Gaston H. Gonnet, PhD - Publications

Affiliations: 
Computer Science ETH/Uni Zurich, Zürich, Zürich, Switzerland 

86 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  0.72
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  0.72
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.44
2009 Gonnet GH, Scholl R. Scientific computation Scientific Computation. 1-236. DOI: 10.1017/CBO9780511815027  0.64
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  0.64
2008 Shcheprova Z, Baldi S, Frei SB, Gonnet G, Barral Y. A mechanism for asymmetric segregation of age during yeast budding Nature. 454: 728-734. PMID 18660802 DOI: 10.1038/nature07212  0.64
2008 Cannarozzi GM, Schneider A, Gonnet GH. Probabilistic ancestral sequences based on the Markovian model of evolution: algorithms and applications Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.003.0005  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
2006 Gil M, Gonnet GH, Petersen WP. A repetition test for pseudo-random number generators Monte Carlo Methods and Applications. 12: 385-393. DOI: 10.1163/156939606779329017  0.64
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  0.64
2006 Schneider A, Gonnet GH, Cannarozzi GM. Synonymous codon substitution matrices Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3992: 630-637. DOI: 10.1007/11758525_86  0.64
2006 Friberg MT, Gonnet P, Barral Y, Schraudolph NN, Gonnet GH. Measures of codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4175: 1-11.  0.64
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  0.64
2005 Schneider A, Cannarozzi GM, Gonnet GH. Empirical codon substitution matrix Bmc Bioinformatics. 6. PMID 15927081 DOI: 10.1186/1471-2105-6-134  0.64
2005 Friberg M, von Rohr P, Gonnet G. Scoring functions for transcription factor binding site prediction Bmc Bioinformatics. 6. PMID 15807889 DOI: 10.1186/1471-2105-6-84  0.64
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  0.64
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  0.64
2004 Gonnet GH. Some string matching problems from Bioinformatics which still need better solutions Journal of Discrete Algorithms. 2: 3-15. DOI: 10.1016/S1570-8667(03)00062-5  0.64
2004 Gonnet GH. The tPI (tRNA pairing index), a mathematical measure of repetition in a (biological) sequence Ifip Advances in Information and Communication Technology. 155: 1-2.  0.64
2003 Buchberger B, Gonnet G, Hazewinkel M. Annals of Mathematics and Artificial Intelligence: Preface Annals of Mathematics and Artificial Intelligence. 38: 1-2. DOI: 10.1023/A:1022900528196  0.64
2003 Gonnet G, Panario D, Viola A. Theoretical Computer Science: Preface Theoretical Computer Science. 297: 1. DOI: 10.1016/S0304-3975(02)00615-1  0.64
2002 Gonnet GH. String matching problems from bioinformatics which still need better solutions Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2476: 27-30. DOI: 10.1007/3-540-45735-6_3  0.64
2001 Zhou X, Gonnet G, Hallett M, Münchbach M, Folkers G, James P. Cell fingerprinting: An approach to classifying cells according to mass profiles of digests of protein extracts Proteomics. 1: 683-690. PMID 11678037  0.64
2000 Korostensky C, Gonnet GH. Using traveling salesman problem algorithms for evolutionary tree construction Bioinformatics. 16: 619-627. PMID 11038332  0.64
2000 Zhou X, Alber F, Folkers G, Gonnet GH, Chelvanayagam G. An analysis of the helix-to-strand transition between peptides with identical sequence Proteins: Structure, Function and Genetics. 41: 248-256. PMID 10966577 DOI: 10.1002/1097-0134(20001101)41:2<248::AID-PROT90>3.0.CO;2-J  0.64
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  0.64
2000 Gonnet GH, Hallett MT, Korostensky C, Bernardin L. Darwin v. 2.0: An interpreted computer language for the biosciences Bioinformatics. 16: 101-103. PMID 10842729  0.64
2000 Gonnet G, Panario D, Viola A. Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1776: VI.  0.64
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  0.64
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  0.64
1997 Chelvanayagam G, Eggenschwiler A, Knecht L, Gonnet GH, Benner SA. An analysis of simultaneous variation in protein structures Protein Engineering. 10: 307-316. PMID 9194155  0.64
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  0.64
1997 Gerloff DL, Cohen FE, Korostensky C, Turcotte M, Gonnet GH, Benner SA. A predicted consensus structure for the N-terminal fragment of the heat shock protein HSP90 family. Proteins. 27: 450-8. PMID 9094746 DOI: 10.1002/(SICI)1097-0134(199703)27:3<450::AID-PROT12>3.0.CO;2-K  0.64
1996 Corless RM, Gonnet GH, Hare DEG, Jeffrey DJ, Knuth DE. On the Lambert W function Advances in Computational Mathematics. 5: 329-359.  0.64
1996 Baeza-Yates RA, Gonnet GH. Fast text searching for regular expressions or automaton searching on tries Journal of the Acm. 43: 915-936.  0.64
