Genome-wide analysis of somatic noncoding mutation patterns in cancer

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

The Role of the Transcription Factor EGR1 in Cancer

(2021) Bin Wang et al.   Frontiers in Oncology

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

(2020) Esther Rheinbay et al.   NATURE

Genomic basis for RNA alterations in cancer

(2020) Claudia Calabrese et al.   NATURE

Pan-cancer analysis of whole genomes

(2020)   NATURE

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Patterns of somatic structural variation in human cancer genomes

(2020) Yilong Li et al.   NATURE

Identification of cancer driver genes based on nucleotide context

(2020) Felix Dietlein et al.   NATURE GENETICS

Combined burden and functional impact tests for cancer driver discovery using DriverPower

(2020) Shimin Shuai et al.   Nature Communications

Single-cell RNA sequencing of human kidney

(2020) Jinling Liao et al.   Scientific Data

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

The emerging role of XBP1 in cancer

(2020) Shanshan Chen et al.   BIOMEDICINE & PHARMACOTHERAPY

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

MutSpot: detection of non-coding mutation hotspots in cancer genomes

(2020) Yu Amanda Guo et al.   npj Genomic Medicine

Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator

(2020) Erik N. Bergstrom et al.   BMC BIOINFORMATICS

Inhibition of O-GlcNAc transferase activates tumor-suppressor gene expression in tamoxifen-resistant breast cancer cells

(2020) Anna Barkovskaya et al.   Scientific Reports

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Cauchy combination test: a powerful test with analytic p-value calculation under arbitrary dependency structures

(2019) Yaowu Liu et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Loss of KCNJ15 expression promotes malignant phenotypes and correlates with poor prognosis in renal carcinoma

(2019) Yang Liu et al.   Cancer Management and Research

Local Determinants of the Mutational Landscape of the Human Genome

(2019) Abel Gonzalez-Perez et al.   CELL

Impact of cancer mutational signatures on transcription factor motifs in the human genome

(2019) Calvin Wing Yiu Chan et al.   BMC Medical Genomics

Inherited nonalcoholic fatty liver disease and dyslipidemia due to monoallelic ABHD5 mutations

(2019) Leila Youssefian et al.   JOURNAL OF HEPATOLOGY

Benefits and limitations of genome-wide association studies

(2019) Vivian Tam et al.   NATURE REVIEWS GENETICS

Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes

(2019) Eric Minwei Liu et al.   Cell Systems

A human liver cell atlas reveals heterogeneity and epithelial progenitors

(2019) Nadim Aizarani et al.   NATURE

Mechanisms underlying the activation of TERT transcription and telomerase activity in human cancer: old actors and new players

(2019) Xiaotian Yuan et al.   ONCOGENE

Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features

(2019) Rémi Buisson et al.   SCIENCE

SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events

(2019) Erik N. Bergstrom et al.   BMC GENOMICS

Passenger Hotspot Mutations in Cancer

(2019) Julian M. Hess et al.   CANCER CELL

Pan-cancer whole-genome analyses of metastatic solid tumours

(2019) Peter Priestley et al.   NATURE

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Liver Activation of Hepatocellular Nuclear Factor-4α by Small Activating RNA Rescues Dyslipidemia and Improves Metabolic Profile

(2019) Kai-Wen Huang et al.   Molecular Therapy-Nucleic Acids

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

(2018) Giovanna Ambrosini et al.   BIOINFORMATICS

ncdDetect2: Improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation

(2018) Malene Juul et al.   BIOINFORMATICS

Choosing between methods of combining $p$-values

(2018) N A Heard et al.   BIOMETRIKA

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

(2018) Han Chen et al.   CELL

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

(2018) Katherine A. Hoadley et al.   CELL

Differential roles of ERRFI1 in EGFR and AKT pathway regulation affect cancer proliferation

(2018) Junmei Cairns et al.   EMBO REPORTS

Somatic mutation of the cohesin complex subunit confers therapeutic vulnerabilities in cancer

(2018) Yunhua Liu et al.   JOURNAL OF CLINICAL INVESTIGATION

Phase II Study of BGJ398 in Patients With FGFR-Altered Advanced Cholangiocarcinoma

(2018) Milind Javle et al.   JOURNAL OF CLINICAL ONCOLOGY

Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers

(2018) Yu Amanda Guo et al.   Nature Communications

EGR1 interacts with TBX2 and functions as a tumor suppressor in rhabdomyosarcoma

(2018) Trefa Mohamad et al.   Oncotarget

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Pharmacological targeting of p38 MAP-Kinase 6 (MAP2K6) inhibits the growth of esophageal adenocarcinoma

(2018) Sijie Lin et al.   CELLULAR SIGNALLING

Estrogen receptor antagonist fulvestrant inhibits proliferation and promotes apoptosis of prolactinoma cells by regulating the IRE1/XBP1 signaling pathway

(2018) Chao Wang et al.   Molecular Medicine Reports

T-Cell Leukemia/Lymphoma 1 (TCL1): An Oncogene Regulating Multiple Signaling Pathways

(2018) Francesco Paduano et al.   Frontiers in Oncology

Candidate biomarkers of PARP inhibitor sensitivity in ovarian cancer beyond the BRCA genes

(2018) Darren R. Hodgson et al.   BRITISH JOURNAL OF CANCER

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Atypical GATA transcription factor TRPS1 represses gene expression by recruiting CHD4/NuRD(MTA2) and suppresses cell migration and invasion by repressing TP63 expression

(2018) Yuzhi Wang et al.   Oncogenesis

Recurrent and functional regulatory mutations in breast cancer

(2017) Esther Rheinbay et al.   NATURE

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Suppression of SRCAP chromatin remodelling complex and restriction of lymphoid lineage commitment by Pcid2

(2017) Buqing Ye et al.   Nature Communications

Progression through mitosis promotes PARP inhibitor-induced cytotoxicity in homologous recombination-deficient cancer cells

(2017) Pepijn M. Schoonen et al.   Nature Communications

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

(2017) Henrik Krehenwinkel et al.   Scientific Reports

Deletion of the MAD2L1 spindle assembly checkpoint gene is tolerated in mouse models of acute T-cell lymphoma and hepatocellular carcinoma

(2017) Floris Foijer et al.   eLife

Metabolic zonation of the liver: The oxygen gradient revisited

(2017) Thomas Kietzmann   Redox Biology

Frequent NFKBIE deletions are associated with poor outcome in primary mediastinal B-cell lymphoma

(2016) L. Mansouri et al.   BLOOD

A Landscape of Pharmacogenomic Interactions in Cancer

(2016) Francesco Iorio et al.   CELL

Understanding TERT Promoter Mutations: A Common Path to Immortality

(2016) R. J. A. Bell et al.   MOLECULAR CANCER RESEARCH

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer

(2016) Akihiro Fujimoto et al.   NATURE GENETICS

Data-driven hypothesis weighting increases detection power in genome-scale multiple testing

(2016) Nikolaos Ignatiadis et al.   NATURE METHODS

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search

(2016) Noa Rappaport et al.   NUCLEIC ACIDS RESEARCH

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

NCOA3 coactivator is a transcriptional target of XBP1 and regulates PERK–eIF2α–ATF4 signalling in breast cancer

(2016) A Gupta et al.   ONCOGENE

Evaluating the evaluation of cancer driver genes

(2016) Collin J. Tokheim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes

(2016) Justin S. Becker et al.   TRENDS IN GENETICS

BCR SIGNALING INHIBITORS: AN OVERVIEW OF TOXICITIES ASSOCIATED WITH IBRUTINIB AND IDELALISIB IN PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA

(2016) Lorenzo Falchi et al.   Mediterranean Journal of Hematology and Infectious Diseases

Matrix Gla protein regulates differentiation of endothelial cells derived from mouse embryonic stem cells

(2015) Jiayi Yao et al.   ANGIOGENESIS

Mango: a bias-correcting ChIA-PET analysis pipeline

(2015) Douglas H. Phanstiel et al.   BIOINFORMATICS

Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data

(2015) Runjun D. Kumar et al.   BIOINFORMATICS

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

The regulatory interaction of EVI1 with the TCL1A oncogene impacts cell survival and clinical outcome in CLL

(2015) E Vasyutina et al.   LEUKEMIA

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity

(2015) Matthew T Chang et al.   NATURE BIOTECHNOLOGY

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

A Pilot Study of the Telomerase Inhibitor Imetelstat for Myelofibrosis

(2015) Ayalew Tefferi et al.   NEW ENGLAND JOURNAL OF MEDICINE

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations

(2015) Lucas Lochovsky et al.   NUCLEIC ACIDS RESEARCH

Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact

(2015) Puya G. Yazdi et al.   PLoS One

Comprehensive assessment of cancer missense mutation clustering in protein structures

