Christophe Dessimoz

Publication Activity (10 Years)

Years Active: 2005-2023
Publications (10 Years): 32

Top Topics

Sequenced Genomes

Multiple Data Sources

Horizontal Gene Transfer

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Petros Liakopoulous, Borbala Banfalvi, Xinyi Wang, Sina Majidian, Tarcisio Mendes de Farias, Christophe Dessimoz, Ana Claudia Sima
Towards predicting essential proteins via federated SPARQL queries. SWAT4HCLS (2023)
Tarcisio Mendes de Farias, Tatsuya Kushida, Ana Claudia Sima, Christophe Dessimoz, Hirokazu Chiba, Frédéric B. Bastian, Hiroshi Masuya
Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets. SWAT4HCLS (2023)
Yannis Nevers, Tamsin E. M. Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codó, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Pilizota, Cristina Guijarro-Clarke, Adrian M. Altenhoff, Elspeth A. Bruford, Christophe Dessimoz, Ingo Ebersberger, David M. Emms, Toni Gabaldón, Natasha Glover, Yanhui Hu, Wataru Iwasaki, Odile Lecompte, Benjamin Linard, María J. Martín, David S. Roos, Erik Sonhammer, Paul D. Thomas, David Thybert, Klaas Vandepoele, Salvador Capella-Gutiérrez, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas, Dmitry Repchevsky, Vicky Sundesha, Erik L. L. Sonnhammer
The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Res. 50 (W1) (2022)
Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger
Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation. Distributed Parallel Databases 40 (2) (2022)
Tarcisio Mendes de Farias, Christophe Dessimoz, Aarón Ayllón-Benítez, Chen Yang, Jiao Long, Ana Claudia Sima
Federating and querying heterogeneous and distributed Web APIs and triple stores. CoRR (2022)
Alina Nicheperovich, Adrian M. Altenhoff, Christophe Dessimoz, Sina Majidian
OMAMO: orthology-based alternative model organism selection. Bioinform. 38 (10) (2022)
Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. Bioinform. 37 (18) (2021)
Adrian M. Altenhoff, Clément-Marie Train, Kimberly J. Gilbert, Ishita Mediratta, Tarcisio Mendes de Farias, David Moi, Yannis Nevers, Hale-Seda Radoykova, Victor Rossier, Alex Warwick Vesztrocy, Natasha M. Glover, Christophe Dessimoz
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. Nucleic Acids Res. 49 (Database-Issue) (2021)
Christophe Dessimoz, Teresa M. Przytycka
ISMB/ECCB 2021 proceedings. Bioinform. 37 (Supplement) (2021)
Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger
Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data. SSDBM (2021)
Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger
Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data. CoRR (2021)
David Moi, Laurent Kilchoer, Pablo S. Aguilar, Christophe Dessimoz
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes. PLoS Comput. Biol. 16 (7) (2020)
Stuart Byma, Akash Dhasade, Adrian M. Altenhoff, Christophe Dessimoz, James R. Larus
Parallel and Scalable Precise Clustering. PACT (2020)
Alex Warwick Vesztrocy, Christophe Dessimoz
Benchmarking gene ontology function predictions using negative annotations. Bioinform. 36 (Supplement-1) (2020)
Adrian M. Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M. Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José María Fernández, Laia Codó, The Quest for Orthologs Consortium, Josep Lluis Gelpí, Jaime Huerta-Cepas, Wataru Iwasaki, Steven Kelly, Odile Lecompte, Matthieu Muffato, Maria Jesus Martin, Salvador Capella-Gutiérrez, Paul D. Thomas, Erik L. L. Sonnhammer, Christophe Dessimoz
The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Samuel Briand, Christophe Dessimoz, Nadia El-Mabrouk, Manuel Lafond, Gabriela Lobinska
A generalized Robinson-Foulds distance for labeled trees. BMC Genom. 21 (S-10) (2020)
Tarcisio Mendes de Farias, Christophe Dessimoz
Enhancing interoperable datasets with virtual links. CoRR (2019)
Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
packages for R and Python. F1000Research 8 (2019)
Ivana Pilizota, Clément-Marie Train, Adrian M. Altenhoff, Henning Redestig, Christophe Dessimoz
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome. Bioinform. 35 (7) (2019)
Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz
Enabling semantic queries across federated bioinformatics databases. Database J. Biol. Databases Curation 2019 (2019)
Bristena Oprisanu, Christophe Dessimoz, Emiliano De Cristofaro
How Much Does GenoGuard Really "Guard"? An Empirical Analysis of Long-Term Security for Genomic Data. CoRR (2019)
Ana Claudia Sima, Christophe Dessimoz, Kurt Stockinger, Monique Zahn-Zabal, Tarcisio Mendes de Farias
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL. F1000Research 8 (2019)
Stuart Byma, Akash Dhasade, Adrian M. Altenhoff, Christophe Dessimoz, James R. Larus
Parallel and Scalable Precise Clustering for Homologous Protein Discovery. CoRR (2019)
Tarcisio Mendes de Farias, Kurt Stockinger, Christophe Dessimoz
VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links. OTM Conferences (2019)
Bristena Oprisanu, Christophe Dessimoz, Emiliano De Cristofaro
How Much Does GenoGuard Really "Guard"?: An Empirical Analysis of Long-Term Security for Genomic Data. WPES@CCS (2019)
Clément-Marie Train, Miguel Pignatelli, Adrian M. Altenhoff, Christophe Dessimoz
iHam and pyHam: visualizing and processing hierarchical orthologous groups. Bioinform. 35 (14) (2019)
