John D. Kececioglu

56 papers A* 3B 19C 3Journal 23Unranked 7

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