Bioinformatics at Ohio University
Bioinformatics Journal Club

The Bioinformatics Journal Club will meet weekly to discuss articles published in 2012 Bioinformatics journals (PLOS Computational Biology, Bioinformatics (Oxford University Press), BMC Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics).  Each student will lead one discussion.  Course credit may be obtained by registering for Prof. Welch's sections of CS690 or CS490.

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Journal club papers (Summer Quarter 2012)

  1. Predicting RNA-Protein Interactions Using Only Sequence Information
    Usha K Muppirala, Vasant G Honavar, and Drena Dobbs.
    BMC Bioinformatics 2011, 12:489 doi:10.1186/1471-2105-12-489
    Discussion leader:  Ashwini Naik
    PDF version
    Link to paper

Journal club papers (Spring Quarter 2012, Wednesday 11:10-12:00 PM in Academic & Research Center 212)

  1. 6/6/2012:  Inferring the Number of Contributors to Mixed DNA Profiles
    David R. Paoletti, Dan E. Krane, Michael L. Raymer, Travis E. Doom.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 1, pp. 113-122, Jan.-Feb. 2012, doi:10.1109/TCBB.2011.76
    Discussion leader:  Jens Schmidt
    Link to paper
    PDF version

  2. 5/30/12: InFiRe - a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes
    Olga Shevchuk, Louisa Roselius, Gabriele Günther, Johannes Klein, Dieter Jahn, Michael Steinert, and Richard Münch.
    Bioinformatics (2012) 28(3): 306-310 first published online December 6, 2011
    Discussion leader:  William Broach
    Link to paper
    PDF version
    Journal Club Article Summary

  3. 5/23/12:  Epigenetic priors for identifying active transcription factor binding sites.
    Cuellar-Partida G, Buske FA, McLeay RC, Whitington T, Noble WS, Bailey TL.
    Bioinformatics. 2012 Jan 1;28(1):56-62. Epub 2011 Nov 8.
    Discussion leader:  Rami Al-Ouran
    Link to paper
    PDF version
    Journal Club Article Summary

  4. 5/16/2012:  Great Lakes Bioinformatics(GLBIO) Conference-No Journal Club Meeting

  5. 5/9/12:  TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.
    Seetin MG, Mathews DH.
    Bioinformatics. 2012 Mar 15;28(6):792-8. Epub 2012 Jan 27.
    Discussion leader:  Andrew Kouse
    Link to paper
    Journal Club Article Summary

  6. 5/2/2012:  "Guilt by Association'' Is the Exception Rather Than the Rule in Gene Networks
    Jesse Gillis, Paul Pavlidis.
    PLoS Computational Biology, March, 2012.
    Discussion leader:  Jeffrey Jones
    PDF version
    Journal Club Article Summary

  7. 4/25/2012:  RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction
    Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler, Manolis Kellis.
    Nucleic Acids Research, January 28, 2012.
    Discussion leader:  Joshua Welch
    Link to paper
    PDF version
    Journal Club Article Summary

  8. 4/18/2012:  SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees
     Kevin Liu, Tandy J. Warnow, Tandy J. Warnow,  Mark T. Holder, Serita M. Nelesen, Jiaye Yu, Alexandros P. Stamatakis, C. Randal Linder.
    Syst Biol (2012)61(1): 90-106 doi:10.1093/sysbio/syr095
    Discussion leader:  Eric Salomaki
    Link to paper
    PDF version
    Journal Club Article Summary

  9. 4/11/2012:  SSuMMo: rapid analysis, comparison and visualization of microbial communities
    Leach et al. 
    Bioinformatics (2012) 28 (5): 679-686.
    Link to paper
    PDF  version
    Journal Club Article Summary

  10. 4/4/2012:De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae.
    Chen MJ, Chou LC, Hsieh TT, Lee DD, Liu KW, Yu CY, Oyang YJ, Tsai HK, Chen CY. 
    Bioinformatics. 2012 Mar 1;28(5):701-8. Epub 2012 Jan 11. PubMed PMID: 22238267.
    Link to paper
    PDF version
    Journal Club Article Summary

  11. 3/28/2012:  No Article

Journal club papers (Winter Quarter 2012, Monday 2:10-3:00 PM in Academic & Research Center 315)

  1. 3/5/2012: The Lucretian swerve: the biological basis of human behavior and the criminal justice system.
    Cashmore AR.
    Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4499-504. Epub 2010 Feb 8.
    Link to paper
    PDF version
    Journal Club Article Summary

  2. 2/27/2012: Principal network analysis: identification of subnetworks representing major dynamics using gene expression data.
     Kim Y, Kim TK, Kim Y, Yoo J, You S, Lee I, Carlson G, Hood L, Choi S, Hwang D.
    Bioinformatics. 2011 Feb 1;27(3):391-8. Epub 2010 Dec 30. PubMed PMID: 21193522; PubMed Central PMCID: PMCID: PMC3031040.
    Link to paper
    PDF version
    Journal Club Article Summary

  3. 2/20/2012:  An Eulerian path approach to DNA fragment assembly.
    Pevzner, P. A., Tang, H. & Waterman, M. S.
    Proc. Natl Acad. Sci. USA98, 9748–9753 (2001).PubMed PMID: 22174245.
    Link to paper
    PDF version
    Journal Club Article Summary

  4. 2/13/2012: Next-generation transcriptome assembly
    Jeffrey A. Martin and Zhong Wang
    Nat     Rev. Genet. 2011 Sep 7;12(10):671-82. doi: 10.1038/nrg3068. Review. PubMed PMID: 21897427.
    Link to paper
    PDF version
    Journal Club Article Summary

  5. 2/6/2012:  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
    Langmead B, Trapnell C, Pop M, Salzberg SL.
    Genome Biol. 2009;10(3):R25. Epub 2009 Mar 4. PubMed PMID: 1926117
    Link to paper
    PDF version
    Journal Club Article Summary

  6. 1/30/2012:  Intro to data production and analysis methods: A user's guide to the encyclopedia of DNA elements (ENCODE).
    ENCODE Project Consortium, Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE.
    PLoS Biol. 2011 Apr;9(4):e1001046. Epub 2011 Apr 19. PubMed PMID: 21526222; PubMed Central PMCID:PMC3079585.
    Link to paper
    PDF Version
    Journal Club Article Summary

  7. 1/23/2012: Transcriptional regulation:  Transcriptional regulatory elements in the human genome
    Maston GA, Evans SK, Green MR.
    Annu Rev Genomics Hum Genet. 2006;7:29-59. Review. PubMed PMID:16719718.
    Link to paper
    PDF version
    Journal Club Article Summary

  8. 1/9/2012:  What is a gene, post-ENCODE? History and updated definition.
    Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M.
    Genome Res. 2007 Jun;17(6):669-81. Review. PubMed PMID: 17567988.
    Link to paper
    PDF version
Journal club papers (Fall Quarter 2011-2012, Thursday 2:10-3:00 PM in Academic & Research Center 314 )
  1. 11/10/2011:  The environments of our Hominin ancestors, tool-usage, and scenario visualization
    Department of Philosophy, Saint Louis University, 3800 Lindell Blvd., P.O. Box 56907, St. Louis, MO 63156-0907, USA
    Biology and Philosophy (2006) 21:95–117 DOI 10.1007/s10539-005-0443-z
    Discussion leader: Dr. Scott Carson, Professor of Philosophy at OU
    Link to paper

  2. 11/3/2011: No class

  3. 10/27/2011: LincRNAs act in the circuitry controlling pluripotency and differentiation.
    Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES. Nature. 2011 Aug 28;477(7364):295-300. doi: 10.1038/nature10398.
    Discussion leader:  Josh Welch
    Link to paper

  4. 10/20/2011: REVIEW PAPER FOR JOURNAL EDITOR. ELECTRONIC COPY NOT AVAILABLE. OBTAIN PAPER FROM RAMI (ra102506@ohio.edu).

  5. 10/13/2011: REVIEW PAPER FOR JOURNAL EDITOR. ELECTRONIC COPY NOT AVAILABLE. OBTAIN PAPER FROM RAMI (ra102506@ohio.edu).

  6. 10/6/2011:  Synthetic chromosome arms function in yeast and generate phenotypic diversity by design.
    Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD. Nature. 2011 Sep 14. doi: 10.1038/nature10403
    Discussion leader: Jason Yerardi
    Link to paper

  7. 9/29/2011:  Systematic discovery of nonobvious human disease models through orthologous phenotypes.
    McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM.
    Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6544-9. Epub 2010 Mar 22.
    Link to paper

  8. 9/22/2011:  Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.
    Catania F, Lynch M.
    BMC Evol Biol. 2010 May 4;10:129.
    Link to paper

  9. 9/15/2011:  Rate, molecular spectrum, and consequences of human mutation.
    Lynch M.
    Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):961-8
    Discussion leader: Lonnie Welch
    Link to paper

Journal club papers (Summer Quarter 2011)

  1. The Genomic HyperBrowser: inferential genomics at the sequence level.
    Sandve GK et al.
    Genome Biol. 2010;11(12):R121.
    Link to paper

  2. Making sense of cancer genomic data.
    Chin L, Hahn WC, Getz G, Meyerson M.
    Genes Dev. 2011 Mar 15;25(6):534-55. Review.
    Link to paper

  3. A vision for the future of genomics research.
    Collins et al.; US National Human Genome Research Institute.
    Nature. 2003 Apr 24;422(6934):835-47.
    Link to paper

Spring quarter 2011
Meeting times and location: Tuesdays 9:10am-10:00pm, Stocker Center 326.

