Please look for references linked to the talks on Reference Material page.

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Week1
Time
Place*
Speaker
Title
Comments, Links,...
Tue, Jan 4




Nothing Scheduled
Wed, Jan 5
10:00pm
SSR
All participants
Organizational Meeting


10:20am
Aud
Christopher Marx
TBA

Thu, Jan 6
10:00am
Aud
Rachel Whitaker
TBA

Fri, Jan 7
10:00am
Aud
Paul Sniegowski
TBA


2:00pm
Aud
Marty Einhorn
What's a wiki good for?
(10 min.)

2:15pm
Aud
Matt Kane
Funding Opportunities for Research in Biological Physics

Week 2

Place*
Speaker
Title
Comments, Links,...
Mon, Jan 10
10:00am
Aud
Jeff Gore
Cheating andcooperation in Microbes

Tue, Jan 11
10:00am
Aud
Sergey Kryazhimskiy
How Does Demography Affect Adaptation?
Joshua Plotkin cannot come this week
Wed, Jan 12
10:00am
Aud
Thane Papke
Haloarchaea: Recombination, Outcomes and Mechanism

Thu, Jan 13
10:00am
Aud
Dan Weinreich
The Simplest Questions of Adaptation I Know (and perhaps even some answers!)

Fri, Jan 14
10:00am
Aud
Eugene Shakhnovich
Evolution on Physics-based Fitness Landscapes: Theory and Experiment



Week 3

Place*
Speaker
Title
Comments, Links,...
Mon, Jan 17



Martin Luther King's day: No activities are planned

Tue, Jan 18
10:00am
Aud
Bonnie Bassler
Information Processing in Quorum Sensing Circuits


2:00pm
SSR?
Sheri Simmons
Diversity in microbial populations in the wild

Wed, Jan 19
10:00am
Aud
Michael Desai
Genetic variation and the fate of beneficial mutations in asexual populations


3.45pm
Aud
Namiko Mitarai
Choice of Synonymous Codons and Ribosome Traffic

Thu, Jan 20
10:00am
Aud
Kim Sneppen
Lessons from phage biology


3:45pm
Aud
Dan Weinreich
Tracking Evolutionary Trajectories of Sexual Populations



Aud
Michael Lässig
Can evolution sense the curvature of fitness landscapes?

Fri, Jan 21
9:30am
Aud
Arjan De Visser
Microbial evolution on empirical fitness landscapes
Double ticket! Note the hour!

11:00am
Aud
Lei-Han Tang
Regulation of carbon flow in microbial metabolism

Week 4

Place*
Speaker
Title
Comments, Links,...
Mon, Jan 24
10:00am
Aud
Lilia Perfeito
Fitness landscape of a metabolic pathway


5:00pm
PL

Informal discussion on measurement of fitness

Tue, Jan 25
10:00am
Aud
Erik van Nimwegen
Looking for macroscopic laws in the evolution of genotypes and phenotypes

Wed, Jan 26
10:00am
Aud
Joy Bergelson
The evolution of gene-for-gene interactions in a plant-pathogen system

Thu, Jan 27
9:30am
Aud
Martin Weigt
Interprotein residue contacts and interaction specificity in bacterial signal transduction
Double ticket! Note the hour!!

11:00am
Aud
Alan Perelson
HIV: Data and Models
Title has changed
Fri, Jan 28
10:00am
Aud
Terry Hwa
On growth, antibiotic resistance, and evolution

Week 5

Place*
Speaker
Title
Comments, Links,...
Mon, Jan 31
10:00am
Aud
Ivan Matic
Environmental tuning of mutation rates

Tue, Feb 1
10:00am
Aud
Berenike Maier
The type IV pilus as a multifunctional bacterial motor

Wed, Feb 2
10:00am
Aud
Isabel Gordo
The fitness effects of mutation in Escherichia coli: the good and the bad




Ana M. Sousa

Due to coincidence with the Special Seminar
(of general interest,) it's been moved to Thursday Morning
Thu, Feb 3
9:30am
Aud
Ana M. Sousa
Epistasis and compensatory evolution of antibiotic resistance
Double feature!! Note the hour!!

11:00am
Aud
Olivier Tenaillon
The bases of convergence in experimental adaptation

Fri, Feb 4



No activities are planned

Week 6
Time
Place*
Speaker
Title
Comments, Links,...
Mon, Feb 7
10:00am
Aud
E. Koonin
Tree of Life, Net of Life, Forest of Life - Where are we?


