| 2019 | RECOMB | Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. | Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz |
| 1999 | SODA | Inverse Inbreeding Coefficient Problems with an Application to Linkage Analysis of Recessive Diseases in Inbred Populations. | Richa Agarwala, Leslie G. Biesecker, Alejandro A. Schffer |
| 1997 | WADS | Approximation Algorithms for a Genetic Diagnostics Problem. | S. Rao Kosaraju, Alejandro A. Schffer, Leslie G. Biesecker |
| 1995 | CPM | Making the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment More Space Efficient in Practice (Extended Abstract). | Sandeep K. Gupta, John D. Kececioglu, Alejandro A. Schffer |
| 1994 | CPM | Multiple Matching of Parameterized Patterns. | Ramana M. Idury, Alejandro A. Schffer |
| 1993 | SODA | Improved Dynamic Dictionary Matching. | Amihood Amir, Martin Farach, Ramana M. Idury, Johannes A. La Poutr, Alejandro A. Schffer |
| 1993 | SODA | Optimal Edge Ranking of Trees in Polynomial Time. | Pilar de la Torre, Raymond Greenlaw, Alejandro A. Schffer |
| 1993 | STOC | Multiple matching of rectangular patterns. | Ramana M. Idury, Alejandro A. Schffer |
| 1992 | CPM | Dynamic Dictionary Matching with Failure Functions (Extended Abstract). | Ramana M. Idury, Alejandro A. Schffer |
| 1992 | ICPP | Markov Analysis of Multiple-Disk Prefetching for External Mergesort. | Vinay S. Pai, Alejandro A. Schffer, Peter J. Varman |
| 1990 | STOC | On the Complexity of Local Search (Extended Abstract) | Christos H. Papadimitriou, Alejandro A. Schffer, Mihalis Yannakakis |
| 1988 | STOC | Storing and Searching a Multikey Table (Extended Abstract) | Amos Fiat, Moni Naor, Alejandro A. Schffer, Jeanette P. Schmidt, Alan Siegel |
| 1987 | STOC | Fast Parallel Algorithms for Chordal Graphs (Extended Abstract) | Joseph Naor, Moni Naor, Alejandro A. Schffer |