Bioinformatics at Ohio University

Journal Club

 

2015Fall_smallThe 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

Spring Semester 2015-2016 Schedule
Time: 1:30 pm - 2:10 pm
Location: ARC 159

Article Title: Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus within Silico Modeling for Blood-Based Diagnostic Development
Discussion Leader: Yichao Li
Date: 4-19-2016
Gennady Margolin, Hanna M. Petrykowska, Nader Jameel, Daphne W. Bell, Alice C. Young, Laura Elnitski, Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development, The Journal of Molecular Diagnostics, Volume 18, Issue 2, March 2016, Pages 283-298, ISSN 1525-1578, http://dx.doi.org/10.1016/j.jmoldx.2015.11.004.
Link to the article
Discussion Questions

 

Article Title: Rate, molecular spectrum, and consequences of human mutation.
Discussion Leader: Dr. Welch
Date: 1-26-2016
Lynch M. Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):961-8
PDF version
Discussion Questions

Article Title: The Lucretian swerve: the biological basis of human behavior and the criminal justice system.
Discussion Leader: Dr. Welch
Date: 2-2-2016
Cashmore AR. The Lucretian swerve: the biological basis of human behavior and the criminal justice system. Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4499-504.
PDF version
Discussion Questions:

Article Title: Viral Proteins Acquired from a Host Converge to Simplified Domain Architectures
Discussion Leader: Mark Slayton
Date: 2-16-2016
Rappoport N, Linial M (2012) Viral Proteins Acquired from a Host Converge to Simplified Domain Architectures. PLoS Comput Biol 8(2): e1002364. doi: 10.1371/journal.pcbi.1002364
PDF version
Discussion Questions

Article Title: Associations between host gene expression , the mucosal microbiome , and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.
Discussion Leader: Samantha Shaw
Date: 2-23-2016
Morgan, X. C., Kabakchiev, B., Waldron, L., Tyler, A. D., Tickle, T. L., Milgrom, R., … Huttenhower, C. (2015). Associations between host gene expression , the mucosal microbiome , and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.
PDF version
Discussion Questions

Article Title: Cytokine-dependent and-independent gene expression changes and cell cycle block revealed in Trypanosoma cruzi-infected host cells by comparative mRNA profiling
Discussion Leader: Prashant Kuntala
Date: 3-8-2016
Costales JA, Daily JP, Burleigh BA. Cytokine-dependent and-independent gene expression changes and cell cycle block revealed in Trypanosoma cruzi-infected host cells by comparative mRNA profiling. BMC Genomics 2009 May 29;10:252
PDF version
Discussion Questions

Article Title: BrainSeq: Neurogenomics to Drive Novel Target Discovery for Neuropsychiatric Disorders
Discussion Leader: Abigail Kacpura
Date: 3-15-2016
Christian R. Schubert, Patricio O’Donnell, Jie Quan, Jens R. Wendland, Hualin S. Xi, Ashley R. Winslow, Enrico Domenici, Laurent Essioux, Tony Kam-Thong, David C. Airey, John N. Calley, David A. Collier, Hong Wang, Brian Eastwood, Philip Ebert, Yushi Liu, Laura Nisenbaum, Cara Ruble, James E. Scherschel, Ryan Matthew Smith, Hui-Rong Qian, Kalpana Merchant, Michael Didriksen, Mitsuyuki Matsumoto, Takeshi Saito, Nicholas J. Brandon, Alan J. Cross, Qi Wang, Husseini Manji, Hartmuth Kolb, Maura Furey, Wayne C. Drevets, Joo Heon Shin, Andrew E. Jaffe, Yankai Jia, Richard E. Straub, Amy Deep-Soboslay, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, BrainSeq: Neurogenomics to Drive Novel Target Discovery for Neuropsychiatric Disorders, Neuron, Volume 88, Issue 6, 16 December 2015, Pages 1078-1083, ISSN 0896-6273, http://dx.doi.org/10.1016/j.neuron.2015.10.047.
PDF version
Discussion Questions

Article Title: A New Formulation of the Set Covering Problem for Metaheuristic Approaches
Discussion Leader: Yating Liu
Date: 3-22-2016
Nehme Bilal, Philippe Galinier, and Francois Guibault, “A New Formulation of the Set Covering Problem for Metaheuristic Approaches,” ISRN Operations Research, vol. 2013, Article ID 203032, 10 pages, 2013. doi:10.1155/2013/203032
PDF version
Discussion Questions

Article Title: Comparative study on gene set and pathway topology-based enrichment methods
Discussion Leader: Marilyn Hayden
Date: 3-29-2016
Bayerlová, M., Jung, K., Kramer, F., Klemm, F., Bleckmann, A., & Beißbarth, T. (2015). Comparative study on gene set and pathway topology-based enrichment methods. BMC Bioinformatics, 16(1), 1–15. http://doi.org/10.1186/s12859-015-0751-5
PDF version
Discussion Questions

Article Title: ComiR: combinatorial microRNA target prediction tool.
Discussion Leader: Emilee Holtzapple
Date: 4-5-2016
Coronnello C, Benos PV. ComiR: combinatorial microRNA target prediction tool. Nucleic Acids Research. 2013;41(Web Server issue):W159-W164. doi:10.1093/nar/gkt379.
PDF version
Discussion Questions

Topics: Metagenomics and Disease
Discussion Leader: Wenzhen Cai & Sarah Metro
Date: 4-12-2016
Article 1: Rajpal DK, Klein J-L, Mayhew D, Boucheron J, Spivak AT, Kumar V, et al. (2015)Selective Spectrum Antibiotic Modulation of the Gut Microbiome in Obesity and Diabetes Rodent Models. PLoS ONE 10(12): e0145499. doi:10.1371/journal.pone.0145499
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Article 2: Jinhua Wu, Kaiye Cai and Qiang Feng (2015) The Application of Metagenomic Approaches in the Management of Infectious Diseases. Trop Med Surgery 3:4: http://dx.doi.org/10.4172/2329-9088.1000196
Article 1 PDF
Article 2 PDF
Discussion Questions

Fall Semester 2015-2016 Schedule
Time: 4:35 pm - 5:55 pm
Location: Porter Hall 104

  • Topics: “Antedisciplinary” Science
    Discussion Leader: Mary Gemmel
    Date: 12-1-2015
    Eddy SR (2005) “Antedisciplinary” Science. PLoS Comput Biol 1(1): e6. doi:10.1371/journal.pcbi.0010006
    Link to article
    Discussion Questions

     
  • Topics: Don’t edit the human germ line & Chinese scientists genetically modify human embryos
    Discussion Leader: Shaw Samantha
    Date: 9-1-2015
    Link to article
    Link to article
    Discussion Questions

     
  • Topics: A comparative encyclopedia of DNA elements in the mouse genome.
    Discussion Leader: Dr. Welch
    Date: 9-8-2015
    Yue F, Cheng Y, Breschi A, Vierstra J, et al. Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.
    PDF version
    Discussion Questions
  • Topic: Recent advances in the T box riboswitch research
    Discussion Leader: Chunxi Zeng
    Date: 9-15-2015
    Abstract
    No Discussion Questions!

     
  • Topic: Identification of potential Stat92E target genes that affect hematopoietic output in Drosophila
    Discussion Leader: Aditi Vyas
    Date: 9-22-2015
    No Discussion Questions!

     
  • Topics: Using the ENCODE Resource for Functional Annotation of Genetic Variants
    Discussion Leader: Yichao Li
    Date: 9-29-2015
    Pazin, M. J. (2015). Using the ENCODE Resource for Functional Annotation of Genetic Variants. Cold Spring Harbor Protocols, 2015(6), pdb.top084988.
    PDF version
    Discussion Questions

     
  • Topics: Genome-Wide Mapping of 5mC and 5hmC Identified Differentially Modified Genomic Regions in Late-Onset Severe Preeclampsia: A Pilot Study
    Discussion Leader: Sarah Metro
    Date: 10-6-2015
    Zhu, L., Lv, R., Kong, L., Cheng, H., Lan, F., & Li, X. (2015). Genome-Wide Mapping of 5mC and 5hmC Identified Differentially Modified Genomic Regions in Late-Onset Severe Preeclampsia: A Pilot Study. Plos One, 10(7), e0134119. http://doi.org/10.1371/journal.pone.0134119
    PDF version
    Discussion Questions

     
  • Topics: Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies
    Discussion Leader: Mariah Hazlett
    Date: 10-13-2015
    Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, et al. (2014) Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies. PLoS Comput Biol 10(3): e1003496. doi:10.1371/journal.pcbi.1003496
    Link to article
    Discussion Questions

     
  • Topics: Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
    Discussion Leader: Yichao Li
    Ernst, J., & Kellis, M. (2013). Interplay between chromatin state , regulator binding , and regulatory motifs in six human cell types, 1142-1154. doi:10.1101/gr.144840.112.Freely
    Date: 10-20-2015
    PDF version
    Discussion Questions
    Background Information:
    paper1, paper2, paper3, paper4

     
  • Topics: FTOObesity Variant Circuitry and Adipocyte Browning in Humans
    Discussion Leader: Ashley Patton
    Date: 11-3-2015
    PDF version
    PDF version
    Discussion Questions

     
  • Topics: Systems Biology Applications to Decipher Mechanisms and Novel Biomarkers in CNS Trauma
    Discussion Leader: Hayden Marilyn
    Date: 11-10-2015
    Link to Article
    Discussion Questions

     
  • Topics: Cis and Trans Acting Factors Involved in Human Cytomegalo virus Experimental and Natural Latent Infection
    Discussion Leader: Mark Slayton
    Date: 11-17-2015
    Link to Article
    Discussion Questions

     
  • Topics: Differential analysis of gene regulation at transcript resolution with RNA-seq
    Discussion Leader: Johathan Young

    Date: 11-24-2015
    Link to Article
    Discussion Questions
    Background Article

     
  • Topics: TBD
    Discussion Leader: Sazan Ismael
    Date: 12-8-2015
  • Topics: Watch Video: HBO Special: VICE- Killing Cancer
    Discussion Leader: Amy Lasure
    Date: 4-14-2015
    Discussion Question

     
  • Date: 4-21-2015
    Bioinformatics Distinguished Lecture
    1:30 pm, Walter 235
    Topic: Computational and Systems Medicine: from theoretical models to advancing health care
    Professor Panagiotis (Takis) Benos
    Regulatory Genomics and Systems Medicine laboratory
    Department of Computational and Systems Biology
    Abstract/Personal Statement

     
  • Topics: Gut microbiota and non-alcoholic fatty liver disease: new insights
    Discussion Leader: Shaw Samantha
    Aron-Wisnewsky, J., Gaborit, B., Dutour, a., & Clement, K. (2013). Gut microbiota and non-alcoholic fatty liver disease: new insights. Clinical Microbiology and Infection, 19(4), 338–348. doi:10.1111/1469-0691.12140
    Date: 4-7-2015
    PDF Version
    Discussion Question

     
  • Topics: Effect of Diet on Expression of Genes Involved in Lipid Metabolism, Oxidative Stress, and Inflammation in Mouse Liver–Insights into Mechanisms of Hepatic Steatosis
    Discussion Leader: Patton Ashley
    Renaud H, Cui J, Lu H, Klaassen C. Effect of Diet on Expression of Genes Involved in Lipid Metabolism, Oxidative Stress, and Inflammation in Mouse Liver–Insights into Mechanisms of Hepatic Steatosis. Plos ONE [serial online]. February 2014;9(2):1-17. Available from: Food Science Source, Ipswich, MA.
    Date: 3-31-2015
    PDF Version
    Discussion Question

     
  • Topics: Imaging characteristics of cerebrovascular arteriopathy and stroke in Hutchinson-Gilford progeria syndrome
    Discussion Leader: Amy Lasure
    Silvera, V. M., Gordon, L. B., Orbach, D. B., Campbell, S. E., Machan, J. T., & Ullrich, N. J. (2013). Imaging characteristics of cerebrovascular arteriopathy and stroke in Hutchinson-Gilford progeria syndrome. AJNR. American Journal of Neuroradiology, 34(5), 1091–7. doi:10.3174/ajnr.A3341
    Date: TBD
    PDF version
    Discussion Questions

