Date Speaker Talk August 30 John Kececioglu Overview of research group projects September 6 (None) (Labor Day holiday) 13 John Kececioglu Algorithms for protein secondary structure prediction 20 John Kececioglu Algorithms for protein secondary structure prediction, continued 27 Dan DeBlasio Multiple sequence alignment October 4 August Woerner Nearest neighbor searching 11 Ben Salazar Tools for protein secondary structure prediction
Date Speaker Talk January 21 (None) (Organizational meeting) 28 David Perkins Gavin Crooks and Steven Brenner,
"Protein secondary structure: entropy, correlations and prediction,"
Bioinformatics 20:10, 1603-1611, 2004.February 4 John Kececioglu Jieun Jeong, Piotr Berman, and Teresa Przytycka,
"Improving strand pairing prediction through exploring folding cooperativity,"
IEEE/ACM Transactions on Computational Biology and Bioinformatics 5:4, 484-491, 2008.11 John Kececioglu Jianlin Cheng and Pierre Baldi,
"Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms,"
Proceedings of ISMB'05, Bioinformatics 21:1, i75-i84, 2005.18 (None) (Cancelled due to illness) 25 (None) (Cancelled due to illness) March 4 (None) (Participants away) 11 (None) (RECOMB organization) 18 (None) (Spring break week) 25 (None) (Participants away) April 1 (None) (Participants away) 8 Travis Wheeler Kimmen Sjölander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, Saira Mian, and David Haussler,
"Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology,"
CABIOS 12:4, 327-345, 1996.15 Travis Wheeler Sjölander, Karplus, Brown, Hughey, Krogh, Mian, and Haussler, continued. 22 (None) (RECOMB preparations) 29 David Perkins (Practice talk for thesis defense)
Date Speaker Talk August 26 (None) (Participants away) September 2 (None) (Participants away) 9 (None) (Organizational meeting) 16 John Kececioglu Zafer Aydin, Yucel Altunbasak and Mark Borodovsky,
"Protein secondary structure prediction for a single-sequence using hidden semi-Markov models,"
BMC Bioinformatics 7:178, 2006.23 (None) (RECOMB preparation) 30 (None) (RECOMB preparation) October 7 (None) (RECOMB submission deadline) 14 (None) (INFORMS talk) 21 (None) (Dornhaus talk) 28 (None) (NSF proposal deadline) November 4 John Kececioglu Aydin, Altunbasak and Borodovsky, continued. 11 (None) (Veterans Day holiday) 18 Travis Wheeler Olivier Gascuel and Mike Steel,
"Neighbor-joining revealed",
Journal of Molecular Evolution 62, 785-792, 2006.25 (None) (Cancelled) December 2 Travis Wheeler Thomas Mailund, Gerth Brodal, Rolf Fagerberg, Christian Pedersen and Derek Phillips,
"Recrafting the neighbor-joining method",
BMC Bioinformatics 7:29, 1-8, 2006.9 (None) (Participants away) 16 Travis Wheeler Mailund, Brodal, Fagerberg, Pedersen and Phillips, continued.
