Dessimoz Lab
Computational Evolutionary Biology
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Publications
All
Selected work
Highly cited ( ≥ 100x)
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Comparative genomics
Benchmarking
Phylogenetics
Statistics
Alignments
Nextgen sequencing
Gene/protein function
Big data
Ontologies
Algorithms
Plant genomics
Original paper
Review
Tutorial
Editorial
Book
Preprint
Quest for Orthologs consortium
Undergraduate co-author
Preprints
David Dylus, Adrian M Altenhoff, Sina Majidian, Fritz J Sedlazeck, Christophe Dessimoz
Read2Tree: scalable and accurate phylogenetic trees from raw reads
bioRxiv 2022.04.18.488678
David Moi, Christophe Dessimoz
Reconstructing protein interactions across time using phylogeny-aware graph neural networks
bioRxiv 2022.07.21.501014
Yannis Nevers, Natasha Glover, Christophe Dessimoz, Odile Lecompte
Protein length distribution is remarkably consistent across Life
bioRxiv 2021.12.03.470944
Tarcisio Mendes de Farias, Christophe Dessimoz, Aaron Ayllon Benitez, Chen Yang, Jiao Long, Ana Claudia Sima
Federating and querying heterogeneous and distributed Web APIs and triple stores
arXiv [csDB] 2206.01594
Ana Lopez Vazquez, Laure Allenbach Petrolati, Christophe Dessimoz, Edwin R Lampugnani, Natasha Glover, Christian Fankhauser
Control of PHYTOCHROME KINASE SUBSTRATE subcellular localization and biological activity by protein S-acylation
bioRxiv 2022.07.08.499325
Brigitte Boeckmann, David Dylus, Sébastien Moretti, Adrian Altenhoff, Clément-Marie Train, Evgenia Kriventseva, Lydie Bougueleret, Ioannis Xenarios, Eyal Privman, Toni Gabaldón, Christophe Dessimoz
Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree
bioRxiv 181966
2022
Samuel Briand, Christophe Dessimoz*, Nadia El-Mabrouk*, Yannis Nevers
(*co-corresponding)
A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem
Syst Biol. Advanced access.
David Moi, Shunsuke Nishio, Xiaohui Li, Clari Valansi, Mauricio Langleib, Nicolas G Brukman, Kateryna Flyak, Christophe Dessimoz, Daniele de Sanctis, Kathryn Tunyasuvunakool, John Jumper, Martin Graña, Héctor Romero, Pablo S Aguilar, Luca Jovine, Benjamin Podbilewicz
Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins
Nat Commun 13:3880.
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 and Parallel Databases 40:409–440. 2022.
Thomas FM Cummings, Kevin Gori, Luis Sanchez-Pulido, Gabriel Gavriilidis, David Moi, Abigail R. Wilson, Elizabeth P Murchison, Christophe Dessimoz, Chris Ponting, Maria A. Christophorou
Protein citrullination was introduced into animals by horizontal gene transfer from cyanobacteria
Mol Biol Evol 2022, 39:2, msab317
Christophe Dessimoz, Sushmita Roy
ISMB 2022 proceedings
Bioinformatics 38:i8–i9.
Alina Nicheperovich, Adrian M Altenhoff, Christophe Dessimoz, Sina Majidian
OMAMO: orthology-based alternative model organism selection
Bioinformatics 38:2965–2966. 2022.
Yannis Nevers, Tamsin EM Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codo, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Piližota, Cristina Guijarro-Clarke, OpenEBench team the Quest for Orthologs Consortium, Wataru Iwasaki, Odile Lecompte, Erik Sonnhammer, David S Roos, Toni Gabaldón, David Thybert, Paul D Thomas, Yanhui Hu, David M Emms, Elspeth Bruford, Salvador Capella-Gutierrez, Maria J Martin, Christophe Dessimoz, Adrian Altenhoff
The Quest for Orthologs orthology benchmark service in 2022
Nucleic Acids Res 50:W623–W632. 2022
David Dylus, Yannis Nevers, Adrian M Altenhoff, Antoine Gürtler, Christophe Dessimoz, Natasha M Glover
How to build phylogenetic species trees with OMA
F1000Research, 2022, 9:511
2021
Christophe Dessimoz, Teresa M Przytycka
ISMB/ECCB 2021 proceedings
Bioinformatics 37:i7–i8.
