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...

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...

Promoter region-based classification of genes.

Published in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

In this paper we consider the problem of extracting information from the upstream untranslated regions of genes to make predictions about their transcriptional regulation. We present a method for classifying genes based on motif-based hidden Markov models (HMMs) of their promoter regions. Sequence motifs discovered in yeast promoters are used to co...

Feather development genes and associated regulatory innovation predate the origin of Dinosauria.

Published in Molecular Biology and Evolution

The evolution of avian feathers has recently been illuminated by fossils and the identification of genes involved in feather patterning and morphogenesis. However, molecular studies have focused mainly on protein-coding genes. Using comparative genomics and more than 600,000 conserved regulatory elements, we show that patterns of genome evolution i...

UCSC Data Integrator and Variant Annotation Integrator.

Published in Bioinformatics

Support vector machine classification and validation of cancer tissue samples using microarray expression data.

Published in Bioinformatics