Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy

DNA structural features of eukaryotic TATA-containing and TATA-less promoters

(2017) Venkata Rajesh Yella et al.   FEBS Open Bio

Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression

(2016) Aditya Kumar et al.   DNA RESEARCH

Deconvolving the Recognition of DNA Shape from Sequence

(2015) Namiko Abe et al.   CELL

Core promoters in transcription: old problem, new insights

(2015) Ananda L. Roy et al.   TRENDS IN BIOCHEMICAL SCIENCES

High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

(2015) Federico Comoglio et al.   Cell Reports

Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

(2014) Manju Bansal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

GBshape: a genome browser database for DNA shape annotations

(2014) Tsu-Pei Chiu et al.   NUCLEIC ACIDS RESEARCH

Structural Properties of Prokaryotic Promoter Regions Correlate with Functional Features

(2014) Pieter Meysman et al.   PLoS One

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

(2013) Lin Yang et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Computational Prediction and Analysis of Core Promoter Elements across Plant Monocots and Dicots

(2013) Sunita Kumari et al.   PLoS One

DNA STRUCTURAL FEATURES AND ARCHITECTURE OF PROMOTER REGIONS PLAY A ROLE IN GENE RESPONSIVENESS OF S. cerevisiae

(2013) VENKATA RAJESH YELLA et al.   Journal of Bioinformatics and Computational Biology

Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs

(2012) Aditya Kumar et al.   JOURNAL OF BIOSCIENCES

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites

(2011) Miriam R Kantorovitz et al.   BMC BIOINFORMATICS

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

(2011) C. Morey et al.   PLANT PHYSIOLOGY

Genomic and chromatin signals underlying transcription start-site selection

(2011) Eivind Valen et al.   TRENDS IN GENETICS

High-quality annotation of promoter regions for 913 bacterial genomes

(2010) Vetriselvi Rangannan et al.   BIOINFORMATICS

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

Gene regulation by nucleosome positioning

(2010) Lu Bai et al.   TRENDS IN GENETICS

Toward a gold standard for promoter prediction evaluation

(2009) Thomas Abeel et al.   BIOINFORMATICS

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Intrinsic variability of gene expression encoded in nucleosome positioning sequences

(2009) Jung Kyoon Choi et al.   NATURE GENETICS

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

Links between core promoter and basic gene features influence gene expression

(2008) Sandra Moshonov et al.   BMC GENOMICS

The RNA polymerase II core promoter — the gateway to transcription

(2008) Tamar Juven-Gershon et al.   CURRENT OPINION IN CELL BIOLOGY

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

Generic eukaryotic core promoter prediction using structural features of DNA

(2007) T. Abeel et al.   GENOME RESEARCH