Bioinformatics Study of Structural Patterns in Plant MicroRNA Precursors

New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure

(2016) Maciej Antczak et al.   ACTA BIOCHIMICA POLONICA

StructAnalyzer - a tool for sequence versus structure similarity analysis

(2016) Jakub Wiedemann et al.   ACTA BIOCHIMICA POLONICA

AmiRNA Designer - new method of artificial miRNA design

(2016) Agnieszka Mickiewicz et al.   ACTA BIOCHIMICA POLONICA

Structural determinants of miR156a precursor processing in temperature-responsive flowering in Arabidopsis

(2016) Wanhui Kim et al.   JOURNAL OF EXPERIMENTAL BOTANY

MicroRNA-155-enhanced autophagy in human gastric epithelial cell in response to Helicobacter Pylori

(2016) Kai Wu et al.   Saudi Journal of Gastroenterology

The miRNA biogenesis in marine bivalves

(2016) Umberto Rosani et al.   PeerJ

The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes

(2015) Wenwen Fang et al.   MOLECULAR CELL

Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins

(2015) Simona Baranauskė et al.   NUCLEIC ACIDS RESEARCH

Nucleotide sequence of miRNA precursor contributes to cleavage site selection by Dicer

(2015) Julia Starega-Roslan et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Asymmetric bulges and mismatches determine 20-nt microRNA formation in plants

(2015) Wen-Chi Lee et al.   RNA Biology

Insight into miRNA biogenesis with RNA sequencing

(2015) Thomas Conrad et al.   Oncotarget

Regulation of microRNA biogenesis

(2014) Minju Ha et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Homodimerization of HYL1 ensures the correct selection of cleavage sites in primary miRNA

(2014) Xi Yang et al.   NUCLEIC ACIDS RESEARCH

Plant microRNAs: Recent Advances and Future Challenges

(2014) Humberto J. Debat et al.   PLANT MOLECULAR BIOLOGY REPORTER

Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing

(2013) Vincent C. Auyeung et al.   CELL

MCQ4Structures to compute similarity of molecule structures

(2013) Tomasz Zok et al.   Central European Journal of Operations Research

Introns of plant pri-miRNAs enhance miRNA biogenesis

(2013) Dawid Bielewicz et al.   EMBO REPORTS

Multiple RNA recognition patterns during microRNA biogenesis in plants

(2013) N. G. Bologna et al.   GENOME RESEARCH

MLP accompanied beam search for the resonance assignment problem

(2013) Marta Szachniuk et al.   JOURNAL OF HEURISTICS

Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1

(2013) Hongliang Zhu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Roles for MicroRNAs in Conferring Robustness to Biological Processes

(2012) Margaret S. Ebert et al.   CELL

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

Functions of microRNAs in plant stress responses

(2012) Ramanjulu Sunkar et al.   TRENDS IN PLANT SCIENCE

RNA CoSSMos: Characterization of Secondary Structure Motifs--a searchable database of secondary structure motifs in RNA three-dimensional structures

(2011) P. L. Vanegas et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

(2010) Mariusz Popenda et al.   BMC BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

MicroRNA Processing: Battle of the Bulge

(2010) Blake C. Meyers et al.   CURRENT BIOLOGY

Microprocessor of microRNAs: regulation and potential for therapeutic intervention

(2010) Kevin J Beezhold et al.   Molecular Cancer

Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis

(2010) Josh T Cuperus et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural basis of microRNA length variety

(2010) Julia Starega-Roslan et al.   NUCLEIC ACIDS RESEARCH

22-nucleotide RNAs trigger secondary siRNA biogenesis in plants

(2010) H.-M. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of Arabidopsis HYPONASTIC LEAVES1 and Its Molecular Implications for miRNA Processing

(2010) Seong Wook Yang et al.   STRUCTURE

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Identification of MicroRNA Processing Determinants by Random Mutagenesis of Arabidopsis MIR172a Precursor

(2009) Julieta L. Mateos et al.   CURRENT BIOLOGY

RNA Secondary Structural Determinants of miRNA Precursor Processing in Arabidopsis

(2009) Liang Song et al.   CURRENT BIOLOGY

Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing

(2009) J. T. Cuperus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstituting plant miRNA biogenesis

(2008) J.-K. Zhu   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA