RegulatorTrail: a web service for the identification of key transcriptional regulators

Multi-omics enrichment analysis using the GeneTrail2 web service

(2016) Daniel Stöckel et al.   BIOINFORMATICS

Enforced Expression of Hoxa3 Inhibits Classical and Promotes Alternative Activation of Macrophages In Vitro and In Vivo

(2016) Hadeel Al Sadoun et al.   JOURNAL OF IMMUNOLOGY

A complex cell

(2016)   NATURE IMMUNOLOGY

Analysis of computational footprinting methods for DNase sequencing experiments

(2016) Eduardo G Gusmao et al.   NATURE METHODS

Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data

(2016) Eiryo Kawakami et al.   NUCLEIC ACIDS RESEARCH

Mixed Integer Linear Programming based machine learning approach identifiesregulatorsof telomerase in yeast

(2016) Alexandra M. Poos et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Florian Schmidt et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

HIV-1 Vpr degrades the HLTF DNA translocase in T cells and macrophages

(2016) Hichem Lahouassa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Juhani Kähärä et al.   BIOINFORMATICS

C/EBPα-induced miR-100 expression suppresses tumor metastasis and growth by targeting ZBTB7A in gastric cancer

(2015) Duan-Bo Shi et al.   CANCER LETTERS

ZBTB7A Suppresses Melanoma Metastasis by Transcriptionally Repressing MCAM

(2015) X.-S. Liu et al.   MOLECULAR CANCER RESEARCH

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

(2015) Alvaro J González 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

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

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Eduardo G. Gusmao et al.   BIOINFORMATICS

Mutant p53 in Cancer: New Functions and Therapeutic Opportunities

(2014) Patricia A.J. Muller et al.   CANCER CELL

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

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks

(2013) Dávid Fazekas et al.   BMC Systems Biology

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

Targeting transcription factors

(2013) Jennifer E. Yeh et al.   CURRENT OPINION IN ONCOLOGY

BLUEPRINT: mapping human blood cell epigenomes

(2013) J. H. A. Martens et al.   HAEMATOLOGICA

p63 is an alternative p53 repressor in melanoma that confers chemoresistance and a poor prognosis

(2013) Rubeta N. Matin et al.   JOURNAL OF EXPERIMENTAL MEDICINE

GATA3 suppresses metastasis and modulates the tumour microenvironment by regulating microRNA-29b expression

(2013) Jonathan Chou et al.   NATURE CELL BIOLOGY

DCGL v2.0: An R Package for Unveiling Differential Regulation from Differential Co-expression

(2013) Jing Yang et al.   PLoS One

Transcriptional control of cancer metastasis

(2013) Brian Ell et al.   TRENDS IN CELL BIOLOGY

Genome-wide in silico prediction of gene expression

(2012) Robert C. McLeay et al.   BIOINFORMATICS

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

Regulatory Snapshots: Integrative Mining of Regulatory Modules from Expression Time Series and Regulatory Networks

(2012) Joana P. Gonçalves et al.   PLoS One

A Minimal Connected Network of Transcription Factors Regulated in Human Tumors and Its Application to the Quest for Universal Cancer Biomarkers

(2012) Ahmed Essaghir et al.   PLoS One

TFRank: network-based prioritization of regulatory associations underlying transcriptional responses

(2011) Joana P. Gonçalves 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

The structure of the Klf4 DNA-binding domain links to self-renewal and macrophage differentiation

(2011) Anja Schuetz et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Krüppel-like factor 4 regulates macrophage polarization

(2011) Xudong Liao et al.   JOURNAL OF CLINICAL INVESTIGATION

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

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

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

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data

(2010) Antonio Reverter et al.   BIOINFORMATICS

NF-κB promotes epithelial–mesenchymal transition, migration and invasion of pancreatic carcinoma cells

(2010) Harald J. Maier et al.   CANCER LETTERS

An Ets2-Driven Transcriptional Program in Tumor-Associated Macrophages Promotes Tumor Metastasis

(2010) T. Zabuawala et al.   CANCER RESEARCH

NF-kappaB in lung cancer, a carcinogenesis mediator and a prevention and therapy target

(2010) Wenshu Chen   Frontiers in Bioscience-Landmark

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

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

Improved Survival with Ipilimumab in Patients with Metastatic Melanoma

(2010) F. Stephen Hodi et al.   NEW ENGLAND JOURNAL OF MEDICINE

Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data

(2010) Ahmed Essaghir 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

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

(2008) Helge G. Roider et al.   BIOINFORMATICS

NF-kappa B genes have a major role in Inflammatory Breast Cancer

(2008) Florence Lerebours et al.   BMC CANCER

The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis

(2008) Adam I Riker et al.   BMC Medical Genomics