     
  • Topics: The top 100 papers
    Discussion Leader: TBD
    VAN NOORDEN, R; MAHER, B; NUZZO, R. The top 100 papers: nature explores the most-cited research of all time. Nature. 7524, 550, 2014. ISSN: 0028-0836.
    Date: TBD
    PDF version
    Discussion Questions

     
  • Topics: Medical Fraud Missing From Public Record
    Discussion Leader: Mary Gemmel
    Date: 3-10-2015
    Link to article
    Discussion Questions

     
  • Topics: Sex redefined
    Discussion Leader: TBD
    Claire Ainsworth. Sex redefined, NATURE | NEWS FEATURE, 18 February 2015
    Date: TBD
    Link to article
    Discussion Questions

     
  • Topics: Gut Check
    Discussion Leader: TBD
    What's Lurking In Your Microbiome? Possibly, a Cure for Disease
    Date: TBD
    Link to article
    Discussion Questions

     

  • Past Discussions
     
    • Topics: Assessing computational tools for the discovery of transcription factor binding sites
      Discussion Leader: Yating Liu
      TOMPA, M; et al. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology. United States, 23, 1, 137-144, Jan. 2005. ISSN: 1087-0156.
      Date: 3-24-2015
      PDF Version
      Finish Reading Template

       
    • Topics: Estimating recombination rates from population-genetic data
      Discussion Leader: Dr. Frank Drews
      STUMPF, MH; MCVEAN, GT. Estimating recombination rates from population-genetic data. Nature Reviews. Genetics. England, 4, 12, 959-968, Dec. 2003. ISSN: 1471-0056.
      Date: 3-10-2015
      PDF Version
      Discussion Questions

       
    • Topics: A discriminative approach for unsupervised clustering of DNA sequence motifs
      Discussion Leader: Chen Liang
      Stegmaier, P., Kel, A., Wingender, E., & Borlak, J. (n.d). A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs. Plos Computational Biology, 9(3)
      Date: 3-17-2015
      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: 2-24-2015
      PDF Version
      Discussion Questions

       
    • Topics: Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
      Discussion Leader: Veronica
      Khatri P, Sirota M, Butte AJ. Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. Ouzounis CA, ed. PLoS Computational Biology 2012;8(2):e1002375. doi:10.1371/journal.pcbi.1002375.
      Date: 2-3-2015
      PDF version
      Discussion Questions

       
    • Topics: Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
      Discussion Leader: Yichao Li
      Ernst, J., & Kellis, M. (2013). Interplay between chromatin state , regulator binding , and regulatory motifs in six human cell types, 1142-1154. doi:10.1101/gr.144840.112.Freely
      Date: 2-10-2015
      PDF version
      Discussion Questions
      Background Information
      - Function of histone modification: paper1, paper2, paper3, paper4

       
    • Topics: A draft map of the human proteome
      Discussion Leader: Krystine Garcia
      Min-Sik Kim,et al. A draft map of the human proteome. Nature 509, 575–581 (29 May 2014) doi:10.1038/nature13302
      Date: 2-17-2015
      PDF Version
      Discussion Questions

       
    • Topics: Top 10 Things You Should Know About Alternative Medicine
      Discussion Leader: Dr. Welch
      Harriet Hal, 2009, Top 10 Things You Should Know About Alternative Medicine, Skeptics Society and Harriet Hall
      Date: 1-20-2015
      PDF version
      Discussion Questions

       

    • 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: 1-27-2015
      PDF version
      Discussion Questions

       

     

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

    • Date: 11-25-2014 NO CLASS!
       
    • 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
      Youtube Video
      Discussion Questions
    • Date: 11-11-2014 NO CLASS!
       
    • Topics: Genome sequence of a 45,000-year-old modern human from western Siberia
      Discussion Leader: Kellie Rabley
      Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., … Paabo, S. (2014). Genome sequence of a 45,000-year-old modern human from western Siberia. Nature, 514(7523), 445–449. Retrieved from http://dx.doi.org/10.1038/nature13810
      Date: 11-18-2014
      PDF version
      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

       
    • 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: 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
      The Hot Zone
      UCSC Ebola Browser
      Discussion Questions

       
    • 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

       
































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    • 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: 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 
      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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