Integrative prediction of gene expression with chromatin accessibility and conformation data

Condensin II Counteracts Cohesin and RNA Polymerase II in the Establishment of 3D Chromatin Organization

(2019) M. Jordan Rowley et al.   Cell Reports

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

Genome-wide prediction of cis-regulatory regions using supervised deep learning methods

(2018) Yifeng Li et al.   BMC BIOINFORMATICS

On the problem of confounders in modeling gene expression

(2018) Florian Schmidt et al.   BIOINFORMATICS

Nuclear Respiratory Factor 1 (NRF-1) Controls the Activity Dependent Transcription of the GABA-A Receptor Beta 1 Subunit Gene in Neurons

(2018) Zhuting Li et al.   Frontiers in Molecular Neuroscience

TEPIC 2—an extended framework for transcription factor binding prediction and integrative epigenomic analysis

(2018) Florian Schmidt et al.   BIOINFORMATICS

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency

(2018) Deborah Gérard et al.   NUCLEIC ACIDS RESEARCH

Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

(2017) Qin Cao et al.   NATURE GENETICS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Modeling gene regulation from paired expression and chromatin accessibility data

(2017) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

(2017) Yupeng He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DeepChrome: deep-learning for predicting gene expression from histone modifications

(2016) Ritambhara Singh et al.   BIOINFORMATICS

The High Mobility Group A1 (HMGA1) Transcriptome in Cancer and Development

(2016) T.F. Sumter et al.   CURRENT MOLECULAR MEDICINE

Epigenomic Profiling of Human CD4 + T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development

(2016) Pawel Durek et al.   IMMUNITY

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

(2016) Sean Whalen et al.   NATURE GENETICS

Analysis of computational footprinting methods for DNase sequencing experiments

(2016) Eduardo G Gusmao et al.   NATURE METHODS

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

(2016) Florian Schmidt et al.   NUCLEIC ACIDS RESEARCH

Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2

(2016) Soroush Tahmasebi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements

(2016) Elena M. Pugacheva et al.   Epigenetics & Chromatin

Wnt9a deficiency discloses a repressive role of Tcf7l2 on endocrine differentiation in the embryonic pancreas

(2016) G. Pujadas et al.   Scientific Reports

In the loop: promoter–enhancer interactions and bioinformatics

(2015) Antonio Mora et al.   BRIEFINGS IN BIOINFORMATICS

A novel role for Ascl1 in the regulation of mesendoderm formation via HDAC-dependent antagonism of VegT

(2015) Li Gao et al.   DEVELOPMENT

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation

(2015) Alvaro J González 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

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

(2015) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates

(2015) Parameswaran Ramachandran et al.   Epigenetics & Chromatin

Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome

(2015) Alessandro Mammana et al.   GENOME BIOLOGY

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

JAMM: a peak finder for joint analysis of NGS replicates

(2014) Mahmoud M. Ibrahim et al.   BIOINFORMATICS

Predictive modelling of gene expression from transcriptional regulatory elements

(2014) David M. Budden et al.   BRIEFINGS IN BIOINFORMATICS

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

(2014) Suhas S.P. Rao et al.   CELL

Enhancer Malfunction in Cancer

(2014) Hans-Martin Herz et al.   MOLECULAR CELL

Global view of enhancer-promoter interactome in human cells

(2014) B. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci

(2014) Dennis J. Hazelett et al.   PLoS Genetics

A p53 enhancer region regulates target genes through chromatin conformations in cis and in trans

(2013) N. Link et al.   GENES & DEVELOPMENT

DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements

(2013) Tim R Mercer et al.   NATURE GENETICS

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

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

CTCF: the protein, the binding partners, the binding sites and their chromatin loops

(2013) S. J. B. Holwerda et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Epigenomic Annotation of Enhancers Predicts Transcriptional Regulators of Human Neural Crest

(2012) Alvaro Rada-Iglesias et al.   Cell Stem Cell

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Core promoter-selective function of HMGA1 and Mediator in Initiator-dependent transcription

(2011) M. Xu et al.   GENES & DEVELOPMENT

TCF12 Protein Functions as Transcriptional Repressor of E-cadherin, and Its Overexpression Is Correlated with Metastasis of Colorectal Cancer

(2011) Chun-Chung Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis

(2011) Bum-Kyu Lee et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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

The Unique Transcriptional Activation Domain of Nuclear Factor-I-X3 Is Critical to Specifically Induce Marker Gene Expression in Astrocytes

(2010) Sandeep K. Singh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide analysis of YY2 versus YY1 target genes

(2010) Li Chen et al.   NUCLEIC ACIDS RESEARCH

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-Range Enhancer Differentially Regulated by c-Jun and JunD Controls Peptidylarginine Deiminase-3 Gene in Keratinocytes

(2008) Véronique Adoue et al.   JOURNAL OF MOLECULAR BIOLOGY