Christophe Dessimoz

Publications | Mémoires et thèses

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81 publications

2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 |
Advances and Applications in the Quest for Orthologs.
Glover N., Dessimoz C., Ebersberger I., Forslund S.K., Gabaldón T., Huerta-Cepas J., Martin M.J., Muffato M., Patricio M., Pereira C. et al., 2019/10/01. Molecular biology and evolution, 36 (10) pp. 2157-2164. Peer-reviewed.
iHam and pyHam: visualizing and processing hierarchical orthologous groups.
Train C.M., Pignatelli M., Altenhoff A., Dessimoz C., 2019/07/15. Bioinformatics, 35 (14) pp. 2504-2506. Peer-reviewed.
OMA standalone: orthology inference among public and custom genomes and transcriptomes.
Altenhoff A.M., Levy J., Zarowiecki M., Tomiczek B., Warwick Vesztrocy A., Dalquen D.A., Müller S., Telford M.J., Glover N.M., Dylus D. et al., 2019/07. Genome research, 29 (7) pp. 1152-1163. Peer-reviewed.
Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria.
Philippe H., Poustka A.J., Chiodin M., Hoff K.J., Dessimoz C., Tomiczek B., Schiffer P.H., Müller S., Domman D., Horn M. et al., 2019/06/03. Current Biology, 29 (11) pp. 1818-1826.e6. Peer-reviewed.
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.
Piližota I., Train C.M., Altenhoff A., Redestig H., Dessimoz C., 2019/04/01. Bioinformatics, 35 (7) pp. 1159-1166. Peer-reviewed.
Assigning confidence scores to homoeologs using fuzzy logic.
Glover N.M., Altenhoff A., Dessimoz C., 2019. PeerJ, 6 pp. e6231. Peer-reviewed.
Enabling semantic queries across federated bioinformatics databases
Sima Ana Claudia, Mendes de Farias Tarcisio, Zbinden Erich, Anisimova Maria, Gil Manuel, Stockinger Heinz, Stockinger Kurt, Robinson-Rechavi Marc, Dessimoz Christophe, 2019/01/01. Database, 2019. Peer-reviewed.
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python.
Kaleb K., Vesztrocy A.W., Altenhoff A., Dessimoz C., 2019. F1000Research, 8 p. 42. Peer-reviewed.
Inferring Orthology and Paralogy.
Altenhoff A.M., Glover N.M., Dessimoz C., 2019. Methods in molecular biology, 1910 pp. 149-175. Peer-reviewed.
VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links
Mendes de Farias Tarcisio, Stockinger Kurt, Dessimoz Christophe, 2019. Lecture Notes in Computer Science pp. 607-625. Peer-reviewed.
RecPhyloXML: a format for reconciled gene trees.
Duchemin W., Gence G., Arigon Chifolleau A.M., Arvestad L., Bansal M.S., Berry V., Boussau B., Chevenet F., Comte N., Davín A.A. et al., 2018/11/01. Bioinformatics, 34 (21) pp. 3646-3652. Peer-reviewed.
Prioritising candidate genes causing QTL using hierarchical orthologous groups.
Warwick Vesztrocy A., Dessimoz C., Redestig H., 2018/09/01. Bioinformatics, 34 (17) pp. i612-i619. Peer-reviewed.
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.
Altenhoff A.M., Glover N.M., Train C.M., Kaleb K., Warwick Vesztrocy A., Dylus D., de Farias T.M., Zile K., Stevenson C., Long J. et al., 2018/01/04. Nucleic acids research, 46 (D1) pp. D477-D485. Peer-reviewed.
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund K., Pereira C., Capella-Gutierrez S., Sousa da Silva A., Altenhoff A., Huerta-Cepas J., Muffato M., Patricio M., Vandepoele K., Ebersberger I. et al., 2018. Bioinformatics, 34 (2) pp. 323-329. Peer-reviewed.
Submit a Topic Page to PLOS Computational Biology and Wikipedia.
Mietchen D., Wodak S., Wasik S., Szostak N., Dessimoz C., 2018. PLoS Computational Biology, 14 (5) pp. e1006137. Peer-reviewed.
Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree
Boeckmann Brigitte, Dylus David, Moretti Sebastien, Altenhoff Adrian, Train Clement-Marie, Kriventseva Evgenia, Bougueleret Lydie, Xenarios Ioannis, Privman Eyal, Gabaldon Toni et al., 2017/09/05. biorxiv.
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.
A Gene Ontology Tutorial in Python.
Vesztrocy A.W., Dessimoz C., 2017. Methods in molecular biology, 1446 pp. 221-229. Peer-reviewed.
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.
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.
Gene Ontology: Pitfalls, Biases, and Remedies.
Gaudet P., Dessimoz C., 2017. Methods in molecular biology, 1446 pp. 189-205. Peer-reviewed.
