John D. Kececioglu

According to our database, John D. Kececioglu authored at least 52 papers between 1993 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Robust Optimal Metabolic Factories.

Spencer Krieger, John D. Kececioglu

J. Comput. Biol., 2024

Computing Robust Optimal Factories in Metabolic Reaction Networks.

Spencer Krieger, John D. Kececioglu

Proceedings of the Research in Computational Molecular Biology, 2024

2023

Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference.

Spencer Krieger, John D. Kececioglu

J. Comput. Biol., November, 2023

Computing Shortest Hyperpaths for Pathway Inference in Cellular Reaction Networks.

Spencer Krieger, John D. Kececioglu

Proceedings of the Research in Computational Molecular Biology, 2023

2022

Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs.

Spencer Krieger, John D. Kececioglu

Algorithms Mol. Biol., 2022

Heuristic shortest hyperpaths in cell signaling hypergraphs.

Spencer Krieger, John D. Kececioglu

Algorithms Mol. Biol., 2022

2021

Fast Approximate Shortest Hyperpaths for Inferring Pathways in Cell Signaling Hypergraphs.

Spencer Krieger, John D. Kececioglu

Proceedings of the 21st International Workshop on Algorithms in Bioinformatics, 2021

2020

Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization.

Spencer Krieger, John D. Kececioglu

Bioinform., 2020

Predicting protein secondary structure by an ensemble through feature-based accuracy estimation.

Spencer Krieger, John D. Kececioglu

Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020

2018

Adaptive Local Realignment of Protein Sequences.

Dan F. DeBlasio, John D. Kececioglu

J. Comput. Biol., 2018

2017

Parameter Advising for Multiple Sequence Alignment

Dan F. DeBlasio, John D. Kececioglu

Computational Biology 26, Springer, ISBN: 978-3-319-64917-7, 2017

Learning Parameter-Advising Sets for Multiple Sequence Alignment.

Dan F. DeBlasio, John D. Kececioglu

IEEE ACM Trans. Comput. Biol. Bioinform., 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, Cheng Yi

Softw. Pract. Exp., 2017

Core column prediction for protein multiple sequence alignments.

Dan F. DeBlasio, John D. Kececioglu

Algorithms Mol. Biol., 2017

Boosting Alignment Accuracy by Adaptive Local Realignment.

Dan F. DeBlasio, John D. Kececioglu

Proceedings of the Research in Computational Molecular Biology, 2017

2016

Predicting Core Columns of Protein Multiple Sequence Alignments for Improved Parameter Advising.

Dan F. DeBlasio, John D. Kececioglu

Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

Adaptive Local Realignment via Parameter Advising.

Dan F. DeBlasio, John D. Kececioglu

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2015

Parameter advising for multiple sequence alignment.

Dan F. DeBlasio, John D. Kececioglu

BMC Bioinform., 2015

Ensemble multiple sequence alignment via advising.

Dan F. DeBlasio, John D. Kececioglu

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014

Learning parameter sets for alignment advising.

Dan F. DeBlasio, John D. Kececioglu

Proceedings of the 5th ACM Conference on Bioinformatics, 2014

2013

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment.

John D. Kececioglu, Dan F. DeBlasio

J. Comput. Biol., 2013

2012

Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising.

Dan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu

Proceedings of the Research in Computational Molecular Biology, 2012

2010

Aligning Protein Sequences with Predicted Secondary Structure.

John D. Kececioglu, Eagu Kim, Travis J. Wheeler

J. Comput. Biol., 2010

2009

Learning Models for Aligning Protein Sequences with Predicted Secondary Structure.

Eagu Kim, Travis J. Wheeler, John D. Kececioglu

Proceedings of the Research in Computational Molecular Biology, 2009

2008

Learning Scoring Schemes for Sequence Alignment from Partial Examples.

Eagu Kim, John D. Kececioglu

IEEE ACM Trans. Comput. Biol. Bioinform., 2008

2007

Inverse Sequence Alignment from Partial Examples.

Eagu Kim, John D. Kececioglu

Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Multiple alignment by aligning alignments.

