Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays

Identification of Single Nucleotide Non-coding Driver Mutations in Cancer

(2018) Kok A. Gan et al.   Frontiers in Genetics

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

Global landscape of mouse and human cytokine transcriptional regulation

(2018) Sebastian Carrasco Pro et al.   NUCLEIC ACIDS RESEARCH

A map of direct TF–DNA interactions in the human genome

(2018) Marius Gheorghe et al.   NUCLEIC ACIDS RESEARCH

Elucidating Protein–DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry

(2017) Katherine E. Buxton et al.   JOURNAL OF PROTEOME RESEARCH

Recurrent and functional regulatory mutations in breast cancer

(2017) Esther Rheinbay et al.   NATURE

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

A pathology atlas of the human cancer transcriptome

(2017) Mathias Uhlen et al.   SCIENCE

Dynamic Gene Regulatory Networks of Human Myeloid Differentiation

(2017) Ricardo N. Ramirez et al.   Cell Systems

Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis

(2016) Yen-Sin Ang et al.   CELL

Sox11 Balances Dendritic Morphogenesis with Neuronal Migration in the Developing Cerebral Cortex

(2016) Y. Hoshiba et al.   JOURNAL OF NEUROSCIENCE

A gene‐centered C. elegans protein–DNA interaction network provides a framework for functional predictions

(2016) Juan I Fuxman Bass et al.   Molecular Systems Biology

Alu repeats as transcriptional regulatory platforms in macrophage responses toM. tuberculosisinfection

(2016) Manuella Bouttier et al.   NUCLEIC ACIDS RESEARCH

KLF4 downregulates hTERT expression and telomerase activity to inhibit lung carcinoma growth

(2016) Wenxian Hu et al.   Oncotarget

Human Gene-Centered Transcription Factor Networks for Enhancers and Disease Variants

(2015) Juan I. Fuxman Bass et al.   CELL

Krüppel-like Factor 2 Represses Transcription of the Telomerase Catalytic Subunit Human Telomerase Reverse Transcriptase (hTERT) in Human T Cells

(2015) Toshifumi Hara et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer

(2015) R. J. A. Bell et al.   SCIENCE

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Sox2 Regulates Cholinergic Amacrine Cell Positioning and Dendritic Stratification in the Retina

(2014) I. E. Whitney et al.   JOURNAL OF NEUROSCIENCE

The Maize TFome - development of a transcription factor open reading frame collection for functional genomics

(2014) Brett Burdo et al.   PLANT JOURNAL

Transcription Factor Binding Sites Prediction Based on Modified Nucleosomes

(2014) Mohammad Talebzadeh et al.   PLoS One

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Telomerase Reverse Transcriptase Gene Promoter Mutations Help Discern the Origin of Urogenital Tumors: A Genomic and Molecular Study

(2013) Song Wu et al.   EUROPEAN UROLOGY

Extensive Rewiring and Complex Evolutionary Dynamics in a C. elegans Multiparameter Transcription Factor Network

(2013) John S. Reece-Hoyes et al.   MOLECULAR CELL

A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks

(2013) Carine Gubelmann et al.   Molecular Systems Biology

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

(2013) Housheng Hansen He et al.   NATURE METHODS

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins

(2013) Anton V. Persikov et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Hashem Koohy et al.   PLoS One

Probing DNA shape and methylation state on a genomic scale with DNase I

(2013) A. Lazarovici et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TERT Promoter Mutations in Familial and Sporadic Melanoma

(2013) S. Horn et al.   SCIENCE

Towards a theoretical understanding of false positives in DNA motif finding

(2012) Amin Zia et al.   BMC BIOINFORMATICS

Latent Regulatory Potential of Human-Specific Repetitive Elements

(2012) Michelle C. Ward et al.   MOLECULAR CELL

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

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

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

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

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

A stele-enriched gene regulatory network in the Arabidopsis root

(2011) S. M. Brady et al.   Molecular Systems Biology

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping

(2011) John S Reece-Hoyes et al.   NATURE METHODS

Automated protein-DNA interaction screening of Drosophila regulatory elements

(2011) Korneel Hens et al.   NATURE METHODS

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

(2011) Dongjun Chung et al.   PLoS Computational Biology

Alu elements: know the SINEs

(2011) Prescott Deininger   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL