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Dessimoz Group - Computational Evolutionary Biology and Genomics

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At the interface between biology and computer science, our laboratory seeks to better understand evolutionary and functional relationships between genes, genomes, and species.

For more information on our lab, please consult the page http://lab.dessimoz.org

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Publications

2012 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 |

2012

Inferring Orthology and Paralogy

Altenhoff Adrian M, Dessimoz Christophe, 2012. pp. 259--279 dans Anisimova Maria (eds.) Evolutionary Genomics, Humana Press.

[serval:BIB_FF6699240132]

2017

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference.

Train C.M., Glover N.M., Gonnet G.H., Altenhoff A.M., Dessimoz C., 2017/07/15. Bioinformatics, 33 (14) pp. i75-i82. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_CB5253715961]

preview resource BIB_0B9096E627F3.P001

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.

Jeffares D.C., Jolly C., Hoti M., Speed D., Shaw L., Rallis C., Balloux F., Dessimoz C., Bähler J., Sedlazeck F.J., 2017/01/24. Nature communications, 8 p. 14061. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_0B9096E627F3]

preview resource BIB_CBFCF5FD756A.P001

Gene Ontology: Pitfalls, Biases, and Remedies.

Gaudet P., Dessimoz C., 2017. Methods in molecular biology (Clifton, N.J.), 1446 pp. 189-205. Peer-reviewed.

[DOI] [Pmid] [serval:BIB_CBFCF5FD756A]

Primer on the Gene Ontology.

Gaudet P., Škunca N., Hu J.C., Dessimoz C., 2017. Methods in molecular biology (Clifton, N.J.), 1446 pp. 25-37. Peer-reviewed.

[DOI] [Pmid] [serval:BIB_E02D84F1D7CD]

Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: the fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.

Suchan T., Espíndola A., Rutschmann S., Emerson B.C., Gori K., Dessimoz C., Arrigo N., Ronikier M., Alvarez N., 2017. Molecular Phylogenetics and Evolution, 114 pp. 189-198. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_1CBC34940B2F]

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

Train C.-M., Glover N.M., Gonnet G.H., Altenhoff A.M., Dessimoz C., 2017. Bioinformatics, 33 (14) pp. i75-i82.

[DOI] [WoS] [serval:BIB_7D03376859BC]

preview resource BIB_66353CA228EE.P001

Comparative genomics reveals contraction in olfactory receptor genes in bats.

Tsagkogeorga G., Müller S., Dessimoz C., Rossiter S.J., 2017. Scientific Reports, 7 (1) p. 259. Peer-reviewed.

[URN] [DOI] [Pmid] [serval:BIB_66353CA228EE]

A Gene Ontology Tutorial in Python.

Vesztrocy A.W., Dessimoz C., 2017. Methods in molecular biology (Clifton, N.J.), 1446 pp. 221-229. Peer-reviewed.

[DOI] [Pmid] [serval:BIB_6D82D9E2A2D4]

2016

preview resource BIB_3564C07C1354.P001

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y., Oron T.R., Clark W.T., Bankapur A.R., D'Andrea D., Lepore R., Funk C.S., Kahanda I., Verspoor K.M., Ben-Hur A. et al., 2016/09/07. Genome Biology, 17 (1) p. 184. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_3564C07C1354]

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.

Robinson O., Dylus D., Dessimoz C., 2016/08. Molecular biology and evolution, 33 (8) pp. 2163-2166. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_82CD43EFE497]

Clustering Genes of Common Evolutionary History.

Gori K., Suchan T., Alvarez N., Goldman N., Dessimoz C., 2016/06. Molecular biology and evolution, 33 (6) pp. 1590-1605. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_36DE5D65E7A5]

Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome.

Zimmer F., Harrison P.W., Dessimoz C., Mank J.E., 2016/04/25. Genome biology and evolution, 8 (4) pp. 1233-1242.

[DOI] [Pmid] [serval:BIB_7DFE950E8AB0]

Standardized benchmarking in the quest for orthologs.

