Pluralistic and stochastic gene regulation: examples, models and consistent theory

Myc and its interactors take shape

(2015) William B. Tu et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Clinical trial metadata: defining and extracting metadata on the design, conduct, results and costs of 125 randomised clinical trials funded by the National Institute for Health Research Health Technology Assessment programme

(2015) James Raftery et al.   HEALTH TECHNOLOGY ASSESSMENT

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

Repressive histone methylation: A case study in deterministic versus stochastic gene regulation

(2014) David B. Lyons et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Stem cell differentiation as a many-body problem

(2014) B. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

HDAC6 Is a Bruchpilot Deacetylase that Facilitates Neurotransmitter Release

(2014) Katarzyna Miskiewicz et al.   Cell Reports

Genome Recognition by MYC

(2014) A. Sabo et al.   Cold Spring Harbor Perspectives in Medicine

Altered Chromatin Occupancy of Master Regulators Underlies Evolutionary Divergence in the Transcriptional Landscape of Erythroid Differentiation

(2014) Jacob C. Ulirsch et al.   PLoS Genetics

Identifying transcriptional cis -regulatory modules in animal genomes

(2014) Kushal Suryamohan et al.   Wiley Interdisciplinary Reviews-Developmental Biology

The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations

(2013) Gabriele Lillacci et al.   BIOINFORMATICS

IRF-1 responsiveness to IFN-γ predicts different cancer immune phenotypes

(2013) D Murtas et al.   BRITISH JOURNAL OF CANCER

Genome-wide Generation and Systematic Phenotyping of Knockout Mice Reveals New Roles for Many Genes

(2013) Jacqueline K. White et al.   CELL

Extracellular Signal-regulated Kinase (ERK) Phosphorylates Histone Deacetylase 6 (HDAC6) at Serine 1035 to Stimulate Cell Migration

(2013) Kendra A. Williams et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Evolutionary Rewiring of the Ribosomal Protein Transcription Pathway Modifies the Interaction of Transcription Factor Heteromer Ifh1-Fhl1 (Interacts with Forkhead 1-Forkhead-like 1) with the DNA-binding Specificity Element

(2013) Jaideep Mallick et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data

(2013) Robert D. Zeigler et al.   NUCLEIC ACIDS RESEARCH

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

(2013) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

Holo-TFIID controls the magnitude of a transcription burst and fine-tuning of transcription

(2013) K. L. Pennington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Identification of Signal-Activated Stochastic Gene Regulation

(2013) G. Neuert et al.   SCIENCE

Inositol Pyrophosphates Regulate Cell Growth and the Environmental Stress Response by Activating the HDAC Rpd3L

(2013) Jeremy Worley et al.   Cell Reports

Complex dynamics of transcription regulation

(2012) Diana A. Stavreva et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells

(2012) Zuqin Nie et al.   CELL

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

Nucleolar exit of RNF8 and BRCA1 in response to DNA damage

(2012) Marta Guerra-Rebollo et al.   EXPERIMENTAL CELL RESEARCH

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Bcl11a is essential for lymphoid development and negatively regulates p53

(2012) Yong Yu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding

(2012) Cecilia Andresen et al.   NUCLEIC ACIDS RESEARCH

Activation of the Carbon Concentrating Mechanism by CO2 Deprivation Coincides with Massive Transcriptional Restructuring in Chlamydomonas reinhardtii

(2012) A. J. Brueggeman et al.   PLANT CELL

Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit

(2012) Dmitry Nevozhay et al.   PLoS Computational Biology

SAGA and ATAC Histone Acetyl Transferase Complexes Regulate Distinct Sets of Genes and ATAC Defines a Class of p300-Independent Enhancers

(2011) Arnaud R. Krebs et al.   MOLECULAR CELL

From expression QTLs to personalized transcriptomics

(2011) Stephen B. Montgomery et al.   NATURE REVIEWS GENETICS

Mechanisms of nuclear reprogramming by eggs and oocytes: a deterministic process?

(2011) Jerome Jullien et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Finding subtypes of transcription factor motif pairs with distinct regulatory roles

(2011) Abha Singh Bais et al.   NUCLEIC ACIDS RESEARCH

Phosphoproteomic Analysis Identifies Grb10 as an mTORC1 Substrate That Negatively Regulates Insulin Signaling

(2011) Y. Yu et al.   SCIENCE

The mTOR-Regulated Phosphoproteome Reveals a Mechanism of mTORC1-Mediated Inhibition of Growth Factor Signaling

(2011) P. P. Hsu et al.   SCIENCE

Signal integration in budding yeast

(2010) Christian Waltermann et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery

(2010) T. J. Parry et al.   GENES & DEVELOPMENT

Transcription Factor Redundancy Ensures Induction of the Antiviral State

(2010) Sonja Schmid et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The DNA Damage Response: Making It Safe to Play with Knives

(2010) Alberto Ciccia et al.   MOLECULAR CELL

Genetic analysis of variation in transcription factor binding in yeast

(2010) Wei Zheng et al.   NATURE

A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks

(2009) Pedro T Monteiro et al.   BMC BIOINFORMATICS

Signaling to p53: Ribosomal Proteins Find Their Way

(2009) Yanping Zhang et al.   CANCER CELL

How Common Are Extraribosomal Functions of Ribosomal Proteins?

(2009) Jonathan R. Warner et al.   MOLECULAR CELL

Transcription Dynamics

(2009) Gordon L. Hager et al.   MOLECULAR CELL

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

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

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

Genome-wide localization analysis of a complete set of Tafs reveals a specific effect of the taf1 mutation on Taf2 occupancy and provides indirect evidence for different TFIID conformations at different promoters

(2009) Kazushige Ohtsuki et al.   NUCLEIC ACIDS RESEARCH

Facilitated diffusion with DNA coiling

(2009) M. A. Lomholt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A global view of genomic information – moving beyond the gene and the master regulator

(2009) John S. Mattick et al.   TRENDS IN GENETICS

NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly

(2008) D. A. Gilchrist et al.   GENES & DEVELOPMENT

The TSC-mTOR Signaling Pathway Regulates the Innate Inflammatory Response

(2008) Thomas Weichhart et al.   IMMUNITY

Inhibition of mTORC1 leads to MAPK pathway activation through a PI3K-dependent feedback loop in human cancer

(2008) Arkaitz Carracedo et al.   JOURNAL OF CLINICAL INVESTIGATION

Lysine Acetylation Is a Highly Abundant and Evolutionarily Conserved Modification inEscherichia Coli

(2008) Junmei Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

ATAC is a double histone acetyltransferase complex that stimulates nucleosome sliding

(2008) Tamaki Suganuma et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY