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2020 – today
- 2023
[c9]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: 173-174- [c8]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: 177-178 - 2022
- [j41]Alina Nicheperovich
, Adrian M. Altenhoff, Christophe Dessimoz, Sina Majidian:
OMAMO: orthology-based alternative model organism selection. Bioinform. 38(10): 2965-2966 (2022) - [j40]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(2-3): 409-440 (2022) - [j39]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:
The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Res. 50(W1): 623-632 (2022) - [i7]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 abs/2206.01594 (2022) - 2021
- [j38]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): 2866-2873 (2021) - [j37]Christophe Dessimoz, Teresa M. Przytycka:
ISMB/ECCB 2021 proceedings. Bioinform. 37(Supplement): 7-8 (2021) - [j36]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): D373-D379 (2021) - [c7]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: 61-72 - [i6]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 abs/2104.13744 (2021) - 2020
- [j35]Alex Warwick Vesztrocy, Christophe Dessimoz:
Benchmarking gene ontology function predictions using negative annotations. Bioinform. 36(Supplement-1): i210-i218 (2020) - [j34]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) - [j33]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): W538-W545 (2020) - [j32]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) - [c6]Stuart Byma, Akash Dhasade, Adrian M. Altenhoff, Christophe Dessimoz, James R. Larus:
Parallel and Scalable Precise Clustering. PACT 2020: 217-228
2010 – 2019
- 2019
- [j31]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: baz106 (2019) - [j30]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): 1159-1166 (2019) - [j29]Clément-Marie Train, Miguel Pignatelli, Adrian M. Altenhoff, Christophe Dessimoz:
iHam and pyHam: visualizing and processing hierarchical orthologous groups. Bioinform. 35(14): 2504-2506 (2019) - [c5]Tarcisio Mendes de Farias, Kurt Stockinger, Christophe Dessimoz:
VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links. OTM Conferences 2019: 607-625 - [c4]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: 93-105 - [i5]Tarcisio Mendes de Farias, Christophe Dessimoz:
Enhancing interoperable datasets with virtual links. CoRR abs/1906.01950 (2019) - [i4]Stuart Byma, Akash Dhasade, Adrian M. Altenhoff, Christophe Dessimoz, James R. Larus:
Parallel and Scalable Precise Clustering for Homologous Protein Discovery. CoRR abs/1908.10574 (2019) - [i3]Bristena Oprisanu, Christophe Dessimoz, Emiliano De Cristofaro:
How Much Does GenoGuard Really "Guard"? An Empirical Analysis of Long-Term Security for Genomic Data. CoRR abs/1908.11315 (2019) - [i2]Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz:
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python. F1000Research 8: 42 (2019) - [i1]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: 1822 (2019) - 2018
- [j28]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, 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): 323-329 (2018) - [j27]Alex Warwick Vesztrocy, Christophe Dessimoz, Henning Redestig:
Prioritising candidate genes causing QTL using hierarchical orthologous groups. Bioinform. 34(17): i612-i619 (2018) - [j26]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): 3646-3652 (2018) - [j25]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): D477-D485 (2018) - [j24]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) - 2017
- [j23]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): i75-i82 (2017) - 2015
- [j22]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): 240-249 (2015) - [j21]Matt Ravenhall, Nives Skunca, Florent Lassalle, Christophe Dessimoz:
Inferring Horizontal Gene Transfer. PLoS Comput. Biol. 11(5) (2015) - 2014
- [j20]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): 2993-2998 (2014) - 2013
- [j19]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): 77-80 (2013) - [j18]Mikael Sunnåker, Alberto Giovanni Busetto, Elina Numminen, Jukka Corander, Matthieu Foll, Christophe Dessimoz:
Approximate Bayesian Computation. PLoS Comput. Biol. 9(1) (2013) - 2012
- [j17]Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero:
Toward community standards in the quest for orthologs. Bioinform. 28(6): 900-904 (2012) - [j16]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) - [j15]Nives Skunca, Adrian M. Altenhoff, Christophe Dessimoz:
Quality of Computationally Inferred Gene Ontology Annotations. PLoS Comput. Biol. 8(5) (2012) - 2011
- [j14]Christophe Dessimoz:
Editorial: Orthology and applications. Briefings Bioinform. 12(5): 375-376 (2011) - [j13]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): 423-435 (2011) - [j12]Christophe Dessimoz, Stefan Zoller, Tereza Manousaki, Huan Qiu, Axel Meyer, Shigehiro Kuraku:
Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). Briefings Bioinform. 12(5): 474-484 (2011) - [j11]Christian Ledergerber, Christophe Dessimoz:
Base-calling for next-generation sequencing platforms. Briefings Bioinform. 12(5): 489-497 (2011) - [j10]Louis du Plessis, Nives Skunca, Christophe Dessimoz:
The what, where, how and why of gene ontology - a primer for bioinformaticians. Briefings Bioinform. 12(6): 723-735 (2011) - [j9]Adrian M. Altenhoff, Adrian Schneider, Gaston H. Gonnet, Christophe Dessimoz:
OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res. 39(Database-Issue): 289-294 (2011)
2000 – 2009
- 2009
- [j8]Alexander C. J. Roth, Gaston H. Gonnet, Christophe Dessimoz:
Algorithm of OMA for large-scale orthology inference. BMC Bioinform. 10 (2009) - [j7]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): 296-299 (2009) - [j6]Adrian M. Altenhoff, Christophe Dessimoz:
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods. PLoS Comput. Biol. 5(1) (2009) - 2008
- [j5]Alexander C. J. Roth, Gaston H. Gonnet, Christophe Dessimoz:
Algorithm of OMA for large-scale orthology inference. BMC Bioinform. 9 (2008) - [j4]Christian Ledergerber, Christophe Dessimoz:
Alignments with non-overlapping moves, inversions and tandem duplications in O ( n 4) time. J. Comb. Optim. 16(3): 263-278 (2008) - [c3]Christophe Dessimoz, Daniel Margadant, Gaston H. Gonnet:
DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework. RECOMB 2008: 315-330 - 2007
- [j3]Adrian Schneider, Christophe Dessimoz, Gaston H. Gonnet:
OMA Browser - Exploring orthologous relations across 352 complete genomes. Bioinform. 23(16): 2180-2182 (2007) - [c2]Christian Ledergerber, Christophe Dessimoz:
Alignments with Non-overlapping Moves, Inversions and Tandem Duplications in O ( n 4) Time. COCOON 2007: 151-164 - 2006
- [j2]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: 529 (2006) - 2005
- [j1]Manuel Gil, Christophe Dessimoz, Gaston H. Gonnet:
A Dimensionless Fit Measure for Phylogenetic Distance Trees. J. Bioinform. Comput. Biol. 3(6): 1429-1440 (2005) - [c1]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: 61-72
Coauthor Index
Tarcisio M. Farias
aka: Tarcisio Mendes de Farias
aka: Tarcisio Mendes de Farias
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