Romain Studer

Romain Studer

Postdoctoral Fellow - Beltrao research group

My research interest is to study the evolution of biological systems by integrating knowledge from phylogenetic inference, structural information and biochemical function. I did my PhD at University of Lausanne (2005-2009), supervised by Prof. Marc Robinson-Rechavi. I studied the impact of whole-genome duplications in vertebrates’ evolution and initiated the development of Selectome, a database of positive selection. In 2010, I collaborated with Prof. Bernard Rossier (University of Lausanne) to work on the evolution of sodium regulation (Na,K-ATPase and ENaC). I then continued my own research at University College London within the lab of Prof. Christine Orengo (2010-2013). I conducted several evolutionary projects, on the RubisCO enzyme and on the coagulation system, and collaborated on the in-house database projects CATH and Gene3D. Since September 2013, I have been working at the European Bioinformatics Institute (EMBL-EBI) in Cambridge within the lab of Dr. Pedro Beltrao. I am now focusing on another level of complexity by analysing the evolution of posttranslational modification (PTM) of amino acids. I have supervised several students (Msc, PhD) and contributed to the organisation of tutorials at ECCB’12 and ECCB’14.

ORCID iD: 0000-0003-0687-9848

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



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 43 (2015) p.d376-81
DOI: 10.1093/nar/gku947

Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life.
Faddeeva A, Studer RA, Kraaijeveld K, Sie D, Ylstra B, Mariën J, op den Camp HJ, Datema E, den Dunnen JT, van Straalen NM, Roelofs D.
PLoS One Volume 10 (2015) p.e0130600
DOI: 10.1371/journal.pone.0130600

Epithelial sodium transport and its control by aldosterone: the story of our internal environment revisited.
Rossier BC, Baker ME, Studer RA.
Physiol Rev Volume 95 (2015) p.297-340
DOI: 10.1152/physrev.00011.2014

Origin of the response to adrenal and sex steroids: Roles of promiscuity and co-evolution of enzymes and steroid receptors.
Baker ME, Nelson DR, Studer RA.
J Steroid Biochem Mol Biol Volume 151 (2015) p.12-24
DOI: 10.1016/j.jsbmb.2014.10.020


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

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

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

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

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


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

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

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


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


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


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


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

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

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


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