Quantitative Laws of Genome Evolution

Villa del Grumello, Como, Italy

27 June - 5 July 2013 Chair: Marco Cosentino Lagomarsino, Université Pierre et Marie Curie, Paris

Organizing Committee: Luigi Grassi, Sapienza Università di Roma Federico Bassetti, Università di Pavia Uberto Pozzoli, IRCCS Medea

Steering Committee: Joshua Weitz, GA Tech Sergei Maslov, Brookhaven National Laboratory Dominique Schneider, University of Grenoble Rosalind Allen, University of Edinburgh Namiko Mitarai, NBI Copenaghen

University of Insubria Commitee: Vincenzo Gino Benza, Università degli Studi dell’Insubria Giulio Casati, Università degli Studi dell’Insubria

Local organization: Centro di Cultura Scientifica "Alessandro Volta" Lake Como School of Advanced Studies Quantitative Laws of Genome Evolution, 27 June - 5 July 2013, Villa del Grumello, Como, Italy

We are grateful to the following sponsors for their support:

iii Quantitative Laws of Genome Evolution, 27 June - 5 July 2013, Villa del Grumello, Como, Italy

Welcome from The Organizers

TISOURPLEASURETOWELCOMEYOUTOTHISWORKSHOP. We have done our best to I make it attractive in terms of both venue and scientific program, and we truly believe in the potential role of such a meeting in strengthening the interdisciplinary bonds between people asking similar questions using different scientific languages. It will be up to all of us to make this potential come true. We sincerely hope that you will enjoy the meeting and the coasts of Lake Como.

Marco Cosentino Lagomarsino Luigi Grassi Federico Bassetti Uberto Pozzoli

Welcome from the Lake Como School of Advanced Studies

E WELCOME ALL OF YOU to the “Lake Como School of Advanced Studies”, a newly W founded Institution originating from the synergy of four Universities of the area: U. of Insubria, U. of Milano, U. of Milano Bicocca, U. of Pavia. The School having the Complex Systems at the core of its scientific interests, we consider a really special opportunity to start its activity with a meeting on Evolutionary Genomics. We are committed to making this event more than an isolated episode, and hope to organize other workshops on related topics in the near future. We will do our best to make your stay a pleasant and fruitful one.

Vincenzo Gino Benza Giulio Casati

iv Quantitative Laws of Genome Evolution, 27 June - 5 July 2013, Villa del Grumello, Como, Italy

About the Workshop

UANTITATIVE APPROACHES to evolutionary genomics, systems biology, and ecology unravel sev- Q eral universal regularities connecting genome-scale observables, phenotypes and physiological traits. Putting aside any unrealistic ambitions of all-inclusive theories, some of these universal empirical trends might qualify as "biological laws" in a similar sense as "law" is understood in modern physics. Consequently, a current challenge for theoreticians is understanding how different universal features emerging empirically can be accounted for by simple mathematical models exploring quantitative laws at different levels, from physiology to evolutionary genomics. The scope of this workshop is to give an overview of the current state of the field and put a researcher in the condition of performing research at the edge of the current knowledge. The workshop targets PhD students and postdocs, as well as more experienced researchers with background in physics, (evolution- ary) genomics, (evolutionary) biology, bioinformatics, ecology, interested in quantitative work.

HEREWILLBETHREEKINDOFSESSIONS. Three lecture-sets “Ideas & Approaches”, on Popula- T tion Genetics, Evolutionary Ecology, Evolutionary Genomics, will cover a (non-comprehensive) overview of the field for the non-specialists, and a “vision” of the main directions where the field is going (for all). Colloquium and contributed talks will be more traditional scientific talks. Finally, three (light) night sessions will cover more “practical” and specialized tools.

F1000 Young Scientist Presentation Award

Aculty of 1000 will award a prize to the three selected undergraduate and graduate student talks. The F winners will have a year-long subscription to F1000 Prime, and a F1000 T-shirt.

v Quantitative Laws of Genome Evolution, 27 June - 5 July 2013, Villa del Grumello, Como, Italy

Workshop Program

Thursday, June 27, 2013. Morning session, Chairman: S. Maslov 8:40 am - 9:00 am Welcome 9:00 am - 10:00 am L. Peliti, Ideas & approaches: Population Genetics. 10:00 am - 11:00 am L. Peliti, Ideas & approaches: Population Genetics. 11:00 am - 11:30 am Coffee Break 11:30 am - 12:30 pm J. Weitz, Ideas & approaches: Evolutionary Ecology. 12:30 pm - 12:50 pm I. Junier, Synteny in Bacterial Genomes: Inference, Organization and Evolution. 1:00 pm - 2:30 pm Lunch

