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The Bioinformatics Journal Club provides a discussion forum for research articles from the premier journals and conferences in the field of computational biology.  The forum is open to all members of the Ohio University community.  Please email suggestions for discussion topics to welch@ohio.edu. 

Fall Semester 2013-14 Schedule 

• 4/23/13: 
  Systematic discovery of nonobvious human disease models through orthologous phenotypes
  K. L. McGary, T. J. Park, J. O. Woods, H. J. Cha, J. B. Wallingford, and E. M. Marcotte, PNAS, vol. 107, no. 14, pp. 6544–6549, Apr. 2010.
  Discussion leader:  Robert Schmidt
  PDF version
  Discussion questions
  
  
• 4/16/13:
  Genome-wide Epigenetic Data Facilitate Understanding of Disease Susceptibility Association Studies
  J Biol Chem. 2012 Sep 7;287(37):30932-40. doi: 10.1074/jbc.R112.352427. Epub 2012 Sep 5., Hardison RC.
  Discussion leader:  Rami Al-Ouran
  PDF version
  Discussion questions
  
  
• 4/9/13:
  California Ban on GloFish Ignites Debate Over Frankenfish
  Discussion leader:  Samantha Shaw
  Link to article
  PDF version
  Discussion questions
  
  
• 4/2/12: Bioinformatics Distinguished Lecture Series:  Dr. John Sanford, Cornell University
  Comprehensive Numerical Simulation as a Tool for Understanding Dynamic Genetic Systems 
  
  
• 3/26/13:
  The Next Step in Understanding Population Dynamics: Comprehensive Numerical Simulation
  John C. Sanford, Chase W. Nelson, The Next Step in Understanding Population Dynamics: Comprehensive Numerical Simulation, Studies in Population Genetics, ISBN: 978-953-51-0588-6
  Discussion leader:  Jeffrey Jones
  PDF version
  Discussion questions
  
  
• 3/19/13: 
  Faiz Rahman Seminar:
  "Two Decades of Adventures in Solid-State Electronics"
  1:30-2:30, Stocker 103
  
  
• 3/12/13:
  A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins
  Saul B. Needleman, Christian D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, Volume 48, Issue 3, 28 March 1970, Pages 443-453, ISSN 0022-2836, 10.1016/0022-2836(70)90057-4.
  Discussion leader:  Yichao Li
  PDF version
  Discussion questions
  
  
• 3/5/13:
  Spring Break
  
  
• 2/26/13: 
  Phenotype Prediction Using Regularized Regression on Genetic Data in the DREAM5 Systems Genetics B Challenge
  Discussion leader:  Ashwini Naik
  PDF version
  Discussion questions
  
  
• 2/19/13: 
  Join visiting lecturer Victor Jin, assistant professor of biomedial informatics at Ohio State University
  Linking bioinformatics data to cancer cells in Feb. 19 lecture
  
  
• 2/12/13:
  CONTACT PROF. WELCH TO OBTAIN THE RESEARCH ARTICLE AND DISCUSSION QUESTIONS.
  Discussion leader:  Dr. Welch
  
  
• 2/5/13: 
  CONTACT PROF. WELCH TO OBTAIN THE RESEARCH ARTICLE AND DISCUSSION QUESTIONS.
  Discussion leader:  Dr. Welch
  
  
• 1/29/13:
  How to Read a Scientific Article
  Discussion leader:  Krystine Garcia
  Link to article
  Discussion questions
  
  
• 1/22/13:
  A Report of the Curriculum Task Force of the ISCB Education Committee
  Discussion leader: Dr. Welch
  Link to article
  Discussion questions
  
  
• 1/15/13: 
  Planning and overview

• The journal club will discuss selected articles from the following collections:
  

DREAM Challenge Problems

NAR Databases annual issue

NAR Webserver annual issue

Official journals of the ISCB

Overview articles about bioinformatics

The ENCODE project

ISMB Bioinformatics Education page

• Other possible topics:
  

  Self-Assembling Molecules Offer New Clues on Life's Possible Origin
  

Mice Fall Short as Test Subjects for Humans' Deadly Ills

Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs

Transposable elements reveal a stem cell specific class of long noncoding RNAs

Rationally designed bidirection promoter improves the evolutionary stability of synthetic genetic circuits

Dusting off the Turing Test

Beyond Turing's Machines

PLoS Computational Biology: Core Facilities

 

Journal club papers (Fall Semester 2012-13, Tuesday 4:35 PM to 5:25 PM in Academic & Research Center 101)

1. 12/4/12:  Computational Approaches to Developmental Patterning
   Discussion leader:  Andy Kouse
   PDF version
   Journal Club Article Summary
   
   
2. 11/27/12: Cell Polarity:  Quantitative Modeling as a Tool in Cell Biology
   Discussion leader: Bill Broach
   Link to article
   PDF version
   Journal Club Article Summary
   
   
3. 11/20/12: Thanksgiving Break-No Meeting
   
   
4. 11/13/12:  No Meeting
   
   
5. 11/6/12:  Using Gene Expression Noise to Understand Gene Regulation
   Discussion leader:  Ashwini  Naik
   Link to article
   PDF version
   Journal Club Article Summary
   
   
6. 10/30/12:  Differential Gene and Transcript Expression Analysis of RNA-Seq Experiments with TopHat and Cufflinks 
   Discussion leader:  Jens Schmidt  
   PDF version
   Journal Club Article Summary
   
   
7. 10/23/12:  A Deep Sequencing Approach to Comparatively Analyze the Transcription of Lifecycle Stages of the Filarial Worm, Brugia malayi
   Discussion leader:  Rami Al-Ouran
   PDF version
   Journal Club Article Summary
   
   
8. 10/16/12:  Integrating Genomes
   Discussion leader:  Keith Gilland
   PDF version
9. Journal Club Article Summary
   
   
10. 10/9/12: ACLU challenges California DNA collection practice that police use to solve cold cases
    Discussion leader: Samantha Shaw
    Link to article
    Journal Club Article Summary
    
    
11. 10/2/12: National Bioeconomy Blueprint, April 2012
    Discussion leader: Robert Schmidt
    Link to article
    Journal Club Article Summary
    
    
12. 9/25/12: DNA and Computers -- A Marriage Made in Heaven
    Discussion leader: Dr. Lonnie Welch
    Link to article
    Journal Club Article Summary
    
    
    
13. 9/18/12: Website: http://www.iscb.org/iscb-careers
    Review the current listings on the 'job board' of the International Society for Computational Biology.  Find several job opportunities that seem interesting.  Print the listing for the job that most interests you and bring it to class.  Be prepared to describe the job and to tell why it interests you.
    Discussion leader: Dr. Lonnie Welch
    
    
14. 9/11/12: Computational Biologists: The Next Pharma Scientists?
    Discussion leader: Dr. Lonnie Welch
    Link to article
    Journal Club Article Summary
    
    
15. 9/4/12: Creativity at the interface
    Alberts B.
    Science. 2012 Apr 13;336(6078):131. PubMed PMID: 22499904
    Discussion leader: Dr. Lonnie Welch
    PDF version
    Journal Club Article Summary
    
    

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
   
   

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