KITP Program: Microbial and Viral Evolution (Jan 4 - Mar 25, 2011)
Coordinators: Santiago Elena, Michael Lässig, Luca Peliti, Paul Sniegowski

Scientific Advisor: Matthew Kane

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Time Speaker Title
1/05, 10:00 a.m. Organizers Introductory Remarks[Podcast][Aud][Cam]
1/05, 10:20 a.m. Christopher Marx
The Art/science of Experimental Evolution[Slides][Podcast][Aud][Cam]
1/06, 10:00 a.m. Rachel Whitaker
Evolutionary Dynamics in Wild Microbial Populations[Slides][Podcast][Aud][Cam]
1/07, 10:00 a.m. Paul Sniegowski
Univ. of Penn & KITP
Mutation Rates, Hitchhiking and Extinction in Asexuals
1/07, 2:00 p.m. Marty Einhorn
What's a Wiki Good For?[Podcast][Aud][Cam]
1/07, 2:15 p.m. Matt Kane
Funding Opportunities for Research in Biological Physics[Podcast][Aud][Cam]
1/10, 10:00 a.m. Jeff Gore
Cooperation and Cheating in Microbes[Podcast][Aud][Cam]
1/11, 10:00 a.m. Sergey Kryazhimskiy
Harvard & KITP
How Does Demography Affect Adaptation?[Slides][Podcast][Aud][Cam]
1/12, 10:00 a.m. Thane Papke
Haloarchaea: Recombination, Outcomes and Mechanisms[Podcast][Aud][Cam]
1/13, 10:00 a.m. Daniel Weinreich
Brown Univ. & KITP
The Simplest Questions of Adaptation I Know (and perhaps even some answers!)[Slides][Podcast][Aud][Cam]
1/14, 10:00 a.m. Eugene Shakhnovich
Harvard & KITP
Evolution on Physics-based Fitness Landscapes: Theory and Experiment[Podcast][Aud][Cam]
1/18, 10:00 a.m. Bonnie Bassler
Information Processing in Quorum Sensing Circuits[Slides][Podcast][Aud][Cam]
1/18, 2:00 p.m. Sheri Simmons
Marine Biological Laboratory & KITP
Diversity in Microbial Populations in the Wild[Slides][Podcast][Aud][Cam]
1/19, 10:00 a.m. Michael Desai
Harvard & KITP
Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations[Slides][Podcast][Aud][Cam]
1/19, 3:45 p.m. Namiko Mitarai
Niels Bohr Inst. & KITP
Choice of Synonymous Codons and Ribosome Traffic[Podcast][Aud][Cam]
1/20, 10:00 a.m. Kim Sneppen
Niels Bohr Inst. & KITP
Lessons From Phage Biology[Podcast][Aud][Cam]
1/20, 3:45 p.m. Daniel Weinreich
Brown Univ. & KITP
Tracking Evolutionary Trajectories of Sexual Populations[Slides][Podcast][Aud][Cam]
1/20, 3:45 p.m. Michael Lässig
Univ.of Cologne & KITP
Can Evolution Sense the Curvature of Fitness Landscapes?[Podcast][Aud][Cam]
1/21, 10:00 a.m. Arjan de Visser
Wageningen Univ. & KITP
Microbial Evolution on Empirical Fitness Landscapes[Slides][Podcast][Aud][Cam]
1/21, 11:00 a.m. Lei-Han Tang
Hong Kong Baptist
Regulation of Carbon Flow in Microbial Metabolism[Slides][Podcast][Aud][Cam]
1/24, 10:00 a.m. Lilia Perfeito
Univ. Cologne & KITP
Fitness Landscape of a Metabolic Pathway[Slides][Podcast][Aud][Cam]
1/25, 10:00 a.m. Erik van Nimwegen
Univ. of Basel & KITP
Looking for Macroscopic Laws in the Evolution of Genotypes and Phenotypes[Podcast][Aud][Cam]
1/26, 10:00 a.m. Joy Bergelson
Univ. Chicago & KITP
The Evolution of Gene-for-gene Interactions in a Plant-pathogen System[Podcast][Aud][Cam]
1/27, 9:30 a.m. Martin Weigt
Human Genetics Foundation & KITP
Interprotein Residue Contacts and Interaction Specificity in Bacterial Signal Transduction[Slides][Podcast][Aud][Cam]
1/27, 11:00 a.m. Alan Perelson
HIV: Data and Models[Slides][Podcast][Aud][Cam]
1/28, 10:00 a.m. Terry Hwa
On Growth, Antibiotic Resistance, and Evolution[Slides][Podcast][Aud][Cam]
1/31, 10:00 a.m. Ivan Matic
Univ. Paris
Environmental Tuning of Mutation Rates[Podcast][Aud][Cam]
2/01, 10:00 a.m. Berenike Maier
WWU Münster & KITP
The Type IV Pilus as a Multifunctional Bacterial Motor[Slides][Podcast][Aud][Cam]
2/02, 10:00 a.m. Isabel Gordo
Instituto Gulbenkian de Ciência & KITP
The Fitness Effects of Mutation in Escherichia Coli: The Good and the Bad[Podcast][Aud][Cam]
2/03, 9:30 a.m. Ana Margarida Sousa
Instituto Gulbenkian de Ciência & KITP
Epistasis and Compensatory Evolution of Antibiotic Resistance[Slides][Podcast][Aud][Cam]
2/03, 11:00 a.m. Olivier Tenaillon
Inserm U722
The Bases of Convergence in Experimental Adaptation[Slides][Podcast][Aud][Cam]
2/07, 10:00 a.m. Eugene Koonin
Tree of Life, Net of Life, Forest of Life - Where Are We?[Slides][Podcast][Aud][Cam]
2/07, 3:45 p.m. Gavin Sherlock
Stanford Medical
Watching Yeast Change: Using Genomics to Understand the Influence of Epistasis on the Adaptive Landscape[Slides][Podcast][Aud][Cam]
2/08, 9:30 a.m. Stephan Schiffels
Univ. Cologne & KITP
Emergent Neutrality in Adaptive Genome Evolution[Slides][Podcast][Aud][Cam]
2/08, 11:00 a.m. Aleksandra Walczak
The Effects of Negative Selection on the Evolution of Linked Sites[Slides][Podcast][Aud][Cam]
2/09, 9:30 a.m. Christian Schlötterer
Univ. Wien
New-generation Sequencing and the Detection of Selection in Drosophila and Its Endosymbionts
2/09, 11:15 a.m. Armita Nour Mohammad
Univ. Köln & KITP
Evolutionary Modes of Regulatory Sequences in Eukaryotes[Slides][Podcast][Aud][Cam]
2/10, 10:00 a.m. Edo Kussell
Dynamics of Bacterial Sequence Evolution
2/10, 4:00 p.m. Ha Youn Lee
Univ. Rochester & KITP
Modeling and Quantification of HIV-1 and SIV Intrahost Sequence Evolution[Slides][Podcast][Aud][Cam]
2/10, 5:00 p.m. Jose Fontanari
Univ. of Sao Paulo & KITP
On Cultural Evolution[Slides][Podcast][Aud][Cam]
2/14, 9:30 a.m. Nick Barton
IST Austria
Branching Processes in Population Genetics[Podcast][Aud][Cam]
2/14, 10:45 a.m. Daniel Weissman
Institute of Science and Technology & KITP
The Rate of Adaptation in Large Sexual Populations[Slides][Podcast][Aud][Cam]
2/15, 10:00 a.m. Sally Otto
Recombination and the Deleterious Hitchhiker[Slides][Podcast][Aud][Cam]
2/15, 11:00 a.m. Richard Neher
Sex, Draft, and Survival[Slides][Podcast][Aud][Cam]
2/15, 3:45 p.m. Nigel Goldenfeld
Two Problems in Microbial Genome Evolution: Diversification Fronts and the Evolution of Compositional Bias[Slides][Podcast][Aud][Cam]
2/16, 10:00 a.m. Santiago Elena
Experimental Evolution of Viruses: Model Systems and Questions[Slides][Podcast][Aud][Cam]
2/16, 3:45 p.m. Jonathan Miller
Okinawa Inst. & KITP
Genome Sequence Power-Laws <=> Recombination[Podcast][Aud][Cam]
2/17, 9:30 a.m. James Bull
Univ. Texas, Austin
Quasispecies and Lethal Mutagenesis: Concepts and Practice[Podcast][Aud][Cam]
2/17, 11:00 a.m. Eugene Koonin
The Virus World, Its Evolution, Evolution of Antiviral Defense, and the Role of Viruses in the Evolution of Cells[Slides][Podcast][Aud][Cam]
2/18, 9:30 a.m. Forest Rohwer
Virus Metagenomics[Slides][Podcast][Aud][Cam]
