Dempster-Shafer Theory for the Prediction of Auxin-Response Elements (AuxREs) in Plant Genomes

Evaluating tools for transcription factor binding site prediction

(2016) Narayan Jayaram et al.   BMC BIOINFORMATICS

Sequence-based prediction of transcription upregulation by auxin in plants

(2015) Petr M. Ponomarenko et al.   Journal of Bioinformatics and Computational Biology

ppdb: plant promoter database version 3.0

(2013) Ayaka Hieno et al.   NUCLEIC ACIDS RESEARCH

Unipro UGENE: a unified bioinformatics toolkit

(2012) Konstantin Okonechnikov et al.   BIOINFORMATICS

Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription

(2012) Kenneth W Berendzen et al.   BMC PLANT BIOLOGY

Pattern of Auxin and Cytokinin Responses for Shoot Meristem Induction Results from the Regulation of Cytokinin Biosynthesis by AUXIN RESPONSE FACTOR3

(2012) Z. J. Cheng et al.   PLANT PHYSIOLOGY

Epigenetic priors for identifying active transcription factor binding sites

(2011) Gabriel Cuellar-Partida et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data

(2011) Yoshiharu Y Yamamoto et al.   BMC PLANT BIOLOGY

Bipartite Promoter Element Required for Auxin Response

(2011) C. L. Walcher et al.   PLANT PHYSIOLOGY

Hormonal control of the shoot stem-cell niche

(2010) Zhong Zhao et al.   NATURE

MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor

(2010) Alexandra Schlereth et al.   NATURE

Spatio-temporal sequence of cross-regulatory events in root meristem growth

(2010) E. Scacchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Auxin regulates distal stem cell differentiation in Arabidopsis roots

(2010) Z. Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence-ranked motif identification

(2010) Stoyan Georgiev et al.   GENOME BIOLOGY

Regulation of preprocambial cell state acquisition by auxin signaling in Arabidopsis leaves

(2009) T. J. Donner et al.   DEVELOPMENT

DORNROSCHEN is a direct target of the auxin response factor MONOPTEROS in the Arabidopsis embryo

(2009) M. Cole et al.   DEVELOPMENT

Auxin Control of Embryo Patterning

(2009) B. Moller et al.   Cold Spring Harbor Perspectives in Biology

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets

(2008) C. Linhart et al.   GENOME RESEARCH

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

(2008) Jean-Valery Turatsinze et al.   Nature Protocols

The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access

(2008) Hideki Goda et al.   PLANT JOURNAL