Romain Studer

Romain Studer

Scientist - Postdoc - Beltrao research group

ORCID iD: 0000-0003-0687-9848

Tel:+ 44 (0) 1223 492 547 / Fax:+ 44 (0) 1223 494 468

Publications

2014

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO.
Studer RA, Christin PA, Williams MA, Orengo CA.
Proc Natl Acad Sci U S A Volume 111 (2014) p.2223-2228
DOI: 10.1073/pnas.1310811111

Selectome update: quality control and computational improvements to a database of positive selection.
Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M.
Nucleic Acids Res Volume 42 (2014) p.d917-21
DOI: 10.1093/nar/gkt1065

Understanding the functional difference between growth arrest-specific protein 6 and protein S: an evolutionary approach.
Studer RA, Opperdoes FR, Nicolaes GA, Mulder AB, Mulder R.
Open Biol Volume 4 (2014) p.
DOI: 10.1098/rsob.140121

CATH: comprehensive structural and functional annotations for genome sequences.
Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA.
Nucleic Acids Res Volume (2014) p.
DOI: 10.1093/nar/gku947

Positive selection during the evolution of the blood coagulation factors in the context of their disease-causing mutations.
Rallapalli PM, Orengo CA, Studer RA, Perkins SJ.
Mol Biol Evol Volume 31 (2014) p.3040-3056
DOI: 10.1093/molbev/msu248

Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.
Lees JG, Lee D, Studer RA, Dawson NL, Sillitoe I, Das S, Yeats C, Dessailly BH, Rentzsch R, Orengo CA.
Nucleic Acids Res Volume 42 (2014) p.d240-5
DOI: 10.1093/nar/gkt1205

2013

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA.
Nucleic Acids Res Volume 41 (2013) p.d490-8
DOI: 10.1093/nar/gks1211

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes.
Studer RA, Dessailly BH, Orengo CA.
Biochem J Volume 449 (2013) p.581-594
DOI: 10.1042/bj20121221

Vitellogenin underwent subfunctionalization to acquire caste and behavioral specific expression in the harvester ant Pogonomyrmex barbatus.
Corona M, Libbrecht R, Wurm Y, Riba-Grognuz O, Studer RA, Keller L.
PLoS Genet Volume 9 (2013) p.e1003730
DOI: 10.1371/journal.pgen.1003730

2012

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.
Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C.
PLoS Comput Biol Volume 8 (2012) p.e1002514
DOI: 10.1371/journal.pcbi.1002514

2011

Evolution of the epithelial sodium channel and the sodium pump as limiting factors of aldosterone action on sodium transport.
Studer RA, Person E, Robinson-Rechavi M, Rossier BC.
Physiol Genomics Volume 43 (2011) p.844-854
DOI: 10.1152/physiolgenomics.00002.2011

2010

Adaptive divergence of ancient gene duplicates in the avian MHC class II beta.
Burri R, Salamin N, Studer RA, Roulin A, Fumagalli L.
Mol Biol Evol Volume 27 (2010) p.2360-2374
DOI: 10.1093/molbev/msq120

Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution.
Studer RA, Robinson-Rechavi M.
Mol Biol Evol Volume 27 (2010) p.2618-2627
DOI: 10.1093/molbev/msq149

2009

Structural and evolutionary innovation of the heterodimerization interface between USP and the ecdysone receptor ECR in insects.
Iwema T, Chaumot A, Studer RA, Robinson-Rechavi M, Billas IM, Moras D, Laudet V, Bonneton F.
Mol Biol Evol Volume 26 (2009) p.753-768
DOI: 10.1093/molbev/msn302

Selectome: a database of positive selection.
Proux E, Studer RA, Moretti S, Robinson-Rechavi M.
Nucleic Acids Res Volume 37 (2009) p.d404-7
DOI: 10.1093/nar/gkn768

Evidence for an episodic model of protein sequence evolution.
Studer RA, Robinson-Rechavi M.
Biochem Soc Trans Volume 37 (2009) p.783-786
DOI: 10.1042/bst0370783

How confident can we be that orthologs are similar, but paralogs differ?
Studer RA, Robinson-Rechavi M.
Trends Genet Volume 25 (2009) p.210-216
DOI: 10.1016/j.tig.2009.03.004

2008

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes.
Studer RA, Penel S, Duret L, Robinson-Rechavi M.
Genome Res Volume 18 (2008) p.1393-1402
DOI: 10.1101/gr.076992.108