Natasha M Glover, Shaoline Sheppard, Christophe Dessimoz
Homoeolog inference methods requiring bidirectional best hits or synteny miss many pairs
Genome Biol Evol. 2021, 13:6, evab077
Benjamin Linard, Ingo Ebersberger, Shawn E McGlynn, Natasha M Glover, Tomohiro Mochizuki, Mateus Patricio, Odile Lecompte, Yannis Nevers, QFO Consortium, Paul D Thomas, Toni Gabaldón, Erik Sonnhammer, Christophe Dessimoz, Ikuo Uchiyama
Ten years of collaborative progress in the Quest for Orthologs
Mol Biol Evol. 2021, 38:8 pp. 3033–3045
Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches
Bioinformatics, 2021, 37:18 pp. 2866–2873
Code
Emma B Hodcroft, Nicola De Maio, Rob Lanfear, Duncan R MacCannell, Bui Quang Minh, Heiko A Schmidt, Alexandros Stamatakis, Nick Goldman, Christophe Dessimoz
Want to track pandemic variants faster? Fix the bioinformatics bottleneck
Nature, 2021, 591:7848, 30-33.
Natalia Zajac, Stefan Zoller, Katri Seppälä, David Moi, Christophe Dessimoz, Jukka Jokela, Hanna Hartikainen, Natasha Glover
Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism
Genome Biol Evol, 2021, 13:3
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 Research, 2021, 49:D1, D373-D379
2020
Samuel Briand, Christophe Dessimoz*, Nadia El-Mabrouk*, Yannis Nevers
(*co-corresponding)
A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem
bioRxiv 2020.09.14.293522, ver. 4 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology
10.1101/2020.09.14.293522
Richard Benton, Christophe Dessimoz, David Moi
A putative origin of insect chemosensory receptors in the last common eukaryotic ancestor
eLife, 2020, 9:e62507
Natasha M Glover
Making the most of genomic data with OMA
F1000Res, 2020, 9:665
David Dylus, Trestan Pillonel, Onya Opota, Daniel Wüthrich, Helena MB Seth-Smith, Adrian Egli, Stefano Leo, Vladimir Lazarevic, Jacques Schrenzel, Sacha Laurent, Claire Bertelli, Dominique S Blanc, Stefan Neuenschwander, Alban Ramette, Laurent Falquet, Frank Imkamp, Peter M Keller, Andre Kahles, Simone Oberhaensli, Valérie Barbié, Christophe Dessimoz, Gilbert Greub, Aitana Lebrand
NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
Front Microbiol, 2020, 11:2822.
Stuart Byma, Akash Dhasade, Adrian Altenhoff, Christophe Dessimoz, James R. Larus
Parallel and Scalable Precise Clustering
Proceedings of the ACM International Conference on Parallel Architectures and Compilation Techniques, PACT ’20. New York, NY, USA. ACM pp. 217–228.
