Christophe Dessimoz

61 papers B 3Misc 1Journal 52Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
Annotation matters: the effect of structural gene annotation on orthology inference.
Bioinform.
Silvia Prieto-Baños, Yannis Nevers, Adrian M. Altenhoff, Alex Warwick Vesztrocy, Christophe Dessimoz, Natasha M. Glover
2025 J jnl
Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs.
BMC Medical Informatics Decis. Mak.
Tatsuya Kushida, Tarcisio Mendes de Farias, Ana Claudia Sima, Christophe Dessimoz, Hirokazu Chiba, Frederic B. Bastian, Hiroshi Masuya
2025 J jnl
Open and Sustainable AI: challenges, opportunities and the road ahead in the life sciences.
CoRR
Gavin Farrell, Eleni S. Adamidi, Rafael Andrade Buono, Mihail Anton, Omar Abdelghani Attafi, Salvador Capella-Gutiérrez, Emidio Capriotti, Leyla Jael Castro, Davide Cirillo, Lisa C. Crossman, Christophe Dessimoz, Alexandros C. Dimopoulos, Raúl Fernández-Díaz, Styliani-Christina Fragkouli, Carole A. Goble, Wei Gu, John M. Hancock, Alireza Khanteymoori, Tom Lenaerts, Fabio G. Liberante, Peter Maccallum, Alexander Miguel Monzon, Magnus Palmblad, Lucy Poveda, Ovidiu Radulescu, Denis C. Shields, Shoaib Sufi, Thanasis Vergoulis, Fotis E. Psomopoulos, Silvio C. E. Tosatto
2023 — conf
Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets.
SWAT4HCLS
Tarcisio Mendes de Farias, Tatsuya Kushida, Ana Claudia Sima, Christophe Dessimoz, Hirokazu Chiba, Frédéric B. Bastian, Hiroshi Masuya
2023 — conf
Towards predicting essential proteins via federated SPARQL queries.
SWAT4HCLS
Petros Liakopoulous, Borbala Banfalvi, Xinyi Wang, Sina Majidian, Tarcisio Mendes de Farias, Christophe Dessimoz, Ana Claudia Sima
2022 J jnl
Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation.
Distributed Parallel Databases
Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger
2022 J jnl
Federating and querying heterogeneous and distributed Web APIs and triple stores.
CoRR
Tarcisio Mendes de Farias, Christophe Dessimoz, Aarón Ayllón-Benítez, Chen Yang, Jiao Long, Ana Claudia Sima
2022 J jnl
ISMB 2022 proceedings.
Bioinform.
Christophe Dessimoz, Sushmita Roy
2022 J jnl
OMAMO: orthology-based alternative model organism selection.
Bioinform.
Alina Nicheperovich, Adrian M. Altenhoff, Christophe Dessimoz, Sina Majidian
2022 J jnl
The Quest for Orthologs orthology benchmark service in 2022.
Nucleic Acids Res.
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 M. 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
2021 B conf
Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data.
SSDBM
Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger
2021 J jnl
Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data.
CoRR
Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger
2021 J jnl
ISMB/ECCB 2021 proceedings.
Bioinform.
Christophe Dessimoz, Teresa M. Przytycka
2021 J jnl
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.
Nucleic Acids Res.
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
2021 J jnl
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches.
Bioinform.
Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz
2020 J jnl
A generalized Robinson-Foulds distance for labeled trees.
BMC Genom.
Samuel Briand, Christophe Dessimoz, Nadia El-Mabrouk, Manuel Lafond, Gabriela Lobinska
2020 J jnl
Benchmarking gene ontology function predictions using negative annotations.
Bioinform.
Alex Warwick Vesztrocy, Christophe Dessimoz
2020 B conf
Parallel and Scalable Precise Clustering.
PACT
Stuart Byma, Akash Balasaheb Dhasade, Adrian M. Altenhoff, Christophe Dessimoz, James R. Larus
2020 J jnl
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes.
PLoS Comput. Biol.
David Moi, Laurent Kilchoer, Pablo S. Aguilar, Christophe Dessimoz
2020 J jnl
The Quest for Orthologs benchmark service and consensus calls in 2020.
Nucleic Acids Res.
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, Quest for Orthologs Consortium, Josep Lluís 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
2019 J jnl
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL.
F1000Research
Ana Claudia Sima, Christophe Dessimoz, Kurt Stockinger, Monique Zahn-Zabal, Tarcisio Mendes de Farias
2019 J jnl
Enabling semantic queries across federated bioinformatics databases.
Database J. Biol. Databases Curation
Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz
2019 J jnl
Enhancing interoperable datasets with virtual links.
CoRR
Tarcisio Mendes de Farias, Christophe Dessimoz
2019 J jnl
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the
F1000Research
Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
2019 J jnl
How Much Does GenoGuard Really "Guard"? An Empirical Analysis of Long-Term Security for Genomic Data.
CoRR
Bristena Oprisanu, Christophe Dessimoz, Emiliano De Cristofaro
2019 — conf
How Much Does GenoGuard Really "Guard"?: An Empirical Analysis of Long-Term Security for Genomic Data.
WPES@CCS
Bristena Oprisanu, Christophe Dessimoz, Emiliano De Cristofaro
2019 J jnl
Parallel and Scalable Precise Clustering for Homologous Protein Discovery.
CoRR
Stuart Byma, Akash Balasaheb Dhasade, Adrian M. Altenhoff, Christophe Dessimoz, James R. Larus
2019 J jnl
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.
