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Items: 1 to 50 of 68

1.

Assigning confidence scores to homoeologs using fuzzy logic.

Glover NM, Altenhoff A, Dessimoz C.

PeerJ. 2019 Jan 11;6:e6231. doi: 10.7717/peerj.6231. eCollection 2019.

2.

iHam & pyHam: visualizing and processing hierarchical orthologous groups.

Train CM, Pignatelli M, Altenhoff A, Dessimoz C.

Bioinformatics. 2018 Dec 3. doi: 10.1093/bioinformatics/bty994. [Epub ahead of print]

PMID:
30508066
3.

Prioritising candidate genes causing QTL using hierarchical orthologous groups.

Warwick Vesztrocy A, Dessimoz C, Redestig H.

Bioinformatics. 2018 Sep 1;34(17):i612-i619. doi: 10.1093/bioinformatics/bty615.

4.

Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.

Piližota I, Train CM, Altenhoff A, Redestig H, Dessimoz C.

Bioinformatics. 2018 Sep 1. doi: 10.1093/bioinformatics/bty772. [Epub ahead of print]

PMID:
30184069
5.

GOATOOLS: A Python library for Gene Ontology analyses.

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.

Sci Rep. 2018 Jul 18;8(1):10872. doi: 10.1038/s41598-018-28948-z.

6.

Submit a Topic Page to PLOS Computational Biology and Wikipedia.

Mietchen D, Wodak S, Wasik S, Szostak N, Dessimoz C.

PLoS Comput Biol. 2018 May 31;14(5):e1006137. doi: 10.1371/journal.pcbi.1006137. eCollection 2018 May. No abstract available.

7.

RecPhyloXML: a format for reconciled gene trees.

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, Posada D, Scornavacca C, Szöllosi G, Zhang L, Tannier É, Daubin V.

Bioinformatics. 2018 Nov 1;34(21):3646-3652. doi: 10.1093/bioinformatics/bty389.

8.

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

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.

Nucleic Acids Res. 2018 Jan 4;46(D1):D477-D485. doi: 10.1093/nar/gkx1019.

9.

Gearing up to handle the mosaic nature of life in the quest for orthologs.

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; Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S.

Bioinformatics. 2017 Aug 30. doi: 10.1093/bioinformatics/btx542. [Epub ahead of print]

10.

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference.

Train CM, Glover NM, Gonnet GH, Altenhoff AM, Dessimoz C.

Bioinformatics. 2017 Jul 15;33(14):i75-i82. doi: 10.1093/bioinformatics/btx229.

11.

Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.

Suchan T, Espíndola A, Rutschmann S, Emerson BC, Gori K, Dessimoz C, Arrigo N, Ronikier M, Alvarez N.

Mol Phylogenet Evol. 2017 Sep;114:189-198. doi: 10.1016/j.ympev.2017.06.012. Epub 2017 Jun 21.

PMID:
28645767
12.

Comparative genomics reveals contraction in olfactory receptor genes in bats.

Tsagkogeorga G, Müller S, Dessimoz C, Rossiter SJ.

Sci Rep. 2017 Mar 21;7(1):259. doi: 10.1038/s41598-017-00132-9.

13.

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.

Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, Balloux F, Dessimoz C, Bähler J, Sedlazeck FJ.

Nat Commun. 2017 Jan 24;8:14061. doi: 10.1038/ncomms14061.

14.

A Gene Ontology Tutorial in Python.

Vesztrocy AW, Dessimoz C.

Methods Mol Biol. 2017;1446:221-229.

PMID:
27812946
15.

Gene Ontology: Pitfalls, Biases, and Remedies.

Gaudet P, Dessimoz C.

Methods Mol Biol. 2017;1446:189-205.

PMID:
27812944
16.

Primer on the Gene Ontology.

Gaudet P, Škunca N, Hu JC, Dessimoz C.

Methods Mol Biol. 2017;1446:25-37.

PMID:
27812933
17.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

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, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

18.

Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life.

Sojo V, Dessimoz C, Pomiankowski A, Lane N.

Mol Biol Evol. 2016 Nov;33(11):2874-2884. Epub 2016 Aug 8.

19.

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.

Robinson O, Dylus D, Dessimoz C.

Mol Biol Evol. 2016 Aug;33(8):2163-6. doi: 10.1093/molbev/msw080. Epub 2016 Apr 19.

20.

Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome.

Zimmer F, Harrison PW, Dessimoz C, Mank JE.

Genome Biol Evol. 2016 Apr 25;8(4):1233-42. doi: 10.1093/gbe/evw075.

21.

Standardized benchmarking in the quest for orthologs.

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, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.

Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4.

22.

Homoeologs: What Are They and How Do We Infer Them?

Glover NM, Redestig H, Dessimoz C.

Trends Plant Sci. 2016 Jul;21(7):609-621. doi: 10.1016/j.tplants.2016.02.005. Epub 2016 Mar 22. Review.

23.

Clustering Genes of Common Evolutionary History.

Gori K, Suchan T, Alvarez N, Goldman N, Dessimoz C.

Mol Biol Evol. 2016 Jun;33(6):1590-605. doi: 10.1093/molbev/msw038. Epub 2016 Feb 17.

24.

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C.

Syst Biol. 2015 Sep;64(5):778-91. doi: 10.1093/sysbio/syv033. Epub 2015 Jun 1.

25.

Inferring horizontal gene transfer.

Ravenhall M, Škunca N, Lassalle F, Dessimoz C.

PLoS Comput Biol. 2015 May 28;11(5):e1004095. doi: 10.1371/journal.pcbi.1004095. eCollection 2015 May.

26.

A transcriptomic-phylogenomic analysis of the evolutionary relationships of flatworms.

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.

Curr Biol. 2015 May 18;25(10):1347-53. doi: 10.1016/j.cub.2015.03.034. Epub 2015 Apr 9.

27.

Phylogenetic profiling: how much input data is enough?

Škunca N, Dessimoz C.

PLoS One. 2015 Feb 13;10(2):e0114701. doi: 10.1371/journal.pone.0114701. eCollection 2015.

28.

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.

Tan G, Gil M, Löytynoja AP, Goldman N, Dessimoz C.

Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):E99-100. doi: 10.1073/pnas.1417526112. Epub 2015 Jan 6. No abstract available.

29.

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.

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, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG.

Nat Biotechnol. 2014 Dec;32(12):1250-5. doi: 10.1038/nbt.3079. Epub 2014 Nov 17.

30.

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.

Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D240-9. doi: 10.1093/nar/gku1158. Epub 2014 Nov 15.

31.

Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology.

Wittwer LD, Piližota I, Altenhoff AM, Dessimoz C.

PeerJ. 2014 Oct 7;2:e607. doi: 10.7717/peerj.607. eCollection 2014.

32.

Big data and other challenges in the quest for orthologs.

Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C; Quest for Orthologs consortium.

Bioinformatics. 2014 Nov 1;30(21):2993-8. doi: 10.1093/bioinformatics/btu492. Epub 2014 Jul 26.

33.

[Alveolar proteinosis: a cause of immunodeficiency].

Ben Hammoud L, Dessimoz C, Rudaz D, Ravussin P, Oggier S, Tschopp JM.

Rev Med Suisse. 2013 Nov 13;9(406):2078-81. French.

PMID:
24383280
34.

Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.

Iantorno S, Gori K, Goldman N, Gil M, Dessimoz C.

Methods Mol Biol. 2014;1079:59-73. doi: 10.1007/978-1-62703-646-7_4. Review.

PMID:
24170395
35.

CAFA and the open world of protein function predictions.

Dessimoz C, Škunca N, Thomas PD.

Trends Genet. 2013 Nov;29(11):609-10. doi: 10.1016/j.tig.2013.09.005. Epub 2013 Oct 15. No abstract available.

36.

Global regulatory architecture of human, mouse and rat tissue transcriptomes.

Prasad A, Kumar SS, Dessimoz C, Bleuler S, Laule O, Hruz T, Gruissem W, Zimmermann P.

BMC Genomics. 2013 Oct 20;14:716. doi: 10.1186/1471-2164-14-716.

37.

Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals.

Dalquen DA, Dessimoz C.

Genome Biol Evol. 2013;5(10):1800-6. doi: 10.1093/gbe/evt132.

38.

The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study.

Dalquen DA, Altenhoff AM, Gonnet GH, Dessimoz C.

PLoS One. 2013;8(2):e56925. doi: 10.1371/journal.pone.0056925. Epub 2013 Feb 25.

39.

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.

Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E.

Nature. 2013 Feb 7;494(7435):77-80. doi: 10.1038/nature11875. Epub 2013 Jan 23.

40.

Inferring hierarchical orthologous groups from orthologous gene pairs.

Altenhoff AM, Gil M, Gonnet GH, Dessimoz C.

PLoS One. 2013;8(1):e53786. doi: 10.1371/journal.pone.0053786. Epub 2013 Jan 14.

41.

Approximate Bayesian computation.

Sunnåker M, Busetto AG, Numminen E, Corander J, Foll M, Dessimoz C.

PLoS Comput Biol. 2013;9(1):e1002803. doi: 10.1371/journal.pcbi.1002803. Epub 2013 Jan 10.

42.

Guillain-Barré Syndrome Associated with Primary Parvovirus B19 Infection in an HIV-1-Infected Patient.

Bucher Praz C, Dessimoz C, Bally F, Reymond S, Troillet N.

Case Rep Med. 2012;2012:140780. doi: 10.1155/2012/140780. Epub 2012 Nov 6.

43.

Quality of computationally inferred gene ontology annotations.

Skunca N, Altenhoff A, Dessimoz C.

PLoS Comput Biol. 2012 May;8(5):e1002533. doi: 10.1371/journal.pcbi.1002533. Epub 2012 May 31.

44.

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.

Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C.

PLoS Comput Biol. 2012;8(5):e1002514. doi: 10.1371/journal.pcbi.1002514. Epub 2012 May 17.

45.

Inferring orthology and paralogy.

Altenhoff AM, Dessimoz C.

Methods Mol Biol. 2012;855:259-79. doi: 10.1007/978-1-61779-582-4_9. Review.

PMID:
22407712
46.

Toward community standards in the quest for orthologs.

Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J; Quest for Orthologs Consortium.

Bioinformatics. 2012 Mar 15;28(6):900-4. doi: 10.1093/bioinformatics/bts050. Epub 2012 Feb 12.

47.

ALF--a simulation framework for genome evolution.

Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C.

Mol Biol Evol. 2012 Apr;29(4):1115-23. doi: 10.1093/molbev/msr268. Epub 2011 Dec 8.

48.

Editorial: Orthology and applications.

Dessimoz C.

Brief Bioinform. 2011 Sep;12(5):375-6. doi: 10.1093/bib/bbr057. No abstract available.

PMID:
21949264
49.

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.

Boeckmann B, Robinson-Rechavi M, Xenarios I, Dessimoz C.

Brief Bioinform. 2011 Sep;12(5):423-35. doi: 10.1093/bib/bbr034. Epub 2011 Jul 7.

50.

Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes).

Dessimoz C, Zoller S, Manousaki T, Qiu H, Meyer A, Kuraku S.

Brief Bioinform. 2011 Sep;12(5):474-84. doi: 10.1093/bib/bbr038. Epub 2011 Jun 28.

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