Detecting Differential Transcription Factor Activity from ATAC-Seq Data

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Analysis of chromatin accessibility in decidualizing human endometrial stromal cells

(2018) Pavle Vrljicak et al.   FASEB JOURNAL

Enhancer RNA profiling predicts transcription factor activity

(2018) Joseph G. Azofeifa et al.   GENOME RESEARCH

An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq

(2017) Joseph G. Azofeifa et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Transcriptional landscape of the human cell cycle

(2017) Yin Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity

(2017) Songjoon Baek et al.   Cell Reports

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

(2017) Hamish W King et al.   eLife

A Genome-wide Association Study of Nonsyndromic Cleft Palate Identifies an Etiologic Missense Variant in GRHL3

(2016) Elizabeth J. Leslie et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A generative model for the behavior of RNA polymerase

(2016) Joseph G. Azofeifa et al.   BIOINFORMATICS

A comprehensive comparison of tools for differential ChIP-seq analysis

(2016) Sebastian Steinhauser et al.   BRIEFINGS IN BIOINFORMATICS

Mutations in TFAM, encoding mitochondrial transcription factor A, cause neonatal liver failure associated with mtDNA depletion

(2016) Ashlee R. Stiles et al.   MOLECULAR GENETICS AND METABOLISM

Genetics of Congenital Heart Defects: The NKX2-5 Gene, a Key Player

(2016) Ill-Min Chung et al.   Genes

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

(2015) Dawn Thompson et al.   Annual Review of Cell and Developmental Biology

Ligand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity

(2015) Janusz Puc et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

Identification of a novel missense mutation ofMAFin a Japanese family with congenital cataract by whole exome sequencing: A clinical report and review of literature

(2014) Yoko Narumi et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Spurious transcription factor binding: Non-functional or genetically redundant?

(2014) Mikhail Spivakov   BIOESSAYS

Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses

(2014) Xin Luo et al.   BMC GENOMICS

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

(2014) P. J. Balwierz et al.   GENOME RESEARCH

TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity

(2014) Morgan A. Sammons et al.   GENOME RESEARCH

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Enhancer RNAs and regulated transcriptional programs

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

Enhancer variants: evaluating functions in common disease

(2014) Olivia Corradin et al.   Genome Medicine

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms

(2014) Mary Ann Allen et al.   eLife

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

Calculating Sample Size Estimates for RNA Sequencing Data

(2013) Steven N. Hart et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He et al.   NATURE METHODS

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

p53 mutations in cancer

(2012) Patricia A. J. Muller et al.   NATURE CELL BIOLOGY

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

(2012) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Functional analysis of transcription factor binding sites in human promoters

(2012) Troy W Whitfield et al.   GENOME BIOLOGY

Detailed Structural-Functional Analysis of the Krüppel-like Factor 16 (KLF16) Transcription Factor Reveals Novel Mechanisms for Silencing Sp/KLF Sites Involved in Metabolism and Endocrinology

(2011) Gaurang S. Daftary et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data

(2010) Xiaoyu Chen et al.   BIOINFORMATICS

A spectrum of LMX1B mutations in Nail-Patella syndrome: New point mutations, deletion, and evidence of mosaicism in unaffected parents

(2010) Monica Marini et al.   GENETICS IN MEDICINE

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Novel RUNX1 mutations in familial platelet disorder with enhanced risk for acute myeloid leukemia: clues for improved identification of the FPD/AML syndrome

(2009) M C J Jongmans et al.   LEUKEMIA

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Genes targeted by the estrogen and progesterone receptors in the human endometrial cell lines HEC1A and RL95-2

(2009) Karin Tamm et al.   Reproductive Biology and Endocrinology

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

(2008) Leighton J. Core et al.   SCIENCE