Seminar Computational Biology 2022

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 ‘good’



1  RNA miscellanea: GP map and diversification

Insertions and deletions in the RNA sequence–structure map

NS Martin, SE Ahnert - Journal of the Royal Society …, 2021 - royalsocietypublishing.org


Phenotype bias determines how natural RNA structures occupy the morphospace of all possible shapes

K Dingle, F Ghaddar, P Šulc… - … biology and evolution, 2022

href="https://scholar.google.com/citations?user=10IaieEAAAAJ&hl=en&oi=sra">R Mizuuchi, T Furubayashi, N Ichihashi - Nat commun 2022 18 mar



Evolutionary transition from a single RNA replicator to a multiple replicator network

R Mizuuchi, T Furubayashi, N Ichihashi - Nature Communications, 2022 - nature.com





2  Tempo and mode of evolution



Direct observation of adaptive tracking on ecological time scales in Drosophila

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[HTML] Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution

MF Schenk, MP Zwart, S Hwang, P Ruelens… - Nature Ecology & …, 2022 - nature.com





3  Spatial structure in microbial communities



 Droplet printing reveals the importance of micron-scale structure for bacterial ecology

R Krishna Kumar, TA Meiller-Legrand… - Nature …, 2021 - nature.com



Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment

D Ciccarese, G Micali, B Borer, C Ruan, D Or… - The ISME …, 2022 - nature.com



Slow expanders invade by forming dented fronts in microbial colonies

H Lee, J Gore, KS Korolev - Proceedings of the National …, 2022 - National Acad Sciences




4  HGT in structured populations



Transposable elements promote the evolution of genome streamlining

B van Dijk, F Bertels, L Stolk… - … Transactions of the …, 2022 - royalsocietypublishing.org



Harmful behaviour through plasmid transfer: a successful evolutionary strategy of bacteria harbouring conjugative plasmids

CPF Domingues, JS Rebelo… - … of the Royal …, 2022 - royalsocietypublishing.org



5  GP map:  predicting gene expression  and evolution from promotor sequences

The evolution, evolvability and engineering of gene regulatory DNA

…, DA Thompson, JZ Levin, FA Cubillos, A Regev - Nature, 2022 - nature.com



Predicting bacterial promoter function and evolution from random sequences

M Lagator, S Sarikas, M Steinrueck, D Toledo-Aparicio… - eLife, 2022 - elifesciences.org



6  Mutational Priming



Important genomic regions mutate less often than do other regions

J Zhang - 2022 - nature.com


 

 Mutation bias reflects natural selection in Arabidopsis thaliana

J Monroe, T Srikant, P Carbonell-Bejerano, C Becker… - Nature, 2022 - nature.com



A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes

JS Horton, LM Flanagan, RW Jackson… - Nature …, 2021 - nature.com



 7  Collective behaviour and evolution of multicellularity




Formation, collective motion, and merging of macroscopic bacterial aggregates

…, S Lim, X Guo, S Haas, JQ Boedicker - PLoS computational …, 2022



Oxygen suppression of macroscopic multicellularity

…, E Libby, R Pineau, CT Reinhard, WC Ratcliff - Nature …, 2021 - nature.com




Evolution of multicellularity by collective integration of spatial information

ES Colizzi, RMA Vroomans, RMH Merks - Elife, 2020 - elifesciences.org




8   Detailed CPM modeling of  Cell competition, Cell movement and Organogenesis



Cell-scale biophysical determinants of cell competition in epithelia

D Gradeci, A Bove, G Vallardi, AR Lowe, S Banerjee… - Elife, 2021 - elifesciences.org

8 



Computational modelling of nephron progenitor cell movement and aggregation during kidney organogenesis

P Tikka, M Mercker, I Skovorodkin, U Saarela… - Mathematical …, 2022 - Elsevier