Seminar Computational Biology 2025

        Recent computational, experimental and phylogenetic  results

                          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 they are "good"




COPING (OR NOT) WITH HIGH MUTATION RATES

Stochastic parabolic growth promotes coexistence and a relaxed error threshold in RNA-like replicator populations

M Paczkó, E Szathmáry, A Szilágyi - Elife, 2024 - elifesciences.org

How to survive the mutational meltdown: lessons from plant RNA viruses

G Lafforgue, M Lefebvre, T Michon… - Peer Community …, 2024 - peercommunityjournal.org

Evolution of the division of labour between templates and catalysts in spatial replicator models

Y Fu, N Takeuchi - Journal of Evolutionary Biology, 2024 - academic.oup.com

ECO-EVOLUTIONARY DYNAMICS IN MICROBIAL SYSTEMS

Phage predation accelerates the spread of plasmid-encoded antibiotic resistance

C Ruan, J Ramoneda, A Kan, TJ Rudge… - Nature …, 2024 - nature.com

Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species

S Zhu, J Hong, T Wang - Nature Communications, 2024 - nature.com

Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation during extreme cycles of feast and famine

MG Behringer, WC Ho, SF Miller, SB Worthan, Z Cen… - Current Biology, 2024 - cell.com

LANDSCAPES, ROBUSTNESS AND EVOLVABILITY

Mutational robustness and the role of buffer genes in evolvability

…, SK Govers, J Michiels, KJ Verstrepen - The EMBO …, 2024 - embopress.org

High temperature delays and low temperature accelerates evolution of a new protein phenotype

J Zheng, N Guo, Y Huang, X Guo, A Wagner - Nature Communications, 2024 - nature.com

The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR

CA Westmann, L Goldbach, A Wagner - Nature Communications, 2024 - nature.com



EVOLUTION OF EVOLVABILITY

Experimental evolution of evolvability

M Barnett, L Meister, PB Rainey - Science, 2025 - science.org

Evolution takes multiple paths to evolvability when facing environmental change

B Kumawat, A Lalejini, MM Acosta, L Zaman - Proceedings of the National …, 2025 - pnas.org

Aneuploidy can be an evolutionary diversion on the path to adaptation

I Kohanovski, M Pontz, P Vande Zande… - Molecular biology …, 2024 - academic.oup.com

Evolvability predicts macroevolution under fluctuating selection

A Holstad, KL Voje, ØH Opedal, GH Bolstad, S Bourg… - Science, 2024 - science.org


EVOLUTION OF NOVEL FUNCTION

The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss

N Takeuchi, MS Fullmer, DJ Maddock… - The ISME …, 2024 - academic.oup.com

Compensatory mutations potentiate constructive neutral evolution by gene duplication

…, AK Dubé, MÈ Picard, J Grenier, R Shi, CR Landry - Science, 2024 - science.org

Global genetic rewiring during compensatory evolution in the yeast polarity network

E Kingma, L Laan - bioRxiv, 2024 - biorxiv.org


GENOME EVOLUTION

Genome duplication in a long-term multicellularity evolution experiment

K Tong, S Datta, V Cheng, DJ Haas, S Gourisetti… - Nature, 2025 - nature.com

Tandem repeat polymorphisms shape local adaptation

DG King - Trends in Ecology & Evolution, 2025 - cell.com

CELL LEVEL BEHAVIOR AND PROLIFERATION DYNAMICS

    • Cooperative motility emerges in crowds of T cells but not neutrophils

    IMN Wortel, J Postat, M Mihaylova, M Merino… - bioRxiv, 2024 - biorxiv.org

    Morphological basis of the lung adenocarcinoma subtypes

    L Zha, T Matsu-Ura, JP Sluka, T Murakawa, K Tsuta - Iscience, 2024 - cell.com


    ____________________________________________________________________________________________________________
    EXTRA

    Direct and indirect selection in a proofreading polymerase

    K Husain, V Sachdeva, R Ravasio, M Peruzzo, W Liu… - …, 2024 -                     (cf mutation rates)


    Robust genetic codes enhance protein evolvability

    …, C Martí-Gómez, DM McCandlish, JL Payne - PLoS …, 2024 - journals.plos.org  ( cf robustness)

    Transcription– replication interactions reveal bacterial genome regulation

    AW Pountain, P Jiang, T Yao, E Homaee, Y Guan… - Nature, 2024 - nature.com   (crf Genome evolution)