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Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution.
For decades, cytogenetic studies have demonstrated that somatically acquired structural rearrangements of the genome are a common feature of most classes of human cancer. However, the characteristicsExpand
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A SAGE Approach to Discovery of Genes Involved in Autophagic Cell Death
Programmed cell death (PCD), important in normal animal physiology and disease, can be divided into at least two morphological subtypes, including type I, or apoptosis, and type II, or autophagicExpand
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ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
MOTIVATION Our understanding of gene regulation is currently limited by our ability to collectively synthesize and catalogue transcriptional regulatory elements stored in scientific literature. OverExpand
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Estimation of rearrangement phylogeny for cancer genomes.
Cancer genomes are complex, carrying thousands of somatic mutations including base substitutions, insertions and deletions, rearrangements, and copy number changes that have been acquired overExpand
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Assessment of SAGE in transcript identification.
An essential step in Serial Analysis of Gene Expression (SAGE) is tag mapping, which refers to the unambiguous determination of the gene represented by a SAGE tag. Current resources for tag mappingExpand
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cisRED: a database system for genome-scale computational discovery of regulatory elements
We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (). The database and high-throughput predictive pipeline areExpand
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A somatic reference standard for cancer genome sequencing
Large-scale multiplexed identification of somatic alterations in cancer has become feasible with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools has been hamperedExpand
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Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses.
Large amounts of gene expression data from several different technologies are becoming available to the scientific community. A common practice is to use these data to calculate global geneExpand
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Identification and analysis of internal promoters in Caenorhabditis elegans operons.
The current Caenorhabditis elegans genomic annotation has many genes organized in operons. Using directionally stitched promoterGFP methodology, we have conducted the largest survey to date on theExpand
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Personalized Oncogenomics: Clinical Experience with Malignant Peritoneal Mesothelioma Using Whole Genome Sequencing
Peritoneal mesothelioma is a rare and sometimes lethal malignancy that presents a clinical challenge for both diagnosis and management. Recent studies have led to a better understanding of theExpand
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