Past Seasons

Fall 2007 season

Meeting time was Tuesday at 3:00 in 5130 Upson Hall.

• September 25: Csuros M, Holey JA, Rogozin IB. In search of lost introns. Bioinformatics. 2007 Jul 1;23(13):i87-96. Pubmed
  Presenter: Tomas Vinar

• October 2: Narlikar L, Hartemink AJ. Sequence features of DNA binding sites reveal structural class of associated transcription factor. Bioinformatics. 2006 Jan 15;22(2):157-63. Pubmed
  and
  Narlikar L, Gordan R, Hartemink AJ. Nucleosome Occupancy Information Improves de novo Motif Discovery. RECOMB 2007 Download
  We will mention also a third closely-related paper, but feel free to read only the two papers above:
  Narlikar L, Gordan R, Ohler U, Hartemink AJ. Informative priors based on transcription factor structural class improve de novo motif discovery. Bioinformatics. 2006 Jul 15;22(14):e384-92. Pubmed
  Presenter: Brona Brejova

• October 9: fall break

• October 16: Morozov AV, Siggia ED. Connecting protein structure with predictions of regulatory sites. Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7068-73. Pubmed
  Presenter: Kathryn Bushley

• October 23: Shim H, Keles S. Integrating quantitative information from ChIP-chip experiments into motif finding. Biostatistics. 2007 May 28; Pubmed
  Presenter: Patrick Ng

• October 30: cancelled due to CS colloqium

• November 6: Lunter G. Dog as an outgroup to human and mouse. PLoS Comput Biol. 2007 Apr 27;3(4):e74. Pubmed
  AND
  Cannarozzi G, Schneider A, Gonnet G. A phylogenomic study of human, dog, and mouse. PLoS Comput Biol. 2007 Jan 5;3(1):e2. Pubmed
  Presenter: Carolin Kosiol

• November 13: Eden E, Lipson D, Yogev S, Yakhini Z. Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol. 2007 Mar 23;3(3):e39. Pubmed
  If there is enough time, we may mention also
  Chen X, Hughes TR, Morris Q. RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics. 2007 Jul 1;23(13):i72-9. Pubmed
  Presenter: Uri Keich

• November 20: cancelled

• November 27: Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP. Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics. 2007 Jul 1;23(13):i19-28. Pubmed
  We will also mention a related work in gene finding:
  Ratsch G, Sonnenburg S, Srinivasan J, Witte H, Muller KR, Sommer RJ, Scholkopf B. Improving the Caenorhabditis elegans genome annotation using machine learning. PLoS Comput Biol. 2007 Feb 23;3(2):e20. Epub 2006 Dec 21. Pubmed
  Presenter: Tomas Vinar

Spring 2007 season

Meeting time was Wednesday, 2:30pm, in Upson 4135.

• June 27: Margulies EH et al.: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
  Pubmed
  Presenter: Tomas Vinar

• June 20: Zhang J, Jiang B, Li M, Tromp J, Zhang X, Zhang MQ. Computing exact P-values for DNA motifs. Bioinformatics. 2007 Mar 1;23(5):531-7. Epub 2007 Jan 18. Pubmed
  Relevant background can be found in these papers: 1, 2, 3, 4
  Presenter: Uri Keich

• June 13: Shane T. Jensen, X. Shirley Liu, Qing Zhou and Jun S. Liu. Computational Discovery of Gene Regulatory Binding Motifs: A Bayesian Perspective. Statist. Sci. Volume 19, Number 1 (2004), 188-204. (We will cover mostly section 4 of the paper) Download
  and
  Friberg M, von Rohr P, Gonnet G. Scoring functions for transcription factor binding site prediction. BMC Bioinformatics. 2005 Apr 4;6:84. Pubmed
  Presenter: Patrick Ng

• June 6: Li N, Tompa M. Analysis of computational approaches for motif discovery. Algorithms Mol Biol. 2006 May 19;1:8 Pubmed
  Presenter: Brona Brejova

• May 23: Csuros M. Maximum-scoring segment sets. IEEE/ACM Trans Comput Biol Bioinform. 2004 Oct-Dec;1(4):139-50. Pubmed
  Presenter: Tomas Vinar

• April 25: Lazareva-Ulitsky B, Diemer K, Thomas PD. On the quality of tree-based protein classification. Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12. Pubmed
  Presenter: Uri Keich

• April 4: Flannick J, Batzoglou S. Using multiple alignments to improve seeded local alignment algorithms. Nucleic Acids Res. 2005 Aug 12;33(14):4563-77. Print 2005. Pubmed
  Presenter: Brona Brejova

• March 28: Rastas P, Koivisto M, Mannila H and Ukkonen E: A Hidden Markov Technique for Haplotype Reconstruction. 5th Workshop on Algorithms in Bioinformatics - WABI 2005. Springer
  Presenter: Patrick Ng

• March 7: Schultz AK, Zhang M, Leitner T, Kuiken C, Korber B, Morgenstern B, Stanke M. A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes. BMC Bioinformatics. 2006 May 22;7:265. Pubmed
  Presenter: Brona Brejova

Fall 2006 season

Meeting time was Thursday, 3:00pm, in Upson 4135.

• October 5: Chindelevitch L, Li Z, Blais E, Blanchette M. On the inference of parsimonious indel evolutionary scenarios. J Bioinform Comput Biol. 2006 Jun;4(3):721-44. Pubmed Download
  Presenter: Brona Brejova

• October 12: Dewey CN, Huggins PM, Woods K, Sturmfels B, Pachter L. Parametric alignment of Drosophila genomes. PLoS Comput Biol. 2006 Jun 23;2(6):e73. Pubmed
  Presenter: Tomas Vinar

• October 19: Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, Wang JP, Widom J. A genomic code for nucleosome positioning. Nature. 2006 Aug 17;442(7104):772-8. Pubmed
  Presenter: Uri Keich

• October 26: Blanchette M, Bataille AR, Chen X, Poitras C, Laganiere J, Lefebvre C, Deblois G, Giguere V, Ferretti V, Bergeron D, Coulombe B, Robert F. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res. 2006 May;16(5):656-68. Pubmed
  Presenter: Niranjan Nagarajan

• November 2: Jones NC, Pevzner PA. Comparative genomics reveals unusually long motifs in mammalian genomes. Bioinformatics. 2006 Jul 15;22(14):e236-42. Pubmed
  Presenter: Patrick Ng

• November 9: Djordjevic M, Sengupta AM, Shraiman BI. A biophysical approach to transcription factor binding site discovery. Genome Res. 2003 Nov;13(11):2381-90 Pubmed
  Presenter: Ravikant Dintyala

• November 16: Redelings BD, Suchard MA. Joint Bayesian estimation of alignment and phylogeny. Systematic Biology. 2005 Jun;54(3):401-18. Pubmed Download
  and
  Lunter G, Miklos I, Drummond A, Jensen JL, Hein J. Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics. 2005 Apr 1;6:83. Pubmed
  Presenter: Adam Siepel

• November 30: Itzkovitz S, Tlusty T, Alon U.: Coding limits on the number of transcription factors. BMC Genomics. 2006 Sep 19;7:239.
  Presenter: Chris Myers