Alex Warwick Vesztrocy, Christophe Dessimoz
Benchmarking Gene Ontology Function Predictions Using Negative Annotations
ISMB 2020 / Bioinformatics (2020) 36, i210–i218
Supplementary data
Karina Zile, Christophe Dessimoz, Yannick Wurm, Joanna Masel
Only a single taxonomically restricted gene family in the
Drosophila melanogaster
subgroup can be identified with high confidence
Genome Biology and Evolution, 2020, 12(8):1355–1366
Code
Adrian M Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José M Fernández, Laia Codó, the Quest for Orthologs Consortium, Josep Ll Gelpi, Jaime Huerta-Cepas, Wataru Iwasaki, Steven Kelly, Odile Lecompte, Matthieu Muffato, Maria J Martin, Salvador Capella-Gutierrez, Paul D Thomas, Erik Sonnhammer*, Christophe Dessimoz*
(*joint corresponding authors)
The Quest for Orthologs benchmark service and consensus calls in 2020
Nucleic Acids Res, 2020, 48:W1, W538–W545
Project page
David Moi, Laurent Kilchoer, Pablo S. Aguilar, Christophe Dessimoz
Scalable Phylogenetic Profiling using MinHash Uncovers Likely Eukaryotic Sexual Reproduction Genes
PLOS Computational Biology, 2020, 16(7): e1007553
Code
Liam P Shaw, Alethea D Wang, David Dylus, Magda Meier, Grega Pogacnik, Christophe Dessimoz, Francois Balloux
The phylogenetic range of bacterial and viral pathogens of vertebrates
Molecular Ecology, 29(17):3361-3379
Rosa Fernández, Toni Gabaldón, Christophe Dessimoz
Orthology: definitions, inference, and impact on species phylogeny inference
Phylogenetics in the Genomic Era (Eds. S Scornavacca, F Delsuc, N Galtier), Chap. 2.4.
Full text
Robert N. Grass, Reinhard Heckel, Christophe Dessimoz, Wendelin J. Stark
Genomic encryption of digital data stored in synthetic DNA
Angewandte Chemie, 59:22, 8476-8480
Anne-Lyse Ducrest, Samuel Neuenschwander, Emanuel Schmid-Siegert, Marco Pagni, Clément Train, David Dylus, Yannis Nevers, Alex Warwick Vesztrocy, Luis M San-Jose, Mélanie Dupasquier, Christophe Dessimoz, Ioannis Xenarios, Alexandre Roulin*, Jérôme Goudet*
(*joint corresponding authors)
New genome assembly of the barn owl (
Tyto alba alba
)
Ecol. Evol., 2020, 46:D477
Monique Zahn-Zabal, Christophe Dessimoz, Natasha M Glover
Identifying orthologs with OMA: A primer
F1000Research, 2020, 9:27
Samuel Briand, Christophe Dessimoz*, Nadia El-Mabrouk*, Manuel Lafond and Gabriela Lobinska
(*corresponding)
A Generalized Robinson-Foulds Distance for Labeled Trees
The Asia Pacific Bioinformatics Conference (APBC) 2020 & BMC Genomics 21(Suppl 10):779
Preprint
Code
2019
Medhat Mahmoud*, Nastassia Gobet*, Diana Ivette Cruz Dávalos, Ninon Mounier, Christophe Dessimoz° and Fritz J. Sedlazeck°
(*joint first; °joint last)
Structural variant calling: the long and the short of it
Genome Biology, 2019, 20:246
Naihui Zhou et al (223 authors including Adrian Altenhoff, Alex Warwick Vesztrocy, and Christophe Dessimoz)
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Genome Biology, 2019, 20:244
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, 2019, 8:1822
Bristena Oprisanu, Christophe Dessimoz, Emiliano De Cristofaro
How Much Does GenoGuard Really "Guard"? An Empirical Analysis of Long-Term Security for Genomic Data
Proceedings of the 18th ACM CCS Workshop on Privacy in the Electronic Society (WPES'19), 2019, pp 93-105
Full text (ACM)
Tarcisio Mendes de Farias, Kurt Stockinger, Christophe Dessimoz
VoIDext: Vocabulary and patterns for enhancing interoperable datasets with virtual links
Proceedings of The 18th International Conference on Ontologies, DataBases, and Applications of Semantics (ODBASE’19), arXiv 1906.01950, Lecture Notes in Computer Science, vol 11877. Springer, Cham
Ana Claudia Sima*, Tarcisio Mendes de Farias*, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz
(*co-first)
Enabling Semantic Queries Across Federated Bioinformatics Databases
Database, 2019, baz106
Code
Website
Adrian M Altenhoff*, Jeremy Levy*, Magdalena Zarowiecki, Bartłomiej Tomiczek, Alex Warwick Vesztrocy, Daniel A Dalquen, Steven Müller, Maximilian J Telford, Natasha Glover, David Dylus, Christophe Dessimoz
(*co-first)
OMA standalone: orthology inference among public and custom genomes and transcriptomes
Genome Research, 2019, 29:1152-1163
News item
Software
Natasha Glover, Christophe Dessimoz, Ingo Ebersberger, Sofia K Forslund, Toni Gabaldón Jaime Huerta-Cepas, Maria-Jesus Martin, Matthieu Muffato, Mateus Patricio, Cécile Pereira Alan Sousa da Silva, Yan Wang, Erik Sonnhammer, Paul D Thomas, Quest for Orthologs Consortium
Advances and Applications in the Quest for Orthologs
Molecular Biology and Evolution, 2019, 36:10, 2157–2164
Hervé Philippe, Albert J Poustka, Marta Chiodin, Katharina J Hoff, Christophe Dessimoz, Bartlomiej Tomiczek, Philipp H Schiffer, Steven Müller, Daryl Domman, Matthias Horn, Heiner Kuhl, Bernd Timmermann, Noriyuki Satoh, Tomoe Hikosaka-Katayama, Hiroaki Nakano, Matthew L Rowe, Maurice R Elphick, Morgane Thomas-Chollier, Thomas Hankeln, Florian Mertes, Andreas Wallberg, Jonathan P Rast, Richard R Copley, Pedro Martinez, Maximilian J Telford
Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria
Current Biology, 2019, 29:1–9
Adrian M Altenhoff*, Natasha M Glover*, Christophe Dessimoz
(*co-first)
Inferring Orthology and Paralogy
Methods in Molecular Biology, 2019, Humana (New York), Vol 1910.
Ana Claudia Sima, Kurt Stockinger, Tarcisio Mendes de Farias, Manuel Gil
Semantic Integration and Enrichment of Heterogeneous Biological Databases
Methods in Molecular Biology, 2019, Humana (New York), Vol 1910.
Klara Kaleb, Alex Warwick Vesztrocy, Adrian Altenhoff, Christophe Dessimoz
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the
OmaDB
packages for R and Python
F1000 Research, 2019, 8:42
Natasha Glover, Adrian Altenhoff, Christophe Dessimoz
Assigning confidence scores to homoeologs using fuzzy logic
PeerJ 6:e6231
Clément-Marie Train, Miguel Pignatelli, Adrian Altenhoff, Christophe Dessimoz
iHam & pyHam: visualizing and processing hierarchical orthologous groups
Bioinformatics, 2019, 35:14, 2504–2506
Code iHam
Code pyHam
Ivana Piližota, Clément-Marie Train, Adrian Altenhoff, Henning Redestig, Christophe Dessimoz
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome
Bioinformatics, 2019, 35:7, 1159–1166
Software
2018
Alex Warwick Vesztrocy, Christophe Dessimoz*, Henning Redestig*
(*co-last)
Prioritising Candidate Genes Causing QTL using Hierarchical Orthologous Groups
Bioinformatics, 2018, 34:17, pp. i612–i619 (ECCB 2018 proceedings)
Story behind the paper
Software
DV Klopfenstein, Liangsheng Zhang, Brent Pedersen, Fidel Ramírez, Alex Warwick Vesztrocy, Aurelien Naldi, Christopher Mungall, Jeffrey Yunes, Olga Botvinnik, Mark Weigel, William Dampier, Christophe Dessimoz, Patrick Flick, Haibao Tang
GOATOOLS: A Python library for Gene Ontology analyses
Scientific Reports, 2018, 8:10872
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, Celine Scornavacca, Gergely Szöllősi, Louxin Zhang, Éric Tannier, Vincent Daubin
RecPhyloXML: a format for reconciled gene trees
Bioinformatics, 2018, 34:21, 3646–3652
Daniel Mietchen, Shoshana Wodak, Szymon Wasik, Natalia Szostak, Christophe Dessimoz
Submit a Topic Page to PLOS Computational Biology and Wikipedia
PLoS Comput Biol, 2018, 14(5): e1006137
Adrian M Altenhoff, Natasha M Glover, Clément-Marie Train, Klara Kaleb, Alex Warwick Vesztrocy, David Dylus, Tarcisio Mendes de 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, 2018, 46, pp. D477–D485
Kristoffer Forslund, Cecile Pereira, Salvador Capella-Gutierrez, Alan Sousa da Silva, Adrian Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele, Ingo Ebersberger, Judith Blake, Jesualdo Tomás Fernández Breis, the Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik Sonnhammer, Christophe Dessimoz*, Suzanna Lewis*
(*co-last)
Gearing up to handle the mosaic nature of life in the quest for orthologs
Bioinformatics, 2018, 34:2, pp. 323–329
2017
Tarcisio Mendes de Farias, Hirokazu Chiba, Jesualdo T. Fernández-Breis
Leveraging logical rules for efficacious representation of large orthology datasets
Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017)
Tomasz Suchan, Anahí Espíndola, Sereina Rutschmann, Brent C. Emerson, Kevin Gori, Christophe Dessimoz, Nils Arrigo, Michał Ronikier, Nadir Alvarez
Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus
Chiastocheta
(Diptera: Anthomyiidae) as a case study
Molecular Phylogenetics and Evolution, 2017, 114:189-198
Typeset version
Clément-Marie Train, Natasha M Glover, Gaston H Gonnet, Adrian M Altenhoff and Christophe Dessimoz
Orthologous matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference
Bioinformatics, 2017, i1-i8 (ISMB 2017 proceedings)
Georgia Tsagkogeorga, Steven Müller, Christophe Dessimoz, Stephen J. Rossiter
Comparative genomics reveals contraction in olfactory receptor genes in bats
Scientific Reports, 2017, 7:259
Daniel C Jeffares, Clemency Jolly, Mimoza Hoti, Doug Speed, Liam Shaw, Charalampos Rallis, Francois Balloux, Christophe Dessimoz*, Jürg Bähler*, Fritz Sedlazeck*
(*joint corresponding)
Transient structural variations alter gene expression and quantitative traits in Schizosaccharomyces pombe
Nature Communications, 2017, 8:14061
Story behind the paper
Pascale Gaudet, Nives Škunca, James C. Hu, Christophe Dessimoz
Primer on the Gene Ontology
The Gene Ontology Handbook (C Dessimoz, N Škunca, Eds.),
Methods in Molecular Biology, 2017, Springer (New York), Vol. 1446
Pascale Gaudet and Christophe Dessimoz
Gene Ontology: pitfalls, biases, remedies
The Gene Ontology Handbook (C Dessimoz, N Škunca, Eds.),
Methods in Molecular Biology, 2017, Springer (New York), Vol. 1446
Alex Warwick Vesztrocy and Christophe Dessimoz
Gene Ontology tutorial in Python
The Gene Ontology Handbook (C Dessimoz, N Škunca, Eds.),
Methods in Molecular Biology, 2017, Springer (New York), Vol. 1446
Christophe Dessimoz and Nives Škunca, Editors
The Gene Ontology Handbook
Methods in Molecular Biology, 2017, Springer (New York), Vol. 1446
2016
Yuxiang Jiang et al (147 authors including Adrian Altenhoff, Nives Škunca and Christophe Dessimoz)
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Genome Biology, 2016, 17:184
Sojo Victor, Christophe Dessimoz, Andrew Pomiankowski and Nick Lane
Membrane proteins are dramatically less conserved than water-soluble proteins across the tree of life
Molecular Biology and Evolution, advanced access
Supplementary data
Natasha M Glover, Ioanna Antoniadi, Gavin M. George, Lars Götzenberger, Ruben Gutzat, Kadri Koorem, Pierre Liancourt, Kinga Rutowicz, Krishna Saharan, Wanhui You and Philipp Mayer
A Pragmatic Approach to Getting Published: 35 Tips for Early Career Researchers
Frontiers in Plant Science, 2016, 7:610
Oscar Robinson*, David Dylus*, Christophe Dessimoz
(*equal contributions)
Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web
Molecular Biology and Evolution, 2016, 33:8, 2163-2166
Project page
Git repo
Story behind the paper
Demo video
Fabian Zimmer, Peter W Harrison, Christophe Dessimoz, Judith Mank
Compensation of dosage-sensitive genes on the chicken Z chromosome
Genome Biology and Evolution, 2016, 8:4, 1233-1242
Adrian Altenhoff, (25 co-authors including Daniel A Dalquen and Clément-Marie Train), Christophe Dessimoz
Standardized benchmarking in the quest for orthologs
Nature Methods, 2016, 13, 425–430
Story behind the paper
Project page
Natasha M Glover, Henning Redestig, Christophe Dessimoz
Homoeologs: what are they and how do we infer them?
Trends in Plant Science, 2016, 21, 609–621
Story behind the paper
Kevin Gori, Tomasz Suchan, Nadir Alvarez, Nick Goldman, Christophe Dessimoz
Clustering genes of common evolutionary history
Molecular Biology and Evolution, 2016, 33:6, 1590-1605
Git repo
Raw data
Blog post
2015
Ge Tan, Matthieu Muffato, Christian Ledergerber, Javier Herrero, Nick Goldman, Manuel Gil, Christophe Dessimoz
Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference
Systematic Biology, 2015, 64:5, 778-791
Supplementary data
Story behind the paper
Matt Ravenhall*, Nives Škunca*, Florent Lasalle, Christophe Dessimoz
(*equal contributions)
Inferring horizontal gene transfer
PLOS Computational Biology, 2015, 11:5, e1004095
On Wikipedia
Story behind the paper
Bernhard Egger*, François Lapraz*, Bartłomiej Tomiczek*, Steven Müller, Christophe Dessimoz, Johannes Girstmair, Nives Škunca, Kate A Rawlinson, Christopher B Cameron, Elena Beli, M Antonio Todaro, Mehrez Gammoudi, Carolina Noreña, Maximilian J Telford (*co-first)
A transcriptomic-phylogenomic analysis of the evolutionary relationships of flatworms
Current Biology, 2015, 25:10, 1347–1353
Nives Škunca and Christophe Dessimoz
Phylogenetic profiling: how much input data is enough?
PLOS One, 2015, 10:2, e0114701
Ge Tan, Manuel Gil, Ari P Löytynoja, Nick Goldman, Christophe Dessimoz
Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks
PNAS, 2015, 112:2, E99-E100
Preprint
Raw data
Adrian M Altenhoff, Nives Škunca, Natasha Glover, Clément-Marie Train, Anna Sueki, Ivana Piližota, Kevin Gori, Bartlomiej Tomiczek, Steven Müller, Henning Redestig, Gaston H Gonnet and Christophe Dessimoz
The OMA orthology database in 2015: function predictions, better plant support, synteny view, and other improvements
Nucleic Acids Res, 2015, 43:D1, D240-D249
Project page
2014
Xinxia Peng et al. (38 authors including Kevin Gori, Nives Škunca, and Christophe Dessimoz)
The draft genome sequence of the ferret
(Mustela putorius furo)
facilitates study of human respiratory disease
Nature Biotechnology, 2014, 32:12, 1250-1255
Lucas D Wittwer*, Ivana Piližota*, Adrian M Altenhoff, Christophe Dessimoz
(*equal contributions)
Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology
PeerJ, 2014, 2:e607
Story behind the paper
Erik Sonnhammer, Toni Gabaldón, Alan WS da Silva, Maria Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul Thomas, Christophe Dessimoz, and the Quest for Orthologs consortium
Big data and other challenges in the quest for orthologs
Bioinformatics, 2014, 30:21, 2993-2998
Maria Anisimova and Christophe Dessimoz
Preface of Proceedings of GNOME 2014 -- Festschrift for Gaston Gonnet
PeerJ PrePrints, 2014, 2:e426v1
GNOME 2014 Festschrift
Diana Coman, Adrian M Altenhoff, Stefan Zoller, Wilhelm Gruissem and Eva Vranová
Distinct evolutionary strategies in the GGPPS family from plants
Frontiers in Plant Science, 2014, 5:230
Heinz Stockinger, Adrian M Altenhoff, Arnold K, Konstantin Arnold, Amos Bairoch, Frederic Bastian, Sven Bergmann, et al.
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support
Nucleic Acids Res, 2014, 42(W1): W436-W441
Stefano Iantorno*, Kevin Gori*, Nick Goldman, Manuel Gil, Christophe Dessimoz
(*equal contributions)
Who watches the watchmen? an appraisal of benchmarks for multiple sequence alignment
Multiple Sequence Alignment Methods (D Russell, Editor),
Methods in Molecular Biology, 2014, Springer Humana, Vol. 1079.
Preprint
2013
Christophe Dessimoz, Nives Škunca, Paul D. Thomas
CAFA and the open world of protein function predictions
Trends in Genetics, 2013, 29:11, 609-610
Ajay Prasad, Suchitra Suresh Kumar, Christophe Dessimoz, Vincent Jaquet, Stefan Bleuler, Oliver Laule, Tomas Hruz, Wilhelm Gruissem, Philip Zimmermann
Global regulatory architecture of human, mouse and rat tissue transcriptomes
BMC Genomics, 2013, 14:716
Daniel A Dalquen and Christophe Dessimoz
Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals
Genome Biology and Evolution, 2013, 5:10, 1800-1806
Daniel A Dalquen, Adrian M Altenhoff, Gaston H. Gonnet, Christophe Dessimoz
The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study
PLoS One, 2013, 8:2, e56925
Datasets
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
Nature, 2013, 494:7435, 77-80
Media coverage
Full text (PMC)
Adrian M Altenhoff, Manuel Gil, Gaston H. Gonnet, Christophe Dessimoz
Inferring hierarchical orthologous groups from orthologous gene pairs
PLoS One, 2013, 8:1, e53786
Software
Mikael Sunnåker, Alberto G Busetto*, Elina Numminen*, Jukka Corander, Matthieu Foll, Christophe Dessimoz
(*equal contributions)
Approximate Bayesian computation
PLoS Computational Biology, 2013, 9:1, e1002803
On Wikipedia
Story behind the paper
2012
Nives Škunca, Adrian M Altenhoff, Christophe Dessimoz
Quality of computationally inferred gene ontology annotations
PLoS Computational Biology, 2012, 8:5, e1002533
Interactive plots
Story behind the paper
Adrian M Altenhoff, Romain Studer, Marc Robinson-Rechavi, Christophe Dessimoz
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs
PLoS Computational Biology, 2012, 8:5, e1002514
Press release
Story behind the paper
Christophe Dessimoz, Toni Gabaldón, David S Roos, Erik LL Sonnhammer, Javier Herrero, and the Quest for Orthologs Consortium
Toward community standards in the quest for orthologs
Bioinformatics, 2012, 28:6, 900-904
Adrian M Altenhoff and Christophe Dessimoz
Inferring Orthology and Paralogy
Evolutionary Genomics: Statistical and Computational methods (M Anisimova, Editor),
Methods in Molecular Biology, 2012, Springer Humana, Vol. 855.
Daniel A Dalquen, Maria Anisimova, Gaston H. Gonnet, Christophe Dessimoz
ALF - A Simulation Framework for Genome Evolution
Molecular Biology and Evolution, 2012, 29:4, 1115-1123
2011
Christophe Dessimoz
Editorial: Orthology and Applications
Briefings in Bioinformatics, 2011, 12:5, 375-376
Special Issue
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 in Bioinformatics, 2011, 12:5, 423-435
Software
Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz
Conceptual Framework and Pilot Study to Benchmark Phylogenomic Databases Based on Reference Gene Trees
Briefings in Bioinformatics, 2011, 12:5, 474-484
Maria Anisimova, Manuel Gil, Jean-François Dufayard, Christophe Dessimoz, Olivier Gascuel
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes.
Systematic Biology, 2011, 60:5, 685-699
Judith Owiti, Jonas Grossmann, Peter Gehrig, Christophe Dessimoz, Christophe Laloi, Maria Ben Hansen, Wilhelm Gruissem, Hervé Vanderschuren
iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration
The Plant Journal, 2011, 67:1, 145-156
Louis du Plessis, Nives Škunca, Christophe Dessimoz
The What, Where, How, and Why of Gene Ontology -- A Primer for Bioinformaticians
Briefings in Bioinformatics, 2011, 12:6, 723-735
Christian Ledergerber and Christophe Dessimoz
Base-Calling for Next-Generation Sequencing Platforms
Briefings in Bioinformatics, 2011, 12:5, 489-497
Adrian M Altenhoff, Adrian Schneider, Gaston H. Gonnet, Christophe Dessimoz
OMA 2011: Orthology Inference Among 1,000 Complete Genomes
Nucleic Acids Res, 2011, 39 (suppl 1): D289-D294
Project page
2010
Christophe Dessimoz* and Manuel Gil*
(*equal contributions)
Phylogenetic assessment of alignments reveals neglected tree signal in gaps
Genome Biology, 2010, 11:R37
Raw data
2009
Toni Gabaldón, Christophe Dessimoz, Julie Huxley-Jones, Albert J Vilella, Erik LL Sonnhammer, Suzanna Lewis
Joining forces in the quest for orthologs
Genome Biology 2009, 10:403
Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, Jacques Rougemont
The Microbe Browser for Comparative Genomics
Nucleic Acids Res, 2009, 37 (suppl 2): W296-W299.
Project page
Adrian M Altenhoff and Christophe Dessimoz
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
PLoS Computational Biology, 2009, 5:1, e1000262
2008
Alexander Roth, Gaston H. Gonnet, Christophe Dessimoz
Algorithm of OMA for Large-Scale Orthology Inference
BMC Bioinformatics, 2008, 9:518
(Please note the associated
erratum
)
Project page
Mark T. Holder, Derrick J. Zwickl, Christophe Dessimoz
Evaluating the Robustness of Phylogenetic Methods to Among-Site Variability in Substitution Processes
Phil. Trans. R. Soc. B, 2008, 363:1512, 4013-4021
Adam M Szalkowski, Christian Ledergerber, Philipp Krähenbühl, Christophe Dessimoz
SWPS3 - Fast Multi-Threaded Vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2
BMC Research Notes, 2008, 1:107
Project page
Christophe Dessimoz* and Manuel Gil*
(*equal contributions)
Covariance of Maximum Likelihood Evolutionary Distances between Sequences Aligned Pairwise
BMC Evolutionary Biology, 2008, 8:179
Christophe Dessimoz, Daniel Margadant, Gaston H. Gonnet
DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework
RECOMB 2008, LNCS 4955, 315-330
2007
Christian Ledergerber and Christophe Dessimoz
Alignments with Non-overlapping Moves, Inversions and Tandem Duplications in O(n
4
) time
COCOON 2007, LNCS 4598, 151-164
Abstract
selected for publication in
Journal of Combinatorial Optimization, 2008, 16:3
Adrian Schneider, Christophe Dessimoz, Gaston H. Gonnet
OMA Browser - Exploring orthologous relations across 352 complete genomes
Bioinformatics, 2007, 23:16, 2180-2182
Project page
2006
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 Bioinformatics, 2006, 7:529
Christophe Dessimoz, Brigitte Boeckmann, Alexander Roth, Gaston H. Gonnet
Detecting Non-Orthology in the COGs Database and Other Approaches Grouping Orthologs Using Genome-Specific Best Hits
Nucleic Acids Res, 2006 34:11, 3309-3316
2005
Manuel Gil, Christophe Dessimoz, Gaston H. Gonnet
A Dimensionless Fit Measure for Phylogenetic Distance Trees
J Bioinform Comput Biol, 2005, 3:6, 1429-1440
Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander Roth, Adrian Schneider, Gaston H. Gonnet
OMA, a Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements
RECOMB 2005 Workshop on Comparative Genomics, LNCS 3678, 61-72
Project page