The Maximum Weight Trace Problem in Multiple Sequence Alignment. - John D. Kececioglu (CPM, 1993)

Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes. - John D. Kececioglu; David Sankoff (CPM, 1993)

Efficient Bounds for Oriented Chromosome Inversion Distance. - John D. Kececioglu; David Sankoff (CPM, 1994)

Inferring a DNA Sequence from Erroneous Copies (Abstract). - John D. Kececioglu; Ming Li 001; John Tromp (ALT, 1995)

Making the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment More Space Efficient in Practice (Extended Abstract). - Sandeep K. Gupta 002; John D. Kececioglu; Alejandro A. Schäffer (CPM, 1995)

Of Mice and Men: Algorithms for Evolutionary Distances Between Genomes with Translocation. - John D. Kececioglu; R. Ravi 001 (SODA, 1995)

Combinatiorial Algorithms for DNA Sequence Assembly. - John D. Kececioglu; Eugene W. Myers (Algorithmica, 1995)

Exact and Approximation Algorithms for Sorting by Reversals, with Application to Genome Rearrangement. - John D. Kececioglu; David Sankoff (Algorithmica, 1995)

Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment. - Sandeep K. Gupta 002; John D. Kececioglu; Alejandro A. Schäffer (J. Comput. Biol., 1995)

Steiner Points in the Space of Genome Rearrangements. - David Sankoff; Gopal Sundaram; John D. Kececioglu (Int. J. Found. Comput. Sci., 1996)

A branch-and-cut approach to physical mapping with end-probes. - Thomas Christof; Michael Jünger; John D. Kececioglu; Petra Mutzel; Gerhard Reinelt (RECOMB, 1997)

A branch-and-cut algorithm for multiple sequence alignment. - Knut Reinert; Hans-Peter Lenhof; Petra Mutzel; Kurt Mehlhorn; John D. Kececioglu (RECOMB, 1997)

A Branch-and-Cut Approach to Physical Mapping of Chromosomes by Unique End-Probes. - Thomas Christof; Michael Jünger; John D. Kececioglu; Petra Mutzel; Gerhard Reinelt (J. Comput. Biol., 1997)

Inferring a DNA Sequence from Erroneous Copies. - John D. Kececioglu; Ming Li 001; John Tromp (Theor. Comput. Sci., 1997)

Aligning Alignments. - John D. Kececioglu; Weiqing Zhang (CPM, 1998)

Computing Maximum-Cardinality Matchings in Sparse General Graphs. - John D. Kececioglu; A. Justin Pecqueur (WAE, 1998)

Reconstructing a History of Recombinations From a Set of Sequences. - John D. Kececioglu; Dan Gusfield (Discret. Appl. Math., 1998)

Approximation Algorithms for Multiple Sequence Alignment Under a Fixed Evolutionary Tree. - R. Ravi 001; John D. Kececioglu (Discret. Appl. Math., 1998)

Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut. - Thomas Christof; John D. Kececioglu (RECOMB, 1999)

Reconstructing distances in physical maps of chromosomes with nonoverlapping probes. - John D. Kececioglu; Sanjay Shete; Jonathan P. Arnold (RECOMB, 2000)

A polyhedral approach to sequence alignment problems. - John D. Kececioglu; Hans-Peter Lenhof; Kurt Mehlhorn; Petra Mutzel; Knut Reinert; Martin Vingron (Discret. Appl. Math., 2000)

Separtating repeats in DNA sequence assembly. - John D. Kececioglu; Jun Ju (RECOMB, 2001)

Dynamic path-based software watermarking. - Christian S. Collberg; Edward Carter; Saumya K. Debray; Andrew Huntwork; John D. Kececioglu; Cullen Linn; Michael Stepp (PLDI, 2004)

Aligning alignments exactly. - John D. Kececioglu; Dean Starrett (RECOMB, 2004)

Simple and Fast Inverse Alignment. - John D. Kececioglu; Eagu Kim (RECOMB, 2006)

Multiple alignment by aligning alignments. - Travis J. Wheeler; John D. Kececioglu (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Inverse Sequence Alignment from Partial Examples. - Eagu Kim; John D. Kececioglu (WABI, 2007)

Learning Scoring Schemes for Sequence Alignment from Partial Examples. - Eagu Kim; John D. Kececioglu (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Learning Models for Aligning Protein Sequences with Predicted Secondary Structure. - Eagu Kim; Travis J. Wheeler; John D. Kececioglu (RECOMB, 2009)

Aligning Protein Sequences with Predicted Secondary Structure. - John D. Kececioglu; Eagu Kim; Travis J. Wheeler (J. Comput. Biol., 2010)

Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising. - Dan F. DeBlasio; Travis J. Wheeler; John D. Kececioglu (RECOMB, 2012)

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment. - John D. Kececioglu; Dan F. DeBlasio (J. Comput. Biol., 2013)

Learning parameter sets for alignment advising. - Dan F. DeBlasio; John D. Kececioglu (BCB, 2014)

Ensemble multiple sequence alignment via advising. - Dan F. DeBlasio; John D. Kececioglu (BCB, 2015)

Parameter advising for multiple sequence alignment. - Dan F. DeBlasio; John D. Kececioglu (BMC Bioinform., 2015)

Adaptive Local Realignment via Parameter Advising. - Dan F. DeBlasio; John D. Kececioglu (BCB, 2016)

Predicting Core Columns of Protein Multiple Sequence Alignments for Improved Parameter Advising. - Dan F. DeBlasio; John D. Kececioglu (WABI, 2016)

Boosting Alignment Accuracy by Adaptive Local Realignment. - Dan F. DeBlasio; John D. Kececioglu (RECOMB, 2017)

Core column prediction for protein multiple sequence alignments. - Dan F. DeBlasio; John D. Kececioglu (Algorithms Mol. Biol., 2017)

EMP: execution time measurement protocol for compute-bound programs. - Young-Kyoon Suh; Richard T. Snodgrass; John D. Kececioglu; Peter J. Downey; Robert S. Maier 001; Cheng Yi (Softw. Pract. Exp., 2017)

Learning Parameter-Advising Sets for Multiple Sequence Alignment. - Dan F. DeBlasio; John D. Kececioglu (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Parameter Advising for Multiple Sequence Alignment - Dan F. DeBlasio; John D. Kececioglu (Springer, 2017)

Adaptive Local Realignment of Protein Sequences. - Dan F. DeBlasio; John D. Kececioglu (J. Comput. Biol., 2018)

Predicting protein secondary structure by an ensemble through feature-based accuracy estimation. - Spencer Krieger; John D. Kececioglu (BCB, 2020)

Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization. - Spencer Krieger; John D. Kececioglu (Bioinform., 2020)

Fast Approximate Shortest Hyperpaths for Inferring Pathways in Cell Signaling Hypergraphs. - Spencer Krieger; John D. Kececioglu (WABI, 2021)

Heuristic shortest hyperpaths in cell signaling hypergraphs. - Spencer Krieger; John D. Kececioglu (Algorithms Mol. Biol., 2022)

Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs. - Spencer Krieger; John D. Kececioglu (Algorithms Mol. Biol., 2022)

Computing optimal factories in metabolic networks with negative regulation. - Spencer Krieger; John D. Kececioglu (Bioinform., 2022)

Computing Shortest Hyperpaths for Pathway Inference in Cellular Reaction Networks. - Spencer Krieger; John D. Kececioglu (RECOMB, 2023)

Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference. - Spencer Krieger; John D. Kececioglu (J. Comput. Biol., 2023)

Computing Robust Optimal Factories in Metabolic Reaction Networks. - Spencer Krieger; John D. Kececioglu (RECOMB, 2024)

Robust Optimal Metabolic Factories. - Spencer Krieger; John D. Kececioglu (J. Comput. Biol., 2024)