Sequence Analysis Journal Club

Organizers: Uri Keich, Tomas Vinar, Brona Brejova

Mailing list: SEQUENCE-ANALYSIS-L, subscribe at http://www.cit.cornell.edu/computer/elist/lyris/join.html

This journal club will focus on recent papers on all aspects of biological sequence analysis, including but not restricted to papers presenting novel algorithmic, machine learning, and probabilistic methods in sequence analysis, as well as papers presenting new problems in sequence analysis. We hope that this journal club will draw on experience of participants with variety of backgrounds, and therefore we will try to make sure that the presentations will explain necessary background as needed.

Past Seasons

Schedule for Spring 2008

We will meet biweekly on Friday at 1:30 in Upson 5126, starting on February 22

Note: Adam Siepel is teaching a related seminar course BTRY 720: Topics in Computational Genomics http://compgen.bscb.cornell.edu/~acs/btry720.html

May 16: TBA
Presenter: Tomas Vinar

Past meetings

February 22: Jenkins P., Lyngsø R.B., Hein J. How Many Transcripts Does It Take to Reconstruct the Splice Graph? WABI 2006: 103-114 Download
Presenter: Brona Brejova
March 28: Oliver Bembom, Sunduz Keles, and Mark J. van der Laan Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo Stat Appl Genet Mol Biol. 2007 Download
Presenter: Uri Keich
April 11: Habib N, Kaplan T, Margalit H, Friedman N. A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval. PLoS Computational Biology 2008 4(2): e1000010 Download
Presenter: Patrick Ng

Suggested papers

The papers and categories are listed in no particular order. Feel free to suggest new papers.

Sequence alignment

Lunter G. Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes. Bioinformatics. 2007 Jul 1;23(13):i289-96. Pubmed (T&B)

Sheetlin S, Park Y, Spouge JL. The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment. Nucleic Acids Res. 2005 Sep 6;33(15):4987-94. Pubmed (U)

Kantorovitz MR, Robinson GE, Sinha S. A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics. 2007 Jul 1;23(13):i249-55. Pubmed (U)

Mak D, Gelfand Y, Benson G. Indel seeds for homology search. Bioinformatics. 2006 Jul 15;22(14):e341-9. Pubmed (T&B)

Phuong TM, Do CB, Edgar RC, Batzoglou S. Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Res. 2006;34(20):5932-42. Pubmed
Raphael B, Zhi D, Tang H, Pevzner P. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res. 2004 Nov;14(11):2336-46. Pubmed (T&B)

Evolution

Hui Chen and Mathieu Blanchette Detecting non-coding selective pressure in coding regions. BMC Evolutionary Biology 2007 Feb 8;7 Suppl 1:S9. Pubmed (U)

Motifs and Regulation

Kaplan T, Friedman N, Margalit H. Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput Biol. 2005 Jun;1(1) Pubmed

Ofran Y, Mysore V, Rost B. Prediction of DNA-binding residues from sequence. Bioinformatics. 2007 Jul 1;23(13):i347-53. Pubmed (U)

Segal L, Lapidot M, Solan Z, Ruppin E, Pilpel Y, Horn D. Nucleotide variation of regulatory motifs may lead to distinct expression patterns. Bioinformatics. 2007 Jul 1;23(13):i440-9. Pubmed (U)

Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12457-62. Pubmed (U)

Xu W, Aparicio JG, Aparicio OM, Tavare S. Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics. 2006 Oct 26;7:276. Pubmed (U)

Fratkin E, Naughton BT, Brutlag DL, Batzoglou S. Motifcut: regulatory motifs finding with maximum density subgraphs. Bioinformatics. 2006 Jul 15;22(14):e150-7. Pubmed (T&B)

Jensen ST, Shen L, Liu JS. Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes. Bioinformatics. 2005 Oct 15;21(20):3832-9. Pubmed (U)

Sinha S. On counting position weight matrix matches in a sequence, with application to discriminative motif finding. Bioinformatics. 2006 Jul 15;22(14):e454-63 Pubmed (U)

Mustonen V, Lassig M. Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies. Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15936-41 Pubmed (U)

Alternative splicing

Jenkins P., Lyngsø R.B., Hein J. How Many Transcripts Does It Take to Reconstruct the Splice Graph? WABI 2006: 103-114 Download (T&B)

Allen JE, Salzberg SL. A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. Algorithms Mol Biol. 2006 Aug 25;1:14. Pubmed (T&B)

Gene finding

Krause L, Diaz NN, Bartels D, Edwards RA, Puhler A, Rohwer F, Meyer F, Stoye J. Finding novel genes in bacterial communities isolated from the environment. Bioinformatics. 2006 Jul 15;22(14):e281-9. Pubmed (T&B)

Other

Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet. 2007 Oct;39(10):1235-44. Pubmed