(2015) Atanas Kamburov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of novel genes that regulate androgen receptor signaling and growth of androgen-deprived prostate cancer cells

(2015) Elina Levina et al.   Oncotarget

The roles of BTG3 expression in gastric cancer: a potential marker for carcinogenesis and a target molecule for gene therapy

(2015) Wen-feng Gou et al.   Oncotarget

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Identification of Non-Coding RNAs Associated with Telomeres Using a Combination of enChIP and RNA Sequencing

(2015) Toshitsugu Fujita et al.   PLoS One

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

(2014) D. H. Phanstiel et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

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

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

AGR2, an Endoplasmic Reticulum Protein, Is Secreted into the Gastrointestinal Mucus

(2014) Joakim H. Bergström et al.   PLoS One

Transcriptional Silencing by Polycomb-Group Proteins

(2014) U. Grossniklaus et al.   Cold Spring Harbor Perspectives in Biology

Spatial control of the GEN1 Holliday junction resolvase ensures genome stability

(2014) Ying Wai Chan et al.   Nature Communications

The Androgen-Regulated Protease TMPRSS2 Activates a Proteolytic Cascade Involving Components of the Tumor Microenvironment and Promotes Prostate Cancer Metastasis

(2014) J. M. Lucas et al.   Cancer Discovery

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

(2013) David Tamborero et al.   BIOINFORMATICS

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

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

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

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

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

MalaCards: an integrated compendium for diseases and their annotation

(2013) Noa Rappaport et al.   Database-The Journal of Biological Databases and Curation

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation

(2012) Amnon Koren et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

A 50-Gene Intrinsic Subtype Classifier for Prognosis and Prediction of Benefit from Adjuvant Tamoxifen

(2012) S. K. Chia et al.   CLINICAL CANCER RESEARCH

Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

(2012) Y. Drier et al.   GENOME RESEARCH

Chromatin organization is a major influence on regional mutation rates in human cancer cells

(2012) Benjamin Schuster-Böckler et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

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

Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells

(2012) Wanjuan Yang et al.   NUCLEIC ACIDS RESEARCH

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Inducing Cell Proliferation Inhibition, Apoptosis, and Motility Reduction by Silencing Long Noncoding Ribonucleic Acid Metastasis-associated Lung Adenocarcinoma Transcript 1 in Urothelial Carcinoma of the Bladder

(2012) Yonghua Han et al.   UROLOGY

Weighted multiple testing procedures for genomic studies

(2012) Jiang Gui et al.   BioData Mining

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Cells of origin in cancer

(2011) Jane E. Visvader   NATURE

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Fibronectin Protects from Excessive Liver Fibrosis by Modulating the Availability of and Responsiveness of Stellate Cells to Active TGF-β

(2011) Nina Kawelke et al.   PLoS One

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

The Telomerase Antagonist, Imetelstat, Efficiently Targets Glioblastoma Tumor-Initiating Cells Leading to Decreased Proliferation and Tumor Growth

(2010) C. O. Marian et al.   CLINICAL CANCER RESEARCH

MUC2 and MUC6 apomucins expression in human gastric neoplasm: an immunohistochemical analysis

(2010) Abdul-Zaher M. Khattab et al.   MEDICAL ONCOLOGY

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

The metabolic actions of glucagon revisited

(2010) Kirk M. Habegger et al.   Nature Reviews Endocrinology

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

(2010) Anna C. Groner et al.   PLoS Genetics

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Human mutation rate associated with DNA replication timing

(2009) John A Stamatoyannopoulos et al.   NATURE GENETICS

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Weighted Multiple Hypothesis Testing Procedures

(2009) Guolian Kang et al.   Statistical Applications in Genetics and Molecular Biology

Molecular biology of bcr-abl1-positive chronic myeloid leukemia

(2008) A. Quintas-Cardama et al.   BLOOD

Homologous recombination in DNA repair and DNA damage tolerance

(2008) Xuan Li et al.   CELL RESEARCH

miR-21: a small multi-faceted RNA

(2008) Anna M. Krichevsky et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

WikiPathways: Pathway Editing for the People

(2008) Alexander R Pico et al.   PLOS BIOLOGY