A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data

Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors

(2016) Burcu Alptekin et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites

(2015) Jason S. Cumbie et al.   BMC GENOMICS

mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs

(2015) Andrzej Zielezinski et al.   BMC PLANT BIOLOGY

Advances in long noncoding RNAs: identification, structure prediction and function annotation

(2015) Xingli Guo et al.   Briefings in Functional Genomics

Long non-coding RNAs and their functions in plants

(2015) Julia A Chekanova   CURRENT OPINION IN PLANT BIOLOGY

Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress

(2015) Bala Ani Akpinar et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Plant miRNAs: biogenesis, organization and origins

(2015) Hikmet Budak et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites

(2015) María Katherine Mejía-Guerra et al.   PLANT CELL

New insights into pri-miRNA processing and accumulation in plants

(2015) Shuxin Zhang et al.   Wiley Interdisciplinary Reviews-RNA

Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

(2014) H. Wang et al.   GENOME RESEARCH

PNRD: a plant non-coding RNA database

(2014) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

Introns of plant pri-miRNAs enhance miRNA biogenesis

(2013) Dawid Bielewicz et al.   EMBO REPORTS

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

Coordination of Flower Maturation by a Regulatory Circuit of Three MicroRNAs

(2013) Ignacio Rubio-Somoza et al.   PLoS Genetics

PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs

(2013) Annalisa Marsico et al.   GENOME BIOLOGY

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

(2012) W. Zhang et al.   PLANT CELL

Regulation of miR399f Transcription by AtMYB2 Affects Phosphate Starvation Responses in Arabidopsis

(2012) D. Baek et al.   PLANT PHYSIOLOGY

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Coordinated histone modifications are associated with gene expression variation within and between species

(2011) M. Ha et al.   GENOME RESEARCH

cis- andtrans-Regulation of miR163 and Target Genes Confers Natural Variation of Secondary Metabolites in TwoArabidopsisSpecies and Their Allopolyploids

(2011) Danny W-K. Ng et al.   PLANT CELL

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

Nonhierarchical Ribonucleoprotein Assembly Suggests a Strain-Propagation Model for Protein-Facilitated RNA Folding

(2010) Caia D. S. Duncan et al.   BIOCHEMISTRY

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

The Arabidopsis bZIP1 Transcription Factor Is Involved in Sugar Signaling, Protein Networking, and DNA Binding

(2010) Shin Gene Kang et al.   Molecular Plant

MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion

(2009) Kevin J. Peterson et al.   BIOESSAYS

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

Conserved noncoding sequences (CNSs) in higher plants

(2009) Michael Freeling et al.   CURRENT OPINION IN PLANT BIOLOGY

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs

(2009) Bogna Szarzynska et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana

(2009) Xiaoyu Zhang et al.   GENOME BIOLOGY

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY