CENTER FOR ALGORITHMIC SYSTEMS
MSc Programme ``Computing Science"
Seminar: Algorithmic Computational Biology (MACB)
- 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
- Plagiarism is strictly forbidden.
- Language: English.
- Format: A4/A4wide, 11pt.
- 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.)
- 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
- 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
- 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
Orient yourself and find a topic. If you don't find one easily, the suggestions below
may help. (It is allowed to choose a topic someone else already opted for. However,
the term paper should always be your individual effort and cannot be joint with or
similar to someone else's.)
- 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
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:
A (suitable) paper from a key journal such as:
- RECOMB - Research in Computational Molecular Biology (see e.g.
- 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.
- 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
- 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)
(Papers that were chosen as core document for a term paper have been deleted.)
- 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