Science, discussed.

MaxEnt: the Second Law of Thermodynamics as a modeling principle in biology

Most people who’ve taken introductory physics probably remember learning the famous “Second Law of Thermodynamics”: in a closed system, entropy never decreases.  Roughly speaking, we can think of entropy as … Continue reading

15/04/2015 · Leave a comment

A Time for Transcription (Factors)

I’ve been postponing this post for a while, hoping to find the time to expand the analysis, but time seems to elude me at present, so I’ve decided to condense my thoughts … Continue reading

30/03/2015 · Leave a comment

The distribution of mutational effects in yeast

I think it’s fair to say that uncovering the distribution of mutational effects is one of the central problems (if not the central problem) in molecular evolution and genetics today.  … Continue reading


Of Transcription Factors, their Evolution and Mechanism of Action

Transcription factors (TFs) play a key role in any biological system, and not surprisingly are being the centre of a continuous stream of papers. I recently covered the contrasting evidence for … Continue reading

17/02/2015 · 1 Comment

bioRxiv at one: great achievements come with great responsibilities

In a recent piece on Science, Jocelyn Kaiser nicely highlights the reasons why the first 12 months of biorRxiv can be considered a success. Twitter has been echoing of messages of appraisal. … Continue reading

17/11/2014 · Leave a comment

Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites

In their latest submission to bioRxiv, Echave, Jackson, and Wilke present a model to explain site-specific evolutionary rates among amino acids in a protein based on biophysical principles. Relationship between … Continue reading

06/10/2014 · 8 Comments

toyLIFE: a computational framework to study the multi-level organization of the genotype-phenotype map

In this pre-print article on arXiv the authors present a computational toolkit for simulating intra-cellular events and interactions from the level of gene transcription and protein folding to the level … Continue reading

03/10/2014 · Leave a comment

Synthetic biology made circular [preprint]

Clever use of group I permuted intron-exon sequences to obtain circular riboregulators that performs better than their linear counterparts. For the whole story, read the preprint on @bioRxiv Engineering a … Continue reading

25/09/2014 · Leave a comment

On the coupled evolution of protein folding and binding

Michael Manhart and Alexandre V Morozov uploaded on bioRxiv their latest manuscript titled: Protein folding and binding can emerge as evolutionary spandrels through structural coupling where they show the … Continue reading

26/08/2014 · 4 Comments

Fitness landscape analysis illuminates drug treatments [review]

An interesting manuscript in bioRxiv describes the computational analysis of fitness peaks in characterised drug-resistant bacteria to iterate the importance of ‘mixed drugs’ treatments. The use of more than one antibiotic … Continue reading

31/07/2014 · 5 Comments


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