BENG202/CSE282 Class Projects (Winter 2012)
The goal of the project is to understand how to rigorously redefine a biological problem as a computational formulation that can be solved using well-defined algorithmic and statistical approaches . It is expected that the computational formulation may not exactly model the underlying biological question so a rationale must be given as to why the computational formulation is a meaningful step towards solving the biological problem. Making this argument involves understanding the biological problem, identifying a related computational model, proposing an algorithm to solve the biological problem using the computational model , listing the limitations of the proposed approach and identifying specific evaluation criteria to assess the correctness, completeness and statistical significance of the proposed solution.
- Groups of no more than two students
- Group memberships and choice of papers are due by Feb 29th (email)
- The same paper may be assigned to more than one group
- Projects will be presented in class on March 12th and 14th and should explicitly address the following elements:
- Biological question; What is biological question being addressed?
- Input data; What data is being acquired and how is it represented computationally?
- Problem formulation; What is the exact computational problem being solved? If it's unclear how to devise a rigorous formulation, clearly state which aspects of the biological problem are not captured in the computational problem formulation.
- Evaluation of results; How is the quality of the computational results being assessed? What are the possible "pitfalls" that could have lead to false positives and how were these addressed?
- Suggestions for future work; How could this paper's formulation and/or evaluation of results be improved?
- A one-page project write-up addressing the same six elements listed above is due by March 9th (email)
- Evaluation criteria:
- Biological question: 10%
- Input data: 10%
- Problem formulation: 25%
- Evaluation of results: 25%
- Suggestions for future work: 10%
- Comments on other projects' analysis: 20%
List of papers for class projects
- De novo repeat classification and fragment assembly
Pevzner PA, Tang H, Tesler G.
Genome Res. 2004 Sep;14(9):1786-96. PMID: 15342561
- Protein identification by spectral networks analysis
Bandeira N, Tsur D, Frank A, Pevzner PA.
Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6140-5. PMID: 17404225
- Discovery and revision of Arabidopsis genes by proteogenomics
Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP.
Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):21034-8. PMID: 19098097
- Spectrum fusion: using multiple mass spectra for de novo peptide sequencing
Datta R, Bern M.
J Comput Biol. 2009 Aug;16(8):1169-82. PMID: 19645594
- Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
Chi SW, Zang JB, Mele A, Darnell RB. Nature. 2009 Jul 23;460(7254):479-86. Epub 2009 Jun 17. PubMed
PMID: 19536157; PubMed Central PMCID: PMC2733940.
- HITS-CLIP yields genome-wide insights into brain alternative RNA processing
Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer
AC, Blume JE, Wang X, Darnell JC, Darnell RB. Nature. 2008 Nov
27;456(7221):464-9. Epub 2008 Nov 2. PubMed PMID: 18978773; PubMed Central PMCID:
PMC2597294.
- Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK,
Mortazavi A, Williams BA, Song L, Crawford GE, Wold BJ, Willard HF, Myers RM.
Genome Res. 2012 Feb 2. [Epub ahead of print]
PubMed PMID: 22300769.
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg
SL, Wold BJ, Pachter L. Nat
Biotechnol. 2010 May;28(5):511-5. Epub 2010 May 2. PubMed PMID: 20436464; PubMed
Central PMCID: PMC3146043.
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Nat Methods. 2008
Jul;5(7):621-8. Epub 2008 May 30. PubMed PMID: 18516045.
- Genome-wide mapping of in vivo protein-DNA interactions
Johnson DS, Mortazavi A, Myers RM, Wold B. Science. 2007 Jun 8;316(5830):1497-502. Epub 2007 May
31. PubMed PMID: 17540862.
- ChIP-Seq identification of weakly conserved heart enhancers
Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I,
Shoukry M, Wright C, Chen F, Afzal V, Bristow J, Ren B, Black BL, Rubin EM, Visel
A, Pennacchio LA.
Nat Genet. 2010 Sep;42(9):806-10. Epub 2010 Aug 22. PubMed PMID: 20729851; PubMed
Central PMCID: PMC3138496.
- Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs
Girgis HZ, Ovcharenko I. BMC Bioinformatics. 2012 Feb
7;13(1):25. [Epub ahead of print] PubMed PMID: 22313678.
- A high-resolution map of human evolutionary constraint using 29 mammals
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P,
Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S,
Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek
P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins
AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella
AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome
Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young
S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of
Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler
G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J,
Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington
University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx
P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel
A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. Nature. 2011 Oct
12;478(7370):476-82. doi: 10.1038/nature10530. PubMed PMID: 21993624; PubMed
Central PMCID: PMC3207357.