Paper Reading

- Pacific Symposium on Bioinformatics 2007
- 3 Gene-related Papers

Useful Links

Notes 1:

Discovering Motifs With Transcription Factor Domain Knowledge. Pacific Symposium on Biocomputing 12:472-483(2007)
Henry C.M. Leung, Francis Y.L. Chin, Bethany M.Y. Chan

A short summary
Useful link - tutorial PSSM (Position-Specific Scoring Matrices); - a popular motif discovery algorithm MEME
Likelihood - if "probability" allows us to predict unknown outcomes based on known parameters, then "likelihood" allows us to determine unknown parameters based on known outcomes. In a sense, likelihood works backwards from probability: given B, we use the conditional probability Pr(A|B) to reason about A, and, given A, we use the likelihood function L(B|A) to reason about B.


Notes 2:

A Bayesian Network Approach to Operon Prediction. Bioinformatics, 19, pp. 1227-1235.
J. Bockhorst, M. Craven, D. Page, J. Shavlik & J. Glasner (2003).

A short summary

Other links:
Bayesian Network Wiki
An Introduction to Bayesian Networks and their Contemporary Applications

Notes 3:

Evaluation of Gene-Finding Programs on Mammalian Sequences. Genome Research, Vol. 11, Issue 5, 817-832, May 2001
Sanja Rogic, Alan K. Mackworth, and Francis B.F. Ouellette

A short summary

Notes 4:

SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model. Genome Research, Vol 13, Issue 3, 496-502, March 2003
Marina Alexandersson, Simon Cawley and Lior Pachter

A short summary