Mitotic chromosome binding predicts transcription factor properties in interphase

Transcription factor target site search and gene regulation in a background of unspecific binding sites

(2018) J. Hettich et al.   JOURNAL OF THEORETICAL BIOLOGY

The mechanistic basis for chromatin regulation by pioneer transcription factors

(2018) Makiko Iwafuchi-Doi   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Single Live Cell Monitoring of Protein Turnover Reveals Intercellular Variability and Cell-Cycle Dependence of Degradation Rates

(2018) Andrea Brigitta Alber et al.   MOLECULAR CELL

Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape

(2018) Paul Adrian Ginno et al.   Nature Communications

Transcription factor retention on mitotic chromosomes: regulatory mechanisms and impact on cell fate decisions

(2017) Mahé Raccaud et al.   FEBS LETTERS

Electrostatic control of DNA intersegmental translocation by the ETS transcription factor ETV6

(2017) Tam Vo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNA residence time is a regulatory factor of transcription repression

(2017) Karen Clauß et al.   NUCLEIC ACIDS RESEARCH

The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation

(2017) Daosheng Huang et al.   Scientific Reports

Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells

(2017) Yiyuan Liu et al.   Cell Reports

Conformational Dynamics and the Binding of Specific and Nonspecific DNA by the Autoinhibited Transcription Factor Ets-1

(2016) Geneviève Desjardins et al.   BIOCHEMISTRY

How motif environment influences transcription factor search dynamics: Finding a needle in a haystack

(2016) Iris Dror et al.   BIOESSAYS

A role for mitotic bookmarking of SOX2 in pluripotency and differentiation

(2016) Cédric Deluz et al.   GENES & DEVELOPMENT

Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells

(2016) Ferdinand von Meyenn et al.   MOLECULAR CELL

Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network

(2016) Nicola Festuccia et al.   NATURE CELL BIOLOGY

Human mutations affect the epigenetic/bookmarking function of HNF1B

(2016) Jonathan Lerner et al.   NUCLEIC ACIDS RESEARCH

A dynamic mode of mitotic bookmarking by transcription factors

(2016) Sheila S Teves et al.   eLife

protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences

(2015) Nan Xiao et al.   BIOINFORMATICS

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

(2015) Abdenour Soufi et al.   CELL

Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells

(2015) T. K. Mistri et al.   EMBO REPORTS

Identifying Novel Transcriptional Regulators with Circadian Expression

(2015) Sandra Schick et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcription factor binding dynamics during human ES cell differentiation

(2015) Alexander M. Tsankov et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

(2015) Davide Normanno et al.   Nature Communications

Regularization Paths for Generalized Linear Models via Coordinate Descent

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

Sox2 acts as a transcriptional repressor in neural stem cells

(2014) Yu-Ru Liu et al.   BMC NEUROSCIENCE

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Genome Reactivation after the Silence in Mitosis: Recapitulating Mechanisms of Development?

(2014) Kenneth S. Zaret   DEVELOPMENTAL CELL

RBPJ, the Major Transcriptional Effector of Notch Signaling, Remains Associated with Chromatin throughout Mitosis, Suggesting a Role in Mitotic Bookmarking

(2014) Robert J. Lake et al.   PLoS Genetics

Quantifying transcription factor kinetics: At work or at play?

(2013) Florian Mueller et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes

(2013) J. M. Caravaca et al.   GENES & DEVELOPMENT

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

(2013) Carine Gubelmann et al.   Molecular Systems Biology

Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

(2013) J Christof M Gebhardt et al.   NATURE METHODS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models

(2013) E. G. Marklund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

easyFRAP: an interactive, easy-to-use tool for qualitative and quantitative analysis of FRAP data

(2012) Maria Anna Rapsomaniki et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Tissue-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1

(2012) Stephan Kadauke et al.   CELL

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

Circadian Dbp Transcription Relies on Highly Dynamic BMAL1-CLOCK Interaction with E Boxes and Requires the Proteasome

(2012) Markus Stratmann et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

TFClass: an expandable hierarchical classification of human transcription factors

(2012) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

Global mitotic phosphorylation of C2H2zinc finger protein linker peptides

(2011) Raed Rizkallah et al.   CELL CYCLE

Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR

(2011) Y. Takayama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Facilitated DNA Search by Multidomain Transcription Factors: Cross Talk via a Flexible Linker

(2010) Dana Vuzman et al.   BIOPHYSICAL JOURNAL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail

(2010) D. Vuzman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ANCHOR: web server for predicting protein binding regions in disordered proteins

(2009) Z. Dosztanyi et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA

(2009) T. Sekiya et al.   GENES & DEVELOPMENT

Histone Deacetylase 7 and FoxA1 in Estrogen-Mediated Repression of RPRM

(2009) S. Malik et al.   MOLECULAR AND CELLULAR BIOLOGY

Identification of protein functions using a machine-learning approach based on sequence-derived properties

(2009) Bum Lee et al.   Proteome Science

Are DNA Transcription Factor Proteins Maxwellian Demons?

(2008) Longhua Hu et al.   BIOPHYSICAL JOURNAL

Activator-to-Repressor Conversion of T-Box Transcription Factors by the Ripply Family of Groucho/TLE-Associated Mediators

(2008) A. Kawamura et al.   MOLECULAR AND CELLULAR BIOLOGY

Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells

(2008) Jiancong Liang et al.   NATURE CELL BIOLOGY

Highly inclined thin illumination enables clear single-molecule imaging in cells

(2008) Makio Tokunaga et al.   NATURE METHODS

Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter

(2008) T. S. Karpova et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Agonist-mediated docking of androgen receptor onto the mitotic chromatin platform discriminates intrinsic mode of action of prostate cancer drugs

(2007) Sanjay Kumar et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH