Bioinformatics at Ohio University
Bioinformatics Journal Club

2014_fallThe 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


Click here to email the webmaster, Yichao Li


Fall Semester 2014-2015 Schedule
Time: 4:35 pm - 5:55 pm
Location: ARC 314

  • Topics: Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
    Discussion Leader: Kenneth Wheeler
    Gire, S. K., Goba, a., Andersen, K. G., Sealfon, R. S. G., Park, D. J., Kanneh, L., … Sabeti, P. C. (2014). Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science, 1369. doi:10.1126/science.1259657
    Date:10-21-2014
    PDF version
    Link to article 1
    Link to article 2
    Discussion Questions

  • Topics: A genome-wide SNP-association study confirms a sequence variant (g.66493737C>T) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses
    Discussion Leader: Josiah Sifford
    Hill, E. W., Mcgivney, B. A., Gu, J., Whiston, R., & Machugh, D. E. (2010). A genome-wide SNP-association study confirms a sequence variant ( g . 66493737C > T ) in the equine myostatin ( MSTN ) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses A genome-wide SNP-association study confirms a sequence variant ( g . 66493737C > T ) in the equine myostatin ( MSTN ) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses, 552(October).
    Date: 10-28-2014
    Link to article
    Discussion Questions

  • Topics: De Novo Genome Assembly: What Every Biologist Should Know
    Discussion Leader: Yichao Li
    Baker, Monya. "De Novo Genome Assembly: What Every Biologist Should Know: As More Genomes Are Assembled From Scratch, Scientists Are Struggling To Assess And Improve Their Quality." Nature Methods 4 (2012): 333. Academic OneFile. Web. 15 Oct. 2014.
    Date: 11-4-2014
    PDF version
    Discussion Questions

  • Date: 11-11-2014 NO CLASS!

  • Topics: Motif discovery and transcription factor binding sites before and after the next-generation sequencing era
    Discussion Leader: Rami
    Zambelli, F., Pesole, G., & Pavesi, G. (2013). Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. Briefings in Bioinformatics, 14(2), 225–37. doi:10.1093/bib/bbs016
    Date: 11-18-2014
    PDF version
    Discussion Questions

  • Topics: Reproductive medicine: The power of three
    Discussion Leader: Morgan Kohls
    Callaway, Ewen. "Reproductive Medicine: The Power Of Three." Nature 509.7501 (2014): 414-417. MEDLINE with Full Text. Web. 14 Oct. 2014.
    Date: 11-25-2014
    PDF Version
    Discussion Questions

  • Topics: Policy: NIH to balance sex in cell and animal studies
    Discussion Leader: Mary Gemmel
    Clayton, Janine A, and Francis S Collins. "Policy: NIH To Balance Sex In Cell And Animal Studies." Nature 509.7500 (2014): 282-283. MEDLINE with Full Text. Web. 15 Oct. 2014.
    Date: 12-2-2014
    Link to article
    Related Reading1
    Related Reading2
    Related Reading3
    Related Reading4
    Youtube Video


  • Past Discussions

  • Topics: Wikipedia Usage Estimates Prevalence of Influenza-Like Illness in the United States in Near Real-Time
    Discussion Leader: Charlotte Klimovich
    McIver DJ, Brownstein JS (2014) Wikipedia Usage Estimates Prevalence of Influenza-Like Illness in the United States in Near Real-Time. PLoS Comput Biol 10(4): e1003581. doi:10.1371/journal.pcbi.1003581
    Date: 10-14-2014
    PDF version
    Discussion Questions

  • Date: 10-7-2014
    Topics: Darwin and the women
    Discussion Leader: Sarah Nestor
    PDF Version
    Discussion Questions

  • Date:9-30-2014
    Topics: Microbiome science needs a healthy dose of scepticism
    Discussion Leader: Max Rego
    PDF Version
    Youtube Video

    Discussion questions

  • Date: 9-23-2014
    Topcis: Chimeric antigen recceptor-modified T celss in chromic lymphoid leukemia

    Discussion Leader: Samantha Shaw
    PDF version
    Discussion questions

  • Date: 9-16-2014
    Topics: The Fault in our DNA
    Discussion Leader: Samantha Shaw
    Article 1
    Article 2
    Discussion Questions

  • Date: 9-9-2014
    Topics: Bioinformatics careers
    Discussion Leader: Krystine Garcia
    Link to article
    Discussion Questions



  • Date: 9-2-2014
    Topcis: Explain Bioinformatics
    Discussion Leader: Dr. Welch
    Article1
    Article2
    Discussion Questions

  • Date: TBD
    Topics: Writing Funding Proposals
    Discussion Leader: Rami

  • Date: TBD
    Topics: The basics of the prokaryotes
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: The rise of regulatory RNA
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: Technique - $1000 genome
    Discussion Leader: TBD
    PDF version

  • Date: TBD
    Topics: Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: Mobile Genomics
    Discussion Leader:TBD
    Link to article

  • Date: TBD
    Topics: A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
    Discussion Leader: Rami
    PDF Version

  • Date: TBD
    Topics: A draft map of the human proteome
    Discussion Leader: TBD
    PDF Version

  • Date: TBD
    Topics: Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance
    Discussion Leader: TBD
    PDF Version

  • Date: TBD
    Topics: Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: A Statistical Framework for Joint eQTL Analysis in Multiple Tissues
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: Probing DNA shape and methylation state on a genomic scale with DNase I
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: Promoter sequence determines the relationship between expression level and noise.
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay.
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: Linking the signaling cascades and dynamic regulatory networks controlling stress responses.
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: DNase I sensitivity QTLs are a major determinant of human expression variation.
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: "Guilt by association" is the exception rather than the rule in gene networks.
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: An expansive human regulatory lexicon encoded in transcription factor footprints.
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: ADAM: Genomics Formats and Processing Patterns for Cloud Scale Computing
    Discussion Leader: TBD
    PDF Version

  • Date: TBD
    Topics: CLP1 Founder Mutation Links tRNA Splicing and Maturation to Cerebellar Development and Neurodegeneration
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: Human CLP1 Mutations Alter tRNA Biogenesis, Affecting Both Peripheral and Central Nervous System Function
    Discussion Leader: TBD
    Link to article

  • Date: TBD
    Topics: Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies
    Discussion Leader: Dr. Welch
    PDF version

  • Date: TBD
    Topics: Barchart
    Discussion Leader: TBD
    Article 1 PDF
    Article 2 PDF
    Article 3 Link
    Article 4 Link

  • Date: TBD
    Topics: The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
    Discussion Leader: TBD
    Link to Article

  • Date: TBD
    Topics: Noninvasive in vivo monitoring of tissue-specific global gene expression in humans
    Discussion Leader: TBD
    PDF version



Spring Semester 2013-2014 Schedule
Tuesdays 1:30-2:30 PM
Grover Center W113

          Date: 4-30-2014 NO CLASS

  • Date: 4-22-2014
    Topics: Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
    Discussion Leader: Rami

    PDF version
    Discussion questions
  • 3-11-2014
    Topics: Proceed with Caution
    Discussion leader:Robert Schmidt
    Link to article
    Discussion questions

  • 2-25-2014
    Bioinformatics Distinguished Lecture
    1:30 pm - 2:30 pm, Baker University Center 231
    Topic: Churchill: A Cloud-Enabled, Ultra-Fast Computational Approach for the Discovery of Human Genetic Variation
    Peter White, Ph.D.
    Principal Investigator, Center for Microbial Pathogenesis
    Abstract
    Biosketch

  • 2-18-2014
    Topics: Journal article review
    Discussion Leader: Yichao Li

    Article is not available electronically. To obtain the article contact Yichao Li at : yl079811@ohio.edu
    Discussion questions:
    1.  Complete the Template for Taking Notes on Research Articles, link
    2.  Provide your opinion on how well the article address the publication criteria of the PLOS One journal, link
    3.  Your recommendation regarding publication of the article in the PLOS One journal. Choose one of the following: reject, accept after major version, accept after minor revision, accept as it is. Provide the rationale for your selection.

