Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

Transcriptome dynamics of developing maize leaves and genomewide prediction ofciselements and their cognate transcription factors

(2015) Chun-Ping Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maize and millet transcription factors annotated using comparative genomic and transcriptomic data

(2014) Jinn-Jy Lin et al.   BMC GENOMICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Cracking the Kranz enigma with systems biology

(2014) J. P. Fouracre et al.   JOURNAL OF EXPERIMENTAL BOTANY

Short-Root1 Plays a Role in the Development of Vascular Tissue and Kranz Anatomy in Maize Leaves

(2014) Thomas L. Slewinski et al.   Molecular Plant

Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice

(2014) Lin Wang et al.   NATURE BIOTECHNOLOGY

DNA-binding specificities of plant transcription factors and their potential to define target genes

(2014) José M. Franco-Zorrilla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

(2014) Alessandra M. Sullivan et al.   Cell Reports

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4Kranz anatomy

(2013) Peng Wang et al.   PLANT JOURNAL

Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination

(2013) W.-Y. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Scarecrow Plays a Role in Establishing Kranz Anatomy in Maize Leaves

(2012) Thomas L. Slewinski et al.   PLANT AND CELL PHYSIOLOGY

Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis

(2012) Y.-M. Chang et al.   PLANT PHYSIOLOGY

The Development of C4 Rice: Current Progress and Future Challenges

(2012) S. von Caemmerer et al.   SCIENCE

Auxin–Cytokinin Interaction Regulates Meristem Development

(2011) Ying-Hua Su et al.   Molecular Plant

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Using C4 photosynthesis to increase the yield of rice—rationale and feasibility

(2008) Julian M Hibberd et al.   CURRENT OPINION IN PLANT BIOLOGY