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ORCIDJohn D. Kececioglu
Person information
- affiliation: University of Arizona, Tucson, USA
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Books and Theses
- 2017
[b1]Dan F. DeBlasio
, John D. Kececioglu:
Parameter Advising for Multiple Sequence Alignment. Computational Biology 26, Springer 2017, ISBN 978-3-319-64917-7, pp. 1-142
Journal Articles
- 2023
- [j21]Spencer Krieger, John D. Kececioglu:
Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference. J. Comput. Biol. 30(11): 1198-1225 (2023) - 2022
- [j20]Spencer Krieger, John D. Kececioglu:
Heuristic shortest hyperpaths in cell signaling hypergraphs. Algorithms Mol. Biol. 17(1): 12 (2022) - [j19]Spencer Krieger, John D. Kececioglu:
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs. Algorithms Mol. Biol. 17(1): 17 (2022) - 2020
- [j18]Spencer Krieger, John D. Kececioglu:
Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization. Bioinform. 36(Supplement-1): i317-i325 (2020) - 2018
- [j17]Dan F. DeBlasio, John D. Kececioglu:
Adaptive Local Realignment of Protein Sequences. J. Comput. Biol. 25(7): 780-793 (2018) - 2017
- [j16]Dan F. DeBlasio, John D. Kececioglu:
Core column prediction for protein multiple sequence alignments. Algorithms Mol. Biol. 12(1): 11:1-11:16 (2017) - [j15]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): 559-597 (2017) - [j14]Dan F. DeBlasio, John D. Kececioglu:
Learning Parameter-Advising Sets for Multiple Sequence Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 14(5): 1028-1041 (2017) - 2015
- [j13]Dan F. DeBlasio, John D. Kececioglu:
Parameter advising for multiple sequence alignment. BMC Bioinform. 16(S-2): A3 (2015) - 2013
- [j12]John D. Kececioglu, Dan F. DeBlasio:
Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment. J. Comput. Biol. 20(4): 259-279 (2013) - 2010
- [j11]John D. Kececioglu, Eagu Kim, Travis J. Wheeler:
Aligning Protein Sequences with Predicted Secondary Structure. J. Comput. Biol. 17(3): 561-580 (2010) - 2008
- [j10]Eagu Kim, John D. Kececioglu:
Learning Scoring Schemes for Sequence Alignment from Partial Examples. IEEE ACM Trans. Comput. Biol. Bioinform. 5(4): 546-556 (2008) - 2000
- [j9]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): 143-186 (2000) - 1998
- [j8]John D. Kececioglu, Dan Gusfield:
Reconstructing a History of Recombinations From a Set of Sequences. Discret. Appl. Math. 88(1-3): 239-260 (1998) - [j7]R. Ravi, John D. Kececioglu:
Approximation Algorithms for Multiple Sequence Alignment Under a Fixed Evolutionary Tree. Discret. Appl. Math. 88(1-3): 355-366 (1998) - 1997
- [j6]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): 433-447 (1997) - [j5]John D. Kececioglu, Ming Li, John Tromp:
Inferring a DNA Sequence from Erroneous Copies. Theor. Comput. Sci. 185(1): 3-13 (1997) - 1996
- [j4]David Sankoff, Gopal Sundaram, John D. Kececioglu:
Steiner Points in the Space of Genome Rearrangements. Int. J. Found. Comput. Sci. 7(1): 1-9 (1996) - 1995
- [j3]John D. Kececioglu, Eugene W. Myers:
Combinatiorial Algorithms for DNA Sequence Assembly. Algorithmica 13(1/2): 7-51 (1995) - [j2]John D. Kececioglu, David Sankoff:
Exact and Approximation Algorithms for Sorting by Reversals, with Application to Genome Rearrangement. Algorithmica 13(1/2): 180-210 (1995) - [j1]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): 459-472 (1995)
Conference and Workshop Papers
- 2024
- [c32]Spencer Krieger, John D. Kececioglu:
Computing Robust Optimal Factories in Metabolic Reaction Networks. RECOMB 2024: 253-269 - 2023
- [c31]Spencer Krieger, John D. Kececioglu:
Computing Shortest Hyperpaths for Pathway Inference in Cellular Reaction Networks. RECOMB 2023: 155-173 - 2021
- [c30]Spencer Krieger, John D. Kececioglu:
Fast Approximate Shortest Hyperpaths for Inferring Pathways in Cell Signaling Hypergraphs. WABI 2021: 20:1-20:20 - 2020
- [c29]Spencer Krieger, John D. Kececioglu:
Predicting protein secondary structure by an ensemble through feature-based accuracy estimation. BCB 2020: 29:1-29:10 - [c28]Spencer Krieger, John D. Kececioglu:
Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization. BCB 2020: 30:1 - 2017
- [c27]Dan F. DeBlasio, John D. Kececioglu:
Boosting Alignment Accuracy by Adaptive Local Realignment. RECOMB 2017: 1-17 - 2016
- [c26]Dan F. DeBlasio, John D. Kececioglu:
Adaptive Local Realignment via Parameter Advising. BCB 2016: 510-511 - [c25]Dan F. DeBlasio, John D. Kececioglu:
Predicting Core Columns of Protein Multiple Sequence Alignments for Improved Parameter Advising. WABI 2016: 77-89 - 2015
- [c24]Dan F. DeBlasio, John D. Kececioglu:
Ensemble multiple sequence alignment via advising. BCB 2015: 452-461 - 2014
- [c23]Dan F. DeBlasio, John D. Kececioglu:
Learning parameter sets for alignment advising. BCB 2014: 230-239 - 2012
- [c22]Dan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu:
Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising. RECOMB 2012: 45-59 - 2009
- [c21]Eagu Kim, Travis J. Wheeler, John D. Kececioglu:
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure. RECOMB 2009: 512-531 - 2007
- [c20]Travis J. Wheeler, John D. Kececioglu:
Multiple alignment by aligning alignments. ISMB/ECCB (Supplement of Bioinformatics) 2007: 559-568 - [c19]Eagu Kim, John D. Kececioglu:
Inverse Sequence Alignment from Partial Examples. WABI 2007: 359-370 - 2006
- [c18]John D. Kececioglu, Eagu Kim:
Simple and Fast Inverse Alignment. RECOMB 2006: 441-455 - 2004
- [c17]Christian S. Collberg, Edward Carter, Saumya K. Debray, Andrew Huntwork, John D. Kececioglu, Cullen Linn, Michael Stepp:
Dynamic path-based software watermarking. PLDI 2004: 107-118 - [c16]John D. Kececioglu, Dean Starrett:
Aligning alignments exactly. RECOMB 2004: 85-96 - 2001
- [c15]John D. Kececioglu, Jun Ju:
Separtating repeats in DNA sequence assembly. RECOMB 2001: 176-183 - 2000
- [c14]John D. Kececioglu, Sanjay Shete, Jonathan P. Arnold:
Reconstructing distances in physical maps of chromosomes with nonoverlapping probes. RECOMB 2000: 183-192 - 1999
- [c13]Thomas Christof, John D. Kececioglu:
Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut. RECOMB 1999: 115-123 - 1998
- [c12]John D. Kececioglu, Weiqing Zhang:
Aligning Alignments. CPM 1998: 189-208 - [c11]John D. Kececioglu, A. Justin Pecqueur:
Computing Maximum-Cardinality Matchings in Sparse General Graphs. WAE 1998: 121-132 - 1997
- [c10]Thomas Christof, Michael Jünger, John D. Kececioglu, Petra Mutzel, Gerhard Reinelt:
A branch-and-cut approach to physical mapping with end-probes. RECOMB 1997: 84-92 - [c9]Knut Reinert, Hans-Peter Lenhof, Petra Mutzel, Kurt Mehlhorn, John D. Kececioglu:
A branch-and-cut algorithm for multiple sequence alignment. RECOMB 1997: 241-250 - 1995
- [c8]John D. Kececioglu, Ming Li, John Tromp:
Inferring a DNA Sequence from Erroneous Copies (Abstract). ALT 1995: 151-152 - [c7]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: 128-143 - [c6]R. Ravi, John D. Kececioglu:
Approximation Algorithms for Multiple Sequence Alignment Under a Fixed Evolutionary Tree. CPM 1995: 330-339 - [c5]John D. Kececioglu, R. Ravi:
Of Mice and Men: Algorithms for Evolutionary Distances Between Genomes with Translocation. SODA 1995: 604-613 - 1994
- [c4]John D. Kececioglu, David Sankoff:
Efficient Bounds for Oriented Chromosome Inversion Distance. CPM 1994: 307-325 - [c3]John D. Kececioglu, Dan Gusfield:
Reconstructing a History of Recombinations from a Set of Sequences. SODA 1994: 471-480 - 1993
- [c2]John D. Kececioglu, David Sankoff:
Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes. CPM 1993: 87-105 - [c1]John D. Kececioglu:
The Maximum Weight Trace Problem in Multiple Sequence Alignment. CPM 1993: 106-119
Coauthor Index
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