| Year |
Citation |
Score |
| 2023 |
Altenhoff AM, Warwick Vesztrocy A, Bernard C, Train CM, Nicheperovich A, Prieto Baños S, Julca I, Moi D, Nevers Y, Majidian S, Dessimoz C, Glover NM. OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem. Nucleic Acids Research. PMID 37962356 DOI: 10.1093/nar/gkad1020 |
0.464 |
|
| 2023 |
Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nature Biotechnology. PMID 37081138 DOI: 10.1038/s41587-023-01753-4 |
0.388 |
|
| 2022 |
Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Read2Tree: scalable and accurate phylogenetic trees from raw reads. Biorxiv : the Preprint Server For Biology. PMID 36561179 DOI: 10.1101/2022.04.18.488678 |
0.367 |
|
| 2022 |
Nevers Y, Jones TEM, Jyothi D, Yates B, Ferret M, Portell-Silva L, Codo L, Cosentino S, Marcet-Houben M, Vlasova A, Poidevin L, Kress A, Hickman M, Persson E, Piližota I, ... ... Dessimoz C, et al. The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Research. PMID 35552456 DOI: 10.1093/nar/gkac330 |
0.823 |
|
| 2021 |
Cummings TFM, Gori K, Sanchez-Pulido L, Gavriilidis G, Moi D, Wilson AR, Murchison E, Dessimoz C, Ponting CP, Christophorou MA. Citrullination was introduced into animals by horizontal gene transfer from cyanobacteria. Molecular Biology and Evolution. PMID 34730808 DOI: 10.1093/molbev/msab317 |
0.74 |
|
| 2021 |
Glover N, Sheppard S, Dessimoz C. Homoeolog inference methods requiring bidirectional best hits or synteny miss many pairs. Genome Biology and Evolution. PMID 33871639 DOI: 10.1093/gbe/evab077 |
0.419 |
|
| 2021 |
Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I. Ten years of collaborative progress in the Quest for Orthologs. Molecular Biology and Evolution. PMID 33822172 DOI: 10.1093/molbev/msab098 |
0.41 |
|
| 2021 |
Rossier V, Vesztrocy AW, Robinson-Rechavi M, Dessimoz C. OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. Bioinformatics (Oxford, England). PMID 33787851 DOI: 10.1093/bioinformatics/btab219 |
0.357 |
|
| 2021 |
Hodcroft EB, De Maio N, Lanfear R, MacCannell DR, Minh BQ, Schmidt HA, Stamatakis A, Goldman N, Dessimoz C. Want to track pandemic variants faster? Fix the bioinformatics bottleneck. Nature. 591: 30-33. PMID 33649511 DOI: 10.1038/d41586-021-00525-x |
0.433 |
|
| 2021 |
Zajac N, Zoller S, Seppälä K, Moi D, Dessimoz C, Jokela J, Hartikainen H, Glover N. Gene Duplication and Gain in the Trematode Atriophallophorus Winterbourni Contributes to Adaptation to Parasitism. Genome Biology and Evolution. PMID 33484570 DOI: 10.1093/gbe/evab010 |
0.386 |
|
| 2020 |
Dylus D, Nevers Y, Altenhoff AM, Gürtler A, Dessimoz C, Glover NM. How to build phylogenetic species trees with OMA. F1000research. 9: 511. PMID 35722083 DOI: 10.12688/f1000research.23790.2 |
0.314 |
|
| 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 |
0.787 |
|
| 2020 |
Moi D, Kilchoer L, Aguilar PS, Dessimoz C. Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes. Plos Computational Biology. 16: e1007553. PMID 32697802 DOI: 10.1371/Journal.Pcbi.1007553 |
0.515 |
|
| 2020 |
Warwick Vesztrocy A, Dessimoz C. Benchmarking gene ontology function predictions using negative annotations. Bioinformatics (Oxford, England). 36: i210-i218. PMID 32657372 DOI: 10.1093/Bioinformatics/Btaa466 |
0.477 |
|
| 2020 |
Zile K, Dessimoz C, Wurm Y, Masel J. Only a single taxonomically restricted gene family in the Drosophila melanogaster subgroup can be identified with high confidence. Genome Biology and Evolution. PMID 32589737 DOI: 10.1093/Gbe/Evaa127 |
0.464 |
|
| 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 |
0.534 |
|
| 2020 |
Ducrest AL, Neuenschwander S, Schmid-Siegert E, Pagni M, Train C, Dylus D, Nevers Y, Warwick Vesztrocy A, San-Jose LM, Dupasquier M, Dessimoz C, Xenarios I, Roulin A, Goudet J. New genome assembly of the barn owl (). Ecology and Evolution. 10: 2284-2298. PMID 32184981 DOI: 10.1002/Ece3.5991 |
0.473 |
|
| 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 |
0.466 |
|
| 2020 |
Grass RN, Heckel R, Dessimoz C, Stark WJ. Genomic encryption of digital data stored in synthetic DNA. Angewandte Chemie (International Ed. in English). PMID 32083389 DOI: 10.1002/Anie.202001162 |
0.335 |
|
| 2020 |
Dylus D, Nevers Y, Altenhoff AM, Gürtler A, Dessimoz C, Glover NM. How to build phylogenetic species trees with OMA F1000research. 9: 511. DOI: 10.12688/F1000Research.23790.1 |
0.426 |
|
| 2020 |
Altenhoff AM, Levy J, Zarowiecki M, Tomiczek B, Vesztrocy AW, Dalquen DA, Müller S, Telford MJ, Glover NM, Dylus D, Dessimoz C. Corrigendum: OMA standalone: orthology inference among public and custom genomes and transcriptomes Genome Research. 30. DOI: 10.1101/Gr.266809.120 |
0.8 |
|
| 2019 |
Sima AC, Dessimoz C, Stockinger K, Zahn-Zabal M, Mendes de Farias T. A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL. F1000research. 8: 1822. PMID 32612807 DOI: 10.12688/F1000Research.21027.1 |
0.386 |
|
| 2019 |
Mahmoud M, Gobet N, Cruz-Dávalos DI, Mounier N, Dessimoz C, Sedlazeck FJ. Structural variant calling: the long and the short of it. Genome Biology. 20: 246. PMID 31747936 DOI: 10.1186/S13059-019-1828-7 |
0.345 |
|
| 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 |
0.379 |
|
| 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 |
0.339 |
|
| 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 |
0.461 |
|
| 2019 |
Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD. Advances and Applications in the Quest for Orthologs. Molecular Biology and Evolution. PMID 31241141 DOI: 10.1093/Molbev/Msz150 |
0.521 |
|
| 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 |
0.831 |
|
| 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.17548.2 |
0.339 |
|
| 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 |
0.396 |
|
| 2019 |
Farias TMd, Stockinger K, Dessimoz C. VoIDext : vocabulary and patterns for enhancing interoperable datasets with virtual links Lecture Notes in Computer Science. 11877: 607-625. DOI: 10.1007/978-3-030-33246-4_38 |
0.34 |
|
| 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 |
0.475 |
|
| 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 |
0.456 |
|
| 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 |
0.842 |
|
| 2018 |
Klopfenstein DV, Zhang L, Pedersen BS, Ramírez F, Warwick Vesztrocy A, Naldi A, Mungall CJ, Yunes JM, Botvinnik O, Weigel M, Dampier W, Dessimoz C, Flick P, Tang H. GOATOOLS: A Python library for Gene Ontology analyses. Scientific Reports. 8: 10872. PMID 30022098 DOI: 10.1038/S41598-018-28948-Z |
0.473 |
|
| 2018 |
Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, et al. RecPhyloXML - a format for reconciled gene trees. Bioinformatics (Oxford, England). PMID 29762653 DOI: 10.1093/Bioinformatics/Bty389 |
0.386 |
|
| 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 |
0.767 |
|
| 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 |
0.456 |
|
| 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 |
0.791 |
|
| 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 |
0.748 |
|
| 2017 |
Tsagkogeorga G, Müller S, Dessimoz C, Rossiter SJ. Comparative genomics reveals contraction in olfactory receptor genes in bats. Scientific Reports. 7: 259. PMID 28325942 DOI: 10.1038/S41598-017-00132-9 |
0.513 |
|
| 2017 |
Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, Balloux F, Dessimoz C, Bähler J, Sedlazeck FJ. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nature Communications. 8: 14061. PMID 28117401 DOI: 10.1038/Ncomms14061 |
0.384 |
|
| 2017 |
Vesztrocy AW, Dessimoz C. A Gene Ontology Tutorial in Python. Methods in Molecular Biology (Clifton, N.J.). 1446: 221-229. PMID 27812946 DOI: 10.1007/978-1-4939-3743-1_16 |
0.417 |
|
| 2017 |
Gaudet P, Dessimoz C. Gene Ontology: Pitfalls, Biases, and Remedies. Methods in Molecular Biology (Clifton, N.J.). 1446: 189-205. PMID 27812944 DOI: 10.1007/978-1-4939-3743-1_14 |
0.446 |
|
| 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 |
0.81 |
|
| 2017 |
Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C. Automated filtering of multiple sequence alignment worsens phylogenetic inference F1000research. 6. DOI: 10.7490/F1000Research.1115083.1 |
0.546 |
|
| 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 |
0.778 |
|
| 2016 |
Robinson O, Dylus D, Dessimoz C. Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web. Molecular Biology and Evolution. PMID 27189561 DOI: 10.1093/Molbev/Msw080 |
0.352 |
|
| 2016 |
