---

• Publications
• Teaching
• Previous Labs
• Academic Services
• Links

---

Christophe Dessimoz

I am a visiting scientist in the group of Nick Goldman at the European Bioinformatics Institute (EBI). I am supported by an advanced researcher fellowship from the Swiss National Science Foundation. My secondary affiliations are: research associate in Gaston Gonnet's group, ETH Zurich; member of Swiss Institute of Bioinformatics; affiliated teaching staff at Cambridge Computational Biology Institute, University of Cambridge.

My research seeks to understand the forces that shape genes, genomes, and species, using computational and statistical methods. Currently, I am particularly interested in

• large-scale identification of orthologs
• phylogenetic tree reconstruction
• model/method assessment using real biological data
• biological sequence analysis
• Gene Ontology and gene function inference
• lateral gene transfer detection methods

Contact information:

European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK

Email: dessimoz at ebi dot ac dot uk
Phone: +44 1223 494 695
Fax: +44 1223 494 522

LinkedIn ⋅ Twitter ⋅ ReaderMeter ⋅ Mendeley ⋅ Google Scholar

For internship opportunities, please consult this page.

 

Publications

2012

28. Nives Škunca, Adrian Altenhoff, Christophe Dessimoz
    Quality of Computationally Inferred Gene Ontology Annotations
    PLoS Computational Biology, in press [email me for a preprint]
27. Adrian Altenhoff, Romain Studer, Marc Robinson-Rechavi, Christophe Dessimoz
    Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs
    PLoS Computational Biology, in press [email me for a preprint]
26. Christophe Dessimoz, Toni Gabaldón, David S Roos, Erik LL Sonnhammer, Javier Herrero, and the Quest for Orthologs Consortium
    Toward community standards in the quest for orthologs
    Bioinformatics, 2012, 28:6 (pp.900-904) [Open Access]
25. Adrian Altenhoff and Christophe Dessimoz
    Inferring Orthology and Paralogy
    Evolutionary Genomics: Statistical and Computational methods (M Anisimova, Editor),
    Methods in Molecular Biology, 2012, Springer Humana, Vol. 855. [Abstract]
24. Daniel A. Dalquen, Maria Anisimova, Gaston H. Gonnet, Christophe Dessimoz
    ALF - A Simulation Framework for Genome Evolution
    Molecular Biology and Evolution, 2012, 29:4 (pp. 1115-1123) [Open Access]

2011

23. Christophe Dessimoz
    Editorial: Orthology and Applications
    Briefings in Bioinformatics, 2011, 12:5 (pp. 375-376) [Extract]
22. Christophe Dessimoz, Stefan Zoller, Tereza Manousaki, Huan Qiu, Axel Meyer, Shigehiro Kuraku
    Comparative genomics approach to detecting split coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)
    Briefings in Bioinformatics, 2011, 12:5 (pp. 423-435) [Open Access]
21. Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz
    Conceptual Framework and Pilot Study to Benchmark Phylogenomic Databases Based on Reference Gene Trees
    Briefings in Bioinformatics, 2011, 12:5 (pp. 474-484) [Open Access]
20. Maria Anisimova, Manuel Gil, Jean-François Dufayard, Christophe Dessimoz, Olivier Gascuel
    Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes.
    Systematic Biology, 2011, 60:5 (pp. 685-699) [Open Access]
19. Judith Owiti, Jonas Grossmann, Peter Gehrig, Christophe Dessimoz, Christophe Laloi, Maria Ben Hansen, Wilhelm Gruissem, Hervé Vanderschuren
    iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration
    The Plant Journal, 2011, 67:1 (pp. 145-156) [Abstract]
18. Louis du Plessis, Nives Škunca, Christophe Dessimoz
    The What, Where, How, and Why of Gene Ontology -- A Primer for Bioinformaticians
    Briefings in Bioinformatics, 2011, 12:6 (pp. 723-735) [Open Access]
17. Christian Ledergerber and Christophe Dessimoz
    Base-Calling for Next-Generation Sequencing Platforms
    Briefings in Bioinformatics, 2011, 12:5 (pp. 489-497) [Open Access]
16. Adrian Altenhoff, Adrian Schneider, Gaston H Gonnet, Christophe Dessimoz
    OMA 2011: Orthology Inference Among 1,000 Complete Genomes
    Nucleic Acids Research, 2011, 39 (suppl 1): D289-D294 [Open Access] [Project Page]

2010

15. Christophe Dessimoz and Manuel Gil ^{(equal contribution)}
    Phylogenetic assessment of alignments reveals neglected tree signal in gaps
    Genome Biology, 2010, 11:R37 [Open Access] [Raw Data]
    

2009

14. Toni Gabaldón, Christophe Dessimoz, Julie Huxley-Jones, Albert J Vilella, Erik LL Sonnhammer, Suzanna Lewis
    Joining forces in the quest for orthologs
    Genome Biology 2009, 10:403 [Free Access]
    
13. Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, Jacques Rougemont
    The Microbe Browser for Comparative Genomics
    Nucleic Acids Research, 2009, 37 (suppl 2): W296-W299. [Open Access] [Project Page]
12. Adrian Altenhoff and Christophe Dessimoz
    Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
    PLoS Computational Biology, 2009, 5:1, e1000262 [Open Access]

