Publications

  1. Preprints
  2. 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
  3. David Moi, Christophe Dessimoz
    Reconstructing protein interactions across time using phylogeny-aware graph neural networks
    bioRxiv 2022.07.21.501014
  4. Yannis Nevers, Natasha Glover, Christophe Dessimoz, Odile Lecompte
    Protein length distribution is remarkably consistent across Life
    bioRxiv 2021.12.03.470944
  5. 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
  6. 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
  7. 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
  8. 2022
  9. 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.
  10. 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.
  11. 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.
  12. 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
  13. Christophe Dessimoz, Sushmita Roy
    ISMB 2022 proceedings
    Bioinformatics 38:i8–i9.
  14. Alina Nicheperovich, Adrian M Altenhoff, Christophe Dessimoz, Sina Majidian
    OMAMO: orthology-based alternative model organism selection
    Bioinformatics 38:2965–2966. 2022.
  15. 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
  16. 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
  17. 2021
  18. Christophe Dessimoz, Teresa M Przytycka
    ISMB/ECCB 2021 proceedings
    Bioinformatics 37:i7–i8.
  19. 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
  20. 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
  21. 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
  22. 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.
  23. 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
  24. 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
  25. 2020
  26. 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
  27. Richard Benton, Christophe Dessimoz, David Moi
    A putative origin of insect chemosensory receptors in the last common eukaryotic ancestor
    eLife, 2020, 9:e62507
  28. Natasha M Glover
    Making the most of genomic data with OMA
    F1000Res, 2020, 9:665
  29. 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.
  30. 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.
  31. Alex Warwick Vesztrocy, Christophe Dessimoz
    Benchmarking Gene Ontology Function Predictions Using Negative Annotations
    ISMB 2020 / Bioinformatics (2020) 36, i210–i218 Supplementary data
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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. Open access Full text
  37. 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
  38. 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
  39. Monique Zahn-Zabal, Christophe Dessimoz, Natasha M Glover
    Identifying orthologs with OMA: A primer
    F1000Research, 2020, 9:27
  40. 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
  41. 2019
  42. 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
  43. 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
  44. 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
  45. 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)
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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 PDF
  51. Adrian M Altenhoff*, Natasha M Glover*, Christophe Dessimoz (*co-first)
    Inferring Orthology and Paralogy
    Methods in Molecular Biology, 2019, Humana (New York), Vol 1910.
  52. 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.
  53. 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
  54. Natasha Glover, Adrian Altenhoff, Christophe Dessimoz
    Assigning confidence scores to homoeologs using fuzzy logic
    PeerJ 6:e6231
  55. 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
  56. 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
  57. 2018
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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 PDF
  64. 2017
  65. 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) PDF
  66. 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 PDF Typeset version
  67. 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)
  68. Georgia Tsagkogeorga, Steven Müller, Christophe Dessimoz, Stephen J. Rossiter
    Comparative genomics reveals contraction in olfactory receptor genes in bats
    Scientific Reports, 2017, 7:259
  69. 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
  70. 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
  71. 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
  72. 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
  73. Christophe Dessimoz and Nives Škunca, Editors
    The Gene Ontology Handbook
    Methods in Molecular Biology, 2017, Springer (New York), Vol. 1446
  74. 2016
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. 2015
  84. 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
  85. 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
  86. 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
  87. Nives Škunca and Christophe Dessimoz
    Phylogenetic profiling: how much input data is enough?
    PLOS One, 2015, 10:2, e0114701
  88. 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
  89. 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
  90. 2014
  91. 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
  92. 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
  93. 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
  94. Maria Anisimova and Christophe Dessimoz
    Preface of Proceedings of GNOME 2014 -- Festschrift for Gaston Gonnet
    PeerJ PrePrints, 2014, 2:e426v1 GNOME 2014 Festschrift
  95. 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
  96. 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
  97. 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
  98. 2013
  99. Christophe Dessimoz, Nives Škunca, Paul D. Thomas
    CAFA and the open world of protein function predictions
    Trends in Genetics, 2013, 29:11, 609-610
  100. 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
  101. 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
  102. 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
  103. 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)
  104. 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
  105. 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
  106. 2012
  107. 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
  108. 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
  109. 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
  110. 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. PDF
  111. 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
  112. 2011
  113. Christophe Dessimoz
    Editorial: Orthology and Applications
    Briefings in Bioinformatics, 2011, 12:5, 375-376 PDF Special Issue
  114. 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
  115. 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
  116. 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
  117. 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
  118. 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
  119. Christian Ledergerber and Christophe Dessimoz
    Base-Calling for Next-Generation Sequencing Platforms
    Briefings in Bioinformatics, 2011, 12:5, 489-497
  120. 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
  121. 2010
  122. Christophe Dessimoz* and Manuel Gil* (*equal contributions)
    Phylogenetic assessment of alignments reveals neglected tree signal in gaps
    Genome Biology, 2010, 11:R37 Raw data
  123. 2009
  124. 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
  125. 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
  126. Adrian M Altenhoff and Christophe Dessimoz
    Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
    PLoS Computational Biology, 2009, 5:1, e1000262
  127. 2008
  128. 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
  129. 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
  130. 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
  131. Christophe Dessimoz* and Manuel Gil* (*equal contributions)
    Covariance of Maximum Likelihood Evolutionary Distances between Sequences Aligned Pairwise
    BMC Evolutionary Biology, 2008, 8:179
  132. 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 PDF
  133. 2007
  134. Christian Ledergerber and Christophe Dessimoz
    Alignments with Non-overlapping Moves, Inversions and Tandem Duplications in O(n4) time
    COCOON 2007, LNCS 4598, 151-164 PDF Abstract
    selected for publication in Journal of Combinatorial Optimization, 2008, 16:3 PDF
  135. Adrian Schneider, Christophe Dessimoz, Gaston H. Gonnet
    OMA Browser - Exploring orthologous relations across 352 complete genomes
    Bioinformatics, 2007, 23:16, 2180-2182 Project page
  136. 2006
  137. 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
  138. 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
  139. 2005
  140. Manuel Gil, Christophe Dessimoz, Gaston H. Gonnet
    A Dimensionless Fit Measure for Phylogenetic Distance Trees
    J Bioinform Comput Biol, 2005, 3:6, 1429-1440
  141. 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 PDF Project page