Zimmer F, Harrison PW, Dessimoz C, Mank JE. Compensation of dosage-sensitive genes on the chicken Z chromosome. Genome Biology and Evolution. PMID 27044516 DOI: 10.1093/Gbe/Evw075 |
0.332 |
|
| 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 |
0.8 |
|
| 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 |
0.476 |
|
| 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 |
0.766 |
|
| 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 |
0.573 |
|
| 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 |
0.838 |
|
| 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 |
0.781 |
|
| 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 |
0.838 |
|
| 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 |
0.76 |
|
| 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 |
0.801 |
|
| 2015 |
Altenhoff A, Škunca N, Glover N, Train C, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet G, Dessimoz C. The OMA orthology database in 2015 F1000research. 6. DOI: 10.7490/F1000Research.1098334.1 |
0.773 |
|
| 2015 |
Škunca N, Dessimoz C. Phylogenetic profiling: How much input data is enough? Plos One. 10. DOI: 10.1371/journal.pone.0114701 |
0.775 |
|
| 2015 |
Ravenhall M, Škunca N, Lassalle F, Dessimoz C. Inferring Horizontal Gene Transfer Plos Computational Biology. 11. DOI: 10.1371/journal.pcbi.1004095 |
0.79 |
|
| 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 |
0.77 |
|
| 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 |
0.822 |
|
| 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 |
0.773 |
|
| 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 |
0.761 |
|
| 2014 |
Škunca N, Dessimoz C. Post-modern function annotation F1000research. 5. DOI: 10.7490/F1000Research.1095206.1 |
0.777 |
|
| 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 |
0.82 |
|
| 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 |
0.82 |
|
| 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 |
0.815 |
|
| 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 |
0.636 |
|
| 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 |
0.779 |
|
| 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 |
0.312 |
|
| 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 |
0.821 |
|
| 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 |
0.416 |
|
| 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 |
0.355 |
|
| 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 |
0.36 |
|
| 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 |
0.82 |
|
| 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 |
0.524 |
|
| 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 |
0.519 |
|
| 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 |
0.343 |
|
| 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 |
0.813 |
|
| 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 |
0.381 |
|
| 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 |
0.792 |
|
| 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 |
0.43 |
|
| 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 |
0.504 |
|
| 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 |
0.482 |
|
| 2009 |
Roth AC, Gonnet GH, Dessimoz C. Erratum to: Algorithm of OMA for large-scale orthology inference Bmc Bioinformatics. 10: 220. DOI: 10.1186/1471-2105-10-220 |
0.707 |
|
| 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 |
0.777 |
|
| 2008 |
Szalkowski A, Ledergerber C, Krähenbühl P, Dessimoz C. SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2. Bmc Research Notes. 1: 107. PMID 18959793 DOI: 10.1186/1756-0500-1-107 |
0.327 |
|
| 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 |
0.386 |
|
| 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 |
0.337 |
|
| 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 |
0.741 |
|
| 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 |
0.794 |
|
| 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 |
0.74 |
|
| 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 |
0.786 |
|
| 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 |
0.758 |
|
| 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 |
0.723 |
|
| 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 |
0.764 |
|
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