David Haussler

RNA modeling using Gibbs sampling and stochastic context free grammars.

Published in International Conference on Intelligent Systems for Molecular Biology

A new method of discovering the common secondary structure of a family of homologous RNA sequences using Gibbs sampling and stochastic context-free grammars is proposed. Given an unaligned set of sequences, a Gibbs sampling step simultaneously estimates the secondary structure of each sequence and a set of statistical parameters describing the comm...

The UCSC Known Genes.

Published in Bioinformatics

The University of California Santa Cruz (UCSC) Known Genes dataset is constructed by a fully automated process, based on protein data from Swiss-Prot/TrEMBL (UniProt) and the associated mRNA data from Genbank. The detailed steps of this process are described. Extensive cross-references from this dataset to other genomic and proteomic data were cons...

Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots.

Published in Genome Biology and Evolution

Fast evolving regions of many metazoan genomes show a bias toward substitutions that change weak (A,T) into strong (G,C) base pairs. Single-nucleotide polymorphisms (SNPs) do not share this pattern, suggesting that it results from biased fixation rather than biased mutation. Supporting this hypothesis, analyses of polymorphism in specific regions o...

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.

Published in Genome Research

Six measures of evolutionary change in the human genome were studied, three derived from the aligned human and mouse genomes in conjunction with the Mouse Genome Sequencing Consortium, consisting of (1) nucleotide substitution per fourfold degenerate site in coding regions, (2) nucleotide substitution per site in relics of transposable elements act...

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.

Published in Cell

Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify ...

Computational reconstruction of ancestral DNA sequences.

Published in Methods in Molecular Biology

This chapter introduces the problem of ancestral sequence reconstruction: given a set of extant orthologous DNA genomic sequences (or even whole-genomes), together with a phylogenetic tree relating these sequences, predict the DNA sequence of all ancestral species in the tree. Blanchette et al. (1) have shown that for certain sets of species (in pa...

UCSC Data Integrator and Variant Annotation Integrator.

Published in Bioinformatics