Brian Craft
University of California, Santa Cruz
GeneThe InternetCancerWorld Wide WebGenomeFunctional genomicsData visualizationSet (abstract data type)GenomicsDNA methylationData scienceCancer genomePan cancerVisualizationComputer scienceGeneticsResource (project management)BioinformaticsComputational biologyBiology
35Publications
19H-index
21.9kCitations
Publications 34
Newest
#1Mary Goldman (UCSC: University of California, Santa Cruz)H-Index: 20
#2Brian Craft (UCSC: University of California, Santa Cruz)H-Index: 19
Last. David Haussler (UCSC: University of California, Santa Cruz)H-Index: 177
view all 4 authors...
UCSC Xena (http://xena.ucsc.edu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Researchers can easily view and explore public data, their own private data, or both using the Xena Browser. Data is kept on the researcher9s computer (we support Mac, Windows, and Linux) and is never uploaded to public servers. null Questions Xena can help you answer: null * Is overexpression of this gene associated with lower/higher su...
Source
#1Jian Carrot-ZhangH-Index: 12
#2Xiaotong YaoH-Index: 9
Last. Marcin ImielinskiH-Index: 50
view all 82 authors...
Summary RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to be RPA(−) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of LUADs lacking apparent alterations in this pathway. We show that WGS analysis uncovers RPA(+) in 28 (33%) of the 85 samples. Among the remaining 57 cases, we observe focal deletions targeting the promoter or transcription start site of ...
Source
#1Mary Goldman (UCSC: University of California, Santa Cruz)H-Index: 20
#2Junjun Zhang (OICR: Ontario Institute for Cancer Research)H-Index: 17
Last. Miguel Vazquez (NTNU: Norwegian University of Science and Technology)H-Index: 19
view all 24 authors...
The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we provide a user’s guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper. These tools are ICGC Data Portal, UCSC Xena, Chromot...
6 CitationsSource
#1Mary Goldman (UCSC: University of California, Santa Cruz)H-Index: 20
#2Brian Craft (UCSC: University of California, Santa Cruz)H-Index: 19
Last. David Haussler (UCSC: University of California, Santa Cruz)H-Index: 177
view all 12 authors...
269 CitationsSource
#1Peter J. Campbell (Broad Institute)H-Index: 128
#2abpEmailH-Index: 1
Last. Jiashan Zhang (NIH: National Institutes of Health)H-Index: 6
view all 1330 authors...
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource...
647 CitationsSource
#1Mary Goldman (UCSC: University of California, Santa Cruz)H-Index: 20
#2Brian Craft (UCSC: University of California, Santa Cruz)H-Index: 19
Last. David Haussler (UCSC: University of California, Santa Cruz)H-Index: 177
view all 12 authors...
UCSC Xena is a visual exploration resource for both public and private omics data, supported through the web-based Xena Browser and multiple turn-key Xena Hubs. This unique archecture allows researchers to view their own data securely, using private Xena Hubs, simultaneously visualizing large public cancer genomics datasets, including TCGA and the GDC. Data integration occurs only within the Xena Browser, keeping private data private. Xena supports virtually any functional genomics data, includi...
257 CitationsSource
#1Mary Goldman (UCSC: University of California, Santa Cruz)H-Index: 20
#2Junjun Zhang (OICR: Ontario Institute for Cancer Research)H-Index: 17
Last. Miguel Vazquez (Barcelona Supercomputing Center)H-Index: 2
view all 24 authors...
Pan-Cancer Analysis of Whole Genomes (PCAWG) encompasses the largest collection, to date, of uniformly-processed, cancer whole-genome sequencing data sets. While this dataset has the power to elucidate many cancer biology mechanisms, it also poses serious challenges for visualization tools because of its size and complexity. Here we describe five publicly available tools, each either designed or augmented to derive insights from this unique resource: The ICGC Data Portal, UCSC Xena, Expression A...
Source
#1Mary GoldmanH-Index: 20
#2Brian CraftH-Index: 19
Last. David HausslerH-Index: 177
view all 4 authors...
Source
#1Melissa S. Cline (UCSC: University of California, Santa Cruz)H-Index: 16
#1Melissa S. Cline (UCSC: University of California, Santa Cruz)H-Index: 29
Last. Amanda B. Spurdle (QIMR: QIMR Berghofer Medical Research Institute)H-Index: 86
view all 46 authors...
The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data to support highly collaborative research activities. Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2. Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, ne...
75 CitationsSource
#1Mary Goldman (UCSC: University of California, Santa Cruz)H-Index: 20
#2Brian Craft (UCSC: University of California, Santa Cruz)H-Index: 19
Last. David Haussler (UCSC: University of California, Santa Cruz)H-Index: 177
view all 4 authors...
The UCSC Xena platform (http://xena.ucsc.edu/) allows biologists and bioinformaticians to securely analyze and visualize functional genomics data. Our unique Visual Spreadsheet shows multiple data types side by side enabling discovery of correlations across and within genes and genomic regions. Dynamic Kaplan-Meier survival analysis assesses survival stratification in addition to scatter plots, bar graphs, and boxplots all shown with statistical tests. In addition to the commonly available SNPs,...
1 CitationsSource