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Results: 1 to 20 of 26

1.

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.

PMID:
23451112
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
23342000
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Surprising results on phylogenetic tree building methods based on molecular sequences.

Gonnet GH.

BMC Bioinformatics. 2012 Jun 27;13:148.

PMID:
22738078
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
22160766
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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. Epub 2010 Nov 27.

PMID:
21113020
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
20333182
[PubMed]
Free PMC Article
7.

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.

PMID:
19055798
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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

Schneider A, Dessimoz C, Gonnet GH.

Bioinformatics. 2007 Aug 15;23(16):2180-2. Epub 2007 Jun 1.

PMID:
17545180
[PubMed - indexed for MEDLINE]
Free Article
9.

Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences.

Dessimoz C, Gil M, Schneider A, Gonnet GH.

BMC Bioinformatics. 2006 Dec 5;7:529.

PMID:
17147817
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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. Print 2006.

PMID:
16835308
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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
[PubMed - indexed for MEDLINE]
12.

Empirical codon substitution matrix.

Schneider A, Cannarozzi GM, Gonnet GH.

BMC Bioinformatics. 2005 Jun 1;6:134.

PMID:
15927081
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Using traveling salesman problem algorithms for evolutionary tree construction.

Korostensky C, Gonnet GH.

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

PMID:
11038332
[PubMed - indexed for MEDLINE]
Free Article
14.

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
[PubMed - indexed for MEDLINE]
15.

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
[PubMed - indexed for MEDLINE]
16.

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.

PMID:
10842729
[PubMed - indexed for MEDLINE]
Free Article
17.

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.

PMID:
9562545
[PubMed - indexed for MEDLINE]
18.

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.

PMID:
9194155
[PubMed - indexed for MEDLINE]
Free Article
19.

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
[PubMed - indexed for MEDLINE]
20.

Amino acid substitution during functionally constrained divergent evolution of protein sequences.

Benner SA, Cohen MA, Gonnet GH.

Protein Eng. 1994 Nov;7(11):1323-32.

PMID:
7700864
[PubMed - indexed for MEDLINE]

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