Paper Presentations

Mondays

Each student will have the opportunity to present one to two papers about topics related to our class:
Date Student Paper(s) (Choose one and announce it to the class)
4 Feb Ankit Human Genome Project 1: Initial sequencing and analysis of the human genome

More Human Genome Project papers if you're interested:
4 Feb Filmon Human Genome Project 2: Quality assessment of the human genome sequence

More Human Genome Project papers if you're interested:
11 Feb Matthew Pairwise Alignment:
  • Lobo, I. (2008) Basic Local Alignment Search Tool (BLAST). Nature Education 1(1). (web, pdf)
    • and
  • Eddy, S.R., (2004) Where did BLOSUM62 alignment score matrix come from? Nature Biotechnology 22 pp 1035-1036 (web, pdf)
11 Feb Rafet Multiple Sequence Alignment:
  • Edgar, R. and Batzoglou, S., (2006) Multiple sequence alignment. Current Opinion in Structural Biology, 16:3 pp 368–373. (web, pdf)
Feb 18 Awa Assembly Review (1 of 2):
  • Schatz, M.C., Delcher, A.L., and Salzberg, S.L., (2010) Assembly of large genomes using second-generation sequencing. Genome Research 20 pp 1165-1173. (web, pdf)
Feb 18 Richard Assembly Review (2 of 2):
  • Salzberg, S.L, et al. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research 22 pp 557-567 (web, pdf)
Feb 25 Jingsai Assembly (1 of 2):
  • (Velvet) Zerbino DR, Birney E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18 pp 821–829. (web, pdf)
Feb 25 Xin Assembly (2 of 2):
  • (SOAPdenovo) Li R, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 20 pp 265–272. (web, pdf)
Mar 4 Sachintha Assembly:
  • Flicek, P. and E. Birney, 2009. Sense from sequence reads: methods for alignment and assembly. Nature Methods Supplement 6 pp S6-S12. (web, pdf)
Mar 4 Volodymyr Assembly:
  • Compeau, P.E.C., P.A. Pevzner, and G. Tesler, 2011. How to apply de Bruijn graphs to genome assembly. Nature Biotechnology 29 pp 987-991. (web, pdf)
Mar 18 Ankit Genome Annotation:
  • Brent, M.R., 2008. Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nature Reviews Genetics 9 pp 62-73. (web, pdf)
Mar 18 Hui Genome Annotation:
  • Yandell, M. and D. Ence, 2012. A beginner's guide to eukaryotic genome annotation. Nature Reviews Genetics 13 pp 329-342. (web, pdf)
Mar 25 Filmon Genomic Variation:
  • Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude (Science, 2010)
Mar 25 Awa Genomic Variation:
  • Pathways: Analysing biological pathways in genome-wide association studies (Nature Reviews, 2010)
Apr 1 Matthew Genomic Variation:
  • Exemplary GWAS: "Genomewide Association Studies: History, Rationale, and Prospects for Psychiatric Disorders" (Am J Psychiatry, 2009)
Apr 8 Jingsai Genomic Variation:
  • The International HapMap Project (Nature, 2003)
Apr 8 Xin Genomic Variation:
  • A HapMap harvest of insights into the genetics of common disease (J Clin Invest., 2008)
Apr 15 Sachintha Gene Expression & Transcriptomes:
  • Cluster analysis and display of genome-wide expression patterns. (Proc Natl Acad Sci USA, 1998)
Apr 15 Richard Gene Expression & Transcriptomes:
  • How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? (BMC Genomics, 2012)
Apr 22 Hui Gene Expression & Transcriptomes:
  • Empirical analysis of transcriptional activity in the Arabidopsis genome. (Science, 2003)
Apr 22 Volodymyr Gene Expression & Transcriptomes (Choose one):
  • The developmental dynamics of the maize leaf transcriptome. (Nature Genetics, 2010)
  • Applications of New Sequencing Technologies for Transcriptome Analysis. (Annu. Rev. Benom. Human Genet., 2009)
Apr 24 Rafet Gene Expression & Transcriptomes:
  • Advancing RNA-Seq analysis. (Nature Biotechnology, 2010)
Presentations should be brief (~15 minutes with 5 minutes for questions). If we get to have two presentations per student, than at least one of the presentations should be a "chalk talk" (no PowerPoint). For the "chalk talk", you're welcome to refer to figures in the paper or use the computer to display graphic(s) that would be difficult to draw. Presentations will be graded based on the Department of Computer Science's Oral Presentation Rubric. Please review it for ideas about good presentation skills. For those not presenting, please read the article and come prepared with at least one question.


Weekly Project Status Updates

Complete by 12:25 PM each Friday

As a group, write a status update of your progress on your project for the last week. Your report needs to include each of the following four sections: Please submit your report via email TO Hyrum.Carroll@mtsu.edu and CC the other group member(s).


Project Descriptions

Complete by 10:00 PM on Friday, February 22, 2013

As a group, write a one page description of your project. Your report needs to explain the hypothesis, why this questions is important, any key papers (if already found), and outline the general steps (as you currently understand them) to answer the hypothesis. Please submit your report into the dropbox for COMS 7840 at https://elearn.mtsu.edu.


Homework #3

Complete by class on Friday, February 8, 2013

Exercise 1.2 (page 22) and Exercise 1.3 (page 33). Please submit your brief write-up into the dropbox for COMS 7840 at https://elearn.mtsu.edu.


Homework #2

Complete by class on Wednesday, January 31, 2013

Read pages 4 - 36 of the National Library of Medicine's "Help Me Understand Genetics" handbook (local copy) And watch these tutorials if you still do not feel comfortable with basic molecular biology topics.

Homework #1

Complete by class on Wednesday, January 23, 2013

Read Sections 1 - 6 (pages 122-131) of Bioinformatics-an introduction for computer scientists (local copy).