12:15pm
Aud
TBA
Galaxy Clusters:the Crossroads of Astrophysics and Cosmology
Blackboard Lunch Seminar

3.45pm
Aud?
G. Sherlock
Watching Yeast Change: Using Genomics to Understand the Influence of
Epistasis on the Adaptive Landscape

Tue, Feb 8
9:30am
Aud
S. Schiffels
Emergent neutrality in adaptive genome evolution
Double feature!! Note the hour!!

11:00am
Aud
A. Walczak
The effects of negative selection on the evolution of linked sites

Wed, Feb 9
9:30am
Aud
C. Schlötterer
New-generation Sequencing and the detection of selection in Drosophila and its endosymbionts
Double feature!! Note the hour!!

11:15am
Aud
A. Nour Mohammad
Evolutionary modes of regulatory sequences in eukaryotes

Thu, Feb 10
10:00 am
Aud
E. Kussell
Age Structure in Bacterial Populations: Paths to Measurements
Title has changed

4:00pm
Aud?
H.Y.Lee
Modeling and Quantification of HIV-1 and SIV Intrahost Sequence Evolution


5:00pm
Aud?
JF Fontanari
On Cultural Evolution

Fri, Feb 11



No activities are planned

Week 7
Time
Place*
Speaker
Title
Comments, Links,...
Mon, Feb 14
9:30am
Aud
N. Barton
Branching processes in population genetics
Double feature!! Note the hour!!

10:45am
Aud
D. Weissman
The rate of adaptation in large sexual populations

Tue, Feb 15
9:30am
Aud
S. Otto
Recombination and the deleterious hitchhiker
Double feature!! Note the hour!!

11:00am
Aud
R. Neher
Sex, Draft, and Survival


3:4pam
Aud?
N. Goldenfeld
Two problems in microbial genome evolution: diversification fronts and the evolution of compositional bias
New entry
Wed, Feb 16
10:00am
Aud
S.F. Elena
Experimental evolution of viruses: model systems and questions


3:45pm
Aud?
J. Miller
Genome sequence power-laws <=> recombination
New entry
Thu, Feb 17
9:30am
Aud
J.J. Bull
Quasispecies and lethal mutagenesis: Concepts and practice
Double feature!! Note the hour!!

11:00am
Aud
E. Koonin
The Virus World, its evolution, evolution of antiviral defense, and the role of viruses in the evolution of cells


4:00pm
PL

Summary and discussion on recombination, selection and hitchhiking
New entry
Fri, Feb 18
9:30am
Aud
F. Rohwer
Virus metagenomics
Double feature!! Note the hour!!

11:00am
Aud
S. K. Remold
Experimental evolution of host-switching and emergence of new viruses

Week 8
Time
Place*
Speaker
Title
Comments, Links,...
Mon, Feb 21


Barry Obama
Presidents' Day Holiday
No regularly scheduled events today.
Tue, Feb 22
10:00am
Aud
P. Turner
Robustness and evolvability in the viral world (tentative)

Wed, Feb 23
9:30am
Aud
L. Wahl
Three surprising predictions from modeling evolution experiments
Double feature!! Note the hour!! Title has changed!

11:00am
Aud
M. Morelli
The use of ultradeep sequencing for characterizing viral populations
New entry

5:00pm
Aud
C. Wilke
Quasispecies vs standard population genetics models
Organized discussion
Thu, Feb 24
10:00am
Aud
A. Perelson
How to model a viral infection: Hepatitis C virus


3:45pm
Aud
S. Maslov
Home Depot model of prokaryotic evolution by horizontal gene transfer


4:45pm
Aud
M. Gerstein
Biological network change and evolution

Fri, Feb 25
9:30am
Aud
P. Gerrish
Antigenic evolution (tentative)
Immunity day!! Note the hour!!

11:00am
Aud
I. Rouzine
Within-host dynamics HIV-1


1:30pm
Aud
A. Weinberger
Persisting low-abundance viruses shape microbial-CRISPR based immunity


Week 9
Time
Place*
Speaker
Title
Symposium on emergent viruses
Mon, Feb 28
9:30am
Aud




11:00am
Aud
J. Gog
Simple models for influenza antigenic drift


4:00pm
Aud
M. Lässig
Clonal interference in the evolution of influenza

Tue, Mar 1st
9:30am
Aud
M. Fares
Dynamics of a re-emerging virus: Foot-and-mouth disease virus
Double feature!! Note the hour!!

