Seminar Computational Biology 2019-2020

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 guarantee ‘good’

1 Eco-evolutionary dynamics and diversity

High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast

Alex N. Nguyen Ba1,9, Ivana Cvijović1,2,3,4,9, José I. Rojas Echenique1,9, Katherine R. Lawrence1,5,
Artur Rego-Costa1,  X Liu, SF Levy, MM Desai - Nature, 2019 -

Consumer-resource dynamics is an eco-evolutionary process in a natural plankton community

LR Schaffner, L Govaert, L De Meester… - Nature ecology & …, 2019 -

Effects of rapid evolution on species coexistence

…, MM Turcotte, JM Levine - Proceedings of the …, 2019 - National Acad Sciences

Simulated evolution assembles more realistic food webs with more functionally similar species than invasion

TN Romanuk, A Binzer, N Loeuille, WMA Carscallen… - Scientific Reports, 2019 -

2 Feedback of Spatial selforganization to cellular differentiation

Cooperation and spatial self-organization determine rate and efficiency of particulate organic matter degradation in marine bacteria

…, J Schwartzman, OX Cordero - Proceedings of the …, 2019 - National Acad Sciences

An evolutionarily stable strategy to colonize spatially extended habitats

W Liu, J Cremer, D Li, T Hwa, C Liu - Nature, 2019 -

Toxin production spontaneously becomes regulated by local cell density in evolving bacterial populations,

H Doekes RJ De Boer, R Hermsen - PLoS computational …, 2019 -

3 Fitness Landscapes

Genotype network intersections promote evolutionary innovation

DP Bendixsen, J Collet, B Østman, EJ Hayden - PLoS biology, 2019 -

5 Mutational Bias, and predictability of evolution

 Predicting mutational routes to new adaptive phenotypes

PA Lind, E Libby, J Herzog, PB Rainey - Elife, 2019 -

Antibiotic production is organized by a division of labour in Streptomyces

…, A Liakopoulos, YH Choi, D Claessen, D Rozen - bioRxiv, 2019 -

DNA fragility in the parallel evolution of pelvic reduction in stickleback fish

KT Xie, G Wang, AC Thompson… - …, 2019 -

6 RNA sequence, structure and regulation in present day organisms

RNA structure duplication in the dengue virus 3′ UTR: redundancy or host specificity?

L de Borba, SM Villordo, FL Marsico, JM Carballeda… - MBio, 2019 - Am Soc Microbiol

Emerging roles for intermolecular RNA-RNA interactions in RNP assemblies

B Van Treeck, R Parker - Cell, 2018 - Elsevier

RNA-mediated gene regulation is less evolvable than transcriptional regulation

JL Payne, F Khalid, A Wagner - Proceedings of the …, 2018 - National Acad Sciences

7 Multilevel modeling of cell differentiation