Archive for the ‘publications’ Category

Evolutionary Computation: literature reviews

October 13, 2008

Here are two good overview articles on evolutionary computation.  The first article is more recent and is targeted primarily at computer scientists; the second article is slightly outdated and targeted primarily at ecologists.

“Evolutionary Computation in Bioinformatics: A Review” Sankar K. Pal et al., IEEE Transactions 2006

“Evolutionary Computation: An Overview” Melanie Mitchell and Charles E. Taylor, Ecology and Systematics 1999

Happy Holidays Everyone: A LaTeX-thesis pack for the University of Oregon

December 12, 2007

A screenshot from Gmail, in which the Graduate School editor approves my thesis.
(view screenshot here)

If you’re writing a thesis or dissertation for the University of Oregon Graduate School (UOGS), here is a set of LaTeX files which will help you produce a document with approved formatting.

Download Here: latex-thesis-pack.zip (6.5 MB)

These files will help you format most of your document, but some hand-crafting might be required if your thesis or dissertation contains non-standard “stuff.” The instructions are in the file README.txt

Thanks to Peter Boothe for being a LaTeX-ninja, sometimes.

Spectral Network Analysis

August 29, 2007

This video is exciting:

Pavzner and his team address the challenge of determining a protein’s sequence, given mass spectrometry data. This problem is challenging because every protein undergoes translational modifications, and therefore mass-specs actually measure proteins which deviate (slightly) from their non-translated nucleotide sequences.

An unsolved challenge is to correctly infer a protein’s sequence, given mass-spec data. However, we CAN compare mass-specs against a database of existing (and known) mass-specs in order to guess the sequences. This process is computationally expensive because it requires a linear search of the database for every queried mass-spec search key.

Pavzner present a more efficient algorithm for “guessing” a protein’s sequence, given its mass-spectrum. His technique involves constructing a network of spectral data, and then using that network as the basis for a search. This is remarkably faster than traditional database searches. Pavzner, et al, apply this technique to whole-genome spectrometric data, and yield promising results.

My obscure notes:

17:00 – Why is the signal-to-noise ratio reduced “six-fold” ?

18:01 – Look-up reference for “anti-symmetric pass approach” to solving an alignment between two sequences of unequal length. Can we use this storage technique for other information domains: phylogenetic trees? Electroencephalographic data?

28:07 – The use of “snake venom” makes any science project sound cool.


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