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Items: 1 to 20 of 27

1.

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.

2.

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.

3.

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.

4.
5.

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.

6.

OMA 2011: orthology inference among 1000 complete genomes.

Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C.

Nucleic Acids Res. 2011 Jan;39(Database issue):D289-94. doi: 10.1093/nar/gkq1238.

7.

Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment.

Schneider A, Souvorov A, Sabath N, Landan G, Gonnet GH, Graur D.

Genome Biol Evol. 2009 Jun 5;1:114-8. doi: 10.1093/gbe/evp012.

8.

Algorithm of OMA for large-scale orthology inference.

Roth AC, Gonnet GH, Dessimoz C.

BMC Bioinformatics. 2008 Dec 4;9:518. doi: 10.1186/1471-2105-9-518. Erratum in: BMC Bioinformatics.2009;10. doi:10.1186/1471-2105-10-220.

9.

OMA Browser--exploring orthologous relations across 352 complete genomes.

Schneider A, Dessimoz C, Gonnet GH.

Bioinformatics. 2007 Aug 15;23(16):2180-2.

10.
11.

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits.

Dessimoz C, Boeckmann B, Roth AC, Gonnet GH.

Nucleic Acids Res. 2006 Jul 11;34(11):3309-16.

12.

A dimensionless fit measure for phylogenetic distance trees.

Gil M, Dessimoz C, Gonnet GH.

J Bioinform Comput Biol. 2005 Dec;3(6):1429-40.

PMID:
16374915
13.

Empirical codon substitution matrix.

Schneider A, Cannarozzi GM, Gonnet GH.

BMC Bioinformatics. 2005 Jun 1;6:134.

14.

Using traveling salesman problem algorithms for evolutionary tree construction.

Korostensky C, Gonnet GH.

Bioinformatics. 2000 Jul;16(7):619-27.

15.

An analysis of the helix-to-strand transition between peptides with identical sequence.

Zhou X, Alber F, Folkers G, Gonnet GH, Chelvanayagam G.

Proteins. 2000 Nov 1;41(2):248-56.

PMID:
10966577
16.

Evaluation measures of multiple sequence alignments.

Gonnet GH, Korostensky C, Benner S.

J Comput Biol. 2000 Feb-Apr;7(1-2):261-76.

PMID:
10890401
17.

Darwin v. 2.0: an interpreted computer language for the biosciences.

Gonnet GH, Hallett MT, Korostensky C, Bernardin L.

Bioinformatics. 2000 Feb;16(2):101-3.

18.

A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure.

Chelvanayagam G, Knecht L, Jenny T, Benner SA, Gonnet GH.

Fold Des. 1998;3(3):149-60.

19.

An analysis of simultaneous variation in protein structures.

Chelvanayagam G, Eggenschwiler A, Knecht L, Gonnet GH, Benner SA.

Protein Eng. 1997 Apr;10(4):307-16.

20.

A predicted consensus structure for the N-terminal fragment of the heat shock protein HSP90 family.

Gerloff DL, Cohen FE, Korostensky C, Turcotte M, Gonnet GH, Benner SA.

Proteins. 1997 Mar;27(3):450-8.

PMID:
9094746
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