DNA research
	RNA research
	Protein research
	Estimating amino acid distributions
		Parallel sequence analysis
		Discriminative models in computational biology
		EST analysis
	Software tools

A review of genefinding methods (pdf file)

Improved splice site detection in genie, from RECOMB97

Integrating database homology in a probabilistic gene structure model

A generalized hidden Markov model for the recognition of human genes in DNA, from ISMB96

EcoParse, a mailserver for finding genes in E. coli DNA that uses a Hidden Markov Model

Optimal parse of DNA, a general gene-finding program for prokaryotes that allows the user to add or remove "sensors" that look for coding signals

Using simple Markov models to search DNA databases

Linear hidden Markov models for protein and nucleic acid modeling (SAM)

  RNA research

Detecting base-pairs in RNA multiple alignments

Stochastic context-free grammars for RNA modeling

Gibbs sampling for creating stochastic context-free grammars for RNA modeling

Pseudoknot modeling using intersections of stochastic context-free grammars with applications to database search

  Estimating amino acid distributions

Dirichlet mixtures, a method for improving the estimation of amino acid distributions

Evaluating regularizers for estimating distributions of amino acids, from ISMB95

Regularizers for estimating distributions of amino acids from small samples, by Kevin Karplus (UCSC-CRL-95-11)

  Parallel sequence analysis

Kestrel parallel processor

SAM-T02 sequence alignment and hidden Markov modeling system

  Discriminative models in computational biology

Support vector machine classification and validation of cancer tissue samples using microarray expression data (Postscript of technical report)

Support vector machine classification of microarray gene expression data (UCSC-CRL-99-09) (Postscript of technical report)

Exploiting generative models in discriminative classifiers (Abstract | Postscript)

A discriminative framework for detecting remote protein homologies (Abstract | Postscript | 56mb compressed)

Classifying G-protein coupled receptors with support vector machines (Karchin R, Karplus K, Haussler D. Bioinformatics 2002; 18(1):147-59)

  EST analysis

A probabilistic approach to consensus multiple alignment (Postscript)

Towards an accurate EST consensus (Postscript)

  Software tools

LaTeX style file for CABIOS