2/18, 11:00 a.m. Susi Remold
Univ. Louisville & KITP
Experimental Evolution of Host-Switching and Emergence of New Viruses[Slides][Podcast][Aud][Cam]
2/22, 10:00 a.m. Paul Turner
Evolution of Robustness[Slides][Podcast][Aud][Cam]
2/23, 9:30 a.m. Lindi Wahl
Univ. Western Ontario
Three Surprising Predictions From Modeling Evolution Experiments[Slides][Podcast][Aud][Cam]
2/23, 11:00 a.m. Marco Morelli
Glasgow Univ. & KITP
The Use of Ultradeep Sequencing for Characterizing Viral Populations[Podcast][Aud][Cam]
2/23, 5:00 p.m. Claus Wilke
Univ. Texas, Austin & KITP
Quasispecies vs Standard Population Genetics Models[Podcast][Aud][Cam]
2/24, 10:00 a.m. Alan Perelson
How to Model a Viral Infection: Hepatitis C Virus[Slides][Podcast][Aud][Cam]
2/24, 3:45 p.m. Sergei Maslov
Home Depot Model of Prokaryotic Evolution by Horizontal Gene Transfer[Slides][Podcast][Aud][Cam]
2/24, 4:45 p.m. Mark Gerstein
Biological Network Change and Evolution[Slides][Podcast][Aud][Cam]
2/25, 9:30 a.m. Philip Gerrish
Univ. New Mexico
Mutation Rate and the Maintenance of Cooperation[Podcast][Aud][Cam]
2/25, 11:00 a.m. Igor Rouzine
Tufts Univ. & KITP
Within-Host Dynamics HIV-1[Slides][Podcast][Aud][Cam]
2/25, 1:30 p.m. Ariel Weinberger
How Persisting Viruses Overcome Adaptive Immunity
2/28, 11:00 a.m. Julia Gog
Univ. of Cambridge & KITP
Simple Models for Influenza Antigenic Drift[Slides][Podcast][Aud][Cam]
02/28, 12:15 p.m. Santiago Elena
The Evolutionary Genetics of Emerging Viruses[Podcast][Aud][Cam]
KITP Blackboard Lunch
2/28, 4:00 p.m. Michael Lässig
Univ.of Cologne & KITP
Clonal Interference in the Evolution of Influenza[Podcast][Aud][Cam]
3/01, 9:30 a.m. Mario Fares
Trinity College
Dynamics of a Re-emerging Virus: Foot-and-Mouth Disease Virus[Podcast][Aud][Cam]
3/01, 11:00 a.m. Joshua Weitz
Georgia Tech.
Bacterial Fate Determination by Co-infecting Viruses[Slides][Podcast][Aud][Cam]
3/01, 4:00 p.m. Colin Parrish
Canine Parvovirus Origin and Evolution[Podcast][Aud][Cam]
3/01, 5:00 p.m. Thomas Leitner
Inferring HIV Epidemics from HIV Phylogenetics[Podcast][Aud][Cam]
3/02, 9:30 a.m. Catherine Macken
Migration Strategies for Pandemic Influenza in the USA[Slides][Podcast][Aud][Cam]
3/02, 11:00 a.m. Richard Neher
HIV-1 Intra-host Dynamics[Slides][Podcast][Aud][Cam]
3/02, 4:00 p.m. Leor Weinberger
Viral Gene Circuitry and Stochastic Noise in Viral Gene Expression (tentative)
3/02, 5:00 p.m. Santiago Elena
(Valencia, Spain & KITP)
Mario Fares
(Trinity College)
Discussion: What Does Experimental Evolution Teach About the Evolution of Emergent Viruses?[Podcast][Aud][Cam]
3/07, 10:00 a.m. Juliette de Meaux
Muenster, Germany: Westfaelische Wilhelms-Universität & KITP
Evolution of Flagellin Perception in Arabidopsis Thaliana and Its Relatives[Podcast][Aud][Cam]
3/07, 2:00 p.m. Bernhard Mehlig
Univ. Gothenburg
Linkage Disequilibrium in Populations of Variable Size[Slides][Podcast][Aud][Cam]
3/08, 9:30 a.m. Claus Wilke
Univ. Texas, Austin & KITP
Biophysical Constraints on Sequence Evolution[Podcast][Aud][Cam]
3/08, 11:00 a.m. Rita Maria Zorzenon dos Santos
UFPE-Brazil & KITP
Intra- and Inter-host Spread and Evolution of Tuberculosis[Aud][Cam]
3/09, 9:30 a.m. Shamil Sunyaev
Harvard Med.
Selection and Migration Inside the Host: Rapid Evolution of Human JC Virus Associated with Development of PML[Podcast][Aud][Cam]
3/09, 11:00 a.m. Joachim Krug
Univ. Cologne
Sign Epistasis and Evolutionary Accessibility[Slides][Podcast][Aud][Cam]
3/10, 9:30 a.m. Leonid Mirny
Accumulation of Deleterious Passenger Mutations in Cancer[Slides][Podcast][Aud][Cam]
3/10, 11:00 a.m. Trevor Lawley
Sanger Inst.
Application of High-throughput Genomics to Clostridium Difficile Evolution and Transmission[Podcast][Aud][Cam]
3/10, 5:00 p.m. Sergio Lukic
Rutgers/SUNY & KITP
Numerical Solutions to Complex Demographic Models[Slides][Podcast][Aud][Cam]
3/14, 9:30 a.m. Oskar Hallatschek
Clonal Interference in Structured Populations: Long Range Jumps Better than Sex[Podcast][Aud][Cam]
3/14, 11:00 a.m. David Nelson
Competition and Cooperation at Frontiers[Slides][Podcast][Aud][Cam]
3/15, 9:30 a.m. Michael Doebeli
Adaptive Diversification[Slides][Podcast][Aud][Cam]
3/15, 11:00 a.m. Ilya Nemenman
Emory Univ. & KITP
Evolutionary Dynamics in Heterogeneous Environments: Three Baby Steps[Slides][Podcast][Aud][Cam]
3/16, 9:30 a.m. Ville Mustonen
Wellcome Trust Sanger Institute & KITP
Quantifying Selective Forces from Allele Frequency Time-series Data of a Yeast Population Under Heat Stress[Podcast][Aud][Cam]
3/16, 11:00 a.m. Pleuni Pennings
Harvard & KITP
What Determines the Rate of Evolution of Resistance in HIV?[Slides][Podcast][Aud][Cam]
3/17, 9:30 a.m. Paul Rainey
Evolution of Bet Hedging[Podcast][Aud][Cam]
3/17, 11:00 a.m. Joao Xavier
Sloan-Kettering Inst.
Conflict and Cooperation in Microbes[Slides][Podcast][Vid][Aud][Cam]
3/17, 5:00 p.m. Bob Austin
Falling Uphill: Acceleration of the Emergence of Bacterial Antibiotic Resistance[Slides][Podcast][Aud][Cam]
3/21, 10:00 a.m. Dustin Brisson
UPenn & KITP
Niche Diversification and Gene-for-Gene Interactions in a Vertebrate-pathogen System
3/21, 11:30 a.m. Seth Blumberg
Disentangling the Transmission Dynamics of Human Monkeypox and Other Emerging Zoonoses[Slides][Podcast][Aud][Cam]
3/22, 9:30 a.m. Dirk Brockmann
Northwestern Univ.
Modelling Disease Dynamics on a Global Scale[Slides][Podcast][Vid][Aud][Cam]
3/22, 11:00 a.m. Ganna Rozhnova
Univ. de Lisboa & KITP
Stochastic Models of Infection Dynamics[Slides][Podcast][Aud][Cam]
3/23, 10:00 a.m. Frank Rosenzweig
Univ. Montana
E Unibus Plurum: How Biodiversity Evolves in a Simple, Homogenous Environment[Podcast][Aud][Cam]
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