11:00am
Aud
J. Weitz
Bacterial fate determination by co-infecting viruses


4:00pm
Aud
C. Parrish
Canine parvovirus origin and evolution


5:00pm
Aud
T. Leitner
Inferring HIV epidemics from HIV phylogenetics

Wed, Mar 2
9:30am
Aud
C. Macken
Evolution of avian influenza A (H5) virus
Double feature!! Note the hour!!

11:00
Aud
R. Neher
HIV-1 Intra-host dynamics


4:00pm
Aud
L. Weinberger
How Persisting Viruses Overcome Adaptive Immunity


5:00pm
Aud
MA Fares & SF Elena
Organized discussion: What does experimental evolution teach about the evolution of emergent viruses?

Thu, Mar 3




No activities are planned
Fri, Mar 4




No activities are planned



Week 10
Time
Place*
Speaker
Title

Mon, Mar 7
10:00 am
Aud
J. de Meaux
Evolution of flagellin perception in Arabidopsis thaliana and its relatives
New: starts at 10:00!

2:00pm
Aud
B. Mehlig
Linkage disequilibrium in populations of variable size

Tue,
Mar 8
09:30am
Aud
C. Wilke
Biophysical constraints on sequence evolution
Starts at 09:30!

11:00am
Aud
R. Zorzenon
> Tuberculosis and its spreading within and between hosts

Wed, Mar 9
09:30am
Aud
S. Sunyaev
Selection and migration inside the host: rapid evolution of human JC virus associated with development of PML
Starts at 09:30!

11:00am
Aud
J. Krug
Sign epistasis and evolutionary accessibility

Thu,
Mar 10
09:30am
Aud
L. Mirny
Accumulation of deleterious passenger mutations in cancer
Starts at 09:30!

11:000am
Aud
T. Lawley
Application of high-throughput genomics to Clostridium difficile evolutionand transmission


5:00pm
Aud
S. Lukic
Numerical solutions to complex demographic models







Fri, Mar 11




No formal activities planned

Week 11
Time
Place*
Speaker
Title

Mon, Mar 14
09:30 am
Aud
O. Hallatschek
Clonal interference in Structured Populations: Long Range Jumps better than Sex
Starts at 09:30!

11:00am
Aud
D. Nelson
Competition and cooperation at frontiers

Tue,
Mar 15
09:30am
Aud
M. Doebeli
Adaptive diversification
Starts at 09:30!

11:00am
Aud
I. Nemenman
Evolutionary dynamics in heterogeneous environments: three baby steps

Wed, Mar 16
09:30am
Aud
V. Mustonen
Quantifying selective forces from allele frequency time-series data of a yeast population under heat stress
Starts at 09:30!

11:00am
Aud
P. Pennings
What determines the rate of evolution of resistance in HIV?

Thu,
Mar 17
09:30am
Aud
P. Rainey
Evolution of bet hedging
Starts at 09:30!

11:000am
Aud
J. Xavier
Conflict and cooperation in microbes



5:00pm
Aud
B. Austin
Falling Uphill: Acceleration of the Emergence of Bacterial Antibiotic Resistance







Fri, Mar 18




No formal activities planned


Week 12
Time
Place*
Speaker
Title

Mon, Mar 21
10:00am
Aud
D. Brisson
Niche diversification and gene-for-gene interactions in a vertebrate-pathogen system


11:30am

S. Blumberg
Disentangling the transmission dynamics of human monkeypox and other emerging zoonoses

Tue,
Mar 22
09:30am
Aud

D. Brockmann

Modelling disease dynamics on a global scale

Starts at 09:30!

11:00am
Aud
G. Rozhnova
Stochastic models of infection dynamics

Wed, Mar 23
10:00am
Aud
F. Rosenzweig
E unibus plurum: How biodiversity evolves in a simple, homogenous environment

Thu,
Mar 24




No formal activities planned
*Aud=Auditorium, SSR=Small Seminar Room, MSR=Main Seminar Room, FR=Founders' Room, PL=Porthole Lounge
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