| 1998 | FOCS | Overcoming the Memory Bottleneck in Suffix Tree Construction. | Martin Farach, Paolo Ferragina, S. Muthukrishnan |
| 1998 | SODA | On Local Register Allocation. | Martin Farach, Vincenzo Liberatore |
| 1997 | FOCS | Nearly Tight Bounds on the Learnability of Evolution. | Andris Ambainis, Richard Desper, Martin Farach, Sampath Kannan |
| 1997 | FOCS | Optimal Suffix Tree Construction with Large Alphabets. | Martin Farach |
| 1997 | PDPTA | DNA Strand Separation Prediction: A Parallel Implementation. | Gabriela Hristescu, Craig J. Benham, Martin Farach |
| 1997 | RECOMB | Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. | Richa Agarwala, Serafim Batzoglou, Vlado Danck, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, S. Muthukrishnan, Steven Skiena |
| 1997 | RECOMB | Numerical taxonomy on data (abstract): experimental results. | Jaime Cohen, Martin Farach |
| 1997 | SODA | Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. | Richa Agarwala, Serafim Batzoglou, Vlado Danck, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, Steven Skiena |
| 1997 | SODA | Numerical Taxonomy on Data: Experimental Results. | Jaime Cohen, Martin Farach |
| 1996 | CPM | Perfect Hashing for Strings: Formalization and Algorithms. | Martin Farach, S. Muthukrishnan |
| 1996 | ESA | The Structure of Circular Decomposable Metrics. | George Christopher, Martin Farach, Michael A. Trick |
| 1996 | ICALP | Optimal Logarithmic Time Randomized Suffix Tree Construction. | Martin Farach, S. Muthukrishnan |
| 1996 | SODA | On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics). | Richa Agarwala, Vineet Bafna, Martin Farach, Babu O. Narayanan, Mike Paterson, Mikkel Thorup |
| 1996 | STOC | Efficient Algorithms for Inverting Evolution. | Martin Farach, Sampath Kannan |
| 1995 | ESA | Computing the Agreement of Trees with Bounded Degrees. | Martin Farach, Teresa M. Przytycka, Mikkel Thorup |
| 1995 | SODA | On the Entropy of DNA: Algorithms and Measurements Based on Memory and Rapid Convergence. | Martin Farach, Michiel O. Noordewier, Serap A. Savari, Larry A. Shepp, Aaron D. Wyner, Jacob Ziv |
| 1995 | STOC | String matching in Lempel-Ziv compressed strings. | Martin Farach, Mikkel Thorup |
| 1995 | SPAA | Optimal Parallel Dictionary Matching and Compression (Extended Abstract). | Martin Farach, S. Muthukrishnan |
| 1994 | FOCS | Optimal Evolutionary Tree Comparison by Sparse Dynamic Programming (Extended Abstract) | Martin Farach, Mikkel Thorup |
| 1994 | ICALP | Optimal Two-Dimensional Compressed Matching. | Amihood Amir, Gary Benson, Martin Farach |
| 1994 | SODA | Let Sleeping Files Lie: Pattern Matching in Z-compressed Files. | Amihood Amir, Gary Benson, Martin Farach |
| 1994 | SODA | Fast Comparison of Evolutionary Trees. | Martin Farach, Mikkel Thorup |
| 1994 | SODA | An Efficient Algorithm for Dynamic Text Indexing. | Ming Gu, Martin Farach, Richard Beigel |
| 1993 | SODA | Improved Dynamic Dictionary Matching. | Amihood Amir, Martin Farach, Ramana M. Idury, Johannes A. La Poutr, Alejandro A. Schffer |
| 1993 | STOC | A robust model for finding optimal evolutionary trees. | Martin Farach, Sampath Kannan, Tandy J. Warnow |
| 1993 | SPAA | Optimal Parallel Two Dimensional Pattern Matching. | Amihood Amir, Gary Benson, Martin Farach |
| 1992 | CPM | Efficient Randomized Dictionary Matching Algorithms (Extended Abstract). | Amihood Amir, Martin Farach, Yossi Matias |
| 1992 | STOC | Alphabet Independent Two Dimensional Matching | Amihood Amir, Gary Benson, Martin Farach |
| 1991 | FOCS | Adaptive Dictionary Matching | Amihood Amir, Martin Farach |
| 1991 | SODA | Efficient 2-dimensional Approximate Matching of Non-Rectangular Figures. | Amihood Amir, Martin Farach |