Thursday, June 27, 2013. Afternoon session, Chairman: M. Cosentino Lagomarsino 2:30 pm - 3:15 pm E. van Nimwegen, Evolution of expression noise in native and synthetic E. coli promoters. 3:15 pm - 4:00 pm R.J. Allen, Using models to understand how antibiotics kill bacteria. 4:00 pm - 4:30 pm Coffe Break 4:30 pm - 5:15 pm R.J. Allen, Exploring the diversity and optimality of metabolic pathways. 5:15 pm - 6:00 pm A. Seminara, Bacterial biofilms: toward a multicellular physiology. 6:00 pm - 6:30 pm E. van Nimwegen, A simple evolutionary model for scaling laws in genome composition.

Friday, June 28, 2013. Morning session, Chairman: R.J. Allen 9:00 am - 10:00 am J. Weitz, Ideas & approaches: Evolutionary Ecology. 10:00 am - 11:00 am O. Tenaillon, Ideas & approaches: Evolutionary Biology. 11:00 am - 11:30 am Coffee Break 11:30 am - 12:30 pm O. Tenaillon, Ideas & approaches: Evolutionary Biology. 12:30 pm - 12:50 pm A. Gilson, Can a protein’s evolutionary fate be predicted from its structure? 1:00 pm - 2:30 pm Lunch

vi Quantitative Laws of Genome Evolution, 27 June - 5 July 2013, Villa del Grumello, Como, Italy

Friday, June 28, 2013. Afternoon session, Chairman: U. Pozzoli 2:30 pm - 3:15 pm J. Weitz, Similar (but different): evolutionary dynamics of the gene composition of bacte- rial genomes. 3:15 pm - 4:00 pm E. Koonin, The universal gene frequency distribution and its origin: neutrality vs selection. 4:00 pm - 4:30 pm Break 4:30 pm - 4:50 pm P. Dixit, Quantifying contributions of mutations and homologous recombination to E. coli genomic diversity. 4:50 pm - 5:35 pm P. Pfaffelhuber, The infinitely many genes model: From models... 5:35 pm - 6:05 pm F. Baumdicker, The infinitely many genes model: ...to data. 6:30 pm - 7:30 pm Happy hour 9:15 pm - 9:15 pm J. Weitz, Late night modeling session

Saturday, June 29, 2013. Chairman: J. Weitz 9:00 am - 10:00 am E. Koonin, Ideas & approaches: Evolutionary Genomics. 10:00 am - 11:00 am E. Koonin, Ideas & approaches: Evolutionary Genomics. 11:00 am - 11:30 am Coffee Break 11:30 am - 1:15 pm 4-minute talk session (see detailed program) 1:15 pm - 2:30 pm Lunch

Monday, July 1, 2013. Morning session, Chairman: N. Mitarai 9:00 am - 10:00 am O. Tenaillon, Ideas & approaches: Evolutionary Biology. 10:00 am - 11:00 am L. Peliti, Ideas & approaches: Population Genetics. 11:00 am - 11:30 am Coffee Break 11:30 am - 12:15 pm S. Maslov, Why bacteria run Linux and eukaryotes run Windows? 12:15 pm - 12:35 pm M. Cosentino Lagomarsino, Inter-species gene-family abundances according to Boltz- mann. 12:35 pm - 12:55 pm J. Grilli, Universal properties of ecological interactions and stability of ecosystems. 1:00 pm - 2:30 pm Lunch

vii Quantitative Laws of Genome Evolution, 27 June - 5 July 2013, Villa del Grumello, Como, Italy

Monday, July 1, 2013. Afternoon session, Chairman: V. G. Benza 2:30 pm - 3:15 pm E. Shakhnovich, Climbing the scale ladder in biology: How protein biophysics sculpts fitness landscape (Experiment). 3:15 pm - 4:00 pm K. Sneppen, Phage strategies: Bet hedging or a “Red queen race”. 4:00 pm - 4:30 pm Coffee Break 4:30 pm - 5:15 pm O. Tenaillon, Quantifying molecular determinants shaping the adaptivelandscape of beta- lactamase TEM-1. 5:15 pm - 5:30 pm Group Photo 5:30 pm - 5:50 pm T. Biancalani, Noise-induced bistability in biochemical networks. 5:50 pm - 6:10 pm A. Serohijos, Imprintsof protein biophysicson the emerging genomic patterns of molecular evolution. 6:10 pm - 6:30 pm I. Vasquez Garcia, Quantifying selection in evolving populations using time resolved ge- netic data.