2008

11. Alexander Roth, Gaston H. Gonnet, Christophe Dessimoz
    Algorithm of OMA for Large-Scale Orthology Inference
    BMC Bioinformatics, 2008, 9:518 [Open Access] [Project Page]
    (Please note the associated erratum)
10. Mark T. Holder, Derrick J. Zwickl, Christophe Dessimoz
    Evaluating the Robustness of Phylogenetic Methods to Among-Site Variability in Substitution Processes
    Phil. Trans. R. Soc. B, 2008, 363:1512 (pp. 4013-4021) [Open Access]
9. Adam M Szalkowski, Christian Ledergerber, Philipp Krähenbühl, Christophe Dessimoz
   SWPS3 - Fast Multi-Threaded Vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2
   BMC Research Notes, 2008, 1:107 [Open Access] [Project Page]
8. Christophe Dessimoz and Manuel Gil ^{(equal contribution)}
   Covariance of Maximum Likelihood Evolutionary Distances between Sequences Aligned Pairwise
   BMC Evolutionary Biology, 2008, 8:179 [Open Access]
7. Christophe Dessimoz, Daniel Margadant, Gaston H. Gonnet
   DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework
   RECOMB 2008, LNCS 4955 (pp. 315-330) [Abstract]

2007

6. Christian Ledergerber and Christophe Dessimoz
   Alignments with Non-overlapping Moves, Inversions and Tandem Duplications in O(n⁴) time
   COCOON 2007, LNCS 4598 (pp. 151-164) [Abstract]
   selected for publication in Journal of Combinatorial Optimization, 2008, 16:3 [Abstract]
5. Adrian Schneider, Christophe Dessimoz, Gaston H. Gonnet
   OMA Browser - Exploring orthologous relations across 352 complete genomes
   Bioinformatics, 2007, 23:16 (pp. 2180-2182) [Open Access] [Project Page]

2006

4. Christophe Dessimoz, Manuel Gil, Adrian Schneider, Gaston H. Gonnet
   Fast Estimation of the Difference between two PAM/JTT Evolutionary Distances in Triplets of Homologous Sequences
   BMC Bioinformatics, 2006, 7:529 [Open Access]
3. Christophe Dessimoz, Brigitte Boeckmann, Alexander Roth, Gaston H. Gonnet
   Detecting Non-Orthology in the COGs Database and Other Approaches Grouping Orthologs Using Genome-Specific Best Hits
   Nucleic Acids Res, 2006 34:11 (pp. 3309-3316) [Open Access]

2005

2. Manuel Gil, Christophe Dessimoz, Gaston H. Gonnet
   A Dimensionless Fit Measure for Phylogenetic Distance Trees
   J Bioinform Comput Biol, 2005, 3:6 (pp. 1429-1440) [Abstract]
1. Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander Roth, Adrian Schneider, Gaston H. Gonnet
   OMA, a Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements
   RECOMB 2005 Workshop on Comparative Genomics, LNCS 3678 (pp. 61-72) [Abstract] [Project Page]

(back to top)

Teaching

Students interested in working on a project with me should consult this page!

• Lecturer:
  • Reviews in Computational Biology, University of Cambridge (2012)
  • Reviews in Computational Biology, ETH Zurich (2010, 2011)
  • Bioinformatics: in-depth, ETH Zurich (2011)
  • Computational Biology, ETH Zurich (2010)
• Guest lecturer:
  • EMBO Bioinformatics and Comparative Genome Analysis course, Institut Pasteur (2011)
  • Bioinformatics and Comparative Genome Analysis, Institut Pasteur (2010)
  • Computational Biology, ETH Zurich (2009)
  • Probabilistic Modeling in Molecular Evolution, ETH Zurich (2008, 2009)
  • Introduction to Bioinformatics I, University of Basel (2006, 2007, 2008, 2009)
  • Bioinformatik: Vertiefung, ETH and Uni Zurich (2008)
• Teaching assistant:
  • Foundations of Computer Science: Computational Science (2007, 2007, 2008, 2008, 2009, 2009)
  • Scientific Computing (2007)
  • Introduction to Computational Science (2006-2007)
  • Datenstrukturen und Algorithmen (2006)
  • Linear Algebra (2005-2006)
  • Informatik II (2005)

(back to top)

Previous Labs

• Group of Gaston Gonnet at ETH Zurich, Switzerland (2004-2011)
• Group of Chidchanok Lursinsap at Chulalongkorn University, Thailand (2004)
• Group of Guo-Qiang Chen at Tsinghua University, China (2003)
• Group of Vassily Hatzimanikatis at Northwestern University (now at EPFL), USA (2002)
• Group of Matt Parsek at Northwestern University (now at University of Washington), USA (2002)

(back to top)

Academic organizations and services

• Guest editor for Briefings in Bioinformatics
• Reviewer for Systematic Biology, Genome Biology, Nucleic Acids Research, Molecular Biology and Evolution, Briefings in Bioinformatics, Bioinformatics, PLoS One, BMC Genomics, BMC Evolutionary Biology, BMC Bioinformatics, Algorithms for Molecular Biology, IEEE Transactions on Signal Processing, Gene, Genomics, Information Sciences.
• Member of programme committee of ECCB 2012
• Co-organizer of Quest for Orthologs 2, Hinxton (UK), 17-19 June 2011
• Co-organizer of Zurich Colloquium for Computational Molecular Evolution
• Co-organizer of PhyloSIB 2009
• Co-founder of Young European Biotech Network
• Co-organizer of conference STARTbiotech 2001

(back to top)

Links

• OMA Browser, which classifies proteins from 1,109 species into families of orthologs.
• Quest for Orthologs, the community website
• Friends and collaborators: Adrian Altenhoff, Maria Anisimova, Brigitte Boeckmann, Gina Cannarozzi, Manuel Gil, Javier Herrero, Katzutaka Katoh, Shigehiro Kuraku, Matthieu Muffato, Marc Robinson-Rechavi, Adrian Schneider, Botond Sipos, Hervé Vanderschuren, Albert Vilella

(back to top)

---

This page was last modified on May 1st, 2012.