Seminar Computational Biology 2016-17

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.

We will assign the topics on Tuesday  Januari 10 2017

1. RNA-world  and some precursors/alternatives

Amplification of RNA by an RNA polymerase ribozyme

DP Horning, GF Joyce - Proceedings of the National …, 2016 - National Acad Sciences

Spontaneous formation and base pairing of plausible prebiotic nucleotides in water

…, J Khanam, R Krishnamurthy, NV Hud - Nature …, 2016 - nature.com

Emergence of Autocatalytic Sets in Chemical Reaction Networks Based on RNA Secondary Structure

W Hordijk - arXiv preprint arXiv:1612.02770, 2016 - arxiv.org

The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism

AD Goldman, JT Beatty, LF Landweber - Journal of molecular evolution, 2016 - Springer


2. Mutation rates: evolution, variation, regulation

Genetic drift, selection and the evolution of the mutation rate

M Lynch, MS Ackerman, JF Gout, H Long… - Nature Reviews …, 2016 - nature.com

Antibiotic treatment enhances the genome-wide mutation rate of target cells

…, R Te, H Lee, CC Chen, M Lynch - Proceedings of the …, 2016 - National Acad Sciences

Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation

S Uphoff, ND Lord, B Okumus, L Potvin-Trottier… - …, 2016 - science.sciencemag.org

Population heterogeneity in mutation rate increases the frequency of higher-order mutants and reduces long-term mutational load

HK Alexander, SI Mayer, S Bonhoeffer - Molecular Biology and Evolution, 2016 - SMBE


3.Neutrality and robustness

Predictable convergence in hemoglobin function has unpredictable molecular underpinnings

C Natarajan, FG Hoffmann, RE Weber, A Fago… - …, 2016 - science.sciencemag.org

Secondary structure impacts patterns of selection in human lncRNAs

C Pegueroles, T Gabaldón - BMC biology, 2016 - bmcbiol.biomedcentral.com

Adaptive genetic robustness of Escherichia coli metabolic fluxes

WC Ho, J Zhang - Molecular biology and evolution, 2016 - SMBE


4. Gene essentiality and conservation and evolvability

Evolution by gene loss

R Albalat, C Cañestro - Nature Reviews Genetics, 2016 - nature.com

Gene Essentiality is a quantitative property linked to cellular evolvability

G Liu, MYJ Yong, M Yurieva, KG Srinivasan, J Liu… - Cell, 2015 - Elsevier

Proteins with Highly Evolvable Domain Architectures Are Nonessential but Highly Retained

CH Hsu, AWT Chiang, MJ Hwang, BY Liao - Molecular biology and evolution, 2016 - SMBE


5. HGT and microbial diversity

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

…, SP Preheim, S Timberlake, EJ Alm, MF Polz - Nature …, 2016 - nature.com

In silico gene-level evolution explains microbial population diversity through differential gene mobility

B van Dijk, P Hogeweg - Genome biology and evolution, 2016 - gbe.oxfordjournals.org

Evolvability of an optimal recombination rate

…, YI Wolf, EV Koonin - Genome biology and …, 2016 - gbe.oxfordjournals.org


6. Cell Differentiation

Mitra Mojtahedi, Alexander Skupin, Joseph Zhou, Ivan G. Castaño, Rebecca Y. Y. Leong-Quong, Hannah Chang, Kalliopi Trachana, Alessandro Giuliani, Sui Huan  http://dx.doi.org/10.1371/journal.pbio.2000640

Symbiotic Cell Differentiation and Cooperative Growth in Multicellular Aggregates

JF Yamagishi, N Saito, K Kaneko - PLoS Comput Biol, 2016 - journals.plos.org

Clonal yeast biofilms can reap competitive advantages through cell differentiation without being obligatorily multicellular
…, KS Andersen, JJ Boomsma - … . R. Soc. B, 2016 - rspb.royalsocietypublishing.org


7. Morphogenesis

Filopodial-Tension Model of Convergent-Extension of Tissues

JM Belmonte, MH Swat, JA Glazier - PLoS Comput Biol, 2016 - journals.plos.org

Segment-specific adhesion as a driver of convergent extension

RMA Vroomans, P Hogeweg… - PLoS Comput …, 2015 - journals.plos.org

Modeling halotropism: a key role for root tip architecture and reflux loop remodeling in redistributing auxin

…, RA Korver, C Testerink, KHWJ ten Tusscher - …, 2016 - dev.biologists.org


8. Behaviour, mechanisms and evolution

To Cooperate or Not to Cooperate: Why Behavioural Mechanisms Matter

A Bernard, JB André, N Bredeche - PLoS Comput Biol, 2016 - journals.plos.org

Skill learning and the evolution of social learning mechanisms

…, M Franz, KN Laland - BMC …, 2016 - bmcevolbiol.biomedcentral.com

Emergent oscillations assist obstacle negotiation during ant cooperative transport

A Gelblum, I Pinkoviezky, E Fonio… - Proceedings of the …, 2016 - National Acad Sciences


Ant groups optimally amplify the effect of transiently informed individuals
A Gelblum, I Pinkoviezky, E Fonio, A Ghosh… - Nature …, 2015 - nature.com