, 11:15 a.m. Fengzhu Sun
Inference of Protein Functions and Domain Interactions from Protein Interactions[Slides][Podcast][Aud][Cam]
3/29, 10:00 a.m. Ilya Nemenman
Does Topology of a Biochemical Network Influence its Function?[Slides][Podcast][Aud][Cam]
3/29, 11:15 a.m. Raya Khanin
University of Glasgow & KITP
How Scale-free are Biological Networks?[Slides][Podcast][Aud][Cam]
4/02, 10:00 a.m. Trisha Wittkopp
University of Michigan
Genetic Basis of Regulatory Variation within and between Species[Podcast][Aud][Cam]
4/03, 10:00 a.m. Michael Doebeli
Adaptive Diversification: Theory and Experiments[Slides][Podcast][Aud][Cam]
4/03, 3:00 p.m. Peter Swain
McGill University & KITP
Stochasticity and Designs of Biochemical Networks[Podcast][Aud][Cam]
4/04, 10:00 a.m. Philip Benfey
Duke University
Getting to the Root of Cell Identity
4/05, 10:00 a.m. Eugene Shakhnovich
Harvard & KITP
How Protein Function Shapes Biological Evolution[Podcast][Aud][Cam]
4/05, 4:00 p.m. Dirk Holste
Institute of Molecular Pathology, Vienna
RNA Splicing: At the Interface of Genomics, Networks, and Evolution[Slides][Podcast][Aud][Cam]
4/09, 10:00 a.m. Gary Litman
U of South Florida
Alternative Mechanisms of Immune Diversity[Slides][Podcast][Vid][Aud][Cam]
4/09, 12:15 p.m. Nikolaus Rajewsky
MDC-Berlin & KITP
Evolution of Molecular Networks[Podcast][Aud][Cam]
KITP Blackboard Lunch
4/10, 10:00 a.m. Ken Kosik
Evolution of the Synapse
4/11, 10:00 a.m. Michael Travisano
U of Minnesota
Sources of Biological Diversity[Podcast][Aud][Cam]
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