• Publications
  • Influence
The human genome browser at UCSC.
A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu. Expand
Initial sequencing and analysis of the human genome.
The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence. Expand
Integrative analysis of 111 reference human epigenomes
It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Expand
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
A comprehensive search for conserved elements in vertebrate genomes is conducted, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu rubripes), using a two-state phylogenetic hidden Markov model (phylo-HMM). Expand
GENCODE: the reference human genome annotation for The ENCODE Project.
This work has examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites, and over one-third of GENCODE protein-Coding genes aresupported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. Expand
The Somatic Genomic Landscape of Glioblastoma
Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Expand
Integrated genomic characterization of endometrial carcinoma
  • D. Levine, Gad Stacey B. Kristian Eric Andrey Carrie Mike Cyriac Getz Gabriel Cibulskis Lander Sivachenko Sougnez L, +271 authors H. Sofia
  • Biology, Medicine
  • Nature
  • 1 May 2013
The genomic features of endometrial carcinomas permit a reclassification that may affect post-surgical adjuvant treatment for women with aggressive tumours, and these features are classified into four categories: POLE ultramutated, microsatellite instability hypermutated, copy- number low, and copy-number high. Expand
The UCSC Table Browser data retrieval tool
The University of California Santa Cruz (UCSC) Table Browser provides text-based access to a large collection of genome assemblies and annotation data stored in the Genome Browser Database and offers an enhanced level of query support that includes restrictions based on field values, free-form SQL queries and combined queries on multiple tables. Expand
Learnability and the Vapnik-Chervonenkis dimension
This paper shows that the essential condition for distribution-free learnability is finiteness of the Vapnik-Chervonenkis dimension, a simple combinatorial parameter of the class of concepts to be learned. Expand
Exploiting Generative Models in Discriminative Classifiers
A natural way of achieving this combination by deriving kernel functions for use in discriminative methods such as support vector machines from generative probability models is developed. Expand