January 30 (None) (Organizational meeting) February 6 (None) (Cancelled) 13 (None) (Cancelled) 20 Travis Wheeler (Practice talk) 27 Travis Wheeler (Practice talk) March 5 John Kececioglu Thorsten Joachims, Tamara Galor and Ron Elber,
"Learning to align sequences: a maxium margin approach,"
New Algorithms for Macromolecular Simulation, Springer-Verlag LNCS 49, 57-68, 2005.12 John Kececioglu Joachims, Galor and Elber, continued. 19 (None) (Spring break) 26 John Kececioglu Joachims, Galor and Elber, continued. April 2 (None) (RECOMB conference) 9 (None) (Cancelled) 16 John Kececioglu Joachims, Galor and Elber, continued. 23 Travis Wheeler Sean Eddy and Richard Durbin,
"RNA sequence analysis using covariance models,"
Nucleic Acids Research 22, 2079-2088, 1994.30 Eagu Kim (Practice talk) May 7 Eagu Kim (Practice talk)
Date Speaker Talk August 23 (None) (Organizational meeting) 30 (None) (Participants away) September 6 Eagu Kim (Practice talk for WABI) 13 (None) (RECOMB submission deadline) 20 (None) (RECOMB submission deadline) 27 (None) (Participants away) October 4 (None) (Participants away) 11 John Kececioglu Ydo Wexler, Chaya Zilberstein and Michal Ziv-Ukelson,
"A study of accessible motifs and RNA folding complexity,"
Journal of Computational Biology 14:6, 856-872, 2007.18 John Kececioglu Wexler, Zilberstein and Ziv-Ukelson, continued. 25 Eagu Kim Mirela Andronescu, Anne Condon, Holger Hoos, David Mathews and Kevin Murphy,
"Efficient parameter estimation for RNA secondary structure prediction,"
ISMB/ECCB 15, Bioinformatics 23, i19-i28, 2007.November 1 Eagu Kim Andronescu, Condon, Hoos, Mathews and Murphy, continued. 8 (None) (Cancelled) 15 (None) (Cancelled) 22 (None) (Thanksgiving recess) 29 (None) (Grant proposal deadline)
Date Speaker Talk January 17 (None) (Organizational meeting) 24 (None) (ISMB submission deadline) 31 (None) (ISMB submission deadline) February 7 John Kececioglu Marcella McClure, Hugh Richardson, Rochelle Clinton, Crystal Hepp, Brad Crowther and Eric Donaldson,
"Automated characterization of potentially active retroid agents in the human genome,"
Genomics 85, 512-523, 2005.14 (None) (At ASU Biodesign Institute) 21 John Kececioglu Stefan Burkhardt and Juha Kärkkäinen,
"One-gapped q-gram filters for Levenshtein distance,"
Combinatorial Pattern Matching 13, Springer LNCS 2373, 225-234, 2002.28 John Kececioglu Juha Kärkkäinen,
"Computing the threshold for q-gram filters,"
Scandinavian Workshop on Algorithm Theory 6, Springer LNCS 2368, 348-357, 2002.March 7 Kyri Pavlou Denise Mak, Yevgeniy Gelfand and Gary Benson,
"Indel seeds for homology search,"
Bioinformatics 22:14, e341-e349, 2006.14 (None) (Spring break) 21 Kyri Pavlou Mak, Gelfand and Benson, continued.
28 Kyri Pavlou Mak, Gelfand and Benson, continued.
April 4 John Kececioglu Jie Zheng and Stefano Lonardi,
"Discovery of repetitive patterns in DNA with accurate boundaries,"
BIBE 5, 105-112, 2005.11 John Kececioglu Zheng and Lonardi, continued.
Date Speaker Talk August 25 (None) (Organizational meeting) September 1 John Kececioglu Anantharaman Kalyanaraman and Srinivas Aluru,
"Efficient algorithms and software for detection of full-length LTR retrotransposons,"
To appear in Journal of Bioinformatics and Computational Biology 11:41, 2006.8 John Kececioglu Kalyanaraman and Aluru, continued. 15 (None) (Out of town) 22 Kyriacos Pavlou Pang Ko and Srinivas Aluru,
"Obtaining provably good performance from suffix trees in secondary storage,"
To appear in Proceedings of Combinatorial Pattern Matching (CPM), 2006.29 (None) (RECOMB submission deadline) October 6 Kyriacos Pavlou Ko and Aluru, continued. 13 Eagu Kim Chuong Do, Samuel Gross and Serafim Batzoglou,
"CONTRAlign: discriminative training for protein sequence alignment."
RECOMB 10, 160-174, 2006.20 Eagu Kim Do, Gross and Batzoglou, continued.
27 Eagu Kim Do, Gross and Batzoglou, continued.
November 3 John Kececioglu Robert Edgar and Gene Myers,
"PILER: identification and classification of genomic repeats,"
ISMB 13, 152-158, 2005.10 John Kececioglu Jie Zheng and Stefano Lonardi,
"Discovery of repetitive patterns in DNA with accurate boundaries,"
BIBE 5, 105-112, 2005.17 (None) (Proposal deadline) 24 (None) (Thanksgiving break) December 1 (None) (Out of town)
Date Speaker Talk May 31 Travis Wheeler Robert Edgar,
"MUSCLE: a multiple sequence alignment method with reduced time and space complexity,"
BMC Bioinformatics 5:113, 1-19, 2004.June 7 Travis Wheeler Robert Edgar,
"MUSCLE: multiple sequence alignment with high accuracy and throughput,"
Nucleic Acids Research 32:5, 1792-1797, 2004.14 Travis Wheeler Kazutaka Katoh, Kei-ichi Kuma, Hiroyiki Toh and Takashi Miyata,
"MAFFT version 5: improvement in accuracy of multiple sequence alignment,"
Nucleic Acids Research 33:2, 511-518, 2005.21 John Kececioglu Toru Kasai, Gunho Lee, Hiroki Arimura, Setsuo Arikawa and Kunsoo Park,
"Linear-time longest-common-prefix computation in suffix arrays and its applications,"
Combinatorial Pattern Matching (CPM), Springer-Verlag LNCS 2089, 181-192, 2001.28 (None) (Participants away) July 5 John Kececioglu Kasai et al., continued. 12 (None) (Speaker ill) 19 John Kececioglu John Kececioglu,
"Solving tree multiple-sequence alignment by iterative weighted sum-of-pairs alignment,"
work in progress, 2006.26 John Kececioglu Gene Myers and Webb Miller,
"Chaining multiple-alignment fragments in sub-quadratic time,"
Symposium on Discrete Algorithms (SODA) 6, 38-47, 1995.August 2 (None) (Away on vacation) 9 John Kececioglu Gene Myers and Webb Miller, continued.
Date Speaker Talk January 31 John Kececioglu David Eppstein,
"Setting parameters by example,"
SIAM Journal on Computing 32:3, 643-653, 2003.February 7 John Kececioglu David Eppstein, continued. 14 John Kececioglu David Eppstein, continued. 21 (None) (ISMB submission preparation) 28 (None) (ISMB submission deadline) March 7 Travis Wheeler Julie Thompson, Desmond Higgins and Toby Gibson,
"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,"
Nucleic Acids Research 22:22, 4673-4680, 1994.14 (None) (Spring break) 21 Eagu Kim (Practice talk for RECOMB) 28 Eagu Kim (Practice talk for RECOMB) April 4 (None) (RECOMB in Italy) 11 (None) (Review of RECOMB and organizational meeting) 18 (None) (Away at NIH grant workshop) 25 Travis Wheeler Chuong Do, Mahathi Mahabhashyam, Michael Brudno and Serafim Batzoglou,
"ProbCons: probabilistic consistency-based multiple sequence alignment,"
Genome Research 15, 330-340, 2005.May 2 Travis Wheeler Cedric Notredame, Desmond Higgins and Jaap Heringa,
"T-Coffee: a novel method for fast and accurate multiple sequence alignnment,"
Journal of Molecular Biology 302, 205-217, 2000.
Date Speaker Talk August 31 John Kececioglu Kim Rasmussen, Jens Stoye, and Gene Myers,
"Efficient q-gram filters for finding all epsilon-matches over a given length,"
RECOMB 9, 189-203, 2005.September 7 John Kececioglu Rassmussen, Stoye, and Myers, continued. 14 John Kececioglu Rassmussen, Stoye, and Myers, continued. 21 (None) (RECOMB submission deadline) 28 Travis Wheeler Jens Gramm, Rolf Niedermeier, and Peter Rossmanith,
"Fixed-parameter algorithms for Closest String and related problems,"
Algorithmica 37:1, 25-42, 2003.October 5 (None) (Cancelled due to emergency) 12 Travis Wheeler Gramm, Niedermeier, and Rossmanith, continued. 19 Travis Wheeler Andrew Smith, Pavel Sumazin, Debopriya Das, and Michael Zhang,
"Mining ChIP-chip data for transcription factor and cofactor binding sites,"
ISMB 13, 403-412, 2005.26 (None) (Birth of Elliot Wheeler) November 2 (None) (Speaking in Montana) 9 Eagu Kim Fangting Sun, David Fernández-Baca, and Wei Yu,
"Inverse parametric sequence alignment,"
Journal of Algorithms 53, 36-54, 2004.16 Eagu Kim Sun, Fernández-Baca, and Yu, continued. 23 Eagu Kim D. Gusfield, K. Balasubramanian, and D. Naor,
"Parametric optimization of sequence alignment,"
Algorithmica 12, 312-326, 1994.30 (None) (Organizational meeting for Spring semester)
Date Speaker Talk May 25 (None) (Organizational meeting) June 1 (None) (Out of town) 8 Dean Starrett Osamu Gotoh,
"Further improvement in methods of group-to-group sequence alignment with generalized profile operations,"
Computer Applications in the Biosciences 10:4, 379-387, 1994.15 Dean Starrett Gotoh, continued. 22 Dean Starrett Gotoh, continued. 29 (None) (ISMB 2005) July 6 Eagu Kim Nicholas Chia and Ralf Bundschuh,
"A practical approach to significance assessment in alignments with gaps,"
RECOMB 9, 474-488, 2005.13 Dean Starrett Robert Edgar,
"MUSCLE: a multiple sequence alignment method with reduced time and space complexity,"
BMC Bioinformatics 5:113, 2004.20 Dean Starrett Chuong Do, Mahathi Mahabhashyam, Michael Brudno, and Serafim Batzoglou,
"ProbCons: probabilistic consistency-based multiple sequence alignment,"
Genome Research 15, 330-340, 2005.27 (None) (Organizational meeting)
Date Speaker Talk January 17 (None) (Martin Luther King Jr. Holiday) 24 (None) (Organizational meeting) 31 John Kececioglu James Driscoll, Neil Sarnak, Daniel Sleator, and Robert Tarjan,
"Making data structures persistent,"
Journal of Computer and System Sciences 38:1, 86-124, 1989.February 7 (None) (Out of town) 14 (None) (Discussion of research of participants) 21 (None) (Cancelled) 28 John Kececioglu Driscoll, Sarnak, Sleator, and Tarjan, continued.
March 7 John Kececioglu Driscoll, Sarnak, Sleator, and Tarjan, continued.
14 (None) (Spring break) 21 John Kececioglu Driscoll, Sarnak, Sleator, and Tarjan, continued.
28 John Kececioglu Driscoll, Sarnak, Sleator, and Tarjan, continued.
April 4 Eagu Kim Jeff Thorne, Hirohisa Kishino, and Joe Felsenstein,
"An evolutionary model for maximum likelihood alignment of DNA sequences,"
Journal of Molecular Evolution 33, 114-124, 1991.11 Eagu Kim Thorne, Kishino, and Felsenstein, continued.
18 Eagu Kim Thorne, Kishino, and Felsenstein, continued.
25 Travis Wheeler (Practice talk for Oral Qualifying Exam presentation) May 2 Eagu Kim Jeff Thorne, Hirohisa Kishino, and Joe Felsenstein,
"Inching toward reality: an improved likelihood model of sequence evolution,"
Journal of Molecular Evolution 34, 3-16, 1992.
Date Speaker Talk August 26 (None) (Organizational meeting) September 2 John Kececioglu David Eppstein,
"Finding the k shortest paths,"
FOCS 1994.9 John Kececioglu Eppstein, continued.
16 John Kececioglu Eppstein, continued.
23 (None) (Discussion of research of participants)
30 Travis WheelerDavid Sankoff,
"Simultaneous solution of the RNA folding, alignment and protosequence problems,"
SIAM Journal on Applied Mathematics, 1985.October 7 Travis Wheeler Sankoff, continued.
14 Travis Wheeler Sankoff, continued.
21 Dean Starrett Gary Benson,
"Composition alignment,"
WABI 2003.28 Eagu Kim Sourav Chatterji and Lior Pachter,
"Multiple organism gene finding by collapsed Gibbs sampling,"
RECOMB 2004.November 4 Eagu Kim Chatterji and Pachter, continued.
11 (None) (Veterans' Day Holiday) 18 John Kececioglu Zvi Galil and Kunsoo Park,
"An improved algorithm for approximate string matching,"
SIAM Journal on Computing 1990.25 (None) (Thanksgiving Break) December 2 John Kececioglu Galil and Park, continued.