Tuesday, July 2, 2013. Morning session, Chairman: D. Schneider 9:00 am - 9:45 am A. Maritan, Emergence of criticality in living systems. 9:45 am - 10:05 am M. Osella, Cell size control in E. coli. 10:05 am - 10:25 am M. Gherardi, Soft bounds in the evolution of software packages (and other animals). 10:25 am - 10:45 am L. Grassi, Horizontal and vertical growth of S. cerevisiae metabolic network. 10:45 am - 11:05 am G. Rozhnova, Requirements for evolutionary stability of TIPs and HIV in high-risk popu- lations. 11:05 am - 11:30 am Coffee Break 11:30 am - 12:15 pm L. Peliti, Life and Information: Thermodynamic implications of life as an information- processing system. 12:15 pm - 1:00 pm M. Laessig, Universality in the evolution of quantitative traits. 1:00 pm - 2:30 pm Lunch

Tuesday, July 2, 2013. Afternoon session, Chairman: M. Cosentino Lagomarsino 2:30 pm - 3:15 pm M. Caselle, The role and functions of microRNA-mediated circuits in the human regulatory network. 3:15 pm - 4:00 pm K. Kaneko, Plasticity and Robustness in Evolution: Macroscopic Theory, Model Simula- tions, and Laboratory Experiments - Part I. 4:00 pm - 4:30 pm Coffee Break 4:30 pm - 5:15 pm U. Pozzoli, Geographically Explicit Models of Human Evolution. 5:15 pm - 6:00 pm F. Ciccarelli, Systems biology to identify novel cancer drivers and negative genetic inter- actions of cancer genes. 6:00 pm - 6:20 pm F. Capuani, Metabolic Networks in Cancer. 6:20 pm - 7:05 pm M.J. Lercher, Quantifying the role of pre-adaptation in metabolic evolution.

viii Quantitative Laws of Genome Evolution, 27 June - 5 July 2013, Villa del Grumello, Como, Italy

Wednesday, July 3, 2013. Afternoon session, Chairman: L. Grassi 1:00 pm - 2:30 pm Lunch 2:30 pm - 3:15 pm A. Maritan (S. Suweis), Emergence of structural and dynamical properties of ecological mutualistic networks. 3:15 pm - 4:00 pm N. Mitarai, Emergency of diversity in a model ecosystem. 4:00 pm - 4:30 pm Break 4:30 pm - 5:15 pm N. Goldenfeld, The evolution of life prior to LUCA and “universal biology” Part I. 5:15 pm - 6:00 pm H. Isambert, On the evolutionary expansion of gene families implicated in cancer and other genetic diseases. 6:00 pm - 6:20 pm N. Saito, Complexity in Genotype-Phenotype Mapping Facilitates Evolution of Genetic Redundancy. 6:20 pm - 6:40 pm L. Ferretti, Evolution in the protein universe. 7:00 pm - 8:00 pm Happy hour 8:00 pm - 9:00 pm H. Isambert, Causal inference analysis.

Thursday, July 4, 2013. Morning session, Chairman: U. Pozzoli 9:00 am - 9:45 am K. Sneppen, DNA Methylation in bacterial warfare and in epigenetics. 9:45 am - 10:30 am K. Kaneko, Plasticity and Robustness in Evolution: Macroscopic Theory, Model Simula- tions, and Laboratory Experiments - PartII. 10:30 am - 10:50 am A. Melbinger, Evolution of cooperation in group-structured population. 10:50 am - 11:20 am Coffee Break 11:20 am - 12:05 pm E. Koonin, Evolution of microbial pangenomes: closed and isolated? 12:05 pm - 12:50 pm N. Mitarai, Control translation in bacteria. 12:50 pm- 1:10 pm R. Braakman, A metabolic tree of life. 1:10 pm - 2:30 pm Lunch

Thursday, July 4, 2013. Afternoon session, Chairman: F. Bassetti 2:30 pm - 3:15 pm J. Krug, Evolutionary accessibility of modular fitness landscapes. 3:15 pm - 4:00 pm M. Laessig, Fitness flux and predictability of adaptive processes. 4:00 pm - 4:30 pm Coffee Break 4:30 pm - 5:15 pm S. Maslov, Parkinson’s Law in bacterial regulation. 5:15 pm - 6:00 pm E. Shakhnovich, Climbing the scale ladder in Biology: Biophysicsinspired ”ab initio” evo- lutionary models (Theory).

ix Quantitative Laws of Genome Evolution, 27 June - 5 July 2013, Villa del Grumello, Como, Italy

