John D. Kececioglu

Publication Activity (10 Years)

Years Active: 1993-2024
Publications (10 Years): 16

Top Topics

Multiple Sequence Alignment

Protein Sequences

Signal Transduction Pathways

Secondary Structure

Top Venues

Algorithms Mol. Biol.

J. Comput. Biol.

Publications

Spencer Krieger, John D. Kececioglu
Computing Robust Optimal Factories in Metabolic Reaction Networks. RECOMB (2024)
Spencer Krieger, John D. Kececioglu
Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference. J. Comput. Biol. 30 (11) (2023)
Spencer Krieger, John D. Kececioglu
Computing Shortest Hyperpaths for Pathway Inference in Cellular Reaction Networks. RECOMB (2023)
Spencer Krieger, John D. Kececioglu
Heuristic shortest hyperpaths in cell signaling hypergraphs. Algorithms Mol. Biol. 17 (1) (2022)
Spencer Krieger, John D. Kececioglu
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs. Algorithms Mol. Biol. 17 (1) (2022)
Spencer Krieger, John D. Kececioglu
Fast Approximate Shortest Hyperpaths for Inferring Pathways in Cell Signaling Hypergraphs. WABI (2021)
Spencer Krieger, John D. Kececioglu
Predicting protein secondary structure by an ensemble through feature-based accuracy estimation. BCB (2020)
Spencer Krieger, John D. Kececioglu
Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization. Bioinform. 36 (Supplement-1) (2020)
Spencer Krieger, John D. Kececioglu
Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization. BCB (2020)
Dan F. DeBlasio, John D. Kececioglu
Adaptive Local Realignment of Protein Sequences. J. Comput. Biol. 25 (7) (2018)
Dan F. DeBlasio, John D. Kececioglu
Core column prediction for protein multiple sequence alignments. Algorithms Mol. Biol. 12 (1) (2017)
Dan F. DeBlasio, John D. Kececioglu
Boosting Alignment Accuracy by Adaptive Local Realignment. RECOMB (2017)
Dan F. DeBlasio, John D. Kececioglu
Learning Parameter-Advising Sets for Multiple Sequence Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (5) (2017)
Young-Kyoon Suh, Richard T. Snodgrass, John D. Kececioglu, Peter J. Downey, Robert S. Maier, Cheng Yi
EMP: execution time measurement protocol for compute-bound programs. Softw. Pract. Exp. 47 (4) (2017)
Dan F. DeBlasio, John D. Kececioglu
Predicting Core Columns of Protein Multiple Sequence Alignments for Improved Parameter Advising. WABI (2016)
Dan F. DeBlasio, John D. Kececioglu
Adaptive Local Realignment via Parameter Advising. BCB (2016)
Dan F. DeBlasio, John D. Kececioglu
Parameter advising for multiple sequence alignment. BMC Bioinform. 16 (S-2) (2015)
Dan F. DeBlasio, John D. Kececioglu
Ensemble multiple sequence alignment via advising. BCB (2015)
Dan F. DeBlasio, John D. Kececioglu
Learning parameter sets for alignment advising. BCB (2014)
John D. Kececioglu, Dan F. DeBlasio
Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment. J. Comput. Biol. 20 (4) (2013)
Dan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu
Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising. RECOMB (2012)
John D. Kececioglu, Eagu Kim, Travis J. Wheeler
Aligning Protein Sequences with Predicted Secondary Structure. J. Comput. Biol. 17 (3) (2010)
Eagu Kim, Travis J. Wheeler, John D. Kececioglu
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure. RECOMB (2009)
Eagu Kim, John D. Kececioglu
Learning Scoring Schemes for Sequence Alignment from Partial Examples. IEEE ACM Trans. Comput. Biol. Bioinform. 5 (4) (2008)
Travis J. Wheeler, John D. Kececioglu
Multiple alignment by aligning alignments. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Eagu Kim, John D. Kececioglu
