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
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
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
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
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
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
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
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
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 http://dx.doi.org/10.1101/008250 where they show the … Continue reading
[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 http://dx.doi.org/10.1073/pnas.1310811111 … Continue reading
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