9 (None) (End of semester)
Date Speaker Talk June 3 Travis Wheeler Segal and Sharan continued,
``A discriminative model for identifying spatial cis-regulatory modules,''
RECOMB 2004.10 John Kececioglu Myers and Durbin,
``A table-driven, full-sensitivity similarity search algorithm,''
JCB 2003.17 John Kececioglu Myers and Durbin, continued. 24 Eagu Kim He and Goldwasser,
``Identifying conserved gene clusters in the presence of orthologous groups,''
RECOMB 2004.July 1 Eagu Kim He and Goldwasser, continued. 8 Dean Starrett Policriti, Vitacolonna and Morgante,
``Structured motifs search,''
RECOMB 2004.15 Travis Wheeler Li and Jiang,
``A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs,''
RECOMB 2004.22 (None) (Discussion of research of participants) 29 Travis Wheeler Li and Jiang, continued. August 5 John Kececioglu Myers,
``A fast bit-vector algorithm for approximmate string matching based on dynamic programming,''
JACM 1999.12 John Kececioglu Myers, continued.
Date Speaker Talk January 22 John Kececioglu Burkhardt and Kärkkäinen,
``Better filtering with gapped q-grams,''
CPM 2001.29 John Kececioglu Burkhardt and Kärkkäinen, continued. February 5 Dean Starrett Buhler, Keich and Sun,
``Designing seeds for similarity search in genomic DNA,''
RECOMB 2003.12 Dean Starrett Buhler, Keich and Sun, continued.
19 Travis Wheeler Eskin and Pevzner,
``Finding composite regulatory patterns in DNA sequences,''
ISMB 2002.26 Travis Wheeler Eskin and Pevzner, continued. March 4 Eagu Kim Bejerano,
``Efficient exact p-value computation and applications to biosequence analysis,''
RECOMB 2003.11 Eagu Kim Bejerano, continued. 18 Dean Starrett (Practice talk for RECOMB 2004) 25 (None) (Preparation for RECOMB 2004, continued) April 1 (None) (Discussion of RECOMB 2004 highlights) 8 John Kececioglu Siepel and Haussler,
``Computational identification of evolutionarily conserved exons,''
RECOMB 2004.15 Eagu Kim Halperin and Karp,
``Perfect phylogeny and haplotype assignment,''
RECOMB 2004.22 Eagu Kim Halperin and Karp, continued. 29 Dean Starrett Sun and Buhler,
``Designing multiple simultaneous seeds for DNA similarity search,''
RECOMB 2004.May 6 Dean Starrett Sun and Buhler, continued. 13 Travis Wheeler Segal and Sharan,
``A discriminative model for identifying spatial cis-regulatory modules,''
RECOMB 2004.
Date Speaker Talk September 4 (None) (Organizational meeting) 11 John Kececioglu Kececioglu and Starrett,
``Aligning alignments exactly,''
in preparation 2003.18 (None) (RECOMB submission deadline) 25 John Kececioglu Kececioglu and Starrett, continued. October 2 John Kececioglu Kärkkäinen and Sanders,
``Simple linear work suffix array construction,''
ICALP 2003.9 Dean Starrett Kasai, Lee, Arimura, Arikawa and Park,
``Linear-time longest-common-prefix computation in suffix arrays and its applications,''
CPM 2001.16 Dean Starrett Kasai et al., continued.
23 Travis Wheeler Ukkonen,
``Finding founder sequences from a set of recombinants,''
WABI 2002.30 Travis Wheeler Ukkonen, continued. November 6 (None) (PhD Oral Comprehensive Exam) 13 Eagu Kim Roskin, Diekhans and Haussler,
``Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments,''
RECOMB 2003.20 John Kececioglu Manber and Myers,
``Suffix arrays: A new method for on-line string searches,''
SIAM Journal on Computing 1993.27 (None) (Thanksgiving break) December 4 John Kececioglu Burkhardt and Kärkkäinen,
``Better filtering with gapped q-grams,''
CPM 2001.11 (None) (Out of town)
Date Speaker Talk January 23 (None) (Organizational meeting) 30 John Kececioglu Gramm, Niedermeier and Rossmanith,
``Exact solutions for Closest String and related problems,''
ISAAC 2001.February 6 John Kececioglu Gramm, Niedermeier and Rossmanith, continued. 13 (None) (Out of town) 20 Travis Wheeler Gusfield,
``Haplotyping as Perfect Phylogeny: conceptual framework and efficient solutions,''
RECOMB 2002.27 Travis Wheeler Gusfield, continued. March 6 (None) (Out of town) 13 Travis Wheeler Gusfield, continued. 20 (None) (Spring break) 27 John Kececioglu Discussion of the optimal discrete-function evaluation problem. April 3 Dean Starrett Hohl, Kurtz and Ohlebusch,
``Efficient multiple genome alignment,''
ISMB 2002.10 (None) (Attending RECOMB 2003 in Berlin) 17 Dean Starrett Hohl, Kurtz and Ohlebusch, continued. 24 Eagu Kim Leuker,
``Improved bounds on the average length of longest common subsequences,''
SODA 2003.
Date Speaker Talk June 5 (None) (Organizational meeting) 12 John Kececioglu Keich and Pevzner,
``Finding motifs in the twilight zone,''
RECOMB 2002.19 John Kececioglu Kececioglu,
``Finding optimal motifs by branch and bound,''
in preparation.26 John Kececioglu Kececioglu, continued. July 3 Travis Wheeler Rash and Gusfield,
``String barcoding: uncovering optimal virus signatures,''
RECOMB 2002.10 Eagu Kim Buhler,
``Provably sensitive indexing strategies for biosequence similarity search,''
RECOMB 2002.17 Dean Starrett Ben-Dor, Chor, Karp, and Yakhini,
``Discovering local structure in gene expression data: the order-preserving submatrix problem,''
RECOMB 2002.
Date Speaker Talk January 18 (None) (Organizational meeting) 25 John Kececioglu Crochemore, Landau and Ziv-Ukelson,
``A sub-quadratic sequence alignment algorithm for unrestricted cost matrices,''
SODA 2002.February 1 John Kececioglu Crochemore, Landau and Ziv-Ukelson, continued. 8 (None) (Cancelled) 15 Dean Starrett Peer and Shamir,
``Spectrum alignment: efficient resequencing by hybridization,''
ISMB 2000.22 Dean Starrett Peer and Shamir, continued. March 1 (None) (Cancelled) 8 Eagu Kim Kurtz, Ohlebusch, Schleiermacher, Stoye and Giegerich,
``Computation and visualization of degenerate repeats in complete genomes,''
ISMB 2000.15 (None) (Spring break) 22 Zhihong Zhang Marsan and Sagot,
``Extracting structured motifs using a suffix tree: algorithms and application to promoter consensus identification,''
RECOMB 2000.29 (None) (Cancelled) April 5 Travis Wheeler van Someren, Wessels and Reinders,
``Linear modeling of genetic networks from experimental data,''
ISMB 2000.12 Dean Starrett Gotoh,
``Optimal alignment between groups of sequences and its application to multiple sequence alignment,''
CABIOS 1993.19 (None) (Postponed due to RECOMB 2002) 26 Dean Starrett Gotoh, continued.
Date Speaker Talk August 31 (None) (Organizational meeting) September 7 John Kececioglu Karp, Stoughton and Yeung,
``Algorithms for choosing differential gene expression experiments,''
RECOMB 1999.14 John Kececioglu Karp, Stoughton and Yeung, continued. 21 Dean Starrett Sharan and Shamir,
``CLICK: A clustering algorithm with applications to gene expression analysis,''
ISMB 2000.28 Zhihong Zhang Ben-Dor, Friedman and Yakhini,
``Class discovery in gene expression data,''
RECOMB 2001.October 5 Eagu Kim Filkov, Skiena and Zhi,
``Analysis techniques for microarray time-series data,''
RECOMB 2001.12 (None) (Cancelled due to illness) 19 (None) (Cancelled due to conflict) 26 Travis Wheeler Vilo, Brazma, Jonassen, Robinson and Ukkonen,
``Mining for putative regulatory elements in the yeast genome using gene expression data,''
ISBM 2000.November 2 (None) (Cancelled due to midsemester crunch) 9 (None) (Cancelled due to ``Pizza with a Prof'') 16 John Kececioglu Discussion of research projects; handing out new papers. 30 John Kececioglu Navarro and Raffinot,
``Fast and simple character classes and bounded gaps pattern matching, with application to protein searching,''
RECOMB 2001.