Journal club papers (Spring 2011):

  1. April-5-2011
    A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
    Marcais G and  Kingsford C.
    Bioinformatics. 2011; 27 (6): 764-770.
    Discussion leader: Lee Nau.
    Link to paper

  2. April-12-2011
    Computational inference of grammars for larger-than-gene structures from annotated gene sequences.
    Tsafnat G, Schaeffer J, Clayphan A, Iredell JR, Partridge SR, Coiera E.
    Bioinformatics. 2011 Mar 15;27(6):791-6.
    Discussion leader: Xiaoyu Liang.
    Link to paper

  3. April-19-2011
    Genome evolution and adaptation in a long-term experiment with Escherichia coli.
    Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF.
    Nature. 2009 Oct 29;461(7268):1243-7.
    Discussion leader: Dr.Lonnie Welch
    Link to paper

  4. April-26-2011
    Mapping and analysis of chromatin state dynamics in nine human cell types.
    Ernst et al.
    Nature. 2011 doi:10.1038/nature09906.
    Discussion leader: Josh Welch.
    Link to paper

  5. May-3-2011
    NO JOURNAL CLUB – ATTEND THE GREAT LAKES BIOINFORMATICS CONFERENCE

  6. May-10-2011
    A catalog of reference genomes from the human microbiome.
    Nelson KE. et al.
    Science. 2010 May 21;328(5981):994-9.
    Discussion leader: Kevin Plis.
    Link to paper

  7. May-17-2011
    The cancer genome.
    Stratton MR, Campbell PJ, Futreal PA.
    Nature. 2009 Apr 9;458(7239):719-24.
    Discussion leader: Xun Zhao.
    Link to paper

  8. May-24-2011
    Learning a prior on regulatory potential from eQTL data.
    Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe'er D, Koller D.
    PLoS Genet. 2009 Jan;5(1):e1000358.
    Discussion leader: Xiaoyu Liang.
    Link to paper

  9. May-31-2011
    A User's Guide to the Encyclopedia of DNA Elements (ENCODE).
    The ENCODE Project Consortium.
    PLoS Biol. 2011 Apr;9(4):e1001046.
    Discussion leader: Dr.Lonnie Welch.
    Link to paper



Winter quarter 2011
Meeting times and location: Tuesdays 3:10pm-4:00pm, Grover Center W109.

Journal club papers (Winter 2011):

  1. January-11-2011
    Overlapping codes within protein-coding sequences.
    Itzkovitz S, Hodis E, Segal E.
    Genome Res. 2010 Nov;20(11):1582-9.
    Discussion leader: Dr.Lonnie Welch.
    Link to paper

  2. January-18-2011
    TRELLIS+: an effective approach for indexing genome-scale sequences using suffix trees.
    Phoophakdee B, Zaki MJ.
    Pac Symp Biocomput. 2008:90-101.
    Discussion leader: Dr.Frank Drews.
    Link to paper

  3. January-25-2011
    PriorsEditor: a tool for the creation and use of positional priors in motif discovery.
    Klepper K, Drablos F.
    Bioinformatics. 2010 Sep 1;26(17):2195-7.
    Discussion leader: Xiaoyu Liang.
    Link to paper

  4. February-8-2011
    Occurrence probability of structured motifs in random sequences.
    Robin S, Daudin JJ, Richard H, Sagot MF, Schbath S.
    J Comput Biol. 2002;9(6):761-73.
    Discussion leader: Rami Al-ouran.
    Link to paper

  5. February-15-2011
    Human population structure detection via multilocus genotype clustering.
    Gao X, Starmer J.
    BMC Genet. 2007 Jun 25;8:34.
    Discussion leader: Richard Wolfe.
    Link to paper

  6. February-22-2011
    Accurate phylogenetic classification of variable-length DNA fragments.
    McHardy AC, Martín HG, Tsirigos A, Hugenholtz P, Rigoutsos I.
    Nature Methods. 2007 Jan;4(1):63-72.
    Discussion Leader: Kevin Plis
    Link to paper

  7. March-1-2011
    Learning from failures: testing broad taxonomic hypotheses about plant naturalization.
    Diez JM, Williams PA, Randall RP, Sullivan JJ, Hulme PE, Duncan RP.
    Ecol Lett. 2009 Nov;12(11):1174-83
    Discussion Leader: Keith Gilland
    Link to paper

  8. March-8-2011
    Building trees of algae: Some advances in phylogenetic and evolutionary analysis.
    Verbruggen H, Theriot EC.
    Eur. J. Phycol. 2008;43(3):229–252
    Discussion Leader: Eric Salomaki
    Link to paper
 
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