| 2024 | RECOMB | Computing Robust Optimal Factories in Metabolic Reaction Networks. | Spencer Krieger, John D. Kececioglu |
| 2023 | RECOMB | Computing Shortest Hyperpaths for Pathway Inference in Cellular Reaction Networks. | Spencer Krieger, John D. Kececioglu |
| 2021 | WABI | Fast Approximate Shortest Hyperpaths for Inferring Pathways in Cell Signaling Hypergraphs. | Spencer Krieger, John D. Kececioglu |
| 2017 | RECOMB | Boosting Alignment Accuracy by Adaptive Local Realignment. | Dan F. DeBlasio, John D. Kececioglu |
| 2016 | WABI | Predicting Core Columns of Protein Multiple Sequence Alignments for Improved Parameter Advising. | Dan F. DeBlasio, John D. Kececioglu |
| 2012 | RECOMB | Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising. | Dan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu |
| 2009 | RECOMB | Learning Models for Aligning Protein Sequences with Predicted Secondary Structure. | Eagu Kim, Travis J. Wheeler, John D. Kececioglu |
| 2007 | ISMB | Multiple alignment by aligning alignments. | Travis J. Wheeler, John D. Kececioglu |
| 2007 | WABI | Inverse Sequence Alignment from Partial Examples. | Eagu Kim, John D. Kececioglu |
| 2006 | RECOMB | Simple and Fast Inverse Alignment. | John D. Kececioglu, Eagu Kim |
| 2004 | PLDI | Dynamic path-based software watermarking. | Christian S. Collberg, Edward Carter, Saumya K. Debray, Andrew Huntwork, John D. Kececioglu, Cullen Linn, Michael Stepp |
| 2004 | RECOMB | Aligning alignments exactly. | John D. Kececioglu, Dean Starrett |
| 2001 | RECOMB | Separtating repeats in DNA sequence assembly. | John D. Kececioglu, Jun Ju |
| 2000 | RECOMB | Reconstructing distances in physical maps of chromosomes with nonoverlapping probes. | John D. Kececioglu, Sanjay Shete, Jonathan P. Arnold |
| 1999 | RECOMB | Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut. | Thomas Christof, John D. Kececioglu |
| 1998 | CPM | Aligning Alignments. | John D. Kececioglu, Weiqing Zhang |
| 1997 | RECOMB | A branch-and-cut approach to physical mapping with end-probes. | Thomas Christof, Michael Jnger, John D. Kececioglu, Petra Mutzel, Gerhard Reinelt |
| 1997 | RECOMB | A branch-and-cut algorithm for multiple sequence alignment. | Knut Reinert, Hans-Peter Lenhof, Petra Mutzel, Kurt Mehlhorn, John D. Kececioglu |
| 1995 | ALT | Inferring a DNA Sequence from Erroneous Copies (Abstract). | John D. Kececioglu, Ming Li, John Tromp |
| 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 |
| 1995 | CPM | Approximation Algorithms for Multiple Sequence Alignment Under a Fixed Evolutionary Tree. | R. Ravi, John D. Kececioglu |
| 1995 | SODA | Of Mice and Men: Algorithms for Evolutionary Distances Between Genomes with Translocation. | John D. Kececioglu, R. Ravi |
| 1994 | CPM | Efficient Bounds for Oriented Chromosome Inversion Distance. | John D. Kececioglu, David Sankoff |
| 1994 | SODA | Reconstructing a History of Recombinations from a Set of Sequences. | John D. Kececioglu, Dan Gusfield |
| 1993 | CPM | The Maximum Weight Trace Problem in Multiple Sequence Alignment. | John D. Kececioglu |
| 1993 | CPM | Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes. | John D. Kececioglu, David Sankoff |