Dr. Carsten Kemena

Postdoctoral Research Associate and Staff Scientist

Email: c.kemena@uni-muenster.de

Tel.: +49-(0)251-83-21632

Room: 100.17



  • since 03/2013: Postdoc, Westfälische Wilhelms-Universität Münster
  • 09/2008 – 12/2012: PhD Biomedicine, Thesis: “Improving the accuracy and efficiency of multiple sequence alignment methods”, Universitat Pompeu Fabra/Centre for Genomic Regulation, Barcelona, Spain
  • 10/2006 – 07/2008: M.Sc. Bioinformatics, Thesis: “Local and Global Alignment Construction using the Seed Approach”, Freie Universität Berlin, Berlin, Germany
  • 10/2003 – 09/2006: B.Sc. Bioinformatics and Genome Research, Thesis: "Algorithms on Enhanced Suffix Arrays and their Application in Bioinformatics”, Universität Bielefeld, Bielefeld Germany

Research Interests

I am currently mainly interested in software development to analyze protein domains, their arrangement and their evolutionary changes. The software that is developed by me and others in the group can be found on the following page: DomainWorld

Furthermore I am interested in multiple sequence alignments and in general methods for sequence analysis.


  • Coban A, Bornberg-Bauer E, Kemena C, "Domain Evolution of Vertebrate Blood Coagulation Cascade Proteins", Journal of Molecular Evolution, 2022
  • Dohmen E, Klasberg S, Bornberg-Bauer E, Perrey S, Kemena C, "The modular nature of protein evolution: domain rearrangement rates across eukaryotic life", BMC Evolutionary Biology, 2020
  • Kemena C, Dohmen E, Bornberg-Bauer E, "DOGMA: A web server for proteome and transcriptome quality assessment", Nucleic Acids Res., 2019
  • Kemena C, Bornberg-Bauer, "A roadmap to domain based proteomics", in Computational Methods in Protein Evolution, 2019
  • Jongepier E, Kemena C, Lopez-Ezquerra A, Belles X, Bornberg-Bauer E, Korb J, "Remodeling of the juvenile hormone pathway through caste-biased gene expression and positive selection along a gradient of termite eusociality", J Exp Zool B Mol Dev Evol, 2018
  • Harrison MC, Jongepier E, Robertson HM, ..., Kemena C, ... ,Belles X, Korb J, Bornberg-Bauer E, "Hemimetabolous genomes reveal molecular basis of termite eusociality", Nature Ecology & Evolution, 2018
  • Dohmen E, Kremer LPM, Bornberg-Bauer E and Kemena C, "DOGMA: Domain-based transcriptome and proteome quality assessment", Bioinformatics 2016
  • Chatzou M, Cedrik M, Chang J, Kemena C, Bussotti G, Erb I and Notredame C, "Multiple sequence alignment modeling: methods and applications", Brief. Bioinformatics 2015
  • Smith CR, Helms Cahan S, Kemena C , Brady SG, Yang W, Bornberg-Bauer E, Eriksson T, Gadau J, Helmpkampf M, Gotzek D, Miyakawa MO, Suarez A, and Mikheyev A, "How do genomes create novel phenotypes? Insights from the loss of the worker caste in ant social parasites", MBE 2015
  • Bitard Feildel T, Kemena C, Greenwood JM and Bornberg-Bauer E, "Domain similarity based orthology detection", BMC Bioionformatics 2015
  • Kemena C, Bitard Feildel T and Bornberg-Bauer E, "MDAT-Aligning multiple domain arrangements", BMC Bioinformatics 2015
  • Schrader L, Kim JW, Ence D, Zimin A, Klein A, Wyschetzki K, Weichselgartner T, Kemena C, Stökl J, Schultner E, Wurm Y, Smith CD, Yandell M, Heinze J, Gadau J and Oettler J, "Transposable element islands facilitate adaptation to novel environments in an invasive species", Nature Communications 2014
  • Earl D, Nguyen NK, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney B, Clawson H, Kim J, Kemena C, Chang J-M, Erb I, Poliakov A, Hou M, Herrero J, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D and Paten B, "Alignathon: A competitive assessment of whole genome alignment methods", Genome Research 2014
  • Di Tommaso P, Bussotti G, Kemena C, Capriotti E, Chatzou M, Prieto P and Notredame C, "SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments", Nucleic Acids Res 2014
  • Kemena C*, Bussotti G*, Capriotti E, Marti-Renom MA and Notredame C "Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package", Bioinformatics, 2013. (*shared first authorship)
  • Breen MS, Kemena C, Vlasov PK, Notredame C and Kondrashov FA, “Epistasis as the primary factor in molecular evolution” Nature, 2012
  • Orobitg M, Cores F, Guirado F, Kemena C, Notredame C and Ripoll A, "Enhancing the Scalability of Consistency-based Progressive Multiple Sequences Alignment Applications", IPDPS, pp 71-82 2012
  • Kemena C, Taly J-F, Kleinjung J and Notredame C, "STRIKE: evaluation of protein MSAs using a single 3D structure", Bioinformatics, vol. 27, no. 24, pp. 3385--3391 2011.
  • Taly J-F, Magis C, Bussotti G, Chang J-M, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C and Notredame C, "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", Nature Protocols, vol. 6, no. 11, pp. 1669--1682, 2011.
  • Kemena C and Notredame C, "Upcoming challenges for multiple sequence alignment methods in the high-throughput era", Bioinformatics, vol. 25, no. 19, pp. 2455--2465, 2009.

Teaching Experience

  • Supervision of Bachelor and Master theses
  • Forschungsmodule
  • Fortgeschrittenenmodule
  • organization and supervision of practicals