Altenhoff A.M., Boeckmann B., Capella-Gutierrez S., Dalquen D.A., DeLuca T., Forslund K., Huerta-Cepas J., Linard B., Pereira C., Pryszcz L.P. et al., 2016. Nature Methods, 13 (5) pp. 425-430. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_E8F5620D5F4F]

preview resource BIB_59A0CA77B84B.P001

Homoeologs: What Are They and How Do We Infer Them?

Glover N.M., Redestig H., Dessimoz C., 2016. Trends in Plant Science, 21 (7) pp. 609-621. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_59A0CA77B84B]

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y., Oron T.R., Clark W.T., Bankapur A.R., D'Andrea D., Lepore R., Funk C.S., Kahanda I., Verspoor K.M., Ben-Hur A. et al., 2016. Genome Biology, 17 (1) p. 184.

[DOI] [Pmid] [serval:BIB_0DA5AAECE9FC]

Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life.

Sojo V., Dessimoz C., Pomiankowski A., Lane N., 2016. Molecular Biology and Evolution, 33 (11) pp. 2874-2884. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_6990F70049C3]

2015

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

Altenhoff Adrian M, Skunca Nives, Glover Natasha, Train Clément-Marie, Sueki Anna, Pilizota Ivana, Gori Kevin, Tomiczek Bartlomiej, Müller Steven, Redestig Henning et al., 2015. Nucleic acids research, 43 (Database issue) pp. D240--9.

[serval:BIB_0E374421DCD4]

A transcriptomic-phylogenomic analysis of the evolutionary relationships of flatworms.

Egger B., Lapraz F., Tomiczek B., Müller S., Dessimoz C., Girstmair J., Škunca N., Rawlinson K.A., Cameron C.B., Beli E. et al., 2015. Current Biology, 25 (10) pp. 1347-1353.

[DOI] [WoS] [Pmid] [serval:BIB_79C6402C984D]

A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms

Egger Bernhard, Lapraz François, Tomiczek Bartlomiej, Müller Steven, Dessimoz Christophe, Girstmair Johannes, Škunca Nives, Rawlinson Kate A, Cameron Christopher B, Beli Elena et al., 2015. Current Biology, 0 (0).

[serval:BIB_0A671BDD4514]

Inferring horizontal gene transfer.

Ravenhall M., Skunca N., Lassalle F., Dessimoz C., 2015. Plos Computational Biology, 11 (5) pp. e1004095.

[DOI] [Pmid] [serval:BIB_FBA48DA66EEC]

preview resource BIB_BCB3501714F5.P001

Phylogenetic profiling: how much input data is enough?

Skunca N., Dessimoz C., 2015. Plos One, 10 (2) pp. e0114701. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_BCB3501714F5]

Phylogenetic profiling: how much input data is enough?

Skunca Nives, Dessimoz Christophe, 2015. PloS one, 10 (2) pp. e0114701.

[serval:BIB_45596BAA4E2A]

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

Tan G., Muffato M., Ledergerber C., Herrero J., Goldman N., Gil M., Dessimoz C., 2015. Systematic Biology, 64 (5) pp. 778-791. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_0502FCD9284A]

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks

Tan Ge, Gil Manuel, Löytynoja Ari P, Goldman Nick, Dessimoz Christophe, 2015. Proceedings of the National Academy of Sciences of the United States of America, 112 (2) pp. E99--100.

[serval:BIB_F254BAC3EDC5]

2014

Preface of Proceedings of GNOME 2014 - Festschrift for Gaston Gonnet

Anisimova Maria, Dessimoz Christophe, 2014/06. dans PeerJ (eds.) Proceedings of GNOME 2014 - Festschrift for Gaston Gonnet, Anisimova Maria Dessimoz Christophe.

[DOI] [serval:BIB_725B398DA464]

Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment

Iantorno Stefano, Gori Kevin, Goldman Nick, Gil Manuel, Dessimoz Christophe, 2014. Methods in molecular biology, 1079 pp. 59--73.

[serval:BIB_31AE496B81C6]

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

Peng Xinxia, Alföldi Jessica, Gori Kevin, Eisfeld Amie J, Tyler Scott R, Tisoncik-Go Jennifer, Brawand David, Law G Lynn, Skunca Nives, Hatta Masato et al., 2014. Nature biotechnology, 32 (12) pp. 1250--1255.

[serval:BIB_26A47AF7E788]

preview resource BIB_172DE4708266.P001

Big data and other challenges in the quest for orthologs.

Sonnhammer E.L., Gabaldón T., Sousa da Silva A.W., Martin M., Robinson-Rechavi M., Boeckmann B., Thomas P.D., Dessimoz C., Quest for Orthologs consortium, 2014. Bioinformatics, 30 (21) pp. 2993-2998. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_172DE4708266]

Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology

Wittwer Lucas D, Pili\v zota Ivana , Altenhoff Adrian M, Dessimoz Christophe, 2014. PeerJ, 2 pp. e607.

[serval:BIB_B76A236F7D81]

2013

CAFA and the Open World of protein function predictions

Dessimoz Christophe, Skunca Nives, Thomas Paul D, 2013/11. Trends in genetics: TIG, 29 (11) pp. 609--610.

[serval:BIB_C85C198416B5]

Global regulatory architecture of human, mouse and rat tissue transcriptomes

Prasad Ajay, Kumar Suchitra Suresh, Dessimoz Christophe, Jaquet Vincent, Bleuler Stefan, Laule Oliver, Hruz Tomas, Gruissem Wilhelm, Zimmermann Philip, 2013/10. BMC genomics, 14 (1) p. 716.

[serval:BIB_D8F8780B6342]

Inferring hierarchical orthologous groups from orthologous gene pairs

Altenhoff Adrian M, Gil Manuel, Gonnet Gaston H, Dessimoz Christophe, 2013/01. PloS one, 8 (1) pp. e53786.

[serval:BIB_DEA8020C3933]

The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study

Dalquen Daniel a, Altenhoff Adrian M, Gonnet Gaston H, Dessimoz Christophe, 2013/01. PloS one, 8 (2) pp. e56925.

[serval:BIB_652F89310896]

Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals

Dalquen Daniel a, Dessimoz Christophe, 2013/01. Genome biology and evolution, 5 (10) pp. 1800--1806.

[serval:BIB_7C82C59EB068]

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

Goldman Nick, Bertone Paul, Chen Siyuan, Dessimoz Christophe, LeProust Emily M., Sipos Botond, Birney Ewan, 2013/01. Nature pp. 3--6.

[serval:BIB_091D03CCEC05]

Approximate bayesian computation

Sunn\aaker Mikael , Busetto Alberto Giovanni, Numminen Elina, Corander Jukka, Foll Matthieu, Dessimoz Christophe, 2013/01. PLoS computational biology, 9 (1) pp. e1002803.

[serval:BIB_D54B852FAC4E]

Stocker de l'information dans l'ADN

Dessimoz Christophe, 2013. Pour la Science 433 pp. 100--101.

[serval:BIB_F98818C2C8AC]

2012

Quality of Computationally Inferred Gene Ontology Annotations

\v Skunca Nives , Altenhoff Adrian, Dessimoz Christophe, 2012/05. PLoS computational biology, 8 (5) pp. e1002533.

[serval:BIB_525FDA1869E8]

ALF--a simulation framework for genome evolution

Dalquen Daniel A, Anisimova Maria, Gonnet Gaston H, Dessimoz Christophe, 2012/04. Molecular biology and evolution, 29 (4) pp. 1115-1123.

[serval:BIB_641A5E38B3A5]

preview resource BIB_89CB0AF6A1E2.P001

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.

Altenhoff A.M., Studer R.A., Robinson-Rechavi M., Dessimoz C., 2012. PLoS Computational Biology, 8 (5) pp. e1002514. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_89CB0AF6A1E2]

Toward community standards in the quest for orthologs

Dessimoz Christophe, Gabaldón Toni, Roos David S, Sonnhammer Erik L L, Herrero Javier, Quest for Orthologs Consortium, 2012. Bioinformatics, 28 (6) pp. 900--904.

[serval:BIB_177E579E584A]

2011

The what, where, how and why of gene ontology--a primer for bioinformaticians

du Plessis Louis, Skunca Nives, Dessimoz Christophe, 2011/11. Briefings in bioinformatics, 12 (6) pp. 723--735.

