Christophe Dessimoz

Publications | Mémoires et thèses

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135 publications

Sous presse | 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 |
Quality assessment of gene repertoire annotations with OMArk.
Nevers Y., Warwick Vesztrocy A., Rossier V., Train C.M., Altenhoff A., Dessimoz C., Glover N.M. Nature biotechnology. Peer-reviewed.
Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families.
Rossier V., Train C., Nevers Y., Robinson-Rechavi M., Dessimoz C., 2024/06/04. Genome biology and evolution, 16 (6). Peer-reviewed.
Frequent jumps from human hosts.
Moi D., Dessimoz C., 2024/05. Nature ecology & evolution, 8 (5) pp. 854-855. Peer-reviewed.
AI and the democratization of knowledge.
Dessimoz C., Thomas P.D., 2024/03/05. Scientific data, 11 (1) p. 268. Peer-reviewed.
OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.
Altenhoff A.M., Warwick Vesztrocy A., Bernard C., Train C.M., Nicheperovich A., Prieto Baños S., Julca I., Moi D., Nevers Y., Majidian S. et al., 2024/01/05. Nucleic acids research, 52 (D1) pp. D513-D521. Peer-reviewed.
The SIB Swiss Institute of Bioinformatics Semantic Web of data.
SIB Swiss Institute of Bioinformatics RDF Group Members, Mendes de Farias T., 2024/01/05. Nucleic acids research, 52 (D1) pp. D44-D51. Peer-reviewed.
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.
Dylus D., Altenhoff A., Majidian S., Sedlazeck F.J., Dessimoz C., 2024/01. Nature biotechnology, 42 (1) pp. 139-147. Peer-reviewed.
Protein S-acylation controls the subcellular localization and biological activity of PHYTOCHROME KINASE SUBSTRATE.
Lopez Vazquez A., Allenbach Petrolati L., Legris M., Dessimoz C., Lampugnani E.R., Glover N., Fankhauser C., 2023/06/26. The Plant cell, 35 (7) pp. 2635-2653. Peer-reviewed.
Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets
Mendes de Farias Tarcisio, Kushida Tatsuya, Sima Ana-Claudia, Dessimoz Christophe, Chiba Hirokazu, Bastian Frédéric, Masuya Hiroshi, 2023/06/22. dans SWAT4HCLS 2023: The 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences.
Towards predicting essential proteins via federated SPARQL queries
Liakopoulos Petros, Banfalvi Borbala, Wang Xinyi, Majidian Sina, Mendes de Farias Tarcisio, Dessimoz Christophe, Sima Ana Claudia, 2023/06/22. dans SWAT4HCLS 2023: The 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences.
Protein length distribution is remarkably uniform across the tree of life.
Nevers Y., Glover N.M., Dessimoz C., Lecompte O., 2023/06/08. Genome biology, 24 (1) p. 135. Peer-reviewed.
Phylogenetic profiling in eukaryotes comes of age.
Moi D., Dessimoz C., 2023/05/09. Proceedings of the National Academy of Sciences of the United States of America, 120 (19) pp. e2305013120. Peer-reviewed.
Bringing science to the public in the light of evolution.
Blatter M.C., Zahn-Zabal M., Moix S., Pichon B., Dessimoz C., Glover N., 2023. Biology methods & protocols, 8 (1) pp. bpad040. Peer-reviewed.
DrosOMA: the Drosophila Orthologous Matrix browser.
Thiébaut A., Altenhoff A.M., Campli G., Glover N., Dessimoz C., Waterhouse R.M., 2023. F1000Research, 12 p. 936. Peer-reviewed.
A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem.
Briand S., Dessimoz C., El-Mabrouk N., Nevers Y., 2022/10/12. Systematic biology, 71 (6) pp. 1391-1403. Peer-reviewed.
Federating and querying heterogeneous and distributed Web APIs and triple stores
Mendes de Farias Tarcisio, Dessimoz Christophe, Ayllon Benitez Aaron, Yang Chen, Long Jiao, Sima Ana-Claudia, 2022/08/02. dans 2022 ISMB Bio-Ontologies Community of Special Interest. Peer-reviewed.
Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins.
Moi D., Nishio S., Li X., Valansi C., Langleib M., Brukman N.G., Flyak K., Dessimoz C., de Sanctis D., Tunyasuvunakool K. et al., 2022/07/06. Nature communications, 13 (1) p. 3880. Peer-reviewed.
The Quest for Orthologs orthology benchmark service in 2022.
Nevers Y., Jones TEM, Jyothi D., Yates B., Ferret M., Portell-Silva L., Codo L., Cosentino S., Marcet-Houben M., Vlasova A. et al., 2022/07/05. Nucleic acids research, 50 (W1) pp. W623-W632. Peer-reviewed.
ISMB 2022 proceedings.
Dessimoz C., Roy S., 2022/06/24. Bioinformatics, 38 (Supplement_1) pp. i8-i9. Peer-reviewed.
OMAMO: orthology-based alternative model organism selection.
Nicheperovich A., Altenhoff A.M., Dessimoz C., Majidian S., 2022/05/13. Bioinformatics, 38 (10) pp. 2965-2966. Peer-reviewed.
Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria.
Cummings TFM, Gori K., Sanchez-Pulido L., Gavriilidis G., Moi D., Wilson A.R., Murchison E., Dessimoz C., Ponting C.P., Christophorou M.A., 2022/02/03. Molecular biology and evolution, 39 (2) pp. msab317. Peer-reviewed.
Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation.
Sima A.C., Mendes de Farias T., Anisimova M., Dessimoz C., Robinson-Rechavi M., Zbinden E., Stockinger K., 2022. Distributed and parallel databases, 40 (2-3) pp. 409-440. Peer-reviewed.
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches.
Rossier V., Warwick Vesztrocy A., Robinson-Rechavi M., Dessimoz C., 2021/09/29. Bioinformatics, 37 (18) pp. 2866-2873. Peer-reviewed.
Ten Years of Collaborative Progress in the Quest for Orthologs.
Linard B., Ebersberger I., McGlynn S.E., Glover N., Mochizuki T., Patricio M., Lecompte O., Nevers Y., Thomas P.D., Gabaldón T. et al., 2021/07/29. Molecular biology and evolution, 38 (8) pp. 3033-3045. Peer-reviewed.
ISMB/ECCB 2021 proceedings.
Dessimoz C., Przytycka T.M., 2021/07/12. Bioinformatics, 37 (Suppl_1) pp. i7-i8. Peer-reviewed.
Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data
Sima Ana Claudia, Mendes de Farias Tarcisio, Anisimova Maria, Dessimoz Christophe, Robinson-Rechavi Marc, Zbinden Erich, Stockinger Kurt, 2021/07/06. 33rd International Conference on Scientific and Statistical Database Management. Peer-reviewed.
Homoeolog Inference Methods Requiring Bidirectional Best Hits or Synteny Miss Many Pairs.
Glover N., Sheppard S., Dessimoz C., 2021/06/08. Genome biology and evolution, 13 (6) pp. evab077. Peer-reviewed.
Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism.
Zajac N., Zoller S., Seppälä K., Moi D., Dessimoz C., Jokela J., Hartikainen H., Glover N., 2021/03/01. Genome biology and evolution, 13 (3) pp. evab010. Peer-reviewed.
Want to track pandemic variants faster? Fix the bioinformatics bottleneck.
Hodcroft E.B., De Maio N., Lanfear R., MacCannell D.R., Minh B.Q., Schmidt H.A., Stamatakis A., Goldman N., Dessimoz C., 2021/03. Nature, 591 (7848) pp. 30-33.
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.
Altenhoff A.M., Train C.M., Gilbert K.J., Mediratta I., Mendes de Farias T., Moi D., Nevers Y., Radoykova H.S., Rossier V., Warwick Vesztrocy A. et al., 2021/01/08. Nucleic acids research, 49 (D1) pp. D373-D379. Peer-reviewed.
A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor
Benton R., Dessimoz C., Moi D., 2020/12/04. eLife, 9 pp. e62507.
NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
Dylus David, Pillonel Trestan, Opota Onya, Wüthrich Daniel, Seth-Smith Helena M. B., Egli Adrian, Leo Stefano, Lazarevic Vladimir, Schrenzel Jacques, Laurent Sacha et al., 2020/11/24. Frontiers in Microbiology, 11. Peer-reviewed.
A generalized Robinson-Foulds distance for labeled trees.
Briand S., Dessimoz C., El-Mabrouk N., Lafond M., Lobinska G., 2020/11/18. BMC genomics, 21 (Suppl 10) p. 779. Peer-reviewed.
Parallel and Scalable Precise Clustering
Byma Stuart, Dhasade Akash, Altenhoff Adrian, Dessimoz Christophe, Larus James R., 2020/09/30. dans Proceedings of the ACM International Conference on Parallel Architectures and Compilation Techniques, ACM.
The phylogenetic range of bacterial and viral pathogens of vertebrates.
Shaw L.P., Wang A.D., Dylus D., Meier M., Pogacnik G., Dessimoz C., Balloux F., 2020/09. Molecular ecology, 29 (17) pp. 3361-3379. Peer-reviewed.
Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence.
Zile K., Dessimoz C., Wurm Y., Masel J., 2020/08/01. Genome biology and evolution, 12 (8) pp. 1355-1366. Peer-reviewed.
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 3 approved]
Sima Ana Claudia, Dessimoz Christophe, Stockinger Kurt, Zahn-Zabal Monique, Farias Tarcisio Mendes de, 2020/07/22. F1000Research.
The Quest for Orthologs benchmark service and consensus calls in 2020.
Altenhoff A.M., Garrayo-Ventas J., Cosentino S., Emms D., Glover N.M., Hernández-Plaza A., Nevers Y., Sundesha V., Szklarczyk D., Fernández J.M. et al., 2020/07/02. Nucleic acids research, 48 (W1) pp. W538-W545. Peer-reviewed.
Benchmarking gene ontology function predictions using negative annotations.
Warwick Vesztrocy A., Dessimoz C., 2020/07/01. Bioinformatics, 36 (Supplement_1) pp. i210-i218. Peer-reviewed.
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes.
Moi D., Kilchoer L., Aguilar P.S., Dessimoz C., 2020/07. PLoS computational biology, 16 (7) pp. e1007553. Peer-reviewed.
Genomic Encryption of Digital Data Stored in Synthetic DNA
Grass Robert N., Heckel Reinhard, Dessimoz Christophe, Stark Wendelin J., 2020/05/25. Angewandte Chemie International Edition, 59 (22) pp. 8476-8480. Peer-reviewed.
New genome assembly of the barn owl (Tyto alba alba).
Ducrest A.L., Neuenschwander S., Schmid-Siegert E., Pagni M., Train C., Dylus D., Nevers Y., Warwick Vesztrocy A., San-Jose L.M., Dupasquier M. et al., 2020/03. Ecology and evolution, 10 (5) pp. 2284-2298. Peer-reviewed.
How to build phylogenetic species trees with OMA.
Dylus D., Nevers Y., Altenhoff A.M., Gürtler A., Dessimoz C., Glover N.M., 2020. F1000Research, 9 p. 511. Peer-reviewed.
Identifying orthologs with OMA: A primer.
Zahn-Zabal M., Dessimoz C., Glover N.M., 2020. F1000Research, 9 p. 27. Peer-reviewed.
Orthology: Definitions, Prediction, and Impact on Species Phylogeny Inference
Fernández Rosa, Gabaldón Toni, Dessimoz Christophe, 2020. dans Phylogenetics in the Genomic Era, No commercial publisher | Authors open access book.
Structural variant calling: the long and the short of it.
Mahmoud M., Gobet N., Cruz-Dávalos D.I., Mounier N., Dessimoz C., Sedlazeck F.J., 2019/11/20. Genome biology, 20 (1) p. 246. Peer-reviewed.
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Zhou N., Jiang Y., Bergquist T.R., Lee A.J., Kacsoh B.Z., Crocker A.W., Lewis K.A., Georghiou G., Nguyen H.N., Hamid M.N. et al., 2019/11/19. Genome biology, 20 (1) p. 244. Peer-reviewed.
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL
Sima Ana Claudia, Dessimoz Christophe, Stockinger Kurt, Zahn-Zabal Monique, Mendes de Farias Tarcisio, 2019/10/29. F1000Research, 8 p. 1822. Peer-reviewed.
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 A.C., Mendes de Farias T., Zbinden E., Anisimova M., Gil M., Stockinger H., Stockinger K., Robinson-Rechavi M., Dessimoz C., 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.
How Much Does GenoGuard Really "Guard"? : An Empirical Analysis of Long-Term Security for Genomic Data
Oprisanu Bristena, Dessimoz Christophe, De Cristofaro Emiliano, 2019..
Inferring Orthology and Paralogy
Altenhoff Adrian M., Glover Natasha M., Dessimoz Christophe, 2019. pp. 149-175 dans Methods in Molecular Biology, Springer New York.
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.
GOATOOLS: A Python library for Gene Ontology analyses.
Klopfenstein D.V., Zhang L., Pedersen B.S., Ramírez F., Warwick Vesztrocy A., Naldi A., Mungall C.J., Yunes J.M., Botvinnik O., Weigel M. et al., 2018. Scientific Reports, 8 (1) p. 10872. 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.
Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution.
McGranahan N., Rosenthal R., Hiley C.T., Rowan A.J., Watkins TBK, Wilson G.A., Birkbak N.J., Veeriah S., Van Loo P., Herrero J. et al., 2017/11/30. Cell, 171 (6) pp. 1259-1271.e11. 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..
Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking
Salvador Capella-Gutierrez, Diana de la Iglesia, Juergen Haas, Analia Lourenco, José María Fernández, Dmitry Repchevsky, Christophe Dessimoz, Torsten Schwede, Cedric Notredame, Josep Ll Gelpi et al., 2017/08/31..
Tracking the Evolution of Non-Small-Cell Lung Cancer.
Jamal-Hanjani M., Wilson G.A., McGranahan N., Birkbak N.J., Watkins TBK, Veeriah S., Shafi S., Johnson D.H., Mitter R., Rosenthal R. et al., 2017/06/01. The New England journal of medicine, 376 (22) pp. 2109-2121. Peer-reviewed.
Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution
Abbosh Christopher, Birkbak Nicolai J., Wilson Gareth A., Jamal-Hanjani Mariam, Constantin Tudor, Salari Raheleh, Le Quesne John, Moore David A., Veeriah Selvaraju, Rosenthal Rachel et al., 2017/05/25. Nature, 545 (7655) pp. 446-451.
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.
The Gene Ontology Handbook
Dessimoz Christophe, Škunca Nives (eds.)Dessimoz Christophe, 2017., Springer New York.
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.
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., 2016/05. Nature methods, 13 (5) pp. 425-430. 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.
Transient structural variations alter gene expression and quantitative traits in Schizosaccharomyces pombe.
Daniel Charlton Jeffares, Clemency Jolly, Mimoza Hoti, Doug Speed, Charalampos Rallis, Christophe Dessimoz, Jurg Bahler, Fritz Sedlazeck, 2016/04., University College London.
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.
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.
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 A.M., Škunca N., Glover N., Train C.M., Sueki A., Piližota I., Gori K., Tomiczek B., Müller S., Redestig H. et al., 2015/01. Nucleic acids research, 43 (Database issue) pp. D240-9. Peer-reviewed.
Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology
Wittwer Lucas D., Piližota Ivana, Altenhoff Adrian M., Dessimoz Christophe, 2014/10/07. PeerJ, 2 pp. e607.
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.
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. pp. 59-73 dans Methods in Molecular Biology, Humana Press.
CAFA and the open world of protein function predictions.
Dessimoz C., Škunca N., Thomas P.D., 2013/11. Trends in genetics, 29 (11) pp. 609-610. Peer-reviewed.
