• Office hours: by appointment.
• Email: macb.seminar--at---gmail.com, tel. 030-2534001, BBL kamer 505
• Back to weekly schedule.
• Back to main.

Term paper

• Choose a topic/article(s) within the next two weeks. (See also below.)
• Propose it and get approval, before May 21st.
• Start reading/analysing your topic/article(s) immediately so you have time to get into it and look for any context material you may need.
• The term paper should use common `writing and formatting standards'.
  • The term paper should have at least 5, at most 10 pages. (The lowerbound is strict.)
  • Plagiarism is strictly forbidden.
  • Language: English.
  • Format: A4/A4wide, 11pt.
  • PDF.
• The due date for the term paper is: Friday, June 29 (17.00 hours), 2012. Try to summit your term paper early, i.e. well before this date.
• Submission: PDF to macb.seminar--at--gmail.com. (Submission on paper in my BBL-mailbox is fine too e.g. if you have special illustrations.)

Specification

• Term papers are individual.
• The term paper should give an adequate context assessment/summary/explanation/analysis of the subject area and contributions of the article(s).
• The paper should do so in your own words. Results from other sources should be properly cited etc.
• Every topic has its own characteristics but here are some aspects that should normally be addressed:
  • The specific subject area studied in the article(s).
  • The research questions addressed in the article(s) (their meaning and why they matter).
  • The concepts, model(s) and approach(es) chosen to attack the questions and why these are suitable.
  • The main results that are obtained, their meaning and why they are important.
  • An indication of the techniques in the paper that are especially interesting or noteworthy.
  • An appraisal of the (expected) impact of the results in the area, as seen e.g. from follow-up studies on the same topic.
  • Your own assessement and opinion of the achievements of the article(s). (Does it/do they achieve your expectations, doies it/do they solve the problems satisfactorily, how would you have approached the problem differently, what open problems are left, how would you expect these could be approached, etc).

Some Suggested Topics/Papers

• Choose a key paper referenced in a chapter in the book (for example, a paper digressing on the topic of one of your presentations), or
• choose another topic of interest, select a key paper (and its context) about it, and propose it.

FOR THE SELECTED TOPICS, SEE THE weekly schedule.

Suggestions for Topics and Papers (under construction)

A (suitable) topic from a part of the book that we didn't cover in class

• Topic from chapter 13 (`Molecular structures').

A (suitable) paper from a key conference such as:

• RECOMB - Research in Computational Molecular Biology (see e.g. here).
• WABI - Workshop on Algorithms in Bioinformatics (see e.g. here).

• Bioinformatics (see e.g. here).
• IEEE/ACM Transactions on Computational Biology and Bioinformatics (see e.g. here).
• Journal of Computational Biology (see e.g. here).

• ...

• ...

• R. Sharan, B.V. Halldorsson, S. Istrail: "Islands of tractability for parsimony haplotyping", IEEE/ACM Trans. Computational Biology and Bioinformatics 3 (2006) 303-311.
• R.M. Karp: "Heuristic algorithms in computational molecular biology", J. Comput. Syst. Science 77 (2011) 122-128.

• D.A. Bader: "Computational biology and high-performance computing", Comm. ACM 47 (2004) 35-40.
• M. Kalaev, M. Smoot, T. Ideker, R. Sharan: "NetworkBLAST: comparative analysis of protein networks", Bioinformatics (Applications Note), 24:4 (2008) 594–596.
• J. Ma, L. Zhang: "Modern BLAST Programs", in: L.S. Heath and N. Ramakrishnan (eds.), Problem Solving Handbook in Computational Biology and Bioinformatics, Springer, 2011.
• S.J. Schultheiss, M-C. Munch, G.D. Andreeva, G. Ratsch: "Persistence and availability of web services in computational biology", PLoS ONE 6 (2011) 1-12.

• R.K. Bradley, A. Roberts, M. Smoot, S. Juvekar, J. Do, C. Dewey, I. Holmes, L. Pachter: "Fast statistical alignment", PLoS Computational Biology 5:5 (2009) 1-15.
• R.C. Edgar RC, K. Sjolander: "SATCHMO: sequence alignment and tree construction using hidden Markov models", Bioinformatics 19 (2003) 1404-1411.
• L. Smith, L. Yeganova, W.J. Wilbur: "Hidden Markov models and optimized sequence alignments", Computational Biology and Chemistry 27 (2003) 77-84.

• C. Linhart, R. Shamir: "Matching with don't-cares and a small number of mismatches", Inf. Process. Lett. 109 (2009) 273-277.
• J. Ng, A. Amir and P.A. Pevzner: "Blocked pattern matching problem and its applications in proteomics", in: RECOMB 2011, LNCS Vol 6577, pp. 298-319, 2011.

• N. Atias, R. Sharan: "Comparative analysis of protein networks - hard problems, practical solutions", CACM 55:5 (2012) 88-97.
• M. Kalaev, V. Bafna, R. Sharan: "Fast and accurate alignment of multiple protein networks", J. Comput. Biology 16 (1999) 989-999.
• R. Sharan, S. Suthram, R.M. Kelley, T. Kuhn, S. McCuine, P. Uetz, T. Sittler, R.M. Karp, T. Ideker: "Conserved patterns of protein interaction in multiple species", PNAS 102:6 (2005) 1974-1979.

• M. Bader, M.I. Abouelhoda, E. Ohlebusch: "A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions", BMC Bioinformatics 9 (2008) 516-529.

• G. Myers: "Whole-genome DNA sequencing", Computing in Science & Engineering 1 (1999) 33-43.

• S. Burkhardt, A. Crauser, P. Ferragina, H-P. Lenhof, E. Rivals, M. Vingron: "q-Gram based database searching using a suffix array (QUASAR)", RECOMB 1999, ACM, pp 77-83.

Last modified: May, 2012