Seminar Computational Biology 2017-18

recent theoretical, experimental, and phylogenetic
advances related to topics discussed in the course.

Get an overview of the papers and
choose one topic for presentation and one topic for discussion.

NOTE: be critical: inclusion does not mean ‘good’

Rough schedule

The first two topics will be discussed Tuesday-afternoon (starting at 13.30).
The other topics will be discussed on Thursday (starting at 10.00)

Long term evolutionary experiment (LTEE) : various models dataanalysis and modeling

Presented by: Laurens, Indi, Jan en Sam
Discussed by: Ellen, Daan en Tjerk

The dynamics of molecular evolution over 60,000 generations

BH Good, MJ McDonald, JE Barrick, RE Lenski… - Nature, 2017 -

Genetic Basis of Exploiting Ecological Opportunity During the Long-Term Diversification of a Bacterial Population

…, J Plucain, J Gaffé, T Hindré, D Schneider - Journal of molecular …, 2017 - S

Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment

…, RE Lenski, OS Soyer… - BMC …, 2016

Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification

…, J Consuegra, D Schneider, G Beslon - PLoS computational …, 2017

Evolution of cooperation

Presented by: Reinder en Meine
Discussed by: Thijs en Ugur

Microbes can help explain the evolution of host altruism O Lewin-Epstein, R Aharonov, L Hadany - Nature communications, 2017 -

Mobility can promote the evolution of cooperation via emergent self-assortment dynamics.

Joshi J, Couzin ID, Levin SA, Guttal V. PLoS Comput Biol. 2017

Secondorder cooperation: Cooperative offspring as a living public good arising from secondorder selection on non‐cooperative individuals

A Frénoy, F Taddei, D Misevic - Evolution, 2017 - Wiley Online Library

Spatial dynamics of synthetic microbial mutualists and their parasites

DR Amor, R Montañez… - PLoS computational …, 2017 -

Evolution of ecological communities

Presented by: Thijs en Ugur
Discussed by: Reinder en Meine

Diverse modes of eco-evolutionary dynamics in communities of antibiotic-producing microorganisms

Kalin Vetsigian - Nature Ecology and Evolution

Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment

H Celiker, J Gore - Nature communications, 2014 -

Metabolic evolution and the self-organization of ecosystems

R Braakman, MJ Follows… - Proceedings of the …, 2017 - National Acad Sciences

Evolutionary dynamics of GRN (Yeast)

Presented by: Ellen, Tjerk en Daan
Discussed by: Laurens, Indi, Jan en Sam

Evolutionary dynamics of regulatory changes underlying gene expression divergence among Saccharomyces species

…, PJ Wittkopp, J Coolon - Genome Biology and …, 2017 -

Adaptive Prediction Emerges Over Short Evolutionary Time Scales

Adrián López García de Lomana; Amardeep Kaur; Serdar Turkarslan; Karlyn D. Beer; Fred D. Mast ...

Genome Biology and Evolution, Volume 9, Issue 6, 1 June 2017, Pages 1616–1623,

Effects of mutation and selection on plasticity of a promoter activity in Saccharomyces cerevisiae

F Duveau, DC Yuan, BPH Metzger… - Proceedings of the …, 2017 - National Acad Sciences

Evolution of Robustness and Evolvability

Presented by: Dieter en Stijn
Discussed by: Maarten, Joyce en Olof

A thousand empirical adaptive landscapes and their navigability [PDF] [Supplementary material]

J Aguilar-Rodríguez, JL Payne, A Wagner - Nature Ecology & Evolution, 2017 -

Why phenotype robustness promotes phenotype evolvability

X Wei, J Zhang - Genome biology and evolution, 2017 -

Evolution of drift robustness in small populations

T LaBar, C Adami - Nature communications, 2017 -

Robustness and evolvability of the human signaling network

J Kim, D Vandamme, JR Kim, AG Munoz… - PLoS computational …, 2014 -

Neutrality and complex adaptation

Presented by: Maarten, Joyce en Olof
Discussed by: Margot, Sarah en Ianthe

Evolution of complex adaptations in molecular systems [PDF]

C Pál, B Papp - Nature ecology & evolution, 2017 -

Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery

J Vosseberg, B Snel - Biology direct, 2017

The potential for non-adaptive origins of evolutionary innovations in central carbon metabolism

SR Hosseini, A Wagner - BMC systems biology, 2016 -

HGT: evolution. Regulation and consequences

Presented by: Margot, Sarah en Ianthe
Discussed by: Dieter en Stijn

Inevitability of genetic parasites

…, AE Lobkovsky, YI Wolf, EV Koonin - Genome biology and …, 2016 -

Indirect Fitness Benefits Enable the Spread of Host Genes Promoting Costly Transfer of Beneficial Plasmids…, C Lotton, SP Brown, AB Lindner, F Taddei - PLoS …, 2016 –

Critical mutation rate in a population with horizontal gene transfer

…, DR Gifford, R Krasovec, CG Knight - Proceedings of the …, 2017 -

Gene Transfer Agent Promotes Evolvability within the Fittest Subpopulation of a Bacterial Pathogen

M Québatte, M Christen, A Harms, J Körner, B Christen… - Cell Systems, 2017 - Elsevier

The topic below has been dropped

Modeling Multicellular tissue dynamics: cell shape, cell signling and stability:

Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains

Q Wang, WR Holmes, J Sosnik… - PLoS computational …, 2017 -

Segment-specific adhesion as a driver of convergent extension

RMA Vroomans, P Hogeweg… - PLoS computational …, 2015 -

Virtual cardiac monolayers for electrical wave propagation

N Kudryashova, V Tsvelaya, K Agladze, A Panfilov - Scientific Reports, 2017 -

A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self‐renewal

…, M Witherspoon, N Nishimura, JA Glazier… - Molecular systems …, 2017 -