| 2026 | KR | ABD: Default-Exception Abduction in Finite First-Order Worlds. | Serafim Batzoglou |
| 2025 | EMNLP | Stress-Testing the Reasoning Competence of Language Models With Formal Proofs. | Konstantine Arkoudas, Serafim Batzoglou |
| 2017 | RECOMB | GATTACA: Lightweight Metagenomic Binning Using Kmer Counting. | Victoria Popic, Volodymyr Kuleshov, Michael P. Snyder, Serafim Batzoglou |
| 2016 | RECOMB | Efficient Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting. | Victoria Popic, Serafim Batzoglou |
| 2015 | RECOMB | Read Clouds Uncover Variation in Complex Regions of the Human Genome. | Alex Bishara, Yuling Liu, Dorna Kashef Haghighi, Ziming Weng, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou |
| 2013 | RECOMB | An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test. | Jesse M. Rodriguez, Serafim Batzoglou, Sivan Bercovici |
| 2013 | RECOMB | Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery. | Raheleh Salari, Syed Shayon Saleh, Dorna Kashef Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou |
| 2012 | RECOMB | Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models. | Sivan Bercovici, Jesse M. Rodriguez, Megan Elmore, Serafim Batzoglou |
| 2008 | ISMB | A max-margin model for efficient simultaneous alignment and folding of RNA sequences. | Chuong B. Do, Chuan-Sheng Foo, Serafim Batzoglou |
| 2008 | RECOMB | Automatic Parameter Learning for Multiple Network Alignment. | Jason Flannick, Antal F. Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou |
| 2008 | RECOMB | Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA. | Andreas Sundquist, Eugene Fratkin, Chuong B. Do, Serafim Batzoglou |
| 2006 | ISMB | CONTRAfold: RNA secondary structure prediction without physics-based models. | Chuong B. Do, Daniel A. Woods, Serafim Batzoglou |
| 2006 | ISMB | MotifCut: regulatory motifs finding with maximum density subgraphs. | Eugene Fratkin, Brian T. Naughton, Douglas L. Brutlag, Serafim Batzoglou |
| 2006 | RECOMB | CONTRAlign: Discriminative Training for Protein Sequence Alignment. | Chuong B. Do, Samuel S. Gross, Serafim Batzoglou |
| 2006 | RECOMB | Integrated Protein Interaction Networks for 11 Microbes. | Balaji S. Srinivasan, Antal F. Novak, Jason Flannick, Serafim Batzoglou, Harley H. McAdams |
| 2004 | AAAI | PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences. | Chuong B. Do, Michael Brudno, Serafim Batzoglou |
| 2004 | CPM | A Computational Model for RNA Multiple Structural Alignment.. | Eugene Davydov, Serafim Batzoglou |
| 2004 | WABI | Chaining Algorithms for Alignment of Draft Sequence. | Mukund Sundararajan, Michael Brudno, Kerrin S. Small, Arend Sidow, Serafim Batzoglou |
| 2003 | ISMB | Glocal alignment: finding rearrangements during alignment. | Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou |
| 2003 | PSB | Gene Regulation - Session Introduction. | Serafim Batzoglou, Lior Pachter |
| 2000 | RECOMB | Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). | Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander |
| 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 | CPM | Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem. | Serafim Batzoglou, Sorin Istrail |
| 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 |
| 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 | 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 |