Friday, July 5, 2013. Morning session, Chairman: V. G. Benza 9:00 am - 9:45 am J. Krug, How predictable is evolution? 9:45 am - 10:30 am E. Koonin, Coevolution of viruses and adaptive immunity: when is Lamarckian evolution advantageous? 10:30 am - 11:00 am Coffee Break 11:00 am - 11:45 pm N. Goldenfeld, The evolution of life prior to LUCA and”universal biology” -Part II. 11:45 pm - 12:15 pm Concluding remarks

x Quantitative Laws of Genome Evolution, 27 June - 5 July 2013, Villa del Grumello, Como, Italy

4-minute talk session program

Saturday, June 29, 2013, 11:30 am -13:00 pm 11:30 am - 11:34 am H.-Y. Shih, Rapid evolution and cryptic population cycles emerging from demographic stochasticity and point mutations. 11:34 am - 11:38 am F. Bertels, Assessing the accuracy of phylogenies based on reference alignments of short sequence reads. 11:38 am - 11:42 am A. Teufel, Selective pressures on amino acid substitutions during human-chimpanzee di- vergence. 11:42 am - 11:46 am G. Malaguti, Quantitative analysis of the expansion of “dangerous” gene families during vertebrate evolution: single gene versus whole genome duplication. 11:46 am - 11:50 am A.-F. Bibtol, Population subdivision with migration can facilitate evolution on multi- peaked fitness landscapes. 11:50 am - 12:00 am DISCUSSION 12:00 am - 12:04 pm J. Wong NG, Bacterial Speed Races. 12:04 pm - 12:08 pm M. Mauri, A model for sigma factor competition in bacterial cells. 12:08 pm - 12:12 pm C. Raeside, Genome plasticity during a long-term evolution experiment in Escherichia coli. 12:12 pm - 12:16 pm P. Patra, Population dynamics of bacterial persistence. 12:16 pm - 12:20 pm L. Ciandrini, Quantifying gene expression at the level of translation. 12:20 pm - 12:30 pm DISCUSSION 12:30 pm - 12:34 pm V. Pendino, MiRNAs and the evolution of duplicated genes. 12:34 pm - 12:38 pm C. Bosia, Modeling competing endogenous RNA networks. 12:38 pm - 12:42 pm L. Caniparoli, Synonymous but not the same: a quantification of the information provided by the codon bias. 12:42 pm - 12:46 pm A. Ledda, Thermodynamic interactions and error rates in tRNA recruiting in the ribosome. 12:46 pm - 12:50 pm E. De Leonardis, Prediction of tertiary structure contacts in functional RNAs using direct- coupling analysis. 12:50 pm - 13:00 pm DISCUSSION

xi Quantitative Laws of Genome Evolution, 27 June - 5 July 2013, Villa del Grumello, Como, Italy

Speaker information

Speaker information

Name Affiliation email Arrive Leave

Eugene Koonin NCBS NIH Bethesda [email protected] 6/27/2013 7/5/2013

Luca Peliti Università di Napoli [email protected] 6/27/2013 7/5/2013

Olivier Tenaillon University Paris-Diderot [email protected] 6/27/2013 7/2/2013

Rosalind Allen University of Edinburgh [email protected] 6/27/2013 6/30/2013

Michele Caselle University of Turin [email protected] 7/1/2013 7/4/2013

Francesca Ciccarelli IEO Milano [email protected] 7/1/2013 7/2/2013

Herve Isambert Institut Curie, Paris [email protected] 6/29/2013 7/5/2013

Michael Laessig University of Cologne [email protected] 7/1/2013 7/6/2013

Erik van Nimwegen Biozentrum Basel [email protected] 6/27/2013 6/28/2013

Joachim Krug University of Cologne [email protected] 7/2/2013 7/5/2013

Amos Maritan University of Padua [email protected] 7/1/2013 7/4/2013

Dominique Schneider University of Grenoble dominique.schneider@ujf- 6/27/2013 7/2/2013 grenoble.fr

Sergei Maslov Brookhaven National Lab- [email protected] 6/27/2013 7/5/2013 oratory

Namiko Mitarai Niels Bohr Institute [email protected] 6/30/2013 7/4/2013 Copenhagen

Peter Pfaffelhuber University of Freiburg [email protected] 6/27/2013 6/30/2013 freiburg.de

Agnese Seminara University of Nice [email protected] 6/27/2013 6/28/2013

Kim Sneppen Niels Bohr Institute [email protected] 6/30/2013 7/5/2013 Copenhagen

Joshua Weitz GA Tech [email protected] 6/27/2013 7/1/2013

Eugene Shakhnovich Harvard University [email protected]/30/2013 7/5/2013

Nigel Goldenfeld University of Illinois [email protected] 6/30/2013 7/5/2013

Kunihiko Kaneko University of Tokyo [email protected] 6/30/2013 7/5/2013 tokyo.ac.jp

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