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John Kececioglu is a Professor of Computer Science and the BIO5 Institute at the University of Arizona, which he joined in 2000. John did his PhD with Gene Myers, and his postdoctoral study with David Sankoff and Dan Gusfield.VOSviewer
Courses
- ABAlgorithms in Bioinformatics
- ADSAnalysis of Discrete Structures
- ATAAAdvanced Topics in Algorithm Analysis
- ATSSAdvanced Topics in Software Systems
- AAlgorithms
- ACBAlgorithms for Computational Biology
- DAADesign and Analysis of Algorithms
Grants
- EAGER: Breaking the Speed and Accuracy Barrier for Protein Property Prediction
Principal Investigator (PI)
2020
$199.9K
Active - AF: Small: Collaborative Research: Cell Signaling Hypergraphs: Algorithms and Applications
Principal Investigator (PI)
2016
$212.0K
- INSPIRE Track 1: Arizona- NOAO Temporal Analysis and Response to Events System (ANTARES)
Co-Investigator (COI)
2013
$733.0K
- III: Small: Parameter Interface and Parameter Advising in Computational Biology
Principal Investigator (PI)
2012
$500.1K
- Collaborative: EAGER: A Model Based System for the Automated Design of Synthetic Genetic Circuits by Mathematical Optimization
Principal Investigator (PI)
2011
$28.9K
- Eager: An Exploratory System for Inverse Parametric Optimization
Principal Investigator (PI)
2010
$59.8K
- IGERT Program in Comparative Genomics
Co-Investigator (COI)
2007
$3.0M
- Graduate Assistance in Computer Science: An Area of National Need
Principal Investigator (PI)
2007
$303.6K
News
- A Boost for Analyzing Biological Sequences
2013
- How to Find the Rarest of the Rare in Southern Skies
2013
- UA's BIO5 Institute Hosting International RECOMB 2009 Conference
2009
- Math Awareness Week
2002
Publications (49)
Recent
- The Solar System Notification Alert Processing System (SNAPS): Design, Architecture, and First Data Release (SNAPShot1)
2023
- Computing shortest hyperpaths for pathway inference in cellular reaction networks
2023
- Heuristic shortest hyperpaths in cell signaling hypergraphs
2022
- Computing optimal factories in metabolic networks with negative regulation
2022
- The ANTARES astronomical time-domain event broker
2021
- Fast approximate shortest hyperpaths in cell signaling hypergraphs
2021
- Inferring pathways in cell signaling networks via shortest hyperpaths in directed hypergraphs
2021
- Predicting protein secondary structure via nearest neighbor search and metric learning
2020
- Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization
2020
- ANTARES: a gateway to ZTF and LSST alerts
2020
- Predicting protein secondary structure by an ensemble through feature-based accuracy estimation
2020
- Breaking the speed and accuracy barrier for protein secondary structure prediction
2019
- Adaptive local realignment of protein sequences
2018
- Machine-learning-based brokers for real-time classification of the LSST alert stream
2018
- Learning parameter-advising sets for multiple sequence alignment
2017
- Boosting alignment accuracy by adaptive local realignment
2017
- Core column prediction for protein multiple sequence alignments
2017
- Boosting alignment accuracy through adaptive local realignment
2016
- EMP: Execution Time Measurement Protocol for Compute-Bound Programs
2016
- Predicting core columns of protein multiple sequence alignments for improved parameter advising
2016
- ANTARES: progress towards building a broker of time-domain alerts
2016
- Proceedings of the 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
2016
- Ensemble multiple sequence alignment via advising
2015
- Learning parameter sets for alignment advising
2014
- Accuracy estimation and parameter advising for protein multiple sequence alignment
2013
- Automatic design of synthetic gene circuits through mixed integer non-linear programming
2012
- Estimating the accuracy of multiple alignments and its use in parameter advising
2012
- Aligning protein sequences with predicted secondary structure
2010
- Learning models for aligning protein sequences with predicted secondary structure
2009
- Learning scoring schemes for sequence alignment from partial examples
2008
- Multiple alignment by aligning alignments
2007
- Inverse sequence alignment from partial examples
2007
- Simple and fast inverse alignment
2006
- Aligning alignments exactly
2004
- Separating repeats in DNA sequence assembly
2001
- Reconstructing distances in physical maps of chromosomes with nonoverlapping probes
2000
- A polyhedral approach to sequence alignment problems
2000
- Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut
1999
- Approximation algorithms for multiple sequence alignment under a fixed evolutionary tree
1998
- Branch-and-cut approach to physical mapping with end-probes
1997
- A branch-and-cut approach to physical mapping of chromosomes by unique end-probes
1997
- Inferring a DNA sequence from erroneous copies
1997
- HIV-1 encodes a sequence overlapping env gp41 with highly significant similarity to selenium-dependent glutathione peroxidases.
1997
- Branch-and-cut algorithm for multiple sequence alignment
1997
- Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment.
1995
- Combinatorial algorithms for DNA sequence assembly
1995
- Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement
1995
- Reconstructing a history of recombinations from a set of sequences
1994
- A tool for multiple sequence alignment
1989