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J, Wu David Haussler
Published in
Journal of Computational Biology
We introduce a new system, called shortHMM, for predicting exons, which predicts individual exons using two related genomes. In this system, we build a hidden semi-Markov model to identify exons. In the hidden Markov model, we propose joint probability models of nucleotides in introns, splice sites, 5 UTR, 3 UTR, and intergenic regions by exploitin...
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David Haussler
Published in
PLoS Genetics
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Cb, Lowe M, Kellis A, Siepel Bj, Raney M, Clamp Sr, Salama Dm, Kingsley K, Lindblad-Toh David Haussler
Published in
Science
The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory r...
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C, Wilks Ms, Cline E, Weiler M, Diehkans B, Craft C, Martin D, Murphy H, Pierce J, Black D, Nelson
...
Published in
Database
The Cancer Genomics Hub (CGHub) is the online repository of the sequencing programs of the National Cancer Institute (NCI), including The Cancer Genomics Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects, with data from 25 different types of cancer. ...
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X, Zhou B, Maricque M, Xie D, Li V, Sundaram Ea, Martin Bc, Koebbe C, Nielsen M, Hirst P, Farnham
...
Published in
Nature Methods
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Kr, Rosenbloom J, Armstrong Gp, Barber J, Casper H, Clawson M, Diekhans Tr, Dreszer Pa, Fujita L, Guruvadoo M, Haeussler
...
Published in
Nucleic Acids Research
Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new hu...
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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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Jg, Underwood Av, Uzilov S, Katzman Cs, Onodera Je, Mainzer Dh, Mathews Tm, Lowe Sr, Salama David Haussler
Published in
Nature Methods
Classical approaches to determine structures of noncoding RNA (ncRNA) probed only one RNA at a time with enzymes and chemicals, using gel electrophoresis to identify reactive positions. To accelerate RNA structure inference, we developed fragmentation sequencing (FragSeq), a high-throughput RNA structure probing method that uses high-throughput RNA...
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Ts, Furey N, Cristianini N, Duffy Dw, Bednarski M, Schummer David Haussler
Published in
Bioinformatics
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Vn, Kristensen Cj, Vaske J, Ursini-Siegel P, Van Loo Sh, Nordgard R, Sachidanandam T, Sørlie F, Wärnberg Vd, Haakensen Å, Helland
...
Published in
Proceedings of the National Academy of Sciences
We use an integrated approach to understand breast cancer heterogeneity by modeling mRNA, copy number alterations, microRNAs, and methylation in a pathway context utilizing the pathway recognition algorithm using data integration on genomic models (PARADIGM). We demonstrate that combining mRNA expression and DNA copy number classified the patients ...
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Am, Novak Y, Rosen David Haussler B, Paten
Published in
Bioinformatics
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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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Eo, Paull De, Carlin M, Niepel Pk, Sorger David Haussler Josh Stuart
Published in
Bioinformatics
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T, Jaakkola M, Diekhans David Haussler
Published in
International Conference on Intelligent Systems for Molecular Biology
A new method, called the Fisher kernel method, for detecting remote protein homologies is introduced and shown to perform well in classifying protein domains by SCOP superfamily. The method is a variant of support vector machines using a new kernel function. The kernel function is derived from a hidden Markov model. The general approach of combinin...
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Sw, Hulyk E, Fuh Y, Yuan A, Sneed C, Kowis A, Hodgson Dm, Muzny J, Mcpherson Ra, Gibbs J, Fahey
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Published in
Genome Research
The National Institutes of Health s Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues....
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T, Wang J, Zeng Cb, Lowe Rg, Sellers Sr, Salama M, Yang Sm, Burgess Rk, Brachmann David Haussler
Published in
Proceedings of the National Academy of Sciences
The evolutionary forces that establish and hone target gene networks of transcription factors are largely unknown. Transposition of retroelements may play a role, but its global importance, beyond a few well described examples for isolated genes, is not clear. We report that LTR class I endogenous retrovirus (ERV) retroelements impact considerably ...
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B, Clift David Haussler R, Mcconnell Td, Schneider Gd, Stormo
Published in
Nucleic Acids Research
We describe a method for representing the structure of repeating sequences in nucleic-acids, proteins and other texts. A portion of the sequence is presented at the bottom of a CRT screen. Above the sequence is its landscape, which looks like a mountain range. Each mountain corresponds to a subsequence of the sequence. At the peak of every mountain...
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B, Paten D, Earl N, Nguyen M, Diekhans D, Zerbino David Haussler
Published in
Genome Research
Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced f...
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G, Bejerano Ac, Siepel Wj, Kent David Haussler
Published in
Nature Methods
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Consortium, Roadmap Epigenomics A, Kundaje W, Meuleman J, Ernst M, Bilenky A, Yen A, Heravi-Moussavi P, Kheradpour Z, Zhang J, Wang
...
Published in
Nature
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integ...