A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Pioneer transcription factors, chromatin dynamics, and cell fate control

(2016) Kenneth S Zaret et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Multiparameter functional diversity of human C2H2 zinc finger proteins

(2016) Frank W. Schmitges et al.   GENOME RESEARCH

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Cardiomyocyte differentiation from mouse embryonic stem cells using a simple and defined protocol

(2015) Ioannis Kokkinopoulos et al.   DEVELOPMENTAL DYNAMICS

A Quantitative Proteomics Tool To Identify DNA–Protein Interactions in Primary Cells or Blood

(2015) Nina C. Hubner et al.   JOURNAL OF PROTEOME RESEARCH

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

Retinoic Acid Induces Embryonic Stem Cell Differentiation by Altering Both Encoding RNA and microRNA Expression

(2015) Jingcheng Zhang et al.   PLoS One

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

(2015) Kazuhiro R Nitta et al.   eLife

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

(2015) Swneke D. Bailey et al.   Nature Communications

Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet

(2014) Samantha A. Morris et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Human Hepatocytes with Drug Metabolic Function Induced from Fibroblasts by Lineage Reprogramming

(2014) Yuanyuan Du et al.   Cell Stem Cell

Direct Reprogramming of Human Fibroblasts to Functional and Expandable Hepatocytes

(2014) Pengyu Huang et al.   Cell Stem Cell

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue 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

TGF-β signaling to chromatin: How Smads regulate transcription during self-renewal and differentiation

(2014) Tessa Gaarenstroom et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

A unified model for yeast transcript definition

(2013) C. G. de Boer et al.   GENOME RESEARCH

Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics

(2013) Jovan Simicevic et al.   NATURE METHODS

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

(2013) Rui M M Branca et al.   NATURE METHODS

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation

(2012) Zhaoyu Li et al.   CELL

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Discriminative prediction of mammalian enhancers from DNA sequence

(2011) D. Lee et al.   GENOME RESEARCH

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

(2010) Gong-Hong Wei et al.   EMBO JOURNAL

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

(2010) A. Jolma et al.   GENOME RESEARCH

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

Finding Significant Matches of Position Weight Matrices in Linear Time

(2009) Cinzia Pizzi et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb

(2009) Bo Feng et al.   NATURE CELL BIOLOGY

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

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

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

(2008) Xi Chen et al.   CELL

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

A core Klf circuitry regulates self-renewal of embryonic stem cells

(2008) Jianming Jiang et al.   NATURE CELL BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Distinct functions of Egr gene family members in cognitive processes

(2008) Roseline Poirier   Frontiers in Neuroscience