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.
Primer on the Gene Ontology.
Gaudet P., Škunca N., Hu J.C., Dessimoz C., 2017. Methods in molecular biology, 1446 pp. 25-37. Peer-reviewed.
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. 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.
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.
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.
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.
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.
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.
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).
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.
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.
Inferring horizontal gene transfer.
Ravenhall M., Skunca N., Lassalle F., Dessimoz C., 2015. Plos Computational Biology, 11 (5) pp. e1004095.
Phylogenetic profiling: how much input data is enough?
Skunca N., Dessimoz C., 2015. Plos One, 10 (2) pp. e0114701. Peer-reviewed.
Phylogenetic profiling: how much input data is enough?
Skunca Nives, Dessimoz Christophe, 2015. PloS one, 10 (2) pp. e0114701.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Stocker de l'information dans l'ADN
Dessimoz Christophe, 2013. Pour la Science 433 pp. 100--101.
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.
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.
Quality of Computationally Inferred Gene Ontology Annotations
\v Skunca Nives , Altenhoff Adrian, Dessimoz Christophe, 2012/05. PLoS computational biology, 8 (5) pp. e1002533.
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.
Inferring Orthology and Paralogy
Altenhoff Adrian M., Dessimoz Christophe, 2012. pp. 259-279 dans Anisimova Maria (eds.) Methods in Molecular Biology, Humana Press.
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.
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.
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.
Base-calling for next-generation sequencing platforms
Ledergerber Christian, Dessimoz Christophe, 2011/09. Briefings in bioinformatics, 12 (5) pp. 489--497.
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.
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.
Editorial: Orthology and applications
Dessimoz Christophe, 2011/09. Briefings in bioinformatics, 12 (5) pp. 375--376.
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.
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.
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.
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.
Phylogenetic assessment of alignments reveals neglected tree signal in gaps
Dessimoz Christophe, Gil Manuel, 2010/01. Genome biology, 11 (4) pp. R37.
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.
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.
Phylogenetic and functional assessment of orthologs inference projects and methods
Altenhoff Adrian M, Dessimoz Christophe, 2009/01. PLoS computational biology, 5 (1) pp. e1000262.
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.
Algorithm of OMA for large-scale orthology inference
Roth Alexander C J, Gonnet Gaston H, Dessimoz Christophe, 2008. BMC bioinformatics, 9 p. 518.
Correction: Algorithm of OMA for large-scale orthology inference
Roth Alexander CJ, Gonnet Gaston H, Dessimoz Christophe, 2008. BMC bioinformatics, 9 (1) p. 518.
Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise
Dessimoz Christophe, Gil Manuel, 2008/01. BMC evolutionary biology, 8 p. 179.
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.
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.
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.
OMA Browser--exploring orthologous relations across 352 complete genomes
Schneider Adrian, Dessimoz Christophe, Gonnet Gaston H, 2007/08. Bioinformatics, 23 (16) pp. 2180--2182.
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.
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.
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.
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.
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