Publications
Tags:
- Preprints
- Ivana Piližota, Henning Redestig, Christophe Dessimoz
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome
bioRxiv 182550 - Brigitte Boeckmann, David Dylus, Sébastien Moretti, Adrian Altenhoff, Clément-Marie Train, Evgenia Kriventseva, Lydie Bougueleret, Ioannis Xenarios, Eyal Privman, Christophe Dessimoz
Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree
bioRxiv 181966 - 2018
- 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, in press - 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
Gearing up to handle the mosaic nature of life in the quest for orthologs
Bioinformatics, 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, 114:189-198Typeset version
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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, Charalampos Rallis, 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
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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
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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
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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
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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
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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
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Christophe Dessimoz
Editorial: Orthology and Applications
Briefings in Bioinformatics, 2011, 12:5, 375-376Special Issue
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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
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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
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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
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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
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Christian Ledergerber and Christophe Dessimoz
Alignments with Non-overlapping Moves, Inversions and Tandem Duplications in O(n4) time
COCOON 2007, LNCS 4598, 151-164Abstract
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
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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
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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, 61-72Project page