1996 Gonnet GH, Benner SA. Probabilistic ancestral sequences and multiple alignments Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1097: 380-391.  0.64
1995 Benner SA, Jermann TM, Opitz JG, Stackhouse J, Knecht LJ, Gonnet GH. Uncertainty in ancient phylogenies [7] Nature. 377: 109-110.  0.64
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  0.64
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  0.64
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  0.64
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  0.64
1994 Baeza-Yates RA, Choffrut C, Gonnet GH. On Boyer-Moore automata Algorithmica. 12: 268-292. DOI: 10.1007/BF01185428  0.64
1994 Baezayates RA, Gonnet GH. Fast String Matching with Mismatches Information and Computation. 108: 187-199. DOI: 10.1006/inco.1994.1007  0.64
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  0.64
1993 Gerloff DL, Jenny TF, Knecht LJ, Gonnet GH, Benner SA. The nitrogenase MoFe protein. A secondary structure prediction Febs Letters. 318: 118-124. PMID 8440368 DOI: 10.1016/0014-5793(93)80004-E  0.64
1993 Gonnet GH, Benner SA. A word in your protein [7] Nature. 361: 121. PMID 8421517 DOI: 10.1038/361121b0  0.64
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  0.64
1993 Flajolet P, Gonnet G, Puech C, Robson JM. Analytic variations on quadtrees Algorithmica. 10: 473-500. DOI: 10.1007/BF01891833  0.64
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  0.64
1992 Garvan FG, Gonnet GH. A proof of the two parameter q-cases of the Macdonald - Morris constant term root system conjecture for S(F4) and S(F4)V via Zeilberger's method Journal of Symbolic Computation. 14: 141-177. DOI: 10.1016/0747-7171(92)90033-Z  0.64
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  0.64
1992 Benner SA, Cohen MA, Gonnet GH. Response [2] Science. 257: 1609-1610.  0.64
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.  0.64
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  0.64
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  0.64
1988 Gonnet GH, Larson PA. EXTERNAL HASHING WITH LIMITED INTERNAL STORAGE Journal of the Acm. 35: 161-184. DOI: 10.1145/42267.42274  0.64
1987 Chang EJH, Gonnet GH, Rotem D. On the costs of self-stabilization Information Processing Letters. 24: 311-316. DOI: 10.1016/0020-0190(87)90155-4  0.64
1986 Gonnet GH, Munro JI. HEAPS ON HEAPS Siam Journal On Computing. 15: 964-971.  0.64
1985 Zivani N, Olivie HJ, Gonnet GH. ANALYSIS OF AN IMPROVED SYMMETRIC BINARY B-TREE ALGORITHM Computer Journal. 28: 417-425. DOI: 10.1093/comjnl/28.4.417  0.64
1984 Gonnet GH, Ian Munro J. The analysis of linear probing sort by the use of a new mathematical transform Journal of Algorithms. 5: 451-470. DOI: 10.1016/0196-6774(84)90001-4  0.64
1983 Gonnet GH. BALANCING BINARY TREES BY INTERNAL PATH REDUCTION Communications of the Acm. 26: 1074-1081. DOI: 10.1145/358476.358509  0.64
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  0.64
1983 Gonnet GH, Munro JI, Wood D. Direct dynamic structures for some line segment problems Computer Vision, Graphics and Image Processing. 23: 178-186. DOI: 10.1016/0734-189X(83)90111-1  0.64
1983 Gonnet GH. UNSTRUCTURED DATA BASES OR VERY EFFICIENT TEXT SEARCHING . 117-124.  0.64
1983 Gonnet GH, Olivie HJ, Wood D. HEIGHT-RATIO-BALANCED TREES Computer Journal. 26: 106-108.  0.64
1982 Eisenbarth B, Ziviani N, Gonnet GH, Mehlhorn K, Wood D. The theory of fringe analysis and its application to 23 trees and b-trees Information and Control. 55: 125-174. DOI: 10.1016/S0019-9958(82)90534-4  0.64
1981 Gonnet GH. EXPECTED LENGTH OF THE LONGEST PROBE SEQUENCE IN HASH CODE SEARCHING Journal of the Acm. 28: 289-304. DOI: 10.1145/322248.322254  0.64
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  0.64
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  0.64
1979 Gonnet GH, Morgan DE. Analysis of Closed Queuing Networks with Periodic Servers Ieee Transactions On Software Engineering. 653-659. DOI: 10.1109/TSE.1979.230201  0.64
1979 Gonnet GH, Munro JI, Suwanda H. TOWARD SELF-ORGANIZING LINEAR SEARCH Annual Symposium On Foundations of Computer Science - Proceedings. 169-174.  0.64
1978 Gonnet GH. Notes on the derivation of symptotic expressions from summations Information Processing Letters. 7: 165-169. DOI: 10.1016/0020-0190(78)90059-5  0.64
1977 Gonnet GH, Rogers LD. The interpolation-sequential search algorithm Information Processing Letters. 6: 136-139. DOI: 10.1016/0020-0190(77)90028-X  0.64
1977 Gonnet GH. On the structure of zero finders Bit. 17: 170-183. DOI: 10.1007/BF01932288  0.64
1976 Gonnet GH. A short note on convergence near a high order zero Bit. 16: 338-339. DOI: 10.1007/BF01932277  0.64
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