Global regulatory architecture of human, mouse and rat tissue transcriptomes.
Prasad A., Kumar S.S., Dessimoz C., Bleuler S., Laule O., Hruz T., Gruissem W., Zimmermann P., 2013/10/20. BMC genomics, 14 p. 716. Peer-reviewed.
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, 2013/02/07. Nature, 494 (7435) pp. 77-80.
Approximate Bayesian computation.
Sunnåker M., Busetto A.G., Numminen E., Corander J., Foll M., Dessimoz C., 2013. PLoS computational biology, 9 (1) pp. e1002803. Peer-reviewed.
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 A.M., Gil M., Gonnet G.H., Dessimoz C., 2013. PloS one, 8 (1) pp. e53786. Peer-reviewed.
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 D.A., Altenhoff A.M., Gonnet G.H., Dessimoz C., 2013. PloS one, 8 (2) pp. e56925. Peer-reviewed.
Quality of computationally inferred gene ontology annotations.
Skunca N., Altenhoff A., Dessimoz C., 2012/05. PLoS computational biology, 8 (5) pp. e1002533. Peer-reviewed.
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.
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes.
Anisimova M., Gil M., Dufayard J.F., Dessimoz C., Gascuel O., 2011/10. Systematic biology, 60 (5) pp. 685-699. Peer-reviewed.
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.
Editorial: Orthology and applications
Dessimoz Christophe, 2011/09. Briefings in bioinformatics, 12 (5) pp. 375--376.
iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration.
Owiti J., Grossmann J., Gehrig P., Dessimoz C., Laloi C., Hansen M.B., Gruissem W., Vanderschuren H., 2011/07. The Plant journal, 67 (1) pp. 145-156. Peer-reviewed.
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.
OMA 2011: orthology inference among 1000 complete genomes.
Altenhoff A.M., Schneider A., Gonnet G.H., Dessimoz C., 2011/01. Nucleic acids research, 39 (Database issue) pp. D289-94. Peer-reviewed.
Phylogenetic assessment of alignments reveals neglected tree signal in gaps.
Dessimoz C., Gil M., 2010. Genome biology, 11 (4) pp. R37. Peer-reviewed.
Erratum: Algorithm of OMA for large-scale orthology inference (BMC Bioinformatics (2008) vol. 9 (518))
Dessimoz Christophe, 2009. BMC Bioinformatics.
Joining forces in the quest for orthologs.
Gabaldón T., Dessimoz C., Huxley-Jones J., Vilella A.J., Sonnhammer E.L., Lewis S., 2009. Genome biology, 10 (9) p. 403. Peer-reviewed.
Phylogenetic and functional assessment of orthologs inference projects and methods.
Altenhoff A.M., Dessimoz C., 2009/01. PLoS computational biology, 5 (1) pp. e1000262. Peer-reviewed.
The Microbe browser for comparative genomics.
Gattiker A., Dessimoz C., Schneider A., Xenarios I., Pagni M., Rougemont J., 2009. Nucleic Acids Research, 37 (Web Server issue) pp. W296-W299.
Algorithm of OMA for large-scale orthology inference.
Roth A.C., Gonnet G.H., Dessimoz C., 2008/12/04. BMC bioinformatics, 9 p. 518. Peer-reviewed.
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.
Alignments with non-overlapping moves, inversions and tandem duplications in O(n 4) time
Ledergerber Christian, Dessimoz Christophe, 2008/10., 16 3, Springer Science and Business Media LLC.
Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise
Dessimoz Christophe, Gil Manuel, 2008. BMC Evolutionary Biology, 8 (1) 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 ×86/SSE2
Szalkowski Adam, Ledergerber Christian, Krähenbühl Philipp, Dessimoz Christophe, 2008. BMC Research Notes, 1 (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.
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, 2006/12. BMC Bioinformatics, 7 (1).
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.
A dimensionless fit measure for phylogenetic distance trees.
Gil M., Dessimoz C., Gonnet G.H., 2005/12. Journal of bioinformatics and computational biology, 3 (6) pp. 1429-1440. Peer-reviewed.
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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