Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment

B cells are associated with survival and immunotherapy response in sarcoma

(2020) Florent Petitprez et al.   NATURE

Tertiary lymphoid structures improve immunotherapy and survival in melanoma

(2020) Rita Cabrita et al.   NATURE

B cells and tertiary lymphoid structures promote immunotherapy response

(2020) Beth A. Helmink et al.   NATURE

An approach for normalization and quality control for NanoString RNA expression data

(2020) Arjun Bhattacharya et al.   BRIEFINGS IN BIOINFORMATICS

Genome-Wide CRISPR-Cas9 Screens Expose Genetic Vulnerabilities and Mechanisms of Temozolomide Sensitivity in Glioblastoma Stem Cells

(2019) Graham MacLeod et al.   Cell Reports

Opposing Functions of Interferon Coordinate Adaptive and Innate Immune Responses to Cancer Immune Checkpoint Blockade

(2019) Joseph L. Benci et al.   CELL

B Cells and T Follicular Helper Cells Mediate Response to Checkpoint Inhibitors in High Mutation Burden Mouse Models of Breast Cancer

(2019) Daniel P. Hollern et al.   CELL

Circular ecDNA promotes accessible chromatin and high oncogene expression

(2019) Sihan Wu et al.   NATURE

Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design

(2019) Jo Lynne Rokita et al.   Cell Reports

National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed, Paraffin-Embedded Tissue

(2018) Sarah R. Greytak et al.   BIOPRESERVATION AND BIOBANKING

Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response

(2018) Daniel Temko et al.   JOURNAL OF PATHOLOGY

National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed, Paraffin-Embedded Tissue

(2018) Sarah R. Greytak et al.   Biopreservation and Biobanking

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

(2018) Theo A. Knijnenburg et al.   Cell Reports

Successful Anti-PD-1 Cancer Immunotherapy Requires T Cell-Dendritic Cell Crosstalk Involving the Cytokines IFN-γ and IL-12

(2018) Christopher S. Garris et al.   IMMUNITY

FusionGDB: fusion gene annotation DataBase

(2018) Pora Kim et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2018) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Epigenetic silencing of MLH1 in endometrial cancers is associated with larger tumor volume, increased rate of lymph node positivity and reduced recurrence-free survival

(2017) Casey M. Cosgrove et al.   GYNECOLOGIC ONCOLOGY

Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity

(2017) Kristen M. Turner et al.   NATURE

AACR Project GENIE: Powering Precision Medicine through an International Consortium

(2017)   Cancer Discovery

Gene expression markers of Tumor Infiltrating Leukocytes

(2017) Patrick Danaher et al.   Journal for ImmunoTherapy of Cancer

QuPath: Open source software for digital pathology image analysis

(2017) Peter Bankhead et al.   Scientific Reports

Chemoproteomics-Enabled Discovery of a Potent and Selective Inhibitor of the DNA Repair Protein MGMT

(2016) Chao Wang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia

(2016) Malachi Griffith et al.   EXPERIMENTAL HEMATOLOGY

DNA repair mechanisms and their clinical impact in glioblastoma

(2016) Hélène Erasimus et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

(2016) Sebastian Moran et al.   Epigenomics

Oncotator: Cancer Variant Annotation Tool

(2015) Alex H. Ramos et al.   HUMAN MUTATION

TBCRC009: A Multicenter Phase II Clinical Trial of Platinum Monotherapy With Biomarker Assessment in Metastatic Triple-Negative Breast Cancer

(2015) Steven J. Isakoff et al.   JOURNAL OF CLINICAL ONCOLOGY

PD-L1 Expression as a Predictive Biomarker in Cancer Immunotherapy

(2015) S. P. Patel et al.   MOLECULAR CANCER THERAPEUTICS

APE1/REF-1 down-regulation enhances the cytotoxic effects of temozolomide in a resistant glioblastoma cell line

(2015) Ana P. Montaldi et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

Genomic profiling of Sézary syndrome identifies alterations of key T cell signaling and differentiation genes

(2015) Linghua Wang et al.   NATURE GENETICS

SomaticPOLEmutations cause an ultramutated giant cell high-grade glioma subtype with better prognosis

(2015) E. Zeynep Erson-Omay et al.   NEURO-ONCOLOGY

Vemurafenib in Multiple Nonmelanoma Cancers with BRAF V600 Mutations

(2015) David M. Hyman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

(2014) S. C. Mack et al.   NATURE

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Synthetic Lethality in ATM-Deficient RAD50-Mutant Tumors Underlies Outlier Response to Cancer Therapy

(2014) H. Al-Ahmadie et al.   Cancer Discovery

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

(2013) Gabriela Bindea et al.   IMMUNITY

DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities

(2013) Atsushi Shibata et al.   MOLECULAR CELL

Low-level processing of Illumina Infinium DNA Methylation BeadArrays

(2013) Timothy J. Triche et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

PIK3CA/PTEN Mutations and Akt Activation As Markers of Sensitivity to Allosteric mTOR Inhibitors

(2012) F. Meric-Bernstam et al.   CLINICAL CANCER RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Genome Sequencing Identifies a Basis for Everolimus Sensitivity

(2012) G. Iyer et al.   SCIENCE

Functional significance of mutations in the Snf2 domain of ATRX

(2011) Matthew Mitson et al.   HUMAN MOLECULAR GENETICS

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

The MRE11 complex: starting from the ends

(2011) Travis H. Stracker et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Sunitinib Malate for the Treatment of Pancreatic Neuroendocrine Tumors

(2011) Eric Raymond et al.   NEW ENGLAND JOURNAL OF MEDICINE

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities

(2011) Matthew N Bainbridge et al.   GENOME BIOLOGY

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia

(2010) Maria E. Figueroa et al.   CANCER CELL

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Small molecule inhibitors of DNA repair nuclease activities of APE1

(2010) David M. Wilson et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Anaplastic Lymphoma Kinase Inhibition in Non–Small-Cell Lung Cancer

(2010) Eunice L. Kwak et al.   NEW ENGLAND JOURNAL OF MEDICINE

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS