Science, discussed.

Category Archives: Computational Biology

Data mining & image-based phenotyping: The fight against plant disease

Current predictions for food security in the year 2050 look pretty dire to be honest. If the global population reaches the forecasted ~9 billion, then our overall food production will somehow … Continue reading

02/02/2017 · Leave a comment

Discovering genetic variants from de novo assembly of high-throughput sequencing

High-throughput sequencing is dominating genetics research (and a lot of biotech) because of its speed, low cost, and the resulting abundance of data.  But it still has some major shortcomings.  … Continue reading

02/05/2015 · Leave a comment

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 dual role of Transcription Factors in protein evolution, revisited

In December 2013, Stergachis and colleagues published a high-profile paper on the dual role Transcription Factors (TFs) might have as a consequence of their binding to protein coding regions. This observation could … Continue reading

15/01/2015 · 2 Comments

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

Biophysics of protein evolution and evolutionary protein biophysics

I am the co-author of a recent headline review in the Journal of the Royal Society Interface with the title “Biophysics of protein evolution and evolutionary protein biophysics“. All headline reviews … Continue reading

09/09/2014 · 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

[review] Computational stability analysis to reveal functional hotspot?

I was reading the following paper Stability-activity tradeoffs constrain the adaptive evolution of RubisCO Romain A. Studer, Pascal-Antoine Christin, Mark A. Williams, and Christine A. Orengo PNAS 2014 111 (6) 2223-2228 reading

21/05/2014 · 2 Comments


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