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Gaston H. Gonnet, PhD - Publications

Affiliations: 
Computer Science ETH/Uni Zurich, Zürich, Zürich, Switzerland 
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50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.734
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  0.767
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  0.738
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  0.74
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  0.746
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  0.75
2012 Gonnet GH. Surprising results on phylogenetic tree building methods based on molecular sequences Bmc Bioinformatics. 13. PMID 22738078 DOI: 10.1186/1471-2105-13-148  0.373
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  0.754
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  0.767
2010 Cannarrozzi G, Schraudolph NN, Faty M, von Rohr P, Friberg MT, Roth AC, Gonnet P, Gonnet G, Barral Y. A role for codon order in translation dynamics Cell. 141: 355-367. PMID 20403329 DOI: 10.1016/J.Cell.2010.02.036  0.362
2009 Schneider A, Souvorov A, Sabath N, Landan G, Gonnet GH, Graur D. Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biology and Evolution. 1: 114-8. PMID 20333182 DOI: 10.1093/Gbe/Evp012  0.393
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  0.691
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  0.764
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  0.7
2007 Schneider A, Gonnet G, Cannarozzi G. SynPAM—A Distance Measure Based on Synonymous Codon Substitutions Ieee/Acm Transactions On Computational Biology and Bioinformatics. 4: 553-560. PMID 17975267 DOI: 10.1109/Tcbb.2007.1071  0.334
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  0.764
2007 Cannarozzi G, Schneider A, Gonnet G. A phylogenomic study of human, dog, and mouse Plos Computational Biology. 3: 0009-0014. PMID 17206860 DOI: 10.1371/Journal.Pcbi.0030002  0.438
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  0.712
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  0.771
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  0.725
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  0.694
2005 Schneider A, Cannarozzi GM, Gonnet GH. Empirical codon substitution matrix Bmc Bioinformatics. 6. PMID 15927081 DOI: 10.1186/1471-2105-6-134  0.359
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  0.728
2004 Friberg M, von Rohr P, Gonnet G. Limitations of codon adaptation index and other coding DNA-based features for prediction of protein expression in Saccharomyces cerevisiae Yeast. 21: 1083-1093. PMID 15484285 DOI: 10.1002/Yea.1150  0.377
2000 Korostensky C, Gonnet GH. Using traveling salesman problem algorithms for evolutionary tree construction Bioinformatics. 16: 619-627. PMID 11038332 DOI: 10.3929/Ethz-A-006653341  0.322
2000 Gonnet GH, Korostensky C, Benner S. Evaluation measures of multiple sequence alignments Journal of Computational Biology. 7: 261-276. PMID 10890401 DOI: 10.1089/10665270050081513  0.42
1999 Korostensky C, Gonnet GH. Gap heuristics and tree construction using gaps Ctit Technical Reports Series. 321. DOI: 10.3929/Ethz-A-006653329  0.392
1998 Korostensky C, Staudenmann W, Dainese P, Hoving S, Gonnet G, James P. An algorithm for the identification of proteins using peptides with ragged N- or C-termini generated by sequential endo- and exopeptidase digestions Electrophoresis. 19: 1933-1940. PMID 9740053 DOI: 10.1002/Elps.1150191111  0.307
1998 Chelvanayagam G, Knecht L, Jenny T, Benner SA, Gonnet GH. A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure Folding and Design. 3: 149-160. PMID 9562545 DOI: 10.1016/S1359-0278(98)00023-6  0.32
1997 Dainese P, Staudenmann W, Quadroni M, Korostensky C, Gonnet G, Kertesz M, James P. Probing protein function using a combination of gene knockout and proteome analysis by mass spectrometry Electrophoresis. 18: 432-442. PMID 9150922 DOI: 10.1002/Elps.1150180318  0.373
1996 Baeza-Yates RA, Gonnet GH. Fast text searching for regular expressions or automaton searching on tries Journal of the Acm. 43: 915-936. DOI: 10.1145/235809.235810  0.608
1994 Gonnet GH, Cohen MA, Benner SA. Analysis of amino acid substitution during divergent evolution: the 400 by 400 dipeptide substitution matrix. Biochemical and Biophysical Research Communications. 199: 489-96. PMID 8135790 DOI: 10.1006/Bbrc.1994.1255  0.368
1994 James P, Quadroni M, Carafoli E, Gonnet G. Protein identification in DNA databases by peptide mass fingerprinting Protein Science. 3: 1347-1350. PMID 7987229 DOI: 10.1002/Pro.5560030822  0.39
1994 Benner SA, Jenny TF, Cohen MA, Gonnet GH. Predicting the conformation of proteins from sequences. Progress and future progress. Advances in Enzyme Regulation. 34: 269-353. PMID 7942279 DOI: 10.1016/0065-2571(94)90021-3  0.345
1994 Benner SA, Cohen MA, Gonnet GH. Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Engineering. 7: 1323-32. PMID 7700864 DOI: 10.1093/Protein/7.11.1323  0.308
1994 Baeza-Yates RA, Choffrut C, Gonnet GH. On Boyer-Moore automata Algorithmica. 12: 268-292. DOI: 10.1007/Bf01185428  0.603
1994 Baezayates RA, Gonnet GH. Fast String Matching with Mismatches Information and Computation. 108: 187-199. DOI: 10.1006/Inco.1994.1007  0.324
1993 Benner SA, Cohen MA, Gonnet GH. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. Journal of Molecular Biology. 229: 1065-82. PMID 8445636 DOI: 10.1006/Jmbi.1993.1105  0.36
1993 James P, Quadroni M, Carafoli E, Gonnet G. Protein identification by mass profile fingerprinting Biochemical and Biophysical Research Communications. 195: 58-64. PMID 8363627 DOI: 10.1006/Bbrc.1993.2009  0.335
1992 Gonnet GH, Cohen MA, Benner SA. Exhaustive matching of the entire protein sequence database. Science (New York, N.Y.). 256: 1443-5. PMID 1604319 DOI: 10.1126/Science.1604319  0.423
1992 Baeza-Yates R, Gonnet GH. A new approach to text searching Communications of the Acm. 35: 74-82. DOI: 10.1145/135239.135243  0.589
1992 Baeza-Yates R, Gonnet GH, Ziviani N. Improved bounds for the expected behaviour of AVL trees Bit. 32: 297-315. DOI: 10.1007/Bf01994883  0.609
1991 Cunto W, Gonnet GH, Munro J, Poblete P. Fringe analysis for Extquick. An in situ distributive external sorting algorithm Information and Computation. 92: 141-160. DOI: 10.1016/0890-5401(91)90007-O  0.333
1990 Gonnet GH, Baeza-Yates RA. An analysis of the Karp-Rabin string matching algorithm Information Processing Letters. 34: 271-274. DOI: 10.1016/0020-0190(90)90135-K  0.603
1989 Baeza-Yates RA, Gonnet GH. New approach to text searching Sigir Forum (Acm Special Interest Group On Information Retrieval). 168-175. DOI: 10.1145/75335.75352  0.551
1988 Gonnet GH, Larson PA. EXTERNAL HASHING WITH LIMITED INTERNAL STORAGE Journal of the Acm. 35: 161-184. DOI: 10.1145/42267.42274  0.323
1983 Gonnet GH, Tompa FW. CONSTRUCTIVE APPROACH TO THE DESIGN OF ALGORITHMS AND THEIR DATA STRUCTURES Communications of the Acm. 26: 912-920. DOI: 10.1145/182.358444  0.304
1980 Gonnet GH. Open-addressing hashing with unequal-probability keys Journal of Computer and System Sciences. 21: 354-367. DOI: 10.1016/0022-0000(80)90028-8  0.307
1980 Gonnet GH, Rogers LD, Alan George J. An algorithmic and complexity analysis of interpolation search Acta Informatica. 13: 39-52. DOI: 10.1007/Bf00288534  0.318
1977 Gonnet GH, Rogers LD. The interpolation-sequential search algorithm Information Processing Letters. 6: 136-139. DOI: 10.1016/0020-0190(77)90028-X  0.301
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