| 2006 | RECOMB | Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. | Sagi Snir, Lior Pachter |
| 2004 | RECOMB | Multiple organism gene finding by collapsed gibbs sampling. | Sourav Chatterji, Lior Pachter |
| 2003 | ECCB | HMM sampling and applications to gene finding and alternative splicing. | Simon Cawley, Lior Pachter |
| 2003 | PSB | Gene Regulation - Session Introduction. | Serafim Batzoglou, Lior Pachter |
| 2002 | PSB | Genome-Wide Analysis and Comparative Genomics - Session Introduction. | Inna Dubchak, Lior Pachter, Liping Wei |
| 2002 | RECOMB | Picking alignments from (steiner) trees. | Lior Pachter, Fumei Lam |
| 2001 | RECOMB | Applications of generalized pair hidden Markov models to alignment and gene finding problems. | Lior Pachter, Marina Alexandersson, Simon Cawley |
| 2000 | RECOMB | Human and mouse gene structure: comparative analysis and application to exon prediction. | Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander |
| 1999 | RECOMB | A dictionary based approach for gene annotation. | Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman |