Quantitative modeling of gene expression using DNA shape features of binding sites

A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites

(2015) Jichen Yang et al.   BIOINFORMATICS

Incorporating Chromatin Accessibility Data into Sequence-to-Expression Modeling

(2015) Pei-Chen Peng et al.   BIOPHYSICAL JOURNAL

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

(2015) Charles Blatti et al.   NUCLEIC ACIDS RESEARCH

Quantitative modeling of transcription factor binding specificities using DNA shape

(2015) Tianyin Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts

(2014) Yang I. Li et al.   GENOME RESEARCH

A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data

(2014) Yaron Orenstein et al.   NUCLEIC ACIDS RESEARCH

A General Pairwise Interaction Model Provides an Accurate Description of In Vivo Transcription Factor Binding Sites

(2014) Marc Santolini et al.   PLoS One

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

Flanking sequence context-dependent transcription factor binding in early Drosophila development

(2013) Jessica L Stringham et al.   BMC BIOINFORMATICS

Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data

(2013) Md. Abul Hassan Samee et al.   METHODS

Simulations of Enhancer Evolution Provide Mechanistic Insights into Gene Regulation

(2013) Thyago Duque et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

(2013) Tianyin Zhou et al.   NUCLEIC ACIDS RESEARCH

Protein-DNA binding: complexities and multi-protein codes

(2013) T. Siggers et al.   NUCLEIC ACIDS RESEARCH

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

(2013) Raluca Gordân et al.   Cell Reports

Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy

(2013) Qiong Cheng et al.   PLoS Genetics

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

A flexible integrative approach based on random forest improves prediction of transcription factor binding sites

(2012) Bart Hooghe et al.   NUCLEIC ACIDS RESEARCH

Improved predictions of transcription factor binding sites using physicochemical features of DNA

(2012) Mark Maienschein-Cline et al.   NUCLEIC ACIDS RESEARCH

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

(2011) Tommy Kaplan et al.   PLoS Genetics

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

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

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

From the editors

(2010)   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

An ensemble model of competitive multi-factor binding of the genome

(2009) T. Wasson et al.   GENOME RESEARCH

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

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

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

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

FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution

(2008) A. Pisarev et al.   NUCLEIC ACIDS RESEARCH

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

A Feature-Based Approach to Modeling Protein–DNA Interactions

(2008) Eilon Sharon et al.   PLoS Computational Biology