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John D Kececioglu

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1989 …2023

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  • 2021

    Fast approximate shortest hyperpaths for inferring pathways in cell signaling hypergraphs

    Krieger, S. & Kececioglu, J., Jul 1 2021, 21st International Workshop on Algorithms in Bioinformatics, WABI 2021. Carbone, A. & El-Kebir, M. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 20. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 201).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    2 Scopus citations
  • 2020

    ANTARES: A gateway to ZTF and LSST alerts

    Lee, C. H., Matheson, T., Saha, A., Narayan, G., Soraisam, M., Stubens, C., Wolf, N., Snodgrass, R., Kececioglu, J. & Scheidegger, C., 2020, Observatory Operations: Strategies, Processes, and Systems VIII. Adler, D. S., Seaman, R. L. & Benn, C. R. (eds.). SPIE, 1144923. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 11449).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Scopus citations

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

    Krieger, S. & Kececioglu, J., Sep 21 2020, Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2020. Association for Computing Machinery, Inc, (Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2020).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Scopus citations
  • 2017

    Boosting alignment accuracy by adaptive local realignment

    DeBlasio, D. & Kececioglu, J., 2017, Research in Computational Molecular Biology - 21st Annual International Conference, RECOMB 2017, Proceedings. Sahinalp, S. C. (ed.). Springer-Verlag, p. 1-17 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10229 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    2 Scopus citations
  • 2016

    Adaptive local realignment via parameter advising

    DeBlasio, D. & Kececioglu, J., Oct 2 2016, ACM-BCB 2016 - 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 510-511 2 p. (ACM-BCB 2016 - 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access

  • ANTARES: Progress towards building a 'broker' of time-domain alerts

    Saha, A., Wang, Z., Matheson, T., Narayan, G., Snodgrass, R., Kececioglu, J., Scheidegger, C., Axelrod, T., Jenness, T., Ridgway, S., Seaman, R., Taylor, C., Toeniskoetter, J., Welch, E., Yang, S. & Zaidi, T., 2016, Observatory Operations: Strategies, Processes, and Systems VI. Peck, A. B., Seaman, R. L. & Benn, C. R. (eds.). SPIE, 99100E. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 9910).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    18 Scopus citations

  • Predicting core columns of protein multiple sequence alignments for improved parameter advising

    Deblasio, D. & Kececioglu, J., 2016, Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings. Frith, M. & Pedersen, C. N. S. (eds.). Springer-Verlag, p. 77-89 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9838 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Scopus citations
  • 2015

    Ensemble multiple sequence alignment via advising

    DeBlasio, D. & Kececioglu, J., Sep 9 2015, BCB 2015 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 452-461 10 p. (BCB 2015 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    4 Scopus citations
  • 2014

    ANTARES: A prototype transient broker system

    Saha, A., Matheson, T., Snodgrass, R., Kececioglu, J., Narayan, G., Seaman, R., Jenness, T. & Axelrod, T., 2014, Observatory Operations: Strategies, Processes, and Systems V. Peck, A. B., Benn, C. R. & Seaman, R. L. (eds.). SPIE, 914908. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 9149).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    24 Scopus citations

  • Learning parameter sets for alignment advising

    DeBlasio, D. & Kececioglu, J., Sep 20 2014, ACM BCB 2014 - 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, p. 230-239 10 p. (ACM BCB 2014 - 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    4 Scopus citations
  • 2012

    Estimating the accuracy of multiple alignments and its use in parameter advising

    Deblasio, D. F., Wheeler, T. J. & Kececioglu, J. D., 2012, Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings. p. 45-59 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7262 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    10 Scopus citations
  • 2009

    Learning models for aligning protein sequences with predicted secondary structure

    Kim, E., Wheeler, T. & Kececioglu, J., 2009, Research in Computational Molecular Biology - 13th Annual International Conference, RECOMB 2009, Proceedings. p. 512-531 20 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5541 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Scopus citations
  • 2007

    Inverse sequence alignment from partial examples

    Kim, E. & Kececioglu, J., 2007, Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings. Springer-Verlag, p. 359-370 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4645 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    3 Scopus citations
  • 2006

    Simple and fast inverse alignment

    Kececioglu, J. & Kim, E., 2006, Research in Computational Molecular Biology - 10th Annual International Conference, RECOMB 2006, Proceedings. p. 441-455 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3909 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    23 Scopus citations
  • 1998

    Aligning alignments

    D. Kececioglu, J. & Zhang, W., 1998, Combinatorial Pattern Matching - 9th Annual Symposium, CPM 1998, Proceedings. p. 189-208 20 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 1448 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    20 Scopus citations
  • 1995

    Approximation algorithms for multiple sequence alignment under a fixed evolutionary tree

    Ravi, R. & Kececioglu, J. D., 1995, Combinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings. Galil, Z. & Ukkonen, E. (eds.). Springer-Verlag, p. 330-339 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 937).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    6 Scopus citations

  • Inferring a DNA sequence from erroneous copies

    Kececioglu, J. D., Li, M. & Tromp, J., 1995, Algorithmic Learning Theory - 6th International Workshop, ALT 1995, Proceedings. Jantke, K. P., Shinohara, T. & Zeugmann, T. (eds.). Springer-Verlag, p. 151-152 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 997).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Making the shortest-paths approach to Sum-of-Pairs multiple sequence alignment more space efficient in practice (Extended Abstract)

    Gupta, S. K., Kececioglu, J. D. & Schäffer, A. A., 1995, Combinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings. Galil, Z. & Ukkonen, E. (eds.). Springer-Verlag, p. 128-143 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 937).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    12 Scopus citations

  • Of mice and men: Algorithms for evolutionary distances between genomes with translocation

    Kececioglu, J. D. & Ravi, R., Jan 22 1995, Proceedings of the 6th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1995. Association for Computing Machinery, p. 604-613 10 p. (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    84 Scopus citations
  • 1994

    Efficient bounds for oriented chromosome inversion distance

    Kececioglu, J. & Sankoff, D., 1994, Combinatorial Pattern Matching - 5th Annual Symposium, CPM 1994, Proceedings. Crochemore, M. & Gusfield, D. (eds.). Springer-Verlag, p. 307-325 19 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 807 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    70 Scopus citations

  • Reconstructing a history of recombinations from a set of sequences

    Kececioglu, J. & Gusfield, D., 1994, Proceedings of the Annual ACM SIAM Symposium on Discrete Algorithms. Publ by ACM, p. 471-480 10 p. (Proceedings of the Annual ACM SIAM Symposium on Discrete Algorithms).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    14 Scopus citations
  • 1993

    Exact and approximation algorithms for the inversion distance between two chromosomes

    Kececioglu, J. & Sankoff, D., 1993, Combinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings. Apostolico, A., Apostolico, A., Crochemore, M., Galil, Z., Galil, Z. & Manber, U. (eds.). Springer-Verlag, p. 87-105 19 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 684 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    74 Scopus citations

  • The maximum weight trace problem in multiple sequence alignment

    Kececioglu, J., 1993, Combinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings. Apostolico, A., Apostolico, A., Crochemore, M., Galil, Z., Galil, Z. & Manber, U. (eds.). Springer-Verlag, p. 106-119 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 684 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    98 Scopus citations