Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival

SGK1, the New Player in the Game of Resistance: Chemo-Radio Molecular Target and Strategy for Inhibition

(2016) Cristina Talarico et al.   CELLULAR PHYSIOLOGY AND BIOCHEMISTRY

Nucleotide excision repair is impaired by binding of transcription factors to DNA

(2016) Radhakrishnan Sabarinathan et al.   NATURE

Functional Mutations Form at CTCF-Cohesin Binding Sites in Melanoma Due to Uneven Nucleotide Excision Repair across the Motif

(2016) Rebecca C. Poulos et al.   Cell Reports

Data analysis: Create a cloud commons

(2015) Lincoln D. Stein et al.   NATURE

Non-coding recurrent mutations in chronic lymphocytic leukaemia

(2015) Xose S. Puente et al.   NATURE

Recurrent somatic mutations in regulatory regions of human cancer genomes

(2015) Collin Melton et al.   NATURE GENETICS

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The dark side of ZNF217, a key regulator of tumorigenesis with powerful biomarker value

(2015) Pascale A. Cohen et al.   Oncotarget

Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells

(2015) Elena Grassi et al.   PLoS One

Recurrent targets of aberrant somatic hypermutation in lymphoma

(2015) Alireza Hadj Khodabakhshi et al.   Oncotarget

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

(2014) Nils J Fredriksson et al.   NATURE GENETICS

TCGA-Assembler: open-source software for retrieving and processing TCGA data

(2014) Yitan Zhu et al.   NATURE METHODS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data

(2014) Mehmet Kemal Samur   PLoS One

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Protein tyrosine phosphatase kappa (PTPRK) is a negative regulator of adhesion and invasion of breast cancer cells, and associates with poor prognosis of breast cancer

(2013) Ping-Hui Sun et al.   JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY

Frequent SomaticTERTPromoter Mutations in Thyroid Cancer: Higher Prevalence in Advanced Forms of the Disease

(2013) Iñigo Landa et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal

(2013) P. J. Killela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TERT Promoter Mutations in Familial and Sporadic Melanoma

(2013) S. Horn et al.   SCIENCE

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

(2013) Ekta Khurana et al.   SCIENCE

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

(2013) Hirotaka Nakahashi et al.   Cell Reports

ZNF217 Is a Marker of Poor Prognosis in Breast Cancer That Drives Epithelial-Mesenchymal Transition and Invasion

(2012) J. A. Vendrell et al.   CANCER RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

(2012) Richard Cowper-Sal·lari et al.   NATURE GENETICS

Evolution of the cancer genome

(2012) Lucy R. Yates et al.   NATURE REVIEWS GENETICS

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

The CTCF insulator protein forms an unusual DNA structure

(2011) Melissa J MacPherson et al.   BMC MOLECULAR BIOLOGY

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

An ending is a new beginning: Transcription termination supports re-initiation

(2011) Søren Lykke-Andersen et al.   CELL CYCLE

A frequent somatic mutation in CD274 3′-UTR leads to protein over-expression in gastric cancer by disrupting miR-570 binding

(2011) Weipeng Wang et al.   HUMAN MUTATION

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites

(2010) Savina A. Jaeger et al.   GENOMICS

CDC6 interaction with ATR regulates activation of a replication checkpoint in higher eukaryotic cells

(2010) K. Yoshida et al.   JOURNAL OF CELL SCIENCE

TP53 Mutations in Korean Patients with Non-small Cell Lung Cancer

(2010) Eung Bae Lee et al.   JOURNAL OF KOREAN MEDICAL SCIENCE

Crosstalk between mRNA 3′ End Processing and Transcription Initiation

(2010) Christophe K. Mapendano et al.   MOLECULAR CELL

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Frameshift mutation of MAPRE3, a microtubule-related gene, in gastric and colorectal cancers with microsatellite instability

(2010) Yoo Ri Kim et al.   PATHOLOGY

Cell type specificity of chromatin organization mediated by CTCF and cohesin

(2010) Chunhui Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Low expression of a few genes indicates good prognosis in estrogen receptor positive breast cancer

(2009) Steven Buechler   BMC CANCER

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Loss of miR-122 expression in liver cancer correlates with suppression of the hepatic phenotype and gain of metastatic properties

(2009) C Coulouarn et al.   ONCOGENE

A Transposon-Based Genetic Screen in Mice Identifies Genes Altered in Colorectal Cancer

(2009) T. K. Starr et al.   SCIENCE

Clinical Outcomes and Correlates of TP53 Mutations and Cancer

(2009) A. I. Robles et al.   Cold Spring Harbor Perspectives in Biology

Why Most Discovered True Associations Are Inflated

(2008) John P. A. Ioannidis   EPIDEMIOLOGY