An information theoretic treatment of sequence-to-expression modeling

Modeling gene regulation from paired expression and chromatin accessibility data

(2017) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integration of Orthogonal Signaling by the Notch and Dpp Pathways in Drosophila

(2016) Elizabeth Stroebele et al.   GENETICS

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

(2016) Rupinder Sayal et al.   eLife

Integration of Orthogonal Signaling by the Notch and Dpp Pathways in Drosophila

(2016) Elizabeth Stroebele et al.   GENETICS

Non-coding genetic variants in human disease: Figure 1.

(2015) Feng Zhang et al.   HUMAN MOLECULAR GENETICS

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

(2015) Charles Blatti et al.   NUCLEIC ACIDS RESEARCH

The role and interaction of imprinted genes in human fetal growth

(2015) G. E. Moore et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models

(2015) Dmitry Svetlichnyy et al.   PLoS Computational Biology

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

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

A framework for modelling gene regulation which accommodates non-equilibrium mechanisms

(2014) Tobias Ahsendorf et al.   BMC BIOLOGY

Global parameter estimation for thermodynamic models of transcriptional regulation

(2013) Yerzhan Suleimenov et al.   METHODS

Kinetics of gene derepression by ERK signaling

(2013) B. Lim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mesodermal repression of single-minded in Drosophila embryo is mediated by a cluster of Snail-binding sites proximal to the early promoter

(2012) Kye-Won Park et al.   BMB Reports

A model of spatially restricted transcription in opposing gradients of activators and repressors

(2012) Michael A White et al.   Molecular Systems Biology

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

(2012) Stefan Bonn et al.   NATURE GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Analysis of variation at transcription factor binding sites in Drosophila and humans

(2012) Mikhail Spivakov et al.   GENOME BIOLOGY

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

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

Lateral Gene Expression in Drosophila Early Embryos Is Supported by Grainyhead-Mediated Activation and Tiers of Dorsally-Localized Repression

(2011) Mayra Garcia et al.   PLoS One

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

Systems biology: experimental design

(2009) Clemens Kreutz et al.   FEBS Journal

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE