Christophe Dessimoz - Publications

University College London, London, United Kingdom 
Bioinformatics, Computational Biology

72 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Altenhoff AM, Train CM, Gilbert KJ, Mediratta I, Mendes de Farias T, Moi D, Nevers Y, Radoykova HS, Rossier V, Warwick Vesztrocy A, Glover NM, Dessimoz C. OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. Nucleic Acids Research. PMID 33174605 DOI: 10.1093/nar/gkaa1007  0.72
2020 Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, Gelpi JL, Huerta-Cepas J, Iwasaki W, ... ... Dessimoz C, et al. The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Research. PMID 32374845 DOI: 10.1093/nar/gkaa308  0.72
2020 Zahn-Zabal M, Dessimoz C, Glover NM. Identifying orthologs with OMA: A primer. F1000research. 9: 27. PMID 32089838 DOI: 10.12688/f1000research.21508.1  0.52
2019 Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, ... ... Dessimoz C, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/s13059-019-1835-8  0.4
2019 Sima AC, Mendes de Farias T, Zbinden E, Anisimova M, Gil M, Stockinger H, Stockinger K, Robinson-Rechavi M, Dessimoz C. Enabling semantic queries across federated bioinformatics databases. Database : the Journal of Biological Databases and Curation. 2019. PMID 31697362 DOI: 10.1093/database/baz106  0.76
2019 Altenhoff AM, Glover NM, Dessimoz C. Inferring Orthology and Paralogy. Methods in Molecular Biology (Clifton, N.J.). 1910: 149-175. PMID 31278664 DOI: 10.1007/978-1-4939-9074-0_5  0.72
2019 Altenhoff AM, Levy J, Zarowiecki M, Tomiczek B, Warwick Vesztrocy A, Dalquen DA, Müller S, Telford MJ, Glover NM, Dylus D, Dessimoz C. OMA standalone: orthology inference among public and custom genomes and transcriptomes. Genome Research. PMID 31235654 DOI: 10.1101/gr.243212.118  0.8
2019 Philippe H, Poustka AJ, Chiodin M, Hoff KJ, Dessimoz C, Tomiczek B, Schiffer PH, Müller S, Domman D, Horn M, Kuhl H, Timmermann B, Satoh N, Hikosaka-Katayama T, Nakano H, et al. Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria. Current Biology : Cb. PMID 31104936 DOI: 10.1016/j.cub.2019.04.009  0.44
2019 Kaleb K, Vesztrocy AW, Altenhoff A, Dessimoz C. Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the packages for R and Python. F1000research. 8: 42. PMID 31001419 DOI: 10.12688/f1000research.17548.1  0.4
2019 Glover NM, Altenhoff A, Dessimoz C. Assigning confidence scores to homoeologs using fuzzy logic. Peerj. 6: e6231. PMID 30648004 DOI: 10.7717/peerj.6231  0.52
2018 Train CM, Pignatelli M, Altenhoff A, Dessimoz C. iHam & pyHam: visualizing and processing hierarchical orthologous groups. Bioinformatics (Oxford, England). PMID 30508066 DOI: 10.1093/bioinformatics/bty994  0.52
2018 Warwick Vesztrocy A, Dessimoz C, Redestig H. Prioritising candidate genes causing QTL using hierarchical orthologous groups. Bioinformatics (Oxford, England). 34: i612-i619. PMID 30423067 DOI: 10.1093/bioinformatics/bty615  0.4
2018 Piližota I, Train CM, Altenhoff A, Redestig H, Dessimoz C. Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome. Bioinformatics (Oxford, England). PMID 30184069 DOI: 10.1093/bioinformatics/bty772  0.56
2017 Altenhoff AM, Glover NM, Train CM, Kaleb K, Warwick Vesztrocy A, Dylus D, de Farias TM, Zile K, Stevenson C, Long J, Redestig H, Gonnet GH, Dessimoz C. The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. Nucleic Acids Research. PMID 29106550 DOI: 10.1093/nar/gkx1019  1
2017 Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Boeckmann B, Gabaldón T, ... ... Dessimoz C, et al. Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics (Oxford, England). PMID 28968857 DOI: 10.1093/bioinformatics/btx542  0.6