Bioinform.
Ivana Pilizota, Clément-Marie Train, Adrian M. Altenhoff, Henning Redestig, Christophe Dessimoz
2019 — conf
VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links.
OTM Conferences
Tarcisio Mendes de Farias, Kurt Stockinger, Christophe Dessimoz
2019 J jnl
iHam and pyHam: visualizing and processing hierarchical orthologous groups.
Bioinform.
Clément-Marie Train, Miguel Pignatelli, Adrian M. Altenhoff, Christophe Dessimoz
2018 J jnl
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Bioinform.
Kristoffer Forslund, Cécile 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, Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz, Suzanna Lewis
2018 J jnl
Prioritising candidate genes causing QTL using hierarchical orthologous groups.
Bioinform.
Alex Warwick Vesztrocy, Christophe Dessimoz, Henning Redestig
2018 J jnl
RecPhyloXML: a format for reconciled gene trees.
Bioinform.
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
2018 J jnl
Submit a Topic Page to PLOS Computational Biology and Wikipedia.
PLoS Comput. Biol.
Daniel Mietchen, Shoshana J. Wodak, Szymon Wasik, Natalia Szostak, Christophe Dessimoz
2018 J jnl
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.
Nucleic Acids Res.
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
2017 J jnl
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference.
Bioinform.
Clément-Marie Train, Natasha M. Glover, Gaston H. Gonnet, Adrian M. Altenhoff, Christophe Dessimoz
2015 J jnl
Inferring Horizontal Gene Transfer.
PLoS Comput. Biol.
Matt Ravenhall, Nives Skunca, Florent Lassalle, Christophe Dessimoz
2015 J jnl
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.
Nucleic Acids Res.
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
2014 J jnl
Big data and other challenges in the quest for orthologs.
Bioinform.
Erik L. L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Jesus Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, Quest for Orthologs Consortium
2013 J jnl
Approximate Bayesian Computation.
PLoS Comput. Biol.
Mikael Sunnåker, Alberto Giovanni Busetto, Elina Numminen, Jukka Corander, Matthieu Foll, Christophe Dessimoz
2013 J jnl
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.
Nat.
Nick Goldman, Paul Bertone, Siyuan Chen, Christophe Dessimoz, Emily M. LeProust, Botond Sipos, Ewan Birney
2012 J jnl
Quality of Computationally Inferred Gene Ontology Annotations.
PLoS Comput. Biol.
Nives Skunca, Adrian M. Altenhoff, Christophe Dessimoz
2012 J jnl
Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs.
PLoS Comput. Biol.
Adrian M. Altenhoff, Romain A. Studer, Marc Robinson-Rechavi, Christophe Dessimoz
2012 J jnl
Toward community standards in the quest for orthologs.
Bioinform.
Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero
2011 J jnl
Base-calling for next-generation sequencing platforms.
Briefings Bioinform.
Christian Ledergerber, Christophe Dessimoz
2011 J jnl
Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera
Briefings Bioinform.
Christophe Dessimoz, Stefan Zoller, Tereza Manousaki, Huan Qiu, Axel Meyer, Shigehiro Kuraku
2011 J jnl
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.
Briefings Bioinform.
Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz
2011 J jnl
Editorial: Orthology and applications.
Briefings Bioinform.
Christophe Dessimoz
2011 J jnl
OMA 2011: orthology inference among 1000 complete genomes.
Nucleic Acids Res.
Adrian M. Altenhoff, Adrian Schneider, Gaston H. Gonnet, Christophe Dessimoz
2011 J jnl
The what, where, how and why of gene ontology - a primer for bioinformaticians.
Briefings Bioinform.
Louis du Plessis, Nives Skunca, Christophe Dessimoz
2009 J jnl
Algorithm of OMA for large-scale orthology inference.
BMC Bioinform.
Alexander C. J. Roth, Gaston H. Gonnet, Christophe Dessimoz
2009 J jnl
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods.
PLoS Comput. Biol.
Adrian M. Altenhoff, Christophe Dessimoz
2009 J jnl
The Microbe browser for comparative genomics.
Nucleic Acids Res.
Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, Jacques Rougemont
2008 J jnl
Algorithm of OMA for large-scale orthology inference.
BMC Bioinform.
Alexander C. J. Roth, Gaston H. Gonnet, Christophe Dessimoz
2008 J jnl
Alignments with non-overlapping moves, inversions and tandem duplications in
J. Comb. Optim.
Christian Ledergerber, Christophe Dessimoz
2008 B conf
DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework.
RECOMB
Christophe Dessimoz, Daniel Margadant, Gaston H. Gonnet
2007 Misc conf
Alignments with Non-overlapping Moves, Inversions and Tandem Duplications in
COCOON
Christian Ledergerber, Christophe Dessimoz
2007 J jnl
OMA Browser - Exploring orthologous relations across 352 complete genomes.
Bioinform.
Adrian Schneider, Christophe Dessimoz, Gaston H. Gonnet
2006 J jnl
Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences.
BMC Bioinform.
Christophe Dessimoz, Manuel Gil, Adrian Schneider, Gaston H. Gonnet
2005 J jnl
A Dimensionless Fit Measure for Phylogenetic Distance Trees.
J. Bioinform. Comput. Biol.
Manuel Gil, Christophe Dessimoz, Gaston H. Gonnet
2005 — conf
OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements.
Comparative Genomics
Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander C. J. Roth, Adrian Schneider, Gaston H. Gonnet