Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo

(2019) Clarissa Scholes et al.   Cell Reports

Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression

(2019) Rob Phillips et al.   Annual Review of Biophysics

Ultra-multiplexed analysis of single-cell dynamics reveals logic rules in differentiation

(2019) Ce Zhang et al.   Science Advances

A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation

(2019) Nicholas Bogard et al.   CELL

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation

(2018) Caroline R. Bartman et al.   MOLECULAR CELL

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Synergistic gene expression during the acute phase response is characterized by transcription factor assisted loading

(2017) Ido Goldstein et al.   Nature Communications

The immune checkpoint ligand PD-L1 is upregulated in EMT-activated human breast cancer cells by a mechanism involving ZEB-1 and miR-200

(2017) Muhammad Zaeem Noman et al.   OncoImmunology

Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle

(2017) Clarissa Scholes et al.   Cell Systems

Interactions between pluripotency factors specifycis-regulation in embryonic stem cells

(2016) Chris Fiore et al.   GENOME RESEARCH

The effect of TGF-beta-induced epithelial–mesenchymal transition on the expression of intracellular calcium-handling proteins in T47D and MCF-7 human breast cancer cells

(2015) Shah H.A. Mahdi et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

(2015) Alexander B. Rosenberg et al.   CELL

Transcriptional regulators form diverse groups with context-dependent regulatory functions

(2015) Gerald Stampfel et al.   NATURE

Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo

(2015) Jacques P Bothma et al.   eLife

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

High-throughput functional testing of ENCODE segmentation predictions

(2014) Jamie C. Kwasnieski et al.   GENOME RESEARCH

Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions

(2014) Daphna Rothschild et al.   PLoS Computational Biology

LEVERAGING BIOLOGICAL REPLICATES TO IMPROVE ANALYSIS IN CHIP-SEQ EXPERIMENTS

(2014) Yajie Yang et al.   Computational and Structural Biotechnology Journal

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

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

The hypersensitive sites of the murine  -globin locus control region act independently to affect nuclear localization and transcriptional elongation

(2012) M. A. Bender et al.   BLOOD

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Thermodynamic State Ensemble Models of cis-Regulation

(2012) Marc S. Sherman et al.   PLoS Computational Biology

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

(2011) Sandra Ruf et al.   NATURE GENETICS

Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation

(2010) Sergei Nechaev et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Protein Dynamics in Drug Combinations: a Linear Superposition of Individual-Drug Responses

(2010) Naama Geva-Zatorsky et al.   CELL

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

Genomic Antagonism between Retinoic Acid and Estrogen Signaling in Breast Cancer

(2009) Sujun Hua et al.   CELL

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

Diverse Two-Dimensional Input Functions Control Bacterial Sugar Genes

(2008) Shai Kaplan et al.   MOLECULAR CELL

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE