TSSPlant: a new tool for prediction of plant Pol II promoters

bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria andEscherichia coli

(2016) Ilham Ayub Shahmuradov et al.   BIOINFORMATICS

Dry and wet approaches for genome-wide functional annotation of conventional and unconventional transcriptional activators

(2016) Elisabetta Levati et al.   Computational and Structural Biotechnology Journal

Core promoters in transcription: old problem, new insights

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

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

(2014) Rasika Mundade et al.   CELL CYCLE

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools

(2014) René Dreos et al.   NUCLEIC ACIDS RESEARCH

Identifying transcriptional cis -regulatory modules in animal genomes

(2014) Kushal Suryamohan et al.   Wiley Interdisciplinary Reviews-Developmental Biology

ppdb: plant promoter database version 3.0

(2013) Ayaka Hieno et al.   NUCLEIC ACIDS RESEARCH

Identification and validation of promoters and cis-acting regulatory elements

(2013) Carlos M. Hernandez-Garcia et al.   PLANT SCIENCE

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

(2013) Sunita Kumari et al.   PLoS One

Prediction of plant promoters based on hexamers and random triplet pair analysis

(2011) A K M Azad et al.   Algorithms for Molecular Biology

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

(2011) C. Morey et al.   PLANT PHYSIOLOGY

Identification of TATA and TATA-less promoters in plant genomes by integrating diversity measure, GC-Skew and DNA geometric flexibility

(2010) Yong-Chun Zuo et al.   GENOMICS

Toward a gold standard for promoter prediction evaluation

(2009) Thomas Abeel et al.   BIOINFORMATICS

Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition

(2009) Vetriselvi Rangannan et al.   Molecular BioSystems

Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis

(2009) Yoshiharu Y. Yamamoto et al.   PLANT JOURNAL

Highly Diversified Molecular Evolution of Downstream Transcription Start Sites in Rice and Arabidopsis

(2009) T. Tanaka et al.   PLANT PHYSIOLOGY

The functional consequences of alternative promoter use in mammalian genomes

(2008) Ramana V. Davuluri et al.   TRENDS IN GENETICS

Generic eukaryotic core promoter prediction using structural features of DNA

(2007) T. Abeel et al.   GENOME RESEARCH