Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data

(2015) Md. Abul Hassan Samee et al.   Cell Systems

Enhancer biology and enhanceropathies

(2014) Edwin Smith et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Enhancer variants: evaluating functions in common disease

(2014) Olivia Corradin et al.   Genome Medicine

Deciphering the combinatorial architecture of a Drosophila homeotic gene enhancer

(2013) Robert A. Drewell et al.   MECHANISMS OF DEVELOPMENT

Global parameter estimation for thermodynamic models of transcriptional regulation

(2013) Yerzhan Suleimenov et al.   METHODS

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

(2013) Majid Kazemian et al.   NUCLEIC ACIDS RESEARCH

Functional anatomy of distant-acting mammalian enhancers

(2013) D. E. Dickel et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

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

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design

(2013) Robin P Smith et al.   GENOME BIOLOGY

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Mathematical modeling of gene expression: a guide for the perplexed biologist

(2011) Ahmet Ay et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Long- and Short-Range Transcriptional Repressors Induce Distinct Chromatin States on Repressed Genes

(2011) Li M. Li et al.   CURRENT BIOLOGY

Optimization of reporter gene architecture for quantitative measurements of gene expression in the Drosophila embryo

(2011) Rupinder Sayal et al.   FLY

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

(2011) A. Ozdemir et al.   GENOME RESEARCH

Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects

(2010) Jacqueline M Dresch et al.   BMC Systems Biology

A RSC/Nucleosome Complex Determines Chromatin Architecture and Facilitates Activator Binding

(2010) Monique Floer et al.   CELL

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Transcriptional Repression: Conserved and Evolved Features

(2010) Sandhya Payankaulam et al.   CURRENT BIOLOGY

Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

(2010) Christina I. Swanson et al.   DEVELOPMENTAL CELL

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo

(2010) Walid D Fakhouri et al.   Molecular Systems Biology

Mutations and quantitative genetic variation: lessons from Drosophila

(2010) T. F. C. Mackay   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

(2010) Majid Kazemian et al.   PLOS BIOLOGY

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression

(2010) Xin He et al.   PLoS Computational Biology

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Quantitative imaging of the Dorsal nuclear gradient reveals limitations to threshold-dependent patterning inDrosophila

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

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

(2008) Marcus B. Noyes et al.   NUCLEIC ACIDS RESEARCH

How the Dorsal gradient works: Insights from postgenome technologies

(2008) J.-W. Hong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Image Processing and Analysis for Quantifying Gene Expression from Early Drosophila Embryos

(2008) Ahmet Ay et al.   TISSUE ENGINEERING PART A

Activator Control of Nucleosome Occupancy in Activation and Repression of Transcription

(2008) Gene O Bryant et al.   PLOS BIOLOGY