| 2008 | RECOMB | DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework. | Christophe Dessimoz, Daniel Margadant, Gaston H. Gonnet |
| 2006 | ICCS | Synonymous Codon Substitution Matrices. | Adrian Schneider, Gaston H. Gonnet, Gina Cannarozzi |
| 2006 | WABI | Measures of Codon Bias in Yeast, the tRNA Pairing Index and Possible DNA Repair Mechanisms. | Markus T. Friberg, Pedro Gonnet, Yves Barral, Nicol N. Schraudolph, Gaston H. Gonnet |
| 2005 | RECOMB | OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements. | Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander C. J. Roth, Adrian Schneider, Gaston H. Gonnet |
| 2002 | SPIRE | String Matching Problems from Bioinformatics Which Still Need Better Solutions (Extended Abstract). | Gaston H. Gonnet |
| 1999 | CASC | Partial Inverse Heuristic for the Approximate Solution of Non-linear Equations. | Gaston H. Gonnet, Allan Bonadio |
| 1999 | SPIRE | A Fast Algorithm on Average for All-Against-All Sequence Matching. | Ricardo A. Baeza-Yates, Gaston H. Gonnet |
| 1999 | SPIRE | Near Optimal Multiple Sequence Alignments Using a Traveling Salesman Problem Approach. | Chantal Korostensky, Gaston H. Gonnet |
| 1994 | ESA | Wanna Buy an Algorithm? Cheap! or: Algorithms for Text Searching Which Could Have Commercial Value (Abstract). | Gaston H. Gonnet |
| 1994 | ISSAC | Signature Functions for Algebraic Numbers. | Michael B. Monagan, Gaston H. Gonnet |
| 1994 | PODS | Tutorial: Text Dominated Databases, Theory Practice and Experience. | Gaston H. Gonnet |
| 1991 | ISSAC | An Algebra of Properties. | Trudy Weibel, Gaston H. Gonnet |
| 1991 | SODA | The Analysis of Multidimensional Searching in Quad-Trees. | Philippe Flajolet, Gaston H. Gonnet, Claude Puech, J. M. Robson |
| 1990 | ICCI | Average Case Analysis of Algorithms using Matrix Recurrences. | Ricardo A. Baeza-Yates, Gaston H. Gonnet |
| 1990 | SODA | Analysis of Boyer-Moore-Type String Searching Algorithms. | Ricardo A. Baeza-Yates, Gaston H. Gonnet, Mireille Rgnier |
| 1989 | ICALP | Efficient Text Searching of Regular Expressions (Extended Abstract). | Ricardo A. Baeza-Yates, Gaston H. Gonnet |
| 1989 | SIGIR | A New Approach to Text Searching. | Ricardo A. Baeza-Yates, Gaston H. Gonnet |
| 1989 | WADS | Efficient Text Searching of Regular Expressions. | Ricardo A. Baeza-Yates, Gaston H. Gonnet |
| 1988 | ISSAC | A New Algorithm for Computing Symbolic Limits Using Hierarchical Series. | Keith O. Geddes, Gaston H. Gonnet |
| 1988 | ISSAC | Heuristic Methods for Operations With Algebraic Numbers. (Extended Abstract) | Keith O. Geddes, Gaston H. Gonnet, Trevor J. Smedley |
| 1987 | VLDB | Mind Your Grammar: a New Approach to Modelling Text. | Gaston H. Gonnet, Frank Wm. Tompa |
| 1986 | ISSAC | Computer algebra in the undergraduate mathematics classroom. | Bruce W. Char, Keith O. Geddes, Gaston H. Gonnet, Beverly J. Marshman, Peter J. Ponzo |
| 1986 | ISSAC | New results for random determination of equivalence of expressions. | Gaston H. Gonnet |
| 1986 | ISSAC | An implementation of operators for symbolic algebra systems. | Gaston H. Gonnet |
| 1984 | STOC | Determining Equivalence of Expressions in Random Polynomial Time (Extended Abstract) | Gaston H. Gonnet |
| 1983 | PODS | Unstructured Data Bases or Very Efficient Text Searching. | Gaston H. Gonnet |
| 1982 | ICALP | Heaps on Heaps. | Gaston H. Gonnet, J. Ian Munro |
| 1982 | PODS | External Hashing with Limited Internal Storage. | Gaston H. Gonnet, Per-ke Larson |
| 1981 | STOC | A Linear Probing Sort and its Analysis (Preliminary Draft) | Gaston H. Gonnet, J. Ian Munro |
| 1979 | FOCS | Toward Self-Organizing Linear Search (Preliminary Draught) | Gaston H. Gonnet, J. Ian Munro, Hendra Suwanda |
| 1977 | STOC | The Analysis of an Improved Hashing Technique | Gaston H. Gonnet, J. Ian Munro |