| 2025 | AAAI | The VOROS: Lifting ROC Curves to 3D to Summarize Unbalanced Classifier Performance. | Christopher Ratigan, Lenore Cowen |
| 2025 | RECOMB | Learning a CoNCISE Language for Small-Molecule Binding. | Mert Erden, Kapil Devkota, Lia Varghese, Lenore Cowen, Rohit Singh |
| 2025 | RECOMB | Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC. | Samuel Sledzieski, Charlotte Versavel, Rohit Singh, Faith Ocitti, Kapil Devkota, Lokender Kumar, Polina Shpilker, Liza Roger, Jinkyu Yang, Nastassja Lewinski, Hollie Putnam, Bonnie Berger, Judith Klein-Seetharaman, Lenore Cowen |
| 2024 | RECOMB | Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks. | Kapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen |
| 2022 | CHI | Embodied Notes: A Cognitive Support Tool For Remote Scientific Collaboration in VR. | Monsurat Olaosebikan, Claudia Aranda Barrios, Lenore Cowen, Orit Shaer |
| 2009 | RECOMB | Evaluating Between-Pathway Models with Expression Data. | Benjamin J. Hescott, Mark D. M. Leiserson, Lenore Cowen, Donna K. Slonim |
| 2006 | SPAA | Compact routing with additive stretch using distance labelings. | Arthur Brady, Lenore Cowen |
| 2004 | RECOMB | Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. | Matthew Menke, Eben Scanlon, Jonathan King, Bonnie Berger, Lenore Cowen |
| 2003 | PODC | Compact roundtrip routing with topology-independent node names. | Marta Arias, Lenore Cowen, Kofi A. Laing |
| 2003 | SPAA | Compact routing with name independence. | Marta Arias, Lenore Cowen, Kofi A. Laing, Rajmohan Rajaraman, Orjeta Taka |
| 2001 | RECOMB | Predicting the beta-helix fold from protein sequence data. | Phil Bradley, Lenore Cowen, Matthew Menke, Jonathan King, Bonnie Berger |
| 2000 | PODC | Compact roundtrip routing in directed networks (extended abstract). | Lenore Cowen, Christopher G. Wagner |
| 1999 | SODA | Compact Routing with Minimum Stretch. | Lenore Cowen |
| 1999 | SODA | Compact Roundtrip Routing for Digraphs. | Lenore Cowen, Christopher G. Wagner |
| 1997 | SODA | Coloring with Defect. | Lenore Cowen, Wayne Goddard, C. Esther Jesurum |
| 1996 | ICALP | A Formal Framework for Evaluating Heuristic Programs. | Lenore Cowen, Joan Feigenbaum, Sampath Kannan |
| 1996 | PODC | The Offset Problem (Abstract). | Lenore Cowen, Rudolf Mathar |
| 1994 | STOC | Efficient asynchronous distributed symmetry breaking. | Baruch Awerbuch, Lenore Cowen, Mark A. Smith |
| 1993 | FOCS | Near-Linear Cost Sequential and Distribured Constructions of Sparse Neighborhood Covers | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg |
| 1992 | PODC | Fast Network Decomposition (Extended Abstract). | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg |
| 1991 | SODA | Complexity Results and Algorithms for { <, <=, = }-Constrained Scheduling. | Bonnie Berger, Lenore Cowen |
| 1989 | CRYPTO | On the Structure of Secret Key Exchange Protocols. | Mihir Bellare, Lenore Cowen, Shafi Goldwasser |