TransPrise: a novel machine learning approach for eukaryotic promoter prediction

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

(2018) Jens Keilwagen et al.   BMC BIOINFORMATICS

Comparative genome based cis- elements analysis in the 5′ upstream and 3′ downstream region of cell wall invertase and Phenylalanine ammonia lyase in Nicotiana benthamiana

(2018) S.A. Sheshadri et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Identifying noncoding risk variants using disease-relevant gene regulatory networks

(2018) Long Gao et al.   Nature Communications

PalmXplore: oil palm gene database

(2018) Nik Shazana Nik Mohd Sanusi et al.   Database-The Journal of Biological Databases and Curation

DBTSS/DBKERO for integrated analysis of transcriptional regulation

(2017) Ayako Suzuki et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Ilham A. Shahmuradov et al.   NUCLEIC ACIDS RESEARCH

Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks

(2017) Ramzan Kh. Umarov et al.   PLoS One

Nucleotide patterns aiding in prediction of eukaryotic promoters

(2017) Martin Triska et al.   PLoS One

Nucleotide diversity analysis highlights functionally important genomic regions

(2016) Tatiana V. Tatarinova et al.   Scientific Reports

Nsite, NsiteH and NsiteM computer tools for studying transcription regulatory elements: Fig. 1.

(2015) Ilham A. Shahmuradov et al.   BIOINFORMATICS

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

ZmbZIP91 regulates expression of starch synthesis-related genes by binding to ACTCAT elements in their promoters

(2015) Jiang Chen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genetic fine mapping and candidate gene analysis of the Gossypium hirsutum Ligon lintless-1 (Li1) mutant on chromosome 22(D)

(2015) Yurong Jiang et al.   MOLECULAR GENETICS AND GENOMICS

Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa

(2014) Eran Elhaik et al.   BMC BIOINFORMATICS

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines

(2014) Morten Rye et al.   BMC GENOMICS

Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression

(2014) M. J. Li et al.   BRIEFINGS IN BIOINFORMATICS

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing

(2014) H. Kawaji et al.   GENOME RESEARCH

Unexpected Structure of Plant Promoters:

(2014) Nancy A. Eckardt   PLANT CELL

Paired-End Analysis of Transcription Start Sites inArabidopsisReveals Plant-Specific Promoter Signatures

(2014) Taj Morton et al.   PLANT CELL

Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas

(2013) Christophe Liseron-Monfils et al.   BMC PLANT BIOLOGY

Cross-Species Analysis of Genic GC3 Content and DNA Methylation Patterns

(2013) Tatiana Tatarinova et al.   Genome Biology and Evolution

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Gene Identification Programs in Bread Wheat: A Comparison Study

(2013) Jaber Nasiri et al.   NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS

Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture

(2013) Z. Lu et al.   PLANT CELL

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

(2012) P. Batut et al.   GENOME RESEARCH

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

An examination of targeted gene neighborhoods in strawberry

(2010) Thomas M Davis et al.   BMC PLANT BIOLOGY

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genome-Wide Discovery of cis-Elements in Promoter Sequences Using Gene Expression

(2009) Maxim Troukhan et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

The Prediction of Rice Gene by Fgenesh

(2008) Sheng-li ZHANG et al.   Agricultural Sciences in China

Insights into corn genes derived from large-scale cDNA sequencing

(2008) Nickolai N. Alexandrov et al.   PLANT MOLECULAR BIOLOGY