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

Unique functions of Gata4 in mouse liver induction and heart development

(2016) Matthew J. Borok et al.   DEVELOPMENTAL BIOLOGY

Analysis of computational footprinting methods for DNase sequencing experiments

(2016) Eduardo G Gusmao et al.   NATURE METHODS

Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane

(2016) Savio Siqueira Ferreira et al.   PLANT MOLECULAR BIOLOGY

BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data

(2015) Juhani Kähärä et al.   BIOINFORMATICS

PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R

(2015) Jan Grau et al.   BIOINFORMATICS

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

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

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

A general concept for consistent documentation of computational analyses

(2015) Peter Ebert et al.   Database-The Journal of Biological Databases and Curation

JAMM: a peak finder for joint analysis of NGS replicates

(2014) Mahmoud M. Ibrahim et al.   BIOINFORMATICS

Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications

(2014) Eduardo G. Gusmao 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

DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence

(2014) Myong-Hee Sung et al.   MOLECULAR CELL

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

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection

(2014) Galip Gürkan Yardımcı et al.   NUCLEIC ACIDS RESEARCH

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

(2014) Maxwell A. Hume et al.   NUCLEIC ACIDS RESEARCH

Telomere shortening and telomere position effect in mild ring 17 syndrome

(2014) Cecilia Surace et al.   Epigenetics & Chromatin

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

(2013) Housheng Hansen He et al.   NATURE METHODS

Target analysis by integration of transcriptome and ChIP-seq data with BETA

(2013) Su Wang et al.   Nature Protocols

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

(2013) Jason Piper 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

Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme

(2013) Hashem Koohy et al.   PLoS One

Genome-wide in silico prediction of gene expression

(2012) Robert C. McLeay et al.   BIOINFORMATICS

CTCF-binding sites within theH19ICR differentially regulate local chromatin structures and cis-acting functions

(2012) Sylvain Guibert et al.   Epigenetics

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

(2012) A. Natarajan et al.   GENOME RESEARCH

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

(2012) T. K. Kelly et al.   GENOME RESEARCH

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

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages

(2012) Xun Lan et al.   NUCLEIC ACIDS RESEARCH

Epigenetic priors for identifying active transcription factor binding sites

(2011) Gabriel Cuellar-Partida et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models

(2011) Ivan G Costa et al.   BMC BIOINFORMATICS

IL-12 inhibits glucocorticoid-induced T cell apoptosis by inducing GMEB1 and activating PI3K/Akt pathway

(2011) Kiyokazu Kawabe et al.   IMMUNOBIOLOGY

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

(2011) Morgane Thomas-Chollier et al.   Nature Protocols

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

(2010) Xiaoyu Chen et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

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

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide prediction of transcription factor binding sites using an integrated model

(2010) Kyoung-Jae Won et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells

(2009) Mike J Mason et al.   BMC GENOMICS

Predictive chromatin signatures in the mammalian genome

(2009) G. C. Hon et al.   HUMAN MOLECULAR GENETICS

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

(2009) Jay R Hesselberth et al.   NATURE METHODS

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

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

The Zinc Finger Transcription Factor Zbtb7b Represses CD8-Lineage Gene Expression in Peripheral CD4+ T Cells

(2008) Lie Wang et al.   IMMUNITY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY