Search on UC Santa Cruz Cancer Cluster's publications

UCSC Data Integrator and Variant Annotation Integrator.

As, Hinrichs Bj, Raney Ml, Speir B, Rhead J, Casper D, Karolchik Rm, Kuhn Kr, Rosenbloom As, Zweig David Haussler ...

Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other...

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Ev...

Paull, Eo Carlin, De Niepel, M Sorger, Pk David Haussler Josh Stuart

Published in Bioinformatics

Gene structure-based splice variant deconvolution using a microarray platform.

Wang, H Hubbell, E Hu, Js Mei, G Cline, M Lu, G Clark, T Siani-Rose, Ma Ares, M Kulp, Dc ...

Published in Bioinformatics

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.

Ng, S Collisson, Ea Sokolov, A Goldstein, T Gonzalez-Perez, A Lopez-Bigas, N Benz, C David Haussler Josh Stuart

Published in Bioinformatics

Comparative assembly hubs: web-accessible browsers for comparative genomics.

N, Nguyen G, Hickey Bj, Raney J, Armstrong H, Clawson A, Zweig D, Karolchik Wj, Kent David Haussler B, Paten ...

Published in Bioinformatics

Motivation: Researchers now have access to large volumes of genome sequences for comparative analysis, some generated by the plethora of public sequencing projects and, increasingly, from individual efforts. It is not possible, or necessarily desirable, that the public genome browsers attempt to curate all these data. Instead, a wealth of powerful ...

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

Furey, Ts Cristianini, N Duffy, N Bednarski, Dw Schummer, M David Haussler

Published in Bioinformatics

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

Stanke, M Diekhans, M Baertsch, R David Haussler

Published in Bioinformatics

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.

Karchin, R Diekhans, M Kelly, L Thomas, Dj Pieper, U Eswar, N David Haussler Sali, A

Published in Bioinformatics

Efficient approximations for learning phylogenetic HMM models from data.

Jojic, V Jojic, N Meek, C Geiger, D Siepel, A David Haussler Heckerman, D

Published in Bioinformatics

The UCSC Known Genes.

Hsu, F Kent, Wj Clawson, H Kuhn, Rm Diekhans, M 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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