[serval:BIB_6D5987791C0E]

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

Boeckmann Brigitte, Robinson-Rechavi Marc, Xenarios Ioannis, Dessimoz Christophe, 2011/09. Briefings in bioinformatics, 12 (5) pp. 423--435.

[serval:BIB_681D2626FED2]

Editorial: Orthology and applications

Dessimoz Christophe, 2011/09. Briefings in bioinformatics, 12 (5) pp. 375--376.

[serval:BIB_E0791C68A104]

Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)

Dessimoz Christophe, Zoller Stefan, Manousaki Tereza, Qiu Huan, Meyer Axel, Kuraku Shigehiro, 2011/09. Briefings in bioinformatics, 12 (5) pp. 474--484.

[serval:BIB_96D140B39629]

Base-calling for next-generation sequencing platforms

Ledergerber Christian, Dessimoz Christophe, 2011/09. Briefings in bioinformatics, 12 (5) pp. 489--497.

[serval:BIB_05FCA3137E8F]

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

Anisimova Maria, Gil Manuel, Dufayard Jean-Fran\c cois , Dessimoz Christophe, Gascuel Olivier, 2011/05. Systematic biology, 60 (Mcmc) pp. 685--699.

[serval:BIB_9E20AFF0611F]

OMA 2011: orthology inference among 1000 complete genomes

Altenhoff Adrian M, Schneider Adrian, Gonnet Gaston H, Dessimoz Christophe, 2011/01. Nucleic acids research, 39 (Database issue) pp. D289-94.

[serval:BIB_94EE58DC5EFD]

preview resource BIB_3EF9A7BDC38C.P001

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.

Boeckmann B., Robinson-Rechavi M., Xenarios I., Dessimoz C., 2011. Briefings in Bioinformatics, 12 (5) pp. 423-435. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_3EF9A7BDC38C]

iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration

Owiti Judith, Grossmann Jonas, Gehrig Peter, Dessimoz Christophe, Laloi Christophe, Hansen Maria Benn, Gruissem Wilhelm, Vanderschuren Hervé, 2011. The Plant journal: for cell and molecular biology, 67 (1) pp. 145--156.

[serval:BIB_AED332924163]

2010

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

Dessimoz Christophe, Gil Manuel, 2010/01. Genome biology, 11 (4) pp. R37.

[serval:BIB_4D1B6AAE858E]

2009

The Microbe browser for comparative genomics

Gattiker Alexandre, Dessimoz Christophe, Schneider Adrian, Xenarios Ioannis, Pagni Marco, Rougemont Jacques, 2009/07. Nucleic acids research, 37 (Web Server issue) pp. W296--W299.

[serval:BIB_D85F2A63F2FA]

Phylogenetic and functional assessment of orthologs inference projects and methods

Altenhoff Adrian M, Dessimoz Christophe, 2009/01. PLoS computational biology, 5 (1) pp. e1000262.

[serval:BIB_735B6D029A2B]

Joining forces in the quest for orthologs

Gabaldón Toni, Dessimoz Christophe, Huxley-Jones Julie, Vilella Albert J, Sonnhammer Erik LL, Lewis Suzanna, 2009/01. Genome biology, 10 (9) p. 403.

[serval:BIB_4A536B2784A1]

2008

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes

Holder Mark T, Zwickl Derrick J, Dessimoz Christophe, 2008/12. Philosophical Transactions of the Royal Society of London - Series B: Biological Sciences, 363 (1512) pp. 4013--4021.

[serval:BIB_A5FD05AE6696]

Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise

Dessimoz Christophe, Gil Manuel, 2008/01. BMC evolutionary biology, 8 p. 179.

[serval:BIB_651CD9B99386]

SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2

Szalkowski Adam, Ledergerber Christian, Krähenbühl Philipp, Dessimoz Christophe, 2008/01. BMC research notes, 1 p. 107.

[serval:BIB_4C3D135AFA55]

DLIGHT: lateral gene transfer detection using pairwise evolutionary distances in a statistical framework

Dessimoz Christophe, Margadant Daniel, Gonnet GH, 2008. pp. 315--330 dans Proceedings of the 12th annual international conference on Research in computational molecular biology, Springer-Verlag.

[serval:BIB_CF95F2B7F6EF]

Algorithm of OMA for large-scale orthology inference

Roth Alexander C J, Gonnet Gaston H, Dessimoz Christophe, 2008. BMC bioinformatics, 9 p. 518.

[serval:BIB_2FB29FA83B67]

Correction: Algorithm of OMA for large-scale orthology inference

Roth Alexander CJ, Gonnet Gaston H, Dessimoz Christophe, 2008. BMC bioinformatics, 9 (1) p. 518.

[serval:BIB_7A8BBD358CA3]

2007

Alignments with non-overlapping moves, inversions and tandem duplications in O(n 4) time

Ledergerber Christian, Dessimoz Christophe, 2007/12. Journal of combinatorial optimization, 16 (3) pp. 263--278.

[serval:BIB_A1C5298D8400]

OMA Browser--exploring orthologous relations across 352 complete genomes

Schneider Adrian, Dessimoz Christophe, Gonnet Gaston H, 2007/08. Bioinformatics, 23 (16) pp. 2180--2182.

[serval:BIB_FD23CDB93C4F]

2006

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits

Dessimoz Christophe, Boeckmann Brigitte, Roth Alexander C J, Gonnet Gaston H, 2006/01. Nucleic acids research, 34 (11) pp. 3309--3316.

[serval:BIB_D4B459DAA022]

Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences

Dessimoz Christophe, Gil Manuel, Schneider Adrian, Gonnet Gaston H, 2006/01. BMC bioinformatics, 7 p. 529.

[serval:BIB_CD95449A66C0]

2005

A dimensionless fit measure for phylogenetic distance trees

Gil Manuel, Dessimoz Christophe, Gonnet Gaston H, 2005/12. Journal of bioinformatics and computational biology, 3 (6) pp. 1429--1440.

[serval:BIB_647B72A3D448]

OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements

Dessimoz Christophe, Cannarozzi Gina, Gil Manuel, Margadant Daniel, Roth Alexander, Schneider Adrian, Gonnet G, 2005. pp. 61--72 dans McLysaght Aoife, Huson Daniel H (eds.) RECOMB 2005 Workshop on Comparative Genomics, Springer-Verlag.

[serval:BIB_1F40B385C8DE]

Group leader

Prof. Christophe Dessimoz

Staff & postdocs

Dr. Adrian Altenhoff, OMA Project Manager (based at ETH Zurich)
Dr. Tugce Bilgin Sonay
Dr. David Dylus (based on University of Lausanne)
Dr. Natasha Glover (based on University of Lausanne)
Dr. Tarcisio Mendes De Farias
Dr. Leornado De Oliveira (based on University of Lausanne)
Dr. Nives Škunca (based at ETH Zurich)

PhD students

Kevin Gori (based at EMBL-EBI, co-supervised by Dr. Nick Goldman)
Jessica Joaquim
Jeremy Levy, CoMPLEX student (based at UCL, co-supervised by Prof. Max Telford)
Steven Müller (based at UCL, co-supervised by Prof. Max Telford)
Ivana Piližota, Impact student (based at UCL, co-supervised by Dr. Henning Redestig, Bayer CropScience)
Bartlomiej Tomiczek (based at UCL, co-supervised by Prof. Max Telford)
Clément Train
Tom Watkins (based at Crick, co-supervised by Prof. Charles Swanton, CRUK)

Interns & project students

Abraham Olaoye, CS summer intern
Oscar Robinson, CS summer intern
Jan Koch, Erasmus student
Clément-Marie Train, MSc project student

External collaborators

Raphaëlle Luisier

Search:

Office room: 4155
Phone: +4121 692 4270
Fax: +4121 692 4165
christophe.dessimoz[@]unil.ch

Administrative assistant
Office room: 3106
Phone: +41 21 692 4200
Fax: +41 21 692 4165
anne.cuendet[@]unil.ch

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Biophore - CH-1015 Lausanne - Switzerland - Tel. +41 21 692 41 60 - Fax +41 21 692 41 65