Travis J. Wheeler, John D. Kececioglu

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

Simple and Fast Inverse Alignment.

John D. Kececioglu, Eagu Kim

Proceedings of the Research in Computational Molecular Biology, 2006

2004

Aligning alignments exactly.

John D. Kececioglu, Dean Starrett

Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

Dynamic path-based software watermarking.

Christian S. Collberg, Edward Carter, Saumya K. Debray, Andrew Huntwork, John D. Kececioglu, Cullen Linn, Michael Stepp

Proceedings of the ACM SIGPLAN 2004 Conference on Programming Language Design and Implementation 2004, 2004

2001

Separtating repeats in DNA sequence assembly.

John D. Kececioglu, Jun Ju

Proceedings of the Fifth Annual International Conference on Computational Biology, 2001

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

Reconstructing distances in physical maps of chromosomes with nonoverlapping probes.

John D. Kececioglu, Sanjay Shete, Jonathan P. Arnold

Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

1999

Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut.

Thomas Christof, John D. Kececioglu

Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

1998

Approximation Algorithms for Multiple Sequence Alignment Under a Fixed Evolutionary Tree.

R. Ravi, John D. Kececioglu

Discret. Appl. Math., 1998

Reconstructing a History of Recombinations From a Set of Sequences.

John D. Kececioglu, Dan Gusfield

Discret. Appl. Math., 1998

Computing Maximum-Cardinality Matchings in Sparse General Graphs.

John D. Kececioglu, A. Justin Pecqueur

Proceedings of the Algorithm Engineering, 2nd International Workshop, 1998

Aligning Alignments.

John D. Kececioglu, Weiqing Zhang

Proceedings of the Combinatorial Pattern Matching, 9th Annual Symposium, 1998

1997

Inferring a DNA Sequence from Erroneous Copies.

John D. Kececioglu, Ming Li, John Tromp

Theor. Comput. Sci., 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

A branch-and-cut algorithm for multiple sequence alignment.

Knut Reinert, Hans-Peter Lenhof, Petra Mutzel, Kurt Mehlhorn, John D. Kececioglu

Proceedings of the First Annual International Conference on Research in Computational Molecular Biology, 1997

A branch-and-cut approach to physical mapping with end-probes.

Thomas Christof, Michael Jünger, John D. Kececioglu, Petra Mutzel, Gerhard Reinelt

Proceedings of the First Annual International Conference on Research in Computational Molecular Biology, 1997

1996

Steiner Points in the Space of Genome Rearrangements.

David Sankoff, Gopal Sundaram, John D. Kececioglu

Int. J. Found. Comput. Sci., 1996

1995

Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment.

Sandeep K. Gupta, John D. Kececioglu, Alejandro A. Schäffer

J. Comput. Biol., 1995

Exact and Approximation Algorithms for Sorting by Reversals, with Application to Genome Rearrangement.

John D. Kececioglu, David Sankoff

Algorithmica, 1995

Combinatiorial Algorithms for DNA Sequence Assembly.

John D. Kececioglu, Eugene W. Myers

Algorithmica, 1995

Of Mice and Men: Algorithms for Evolutionary Distances Between Genomes with Translocation.

John D. Kececioglu, R. Ravi

Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 1995

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. Schäffer

Proceedings of the Combinatorial Pattern Matching, 6th Annual Symposium, 1995

Inferring a DNA Sequence from Erroneous Copies (Abstract).

John D. Kececioglu, Ming Li, John Tromp

Proceedings of the Algorithmic Learning Theory, 6th International Conference, 1995

1994

Efficient Bounds for Oriented Chromosome Inversion Distance.

John D. Kececioglu, David Sankoff

Proceedings of the Combinatorial Pattern Matching, 5th Annual Symposium, 1994

1993

Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes.

John D. Kececioglu, David Sankoff

Proceedings of the Combinatorial Pattern Matching, 4th Annual Symposium, 1993

The Maximum Weight Trace Problem in Multiple Sequence Alignment.

John D. Kececioglu

Proceedings of the Combinatorial Pattern Matching, 4th Annual Symposium, 1993