Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression

Hallmarks of Cancer: New Dimensions

(2022) Douglas Hanahan   Cancer Discovery

Walking a tightrope: The complex balancing act of R-loops in genome stability

(2022) Joshua R. Brickner et al.   MOLECULAR CELL

The PAF1 complex promotes 3′ processing of pervasive transcripts

(2022) Xinhong Liu et al.   Cell Reports

A gene–environment-induced epigenetic program initiates tumorigenesis

(2021) Direna Alonso-Curbelo et al.   NATURE

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin

(2021) Alex M. Francette et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural basis of human transcription–DNA repair coupling

(2021) Goran Kokic et al.   NATURE

Epithelial memory of inflammation limits tissue damage while promoting pancreatic tumorigenesis

(2021) Edoardo Del Poggetto et al.   SCIENCE

Regulatory R-loops as facilitators of gene expression and genome stability

(2020) Christof Niehrs et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate

(2020) Preston R. Arnold et al.   Frontiers in Cell and Developmental Biology

Pancreatic cancer

(2020) Jonathan D Mizrahi et al.   LANCET

Enhancer RNAs are an important regulatory layer of the epigenome

(2020) Vittorio Sartorelli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Epigenetic Therapies for Cancer

(2020) Susan E. Bates   NEW ENGLAND JOURNAL OF MEDICINE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma

(2019) Junya Peng et al.   CELL RESEARCH

50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms

(2019) Robert G. Roeder   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Induction of BRCAness in Triple-Negative Breast Cancer by a CDK12/13 Inhibitor Improves Chemotherapy

(2019) Jessica L. Hopkins et al.   CANCER CELL

R Loops: From Physiological to Pathological Roles

(2019) Tatiana García-Muse et al.   CELL

Yeast PAF1 complex counters the pol III accumulation and replication stress on the tRNA genes

(2019) Pratibha Bhalla et al.   Scientific Reports

Loss of KDM6A Activates Super-Enhancers to Induce Gender-Specific Squamous-like Pancreatic Cancer and Confers Sensitivity to BET Inhibitors

(2018) Jaclyn Andricovich et al.   CANCER CELL

A Non-catalytic Function of SETD1A Regulates Cyclin K and the DNA Damage Response

(2018) Takayuki Hoshii et al.   CELL

Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes

(2018) Sebastian Mueller et al.   NATURE

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

(2018) Takayuki Nojima et al.   MOLECULAR CELL

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

(2017) Zefang Tang et al.   NUCLEIC ACIDS RESEARCH

Degrons in cancer

(2017) Bálint Mészáros et al.   Science Signaling

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Degrons in cancer

(2017) Bálint Mészáros et al.   Science Signaling

TGF-β Tumor Suppression through a Lethal EMT

(2016) Charles J. David et al.   CELL

Epigenetic treatment of pancreatic cancer: is there a therapeutic perspective on the horizon?

(2016) Elisabeth Hessmann et al.   GUT

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

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases

(2016) Yasuhiro Murakawa et al.   TRENDS IN GENETICS

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Regeneration and Repair of the Exocrine Pancreas

(2015) L. Charles Murtaugh et al.   Annual Review of Physiology

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

CDK7-Dependent Transcriptional Addiction in Triple-Negative Breast Cancer

(2015) Yubao Wang et al.   CELL

RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity

(2015) Evangelos Pefanis et al.   CELL

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

A small-molecule inhibitor of the aberrant transcription factor CBF -SMMHC delays leukemia in mice

(2015) A. Illendula et al.   SCIENCE

Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor

(2014) Camilla L. Christensen et al.   CANCER CELL

The basal transcription machinery as a target for cancer therapy

(2014) Claudia Villicaña et al.   Cancer Cell International

CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer

(2014) Edmond Chipumuro et al.   CELL

The Mechanisms behind the Therapeutic Activity of BET Bromodomain Inhibition

(2014) Junwei Shi et al.   MOLECULAR CELL

Transcription-Coupled Nucleotide Excision Repair Factors Promote R-Loop-Induced Genome Instability

(2014) Julie Sollier et al.   MOLECULAR CELL

Targeting transcription regulation in cancer with a covalent CDK7 inhibitor

(2014) Nicholas Kwiatkowski et al.   NATURE

Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles

(2014) Susanne Walz et al.   NATURE

Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing

(2014) Dirk Heckl et al.   NATURE BIOTECHNOLOGY

Easy quantitative assessment of genome editing by sequence trace decomposition

(2014) Eva K. Brinkman et al.   NUCLEIC ACIDS RESEARCH

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Roles for KRAS in Pancreatic Tumor Development and Progression

(2013) Marina Pasca di Magliano et al.   GASTROENTEROLOGY

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

Isolation, culture and genetic manipulation of mouse pancreatic ductal cells

(2013) Maximilian Reichert et al.   Nature Protocols

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Modelling Myc inhibition as a cancer therapy

(2008) Laura Soucek et al.   NATURE

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY