Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 42

1.

Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters.

Fresia P, Antelo V, Salazar C, Giménez M, D'Alessandro B, Afshinnekoo E, Mason C, Gonnet GH, Iraola G.

Microbiome. 2019 Feb 28;7(1):35. doi: 10.1186/s40168-019-0648-z.

2.

First Release of the Bacterial Biobank of the Urban Environment (BBUE).

Antelo V, Salazar C, Martínez A, D'Alessandro B, Castro M, Betancor L, Barcala MV, Míguez D, Gonnet GH, Iraola G.

Microbiol Resour Announc. 2018 Oct 25;7(16). pii: e01201-18. doi: 10.1128/MRA.01201-18. eCollection 2018 Oct.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.
9.

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.

10.

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.

11.

A role for codon order in translation dynamics.

Cannarozzi G, Schraudolph NN, Faty M, von Rohr P, Friberg MT, Roth AC, Gonnet P, Gonnet G, Barral Y.

Cell. 2010 Apr 16;141(2):355-67. doi: 10.1016/j.cell.2010.02.036. Erratum in: Cell. 2010 May 14;141(4):728. Cannarrozzi, Gina [corrected to Cannarozzi, Gina].

12.

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.

13.

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.

14.

A mechanism for asymmetric segregation of age during yeast budding.

Shcheprova Z, Baldi S, Frei SB, Gonnet G, Barral Y.

Nature. 2008 Aug 7;454(7205):728-34. doi: 10.1038/nature07212. Epub 2008 Jul 27.

PMID:
18660802
15.

SynPAM-a distance measure based on synonymous codon substitutions.

Schneider A, Gonnet G, Cannarozzi G.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):553-60.

PMID:
17975267
16.

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
17.

A phylogenomic study of human, dog, and mouse.

Cannarozzi G, Schneider A, Gonnet G.

PLoS Comput Biol. 2007 Jan 5;3(1):e2. Epub 2006 Nov 20.

18.
19.

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.

20.

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
21.

Empirical codon substitution matrix.

Schneider A, Cannarozzi GM, Gonnet GH.

BMC Bioinformatics. 2005 Jun 1;6:134.

22.

Scoring functions for transcription factor binding site prediction.

Friberg M, von Rohr P, Gonnet G.

BMC Bioinformatics. 2005 Apr 4;6:84.

24.

Cell fingerprinting: an approach to classifying cells according to mass profiles of digests of protein extracts.

Zhou X, Gonnet G, Hallett M, Münchbach M, Folkers G, James P.

Proteomics. 2001 May;1(5):683-90.

PMID:
11678037
25.

Using traveling salesman problem algorithms for evolutionary tree construction.

Korostensky C, Gonnet GH.

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

PMID:
11038332
26.

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
27.

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
28.

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
29.

An algorithm for the identification of proteins using peptides with ragged N- or C-termini generated by sequential endo- and exopeptidase digestions.

Korostensky C, Staudenmann W, Dainese P, Hoving S, Gonnet G, James P.

Electrophoresis. 1998 Aug;19(11):1933-40.

PMID:
9740053
30.

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.

31.

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
32.

Probing protein function using a combination of gene knockout and proteome analysis by mass spectrometry.

Dainese P, Staudenmann W, Quadroni M, Korostensky C, Gonnet G, Kertesz M, James P.

Electrophoresis. 1997 Mar-Apr;18(3-4):432-42.

PMID:
9150922
33.

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
34.

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
35.

Protein identification in DNA databases by peptide mass fingerprinting.

James P, Quadroni M, Carafoli E, Gonnet G.

Protein Sci. 1994 Aug;3(8):1347-50.

36.

Analysis of amino acid substitution during divergent evolution: the 400 by 400 dipeptide substitution matrix.

Gonnet GH, Cohen MA, Benner SA.

Biochem Biophys Res Commun. 1994 Mar 15;199(2):489-96.

PMID:
8135790
37.

Predicting the conformation of proteins from sequences. Progress and future progress.

Benner SA, Jenny TF, Cohen MA, Gonnet GH.

Adv Enzyme Regul. 1994;34:269-353. Review.

PMID:
7942279
38.

Protein identification by mass profile fingerprinting.

James P, Quadroni M, Carafoli E, Gonnet G.

Biochem Biophys Res Commun. 1993 Aug 31;195(1):58-64.

PMID:
8363627
39.

The nitrogenase MoFe protein. A secondary structure prediction.

Gerloff DL, Jenny TF, Knecht LJ, Gonnet GH, Benner SA.

FEBS Lett. 1993 Mar 1;318(2):118-24.

40.

Empirical and structural models for insertions and deletions in the divergent evolution of proteins.

Benner SA, Cohen MA, Gonnet GH.

J Mol Biol. 1993 Feb 20;229(4):1065-82.

PMID:
8445636
41.

A word in your protein.

Gonnet GH, Benner SA.

Nature. 1993 Jan 14;361(6408):121. No abstract available.

PMID:
8421517
42.

Exhaustive matching of the entire protein sequence database.

Gonnet GH, Cohen MA, Benner SA.

Science. 1992 Jun 5;256(5062):1443-5.

PMID:
1604319

Supplemental Content

Loading ...
Support Center