Daniel Mietchen, Shoshana J. Wodak, Szymon Wasik, Natalia Szostak, Christophe Dessimoz
Submit a Topic Page to PLOS Computational Biology and Wikipedia. PLoS Comput. Biol. 14 (5) (2018)
Adrian M. Altenhoff, Natasha M. Glover, Clément-Marie Train, Klara Kaleb, Alex Warwick Vesztrocy, David Dylus, Tarcisio M. Farias, Karina Zile, Charles Stevenson, Jiao Long, Henning Redestig, Gaston H. Gonnet, Christophe Dessimoz
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. Nucleic Acids Res. 46 (Database-Issue) (2018)
Kristoffer Forslund, Cecile Pereira, Salvador Capella-Gutiérrez, Alan W. Sousa da Silva, Adrian M. Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele, Ingo Ebersberger, Judith A. Blake, Jesualdo Tomás Fernández-Breis, The Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz, Suzanna Lewis
Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinform. 34 (2) (2018)
Alex Warwick Vesztrocy, Christophe Dessimoz, Henning Redestig
Prioritising candidate genes causing QTL using hierarchical orthologous groups. Bioinform. 34 (17) (2018)
Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul S. Bansal, Vincent Berry, Bastien Boussau, François Chevenet, Nicolas Comte, Adrián A. Davín, Christophe Dessimoz, David Dylus, Damir Hasic, Diego Mallo, Rémi Planel, David Posada, Céline Scornavacca, Gergely J. Szöllosi, Louxin Zhang, Eric Tannier, Vincent Daubin
RecPhyloXML: a format for reconciled gene trees. Bioinform. 34 (21) (2018)
Clément-Marie Train, Natasha M. Glover, Gaston H. Gonnet, Adrian M. Altenhoff, Christophe Dessimoz
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference. Bioinform. 33 (14) (2017)
Adrian M. Altenhoff, Nives Skunca, Natasha M. Glover, Clément-Marie Train, Anna Sueki, Ivana Pilizota, Kevin Gori, Bartlomiej Tomiczek, Steven Müller, Henning Redestig, Gaston H. Gonnet, Christophe Dessimoz
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res. 43 (Database-Issue) (2015)
Matt Ravenhall, Nives Skunca, Florent Lassalle, Christophe Dessimoz
Inferring Horizontal Gene Transfer. PLoS Comput. Biol. 11 (5) (2015)
Erik L. L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Jesus Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, The Quest for Orthologs Consortium
Big data and other challenges in the quest for orthologs. Bioinform. 30 (21) (2014)
Mikael Sunnåker, Alberto Giovanni Busetto, Elina Numminen, Jukka Corander, Matthieu Foll, Christophe Dessimoz
Approximate Bayesian Computation. PLoS Comput. Biol. 9 (1) (2013)
Nick Goldman, Paul Bertone, Siyuan Chen, Christophe Dessimoz, Emily M. LeProust, Botond Sipos, Ewan Birney
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nat. 494 (7435) (2013)
Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero
Toward community standards in the quest for orthologs. Bioinform. 28 (6) (2012)
Adrian M. Altenhoff, Romain A. Studer, Marc Robinson-Rechavi, Christophe Dessimoz
Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs. PLoS Comput. Biol. 8 (5) (2012)
Nives Skunca, Adrian M. Altenhoff, Christophe Dessimoz
Quality of Computationally Inferred Gene Ontology Annotations. PLoS Comput. Biol. 8 (5) (2012)
Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Briefings Bioinform. 12 (5) (2011)
Christophe Dessimoz, Stefan Zoller, Tereza Manousaki, Huan Qiu, Axel Meyer, Shigehiro Kuraku
(Holocephali, Chondrichthyes). Briefings Bioinform. 12 (5) (2011)
Christophe Dessimoz
Editorial: Orthology and applications. Briefings Bioinform. 12 (5) (2011)
Louis du Plessis, Nives Skunca, Christophe Dessimoz
The what, where, how and why of gene ontology - a primer for bioinformaticians. Briefings Bioinform. 12 (6) (2011)
Christian Ledergerber, Christophe Dessimoz
Base-calling for next-generation sequencing platforms. Briefings Bioinform. 12 (5) (2011)
Adrian M. Altenhoff, Adrian Schneider, Gaston H. Gonnet, Christophe Dessimoz
OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res. 39 (Database-Issue) (2011)
Adrian M. Altenhoff, Christophe Dessimoz
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods. PLoS Comput. Biol. 5 (1) (2009)
Alexander C. J. Roth, Gaston H. Gonnet, Christophe Dessimoz
Algorithm of OMA for large-scale orthology inference. BMC Bioinform. 10 (2009)
Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, Jacques Rougemont
The Microbe browser for comparative genomics. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Christian Ledergerber, Christophe Dessimoz
) time. J. Comb. Optim. 16 (3) (2008)
Christophe Dessimoz, Daniel Margadant, Gaston H. Gonnet
DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework. RECOMB (2008)
Alexander C. J. Roth, Gaston H. Gonnet, Christophe Dessimoz
Algorithm of OMA for large-scale orthology inference. BMC Bioinform. 9 (2008)
Christian Ledergerber, Christophe Dessimoz
) Time. COCOON (2007)
Adrian Schneider, Christophe Dessimoz, Gaston H. Gonnet
OMA Browser - Exploring orthologous relations across 352 complete genomes. Bioinform. 23 (16) (2007)
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 Bioinform. 7 (2006)
Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander C. J. Roth, Adrian Schneider, Gaston H. Gonnet
OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements. Comparative Genomics (2005)
Manuel Gil, Christophe Dessimoz, Gaston H. Gonnet
A Dimensionless Fit Measure for Phylogenetic Distance Trees. J. Bioinform. Comput. Biol. 3 (6) (2005)