Inverse Sequence Alignment from Partial Examples. WABI (2007)
John D. Kececioglu, Eagu Kim
Simple and Fast Inverse Alignment. RECOMB (2006)
Christian S. Collberg, Edward Carter, Saumya K. Debray, Andrew Huntwork, John D. Kececioglu, Cullen Linn, Michael Stepp
Dynamic path-based software watermarking. PLDI (2004)
John D. Kececioglu, Dean Starrett
Aligning alignments exactly. RECOMB (2004)
John D. Kececioglu, Jun Ju
Separtating repeats in DNA sequence assembly. RECOMB (2001)
John D. Kececioglu, Sanjay Shete, Jonathan Arnold
Reconstructing distances in physical maps of chromosomes with nonoverlapping probes. RECOMB (2000)
John D. Kececioglu, Hans-Peter Lenhof, Kurt Mehlhorn, Petra Mutzel, Knut Reinert, Martin Vingron
A polyhedral approach to sequence alignment problems. Discret. Appl. Math. 104 (1-3) (2000)
Thomas Christof, John D. Kececioglu
Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut. RECOMB (1999)
John D. Kececioglu, Weiqing Zhang
Aligning Alignments. CPM (1998)
John D. Kececioglu, Dan Gusfield
Reconstructing a History of Recombinations From a Set of Sequences. Discret. Appl. Math. 88 (1-3) (1998)
John D. Kececioglu, A. Justin Pecqueur
Computing Maximum-Cardinality Matchings in Sparse General Graphs. WAE (1998)
R. Ravi, John D. Kececioglu
Approximation Algorithms for Multiple Sequence Alignment Under a Fixed Evolutionary Tree. Discret. Appl. Math. 88 (1-3) (1998)
Thomas Christof, Michael Jünger, John D. Kececioglu, Petra Mutzel, Gerhard Reinelt
A branch-and-cut approach to physical mapping with end-probes. RECOMB (1997)
Knut Reinert, Hans-Peter Lenhof, Petra Mutzel, Kurt Mehlhorn, John D. Kececioglu
A branch-and-cut algorithm for multiple sequence alignment. RECOMB (1997)
Thomas Christof, Michael Jünger, John D. Kececioglu, Petra Mutzel, Gerhard Reinelt
A Branch-and-Cut Approach to Physical Mapping of Chromosomes by Unique End-Probes. J. Comput. Biol. 4 (4) (1997)
John D. Kececioglu, Ming Li, John Tromp
Inferring a DNA Sequence from Erroneous Copies. Theor. Comput. Sci. 185 (1) (1997)
David Sankoff, Gopal Sundaram, John D. Kececioglu
Steiner Points in the Space of Genome Rearrangements. Int. J. Found. Comput. Sci. 7 (1) (1996)
John D. Kececioglu, R. Ravi
Of Mice and Men: Algorithms for Evolutionary Distances Between Genomes with Translocation. SODA (1995)
Sandeep K. Gupta, John D. Kececioglu, Alejandro A. Schäffer
Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment. J. Comput. Biol. 2 (3) (1995)
John D. Kececioglu, Eugene W. Myers
Combinatiorial Algorithms for DNA Sequence Assembly. Algorithmica 13 (1/2) (1995)
John D. Kececioglu, Ming Li, John Tromp
Inferring a DNA Sequence from Erroneous Copies (Abstract). ALT (1995)
R. Ravi, John D. Kececioglu
Approximation Algorithms for Multiple Sequence Alignment Under a Fixed Evolutionary Tree. CPM (1995)
Sandeep K. Gupta, John D. Kececioglu, Alejandro A. Schäffer
Making the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment More Space Efficient in Practice (Extended Abstract). CPM (1995)
John D. Kececioglu, David Sankoff
Exact and Approximation Algorithms for Sorting by Reversals, with Application to Genome Rearrangement. Algorithmica 13 (1/2) (1995)
John D. Kececioglu, David Sankoff
Efficient Bounds for Oriented Chromosome Inversion Distance. CPM (1994)
John D. Kececioglu, Dan Gusfield
Reconstructing a History of Recombinations from a Set of Sequences. SODA (1994)
John D. Kececioglu
The Maximum Weight Trace Problem in Multiple Sequence Alignment. CPM (1993)
John D. Kececioglu, David Sankoff
Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes. CPM (1993)