2017 Train CM, Glover NM, Gonnet GH, Altenhoff AM, Dessimoz C. Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference. Bioinformatics (Oxford, England). 33: i75-i82. PMID 28881964 DOI: 10.1093/bioinformatics/btx229  1
2017 Suchan T, Espíndola A, Rutschmann S, Emerson BC, Gori K, Dessimoz C, Arrigo N, Ronikier M, Alvarez N. 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. PMID 28645767 DOI: 10.1016/j.ympev.2017.06.012  0.76
2017 Gaudet P, Škunca N, Hu JC, Dessimoz C. Primer on the Gene Ontology. Methods in Molecular Biology (Clifton, N.J.). 1446: 25-37. PMID 27812933 DOI: 10.1007/978-1-4939-3743-1_3  0.84
2016 Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, ... ... Dessimoz C, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/s13059-016-1037-6  1
2016 Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, ... ... Dessimoz C, et al. Standardized benchmarking in the quest for orthologs. Nature Methods. PMID 27043882 DOI: 10.1038/nmeth.3830  1
2016 Glover NM, Redestig H, Dessimoz C. Homoeologs: What Are They and How Do We Infer Them? Trends in Plant Science. PMID 27021699 DOI: 10.1016/j.tplants.2016.02.005  0.52
2016 Gori K, Suchan T, Alvarez N, Goldman N, Dessimoz C. Clustering genes of common evolutionary history. Molecular Biology and Evolution. PMID 26893301 DOI: 10.1093/molbev/msw038  1
2015 Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C. Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference. Systematic Biology. PMID 26031838 DOI: 10.1093/sysbio/syv033  1
2015 Ravenhall M, Škunca N, Lassalle F, Dessimoz C. Inferring horizontal gene transfer. Plos Computational Biology. 11: e1004095. PMID 26020646 DOI: 10.1371/journal.pcbi.1004095  0.84
2015 Egger B, Lapraz F, Tomiczek B, Müller S, Dessimoz C, Girstmair J, Škunca N, Rawlinson KA, Cameron CB, Beli E, Todaro MA, Gammoudi M, Noreña C, Telford MJ. A transcriptomic-phylogenomic analysis of the evolutionary relationships of flatworms. Current Biology : Cb. 25: 1347-53. PMID 25866392 DOI: 10.1016/j.cub.2015.03.034  1
2015 Škunca N, Dessimoz C. Phylogenetic profiling: how much input data is enough? Plos One. 10: e0114701. PMID 25679783 DOI: 10.1371/journal.pone.0114701  0.84
2015 Tan G, Gil M, Löytynoja AP, Goldman N, Dessimoz C. Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks. Proceedings of the National Academy of Sciences of the United States of America. 112: E99-100. PMID 25564672 DOI: 10.1073/pnas.1417526112  1
2015 Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C. The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Research. 43: D240-9. PMID 25399418 DOI: 10.1093/nar/gku1158  1
2015 Škunca N, Dessimoz C. Phylogenetic profiling: How much input data is enough? Plos One. 10. DOI: 10.1371/journal.pone.0114701  1
2015 Ravenhall M, Škunca N, Lassalle F, Dessimoz C. Inferring Horizontal Gene Transfer Plos Computational Biology. 11. DOI: 10.1371/journal.pcbi.1004095  1
2014 Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, ... ... Dessimoz C, et al. The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. Nature Biotechnology. 32: 1250-5. PMID 25402615 DOI: 10.1038/nbt.3079  1
2014 Wittwer LD, Piližota I, Altenhoff AM, Dessimoz C. Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology. Peerj. 2: e607. PMID 25320677 DOI: 10.7717/peerj.607  0.72
2014 Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C. Big data and other challenges in the quest for orthologs. Bioinformatics (Oxford, England). 30: 2993-8. PMID 25064571 DOI: 10.1093/bioinformatics/btu492  1
2014 Iantorno S, Gori K, Goldman N, Gil M, Dessimoz C. Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment. Methods in Molecular Biology (Clifton, N.J.). 1079: 59-73. PMID 24170395 DOI: 10.1007/978-1-62703-646-7_4  1
2014 Wittwer LD, Pilĭzota I, Altenhoff AM, Dessimoz C. Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology Peerj. 2014. DOI: 10.7717/peerj.607  1
2013 Dessimoz C, Škunca N, Thomas PD. CAFA and the Open World of protein function predictions Trends in Genetics. 29: 609-610. PMID 24138813 DOI: 10.1016/j.tig.2013.09.005  1
2013 Prasad A, Kumar SS, Dessimoz C, Bleuler S, Laule O, Hruz T, Gruissem W, Zimmermann P. Global regulatory architecture of human, mouse and rat tissue transcriptomes. Bmc Genomics. 14: 716. PMID 24138449 DOI: 10.1186/1471-2164-14-716  1
2013 Dalquen DA, Dessimoz C. Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals Genome Biology and Evolution. 5: 1800-1806. PMID 24013106 DOI: 10.1093/gbe/evt132  1
2013 Dalquen DA, Altenhoff AM, Gonnet GH, Dessimoz C. The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study Plos One. 8. PMID 23451112 DOI: 10.1371/journal.pone.0056925  1
2013 Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature. 494: 77-80. PMID 23354052 DOI: 10.1038/nature11875  1
2013 Altenhoff AM, Gil M, Gonnet GH, Dessimoz C. Inferring hierarchical orthologous groups from orthologous gene pairs. Plos One. 8: e53786. PMID 23342000 DOI: 10.1371/journal.pone.0053786  1
2013 Sunnåker M, Busetto AG, Numminen E, Corander J, Foll M, Dessimoz C. Approximate Bayesian computation. Plos Computational Biology. 9: e1002803. PMID 23341757 DOI: 10.1371/journal.pcbi.1002803  1
2012 Škunca N, Altenhoff A, Dessimoz C. Quality of computationally inferred gene ontology annotations Plos Computational Biology. 8. PMID 22693439 DOI: 10.1371/journal.pcbi.1002533  1
2012 Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C. Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. Plos Computational Biology. 8: e1002514. PMID 22615551 DOI: 10.1371/journal.pcbi.1002514  1
2012 Altenhoff AM, Dessimoz C. Inferring orthology and paralogy Methods in Molecular Biology. 855: 259-279. PMID 22407712 DOI: 10.1007/978-1-61779-582-4_9  1
2012 Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J. Toward community standards in the quest for orthologs. Bioinformatics (Oxford, England). 28: 900-4. PMID 22332236 DOI: 10.1093/bioinformatics/bts050  1
2012 Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C. ALF-A simulation framework for genome evolution Molecular Biology and Evolution. 29: 1115-1123. PMID 22160766 DOI: 10.1093/molbev/msr268  1
2011 Dessimoz C. Editorial: Orthology and applications Briefings in Bioinformatics. 12: 375-376. PMID 21949264 DOI: 10.1093/bib/bbr057  1
2011 Boeckmann B, Robinson-Rechavi M, Xenarios I, Dessimoz C. Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Briefings in Bioinformatics. 12: 423-35. PMID 21737420 DOI: 10.1093/bib/bbr034  1
2011 Dessimoz C, Zoller S, Manousaki T, Qiu H, Meyer A, Kuraku S. Comparative genomics approach to detecting split-coding regions in a low-coverage genome: Lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes) Briefings in Bioinformatics. 12: 474-484. PMID 21712341 DOI: 10.1093/bib/bbr038  1
2011 Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Systematic Biology. 60: 685-99. PMID 21540409 DOI: 10.1093/sysbio/syr041  1
2011 Owiti J, Grossmann J, Gehrig P, Dessimoz C, Laloi C, Hansen MB, Gruissem W, Vanderschuren H. ITRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration Plant Journal. 67: 145-156. PMID 21435052 DOI: 10.1111/j.1365-313X.2011.04582.x  1
2011 du Plessis L, Škunca N, Dessimoz C. The what, where, how and why of gene ontology-A primer for bioinformaticians Briefings in Bioinformatics. 12: 723-735. PMID 21330331 DOI: 10.1093/bib/bbr002  1
2011 Ledergerber C, Dessimoz C. Base-calling for next-generation sequencing platforms Briefings in Bioinformatics. 12: 489-497. PMID 21245079 DOI: 10.1093/bib/bbq077  1
2011 Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. OMA 2011: Orthology inference among 1000 complete genomes Nucleic Acids Research. 39: D289-D294. PMID 21113020 DOI: 10.1093/nar/gkq1238  1
2010 Dessimoz C, Gil M. Phylogenetic assessment of alignments reveals neglected tree signal in gaps Genome Biology. 11. PMID 20370897 DOI: 10.1186/gb-2010-11-4-r37  1
2009 Gabaldón T, Dessimoz C, Huxley-Jones J, Vilella AJ, Sonnhammer EL, Lewis S. Joining forces in the quest for orthologs. Genome Biology. 10: 403. PMID 19785718 DOI: 10.1186/gb-2009-10-9-403  1
2009 Gattiker A, Dessimoz C, Schneider A, Xenarios I, Pagni M, Rougemont J. The Microbe browser for comparative genomics Nucleic Acids Research. 37: W296-W299. PMID 19406928 DOI: 10.1093/nar/gkp268  1
2009 Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods Plos Computational Biology. 5. PMID 19148271 DOI: 10.1371/journal.pcbi.1000262  1
2008 Roth ACJ, Gonnet GH, Dessimoz C. Algorithm of OMA for large-scale orthology inference Bmc Bioinformatics. 9. PMID 19055798 DOI: 10.1186/1471-2105-9-518  1
2008 Holder MT, Zwickl DJ, Dessimoz C. Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 4013-21. PMID 18852108 DOI: 10.1098/rstb.2008.0162  1
2008 Dessimoz C, Gil M. Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise Bmc Evolutionary Biology. 8. PMID 18573206 DOI: 10.1186/1471-2148-8-179  1
2008 Szalkowski A, Ledergerber C, Krähenbühl P, Dessimoz C. SWPS3 - Fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2 Bmc Research Notes. 1. DOI: 10.1186/1756-0500-1-107  1
2008 Ledergerber C, Dessimoz C. Alignments with non-overlapping moves, inversions and tandem duplications in O(n 4) time Journal of Combinatorial Optimization. 16: 263-278. DOI: 10.1007/s10878-007-9132-y  1
2008 Dessimoz C, Margadant D, Gonnet GH. DLIGHT - Lateral gene transfer detection using pairwise evolutionary distances in a statistical framework Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4955: 315-330. DOI: 10.1007/978-3-540-78839-3_27  1
2007 Schneider A, Dessimoz C, Gonnet GH. OMA Browser - Exploring orthologous relations across 352 complete genomes Bioinformatics. 23: 2180-2182. PMID 17545180 DOI: 10.1093/bioinformatics/btm295  1
2007 Ledergerber C, Dessimoz C. Alignments with non-overlapping moves, inversions and tandem duplications in O(n4) time Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4598: 151-164.  1
2006 Dessimoz C, Gil M, Schneider A, Gonnet GH. Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences Bmc Bioinformatics. 7. PMID 17147817 DOI: 10.1186/1471-2105-7-529  1
2006 Dessimoz C, Boeckmann B, Roth AC, Gonnet GH. Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits. Nucleic Acids Research. 34: 3309-16. PMID 16835308 DOI: 10.1093/nar/gkl433  1
2006 Dessimoz C, Boeckmann B, Roth ACJ, Gonnet GH. Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits Nucleic Acids Research. 34: 3309-3316. DOI: 10.1093/nar/gkl433  1
2005 Gil M, Dessimoz C, Gonnet GH. A dimensionless fit measure for phylogenetic distance trees Journal of Bioinformatics and Computational Biology. 3: 1429-1440. PMID 16374915 DOI: 10.1142/S0219720005001636  1
2005 Dessimoz C, Cannarozzi G, Gil M, Margadant D, Roth A, Schneider A, Gonnet GH. OMA, a comprehensive, automated project for the identification of orthologs from complete genome data: Introduction and first achievements Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3678: 61-72. DOI: 10.1007/11554714_6  1
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