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A, Siepel David Haussler
Published in
Molecular Biology and Evolution
Nucleotide substitution in both coding and noncoding regions is context-dependent, in the sense that substitution rates depend on the identity of neighboring bases. Context-dependent substitution has been modeled in the case of two sequences and an unrooted phylogenetic tree, but it has only been accommodated in limited ways with more general phylo...
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N, Nguyen G, Hickey Dr, Zerbino B, Raney D, Earl J, Armstrong Wj, Kent David Haussler B, Paten
Published in
Journal of Computational Biology
A reference genome is a high quality individual genome that is used as a coordinate system for the genomes of a population, or genomes of closely related subspecies. Given a set of genomes partitioned by homology into alignment blocks we formalize the problem of ordering and orienting the blocks such that the resulting ordering maximally agrees wit...
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As, Hinrichs Bj, Raney Ml, Speir B, Rhead J, Casper D, Karolchik Rm, Kuhn Kr, Rosenbloom As, Zweig David Haussler
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Published in
Bioinformatics
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M, Goldman B, Craft T, Swatloski K, Ellrott M, Cline M, Diekhans S, Ma C, Wilks Josh Stuart David Haussler
...
Published in
Nucleic Acids Research
The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a set of web-based tools to display, investigate and analyse cancer genomics data and its associated clinical information. The browser provides whole-genome to base-pair level views of several different types of genomics data, including some next-generation sequencing platforms. ...
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M, Blanchette Ed, Green W, Miller David Haussler
Published in
Genome Research
It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral genome sequence an ideal target for reconstruction. Simulations suggest that with methods currently available, we can expect to get 98% of the bases cor...
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Cs, Onodera Jg, Underwood S, Katzman F, Jacobs D, Greenberg Sr, Salama David Haussler
Enhancers and antisense RNAs play key roles in transcriptional regulation through differing mechanisms. Recent studies have demonstrated that enhancers are often associated with non-coding RNAs (ncRNAs), yet the functional role of these enhancer:ncRNA associations is unclear. Using RNA-Sequencing to interrogate the transcriptomes of undifferentiate...
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Cb, Lowe N, Ahituv B, King A, Siepel Sr, Salama Em, Rubin Wj, Kent David Haussler G, Bejerano
Published in
Nature
Hundreds of highly conserved distal cis-regulatory elements have been characterized so far in vertebrate genomes. Many thousands more are predicted on the basis of comparative genomics. However, in stark contrast to the genes that they regulate, in invertebrates virtually none of these regions can be traced by using sequence similarity, leaving the...
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Js, Pedersen G, Bejerano A, Siepel K, Rosenbloom K, Lindblad-Toh Es, Lander J, Kent W, Miller David Haussler
Published in
PLoS Computational Biology
The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general comparative genomics method based on phylogenetic stochastic context-free grammars for identifying functional RNAs encoded in the human geno...
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Ml, Speir As, Zweig Kr, Rosenbloom Bj, Raney B, Paten P, Nejad Bt, Lee K, Learned D, Karolchik As, Hinrichs
...
Published in
Nucleic Acids Research
For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development since its incepti...
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F, Hsu Wj, Kent H, Clawson Rm, Kuhn M, Diekhans David Haussler
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...
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Cw, Sugnet Wj, Kent Jr, Ares M David Haussler
Published in
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Combining mRNA and EST data in splicing graphs with whole genome alignments, we discover alternative splicing events that are conserved in both human and mouse transcriptomes. 1,964 of 19,156 (10%) loci examined contain one or more such alternative splicing events, with 2,698 total events. These events represent a lower bound on the amount of alter...
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D, Kulp David Haussler Mg, Reese Fh, Eeckman
Published in
International Conference on Intelligent Systems for Molecular Biology
We present a statistical model of genes in DNA. A Generalized Hidden Markov Model (GHMM) provides the framework for describing the grammar of a legal parse of a DNA sequence (Stormo & Haussler 1994). Probabilities are assigned to transitions between states in the GHMM and to the generation of each nucleotide base given a particular state. Machine l...
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Sj, Obrien David Haussler O, Ryder
Published in
GigaScience
Everyone loves the birds of the world. From their haunting songs and majesty of flight to dazzling plumage and mating rituals, bird watchers - both amateurs and professionals - have marveled for centuries at their considerable adaptations. Now, we are offered a special treat with the publication of a series of papers in dedicated issues of Science,...
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S, Katzman Ad, Kern Ks, Pollard Sr, Salama David Haussler
Published in
PLoS Genetics
Regions of the genome that have been the target of positive selection specifically along the human lineage are of special importance in human biology. We used high throughput sequencing combined with methods to enrich human genomic samples for particular targets to obtain the sequence of 22 chromosomal samples at high depth in 40 kb neighborhoods o...
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Ja, Bailey R, Baertsch Wj, Kent David Haussler Ee, Eichler
Published in
Genome Biology
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F, Chiaromonte Rj, Weber Km, Roskin M, Diekhans Wj, Kent David Haussler
Published in
Cold Spring Harbor Symposia on Quantitative Biology
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Cb, Lowe G, Bejerano David Haussler
Published in
Proceedings of the National Academy of Sciences
At least 5% of the human genome predating the mammalian radiation is thought to have evolved under purifying selection, yet protein-coding and related untranslated exons occupy at most 2% of the genome. Thus, the majority of conserved and, by extension, functional sequence in the human genome seems to be nonexonic. Recent work has highlighted a han...
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David Haussler
Published in
PLoS Genetics
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A, Siepel David Haussler
Published in
Journal of Computational Biology
A few models have appeared in recent years that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way the process changes from one site to the next. These models combine phylogenetic models of molecular evolution, which apply to individual sites, and hidden Markov models, which allow f...
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Cj, Vaske Sc, Benz Jz, Sanborn D, Earl C, Szeto J, Zhu David Haussler Josh Stuart
Published in
Bioinformatics