Resources for Brendan Frey's plenary talk at ISIT 2006 in Seattle
The web page for Brendan's group
Slides in powerpoint format (ppt)
Slides in portable document format (pdf)
Paper describing biological results from our exploration of the transcriptome
Genome-wide analysis of mouse transcripts using exon
microarrays and factor graphs.
BJ Frey et al, Nature Genetics, Vol 37, No 9, Sep 2005.
Paper describing the factor-graph-based computational method used in our exploration of the transcriptome
(the above version contains some typos corrected in the published version)
GenRate: A generative model that reveals novel transcripts in
genome-tiling microarray data.
BJ Frey, QD Morris, TR Hughes, Journal of Computational Biology, Vol 13, No 2, Mar 2006.
'Heated but friendly debate' between our group and the RIKEN/FANTOM consortium regarding the transcriptome
How many genes are there?
L Lee, TR Hughes, BJ Frey, Science, Vol 311, No 5768, Mar 2006.
Web page containing data sets generated from our exploration of the transcriptome
Paper describing a type of graph-based model that is appropriate
for many problems in computational molecular biology
Factor graphs and the sum-product algorithm.
FR Kschischang, BJ Frey,H-A Loeliger,
IEEE Transactions on Information Theory, Vol 47, No 2, Feb 2001.
Link to on-line book on molecular biology, Human Molecular Genetics 2
This book is quite comprehesive, although it is encyclopedic in its
coverage. However, molecular biology is a huge field, so I don't think
there is an 'easy read' on the entire field. My recommendation is that
you find a problem to work on (even as an exercise) and use this book
as a reference to look up relevant terms, mechanisms and experimental techniques.
Biological sequence analysis: Probabilistic models of proteins and nucleic acids
This book describes computational techniques for analyzing biological
sequences. While it does not comprehensively address all areas
of bioinformatics (no book that I know of properly does), it gives a
refreshingly clear and concise presentation of approaches to a set
of well-defined problems.