Publications

recountmethylation enables flexible analysis of public blood DNA methylation array data
Cite
Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space
Cite
GA4GH: International policies and standards for data sharing across genomic research and healthcare
Cite
A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery
Cite
Sex differences in oncogenic mutational processes
Cite
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Cite
Pan-cancer analysis of whole genomes.
Cite
Neoepiscope improves neoepitope prediction with multivariant phasing
Cite
Exploring integrative analysis using the BioMedical evidence graph
Cite
Butler enables rapid cloud-based analysis of thousands of human genomes
Cite
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer
Cite
A community effort to create standards for evaluating tumor subclonal reconstruction
Cite
Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges
Cite
Creating standards for evaluating tumour subclonal reconstruction
Cite
Valection: design optimization for validation and verification studies
Cite
TBIO-27. GABRIELLA MILLER KIDS FIRST DATA RESOURCE CENTER ADVANCING GENETIC RESEARCH IN CHILDHOOD CANCER AND STRUCTURAL BIRTH DEFECTS THROUGH LARGE SCALE INTEGRATED DATA-DRIVEN DISCOVERY AND CLOUD-BASED PLATFORMS FOR COLLABORATIVE ANALYSIS
Cite
SMMART: Serial measurements of molecular and architectural responses to therapy
Cite
Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines
Cite
Population-level distribution and putative immunogenicity of cancer neoepitopes
Cite
Multi-center mutation calling in multiple cancers: the MC3 project
Cite
Germline contamination and leakage in whole genome somatic single nucleotide variant detection
Cite
Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
Cite
A pan-cancer analysis reveals high-frequency genetic alterations in mediators of signaling by the TGF-$β$ superfamily
Cite
TumorMap: exploring the molecular similarities of cancer samples in an interactive portal
Cite
Prophetic Granger Causality to infer gene regulatory networks
Cite
Large-scale uniform analysis of cancer whole genomes in multiple computing environments
Cite
A community challenge for inferring genetic predictors of gene essentialities through analysis of a functional screen of cancer cell lines
Cite
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
Cite
Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic variant detection
Cite
Abstract PR02: Multiple Pathway Learning accurately predicts gene essentiality in the Cancer Cell Line Encyclopedia
Cite
Abstract B1-37: A signature catalog to classify tumor mixtures: application to recognition of metastatic disease in prostate cancer
Cite
Global optimization of somatic variant identification in cancer genomes with a global community challenge
Cite
Weinstein JN
Cite
The UCSC cancer genomics browser: update 2013
Cite
The somatic genomic landscape of glioblastoma
Cite
The cancer genome atlas pan-cancer analysis project
Cite
Structure of the gamma D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala--D-Glu: Insights into substrate recognition by NlpC/P60 cysteine peptidases
Cite
Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas
Cite
Comprehensive molecular characterization of clear cell renal cell carcinoma
Cancer Genome Atlas Research Network Analysis working group: Baylor College of Medicine Creighton Chad J. 1 2 Morgan Margaret 1 Gunaratne Preethi H. 1 3 Wheeler David A. 1 Gibbs Richard A. 1, BC Cancer Agency Gordon Robertson A. 4 Chu Andy 4, Broad Institute Beroukhim Rameen 5 6 Cibulskis Kristian 6, Brigham & Women’s Hospital Signoretti Sabina 7 54 59, Brown University Vandin Hsin-Ta Wu Fabio 8 8 Raphael Benjamin J. 8, University of Texas MD Anderson Cancer Center Verhaak Roel GW 9 Tamboli Pheroze 10 Torres-Garcia Wandaliz 9 Akbani Rehan 9 Weinstein John N. 9, Memorial Sloan-Kettering Cancer Center Reuter Victor 11 Hsieh James J. 12 Rose Brannon A. 11 Ari Hakimi A. 12 Jacobsen Anders 13 Ciriello Giovanni 13 Reva Boris 13, National Cancer Institute Ricketts Christopher J. 14 Marston Linehan W. agibbs@ bcm. edu 14 c, University of California Santa Cruz Stuart Joshua M. 15, Chapel Hill Kimryn Rathmell W. 16 University of North Carolina, others
Cite
UCSC Cancer Genomics Browser 2.0
Cite
Predicting the impact of mutations in cancer using an integrated pathway approach
Cite
Comprehensive molecular portraits of human breast tumours
Cite
Comprehensive molecular characterization of human colon and rectal cancer
Cite
Comprehensive genomic characterization of squamous cell lung cancers
Cite
Abstract A39: The UCSC Cancer Genomics Browser
Cite
TOPSAN: a dynamic web database for structural genomics
Cite
The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation
Cite
The structure of KPN03535 (gi| 152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold
Cite
The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function
Cite
The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu
Cite
Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved $α$+ $β$ core domain and an auxiliary C-terminal treble-clef zinc finger
Cite
Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism
Cite
Structure of the c-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-c-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases
Cite
Structure of the $γ$-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-$γ$-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases
Cite
Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules
Cite
Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism
Cite
Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron
Cite
Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families
Cite
Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain
Cite
A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution
Cite
Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes
Cite
Improving the performance of protein threading using insertion/deletion frequency arrays
Cite
A historical perspective of template-based protein structure prediction
Cite
Protein Threading for Genome-Scale Structural Analysis
Cite
Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays
Cite
A Generalized Threading Model Using Integer Programming that Allows for Secondary Structure Element Deletion
Cite
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction
Cite
PROSPECT II: protein structure prediction program for genome-scale applications
Cite
A computational pipeline for protein structure prediction and analysis at genome scale
Cite
Restriction enzyme recognition sequence search program
Cite
Identifying transcription factor binding sites through Markov chain optimization
Cite