DESSIMOZ LAB

Publications

Tags:

• All
• Selected work
• Highly cited ( ≥ 30x)
• High altmetrics
• Open access
• Comparative genomics
• Benchmarking
• Phylogenetics
• Statistics
• Alignments
• Nextgen sequencing
• Gene/protein function
• Big data
• Ontologies
• Algorithms
• Plant genomics
• Original paper
• Review
• Editorial
• Book
• Preprint
• Quest for Orthologs consortium
• Undergraduate co-author

1. Preprints
74. Adrian M Altenhoff, Jeremy Levy, Magdalena Zarowiecki, Bartłomiej Tomiczek, Alex Warwick Vesztrocy, Daniel Dalquen, Steven Müller, Maximilian Telford, Natasha Glover, David Dylus, Christophe Dessimoz
    OMA standalone: orthology inference among public and custom genomes and transcriptomes
    bioRxiv 397752
73. 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
74. 2018
72. 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, in press
71. Alex Warwick Vesztrocy, Christophe Dessimoz*, Henning Redestig* (*co-last)
    Prioritising Candidate Genes Causing QTL using Hierarchical Orthologous Groups
    ECCB 2018, accepted
70. 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
69. 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, in press
68. 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
67. 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
66. 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
67. 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)
64. 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
63. 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)
62. Georgia Tsagkogeorga, Steven Müller, Christophe Dessimoz, Stephen J. Rossiter
    Comparative genomics reveals contraction in olfactory receptor genes in bats
    Scientific Reports, 2017, 7:259
61. 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
60. 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
59. 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
58. 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
57. Christophe Dessimoz and Nives Škunca, Editors
    The Gene Ontology Handbook
    Methods in Molecular Biology, 2017, Springer (New York), Vol. 1446
58. 2016
56. 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
55. 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
54. 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
53. 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
52. 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
51. 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
50. 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
49. 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
50. 2015
48. 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
47. 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
46. 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
45. Nives Škunca and Christophe Dessimoz
    Phylogenetic profiling: how much input data is enough?
    PLOS One, 2015, 10:2, e0114701
44. 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
43. 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
44. 2014
42. 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
41. 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
40. 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
39. Maria Anisimova and Christophe Dessimoz
    Preface of Proceedings of GNOME 2014 -- Festschrift for Gaston Gonnet
    PeerJ PrePrints, 2014, 2:e426v1 GNOME 2014 Festschrift
38. 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
37. 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
36. 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
37. 2013
35. Christophe Dessimoz, Nives Škunca, Paul D. Thomas
    CAFA and the open world of protein function predictions
    Trends in Genetics, 2013, 29:11, 609-610
34. 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
33. 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
32. 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
31. 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)
30. 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
29. 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
30. 2012
28. 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
27. 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
26. 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
25. 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.
24. 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
25. 2011
23. Christophe Dessimoz
    Editorial: Orthology and Applications
    Briefings in Bioinformatics, 2011, 12:5, 375-376 Special Issue
22. 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
21. 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
20. 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
19. 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
18. 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
17. Christian Ledergerber and Christophe Dessimoz
    Base-Calling for Next-Generation Sequencing Platforms
    Briefings in Bioinformatics, 2011, 12:5, 489-497
16. 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
17. 2010
15. Christophe Dessimoz* and Manuel Gil* (*equal contributions)
    Phylogenetic assessment of alignments reveals neglected tree signal in gaps
    Genome Biology, 2010, 11:R37 Raw data
16. 2009
14. 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
13. 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
12. Adrian M Altenhoff and Christophe Dessimoz
    Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
    PLoS Computational Biology, 2009, 5:1, e1000262
13. 2008
11. 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
10. 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
9. 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
8. Christophe Dessimoz* and Manuel Gil* (*equal contributions)
   Covariance of Maximum Likelihood Evolutionary Distances between Sequences Aligned Pairwise
   BMC Evolutionary Biology, 2008, 8:179
7. 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
8. 2007
6. Christian Ledergerber and Christophe Dessimoz
   Alignments with Non-overlapping Moves, Inversions and Tandem Duplications in O(n⁴) time
   COCOON 2007, LNCS 4598, 151-164 Abstract
   selected for publication in Journal of Combinatorial Optimization, 2008, 16:3
5. Adrian Schneider, Christophe Dessimoz, Gaston H. Gonnet
   OMA Browser - Exploring orthologous relations across 352 complete genomes
   Bioinformatics, 2007, 23:16, 2180-2182 Project page
6. 2006
4. 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
3. 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
4. 2005
2. Manuel Gil, Christophe Dessimoz, Gaston H. Gonnet
   A Dimensionless Fit Measure for Phylogenetic Distance Trees
   J Bioinform Comput Biol, 2005, 3:6, 1429-1440
1. 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