Fall Semester 2013-14 Schedule
Tuesdays 4:35-5:25 PM
ARC 321

  • TBD
    High-resolution haplotype structure in the human genome
    Discussion leader: Yichao Li
    PDF version
    Discussion questions

  • TBD
    Computing: Out of the Hood
    Discussion leader: TBD
    Link to article
    Discussion questions

  • TBD
    Are We Alone in the Universe?
    Discussion leader: Nestor Sarah
    Link to Article
    Discussion questions

  • TBD
    Human-chimp genome comparison (and other primates)
    Discussion leader: TBD
    PDF version
    Discussion questions

  • TBD
    Topics:
    Proceed with Caution
    Discussion leader:Robert Schmidt
    Link to article
    Discussion questions
  • TBD
    Topics: Artificial Neural Networks

    Discussion leader: Natalie Hanson
    PDF version
    Discussion questions
  • TBD
    Topics: DNA collected at arrest

    Discussion leader: Sam Shaw
    PDF version
    Discussion questions
  • TBD
    Topics: HxNx Predictions

    Discussion leader: Travis Johnson
    PDF version
    Discussion questions
  • 12-3-13
    What is a support vector machine?

    Noble. WS, Nat Biotechnol. 2006 Dec;24(12):1565-7.
    Discussion leader: Al-Ouran Rami
    PDF version
    Discussion questions

  • 11-19-13
    Watch movie: GATTACA

    Discussion leader: David Parisi
    Discussion questions

  • 11-12-13
    Watch movie : GATTACA

    Discussion leader: David Parisi
    Discussion questions

  • 11-5-13
    Watch movie : GATTACA

    Discussion leader: David Parisi

  • 10-29-13
    Reconstructing Population-Level History

    Discussion leader: Yichao Li
    Coursera online course : https://www.coursera.org/course/molevol

    DO ONE OF THE FOLLOWING:
    1.       Attend the Bioinformatics Distinguished Lecture on Monday, October 28th. And write a one paragraph critique of the research presented.
    Location: ARC 106
    Time: Monday, October 28, 2pm - 3pm
    Abstract
    Biosketch

    2.       Read the following article and complete the reading template.
    A consensus tree approach for reconstructing human evolutionary history and detecting population substructure.
    Tsai MC, Blelloch G, Ravi R, Schwartz R.
    PDF version
    Discussion questions

  • 10-22-13
    Genome-wide compatible SNP intervals and their properties

    Wang, J., Hill, C., Moore, K. J., Hill, C., Pardo-manual, F., Hill, C., … Mcmillan, L. (n.d.).
    Discussion leader: Jones Jeffrey
    PDF version
    Discussion questions

  • 10-15-13
    How to Read a Scientific Article

    Discussion leader: Krystine Garcia
    Link to article
    Discussion Questions


  • 10-8-13
    Bioethics Issues Pertaining to the Genetic Engineering of Humanity

    Discussion Leader: Xiaoyou Liang

    Complete one of the activities from the list below.

    1. Attend the Bioethics panel discussion and write a 1 paragraph summary of three key points made during the discussion.
    Panel discussion: Can we safely and successfully re-engineer humanity?
    Panelists: Dr. Chris Hook (Mayo Medical School), Dr. Scott Carson (Dept of Philosophy, Ohio University), Attorney Scott Robe (Robe Law Office, Athens)
    Location: WOUB Studio A, RTV Building
    Time: Wednesday, Oct. 2, Noon-1:30pm (arrive before 11:45am)

    2. Attend the Bioethics lecture and write a 1 paragraph critique of the key ideas presented.
    Lecture: The History of American Eugenics -  Lessons for the Second Genetic Century
    Speaker: Dr. Chris Hook (Mayo Clinic)
    Location: Baker Ballroom
    Time: Wednesday, Oct. 2, 8-9:30pm

    3. Read the following article and answer the discussion questions provided below.
    Miller PS, Levine RL. Avoiding genetic genocide: understanding good intentions and eugenics in the complex dialogue between the medical and disability communities. Genet Med. 2013 Feb;15(2):95-102. doi: 10.1038/gim.2012.102. Epub 2012 Aug 16. PubMed PMID: 22899092; PubMed Central PMCID: PMC3566260.
    PDF version
    Discussion questions
Spring Semester 2012-13 Schedule
Tuesdays 1:30-2:30 PM
Stocker 103
  • 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
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. HolderSerita M. NelesenJiaye 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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