Comprehensive Annotation and Functional Exploration of MicroRNAs in Lettuce

Structural and Functional Analyses of Hub MicroRNAs in an Integrated Gene Regulatory Network of Arabidopsis

(2021) Zhaoxu Gao et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Elucidation of the microRNA Transcriptome in Western Corn Rootworm Reveals Its Dynamic and Evolutionary Complexity

(2021) Xiaozeng Yang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

MicroRNA annotation in plants: current status and challenges

(2021) Yongxin Zhao et al.   BRIEFINGS IN BIOINFORMATICS

Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce

(2021) Tong Wei et al.   NATURE GENETICS

CRISPR/Cas9-mediated mutagenesis of ClBG1 decreased seed size and promoted seed germination in watermelon

(2021) Yanping Wang et al.   Horticulture Research

A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.)

(2020) Kousuke Seki et al.   Horticulture Research

Quo vadis microRNAs?

(2020) Bastian Fromm et al.   TRENDS IN GENETICS

Dissection of the domestication‐shaped genetic architecture of lettuce primary metabolism

(2020) Weiyi Zhang et al.   PLANT JOURNAL

Upregulation of a KN1 homolog by transposon insertion promotes leafy head development in lettuce

(2020) Changchun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant-derived RNAi therapeutics: A strategic inhibitor of HBsAg

(2019) Shuo Zhang et al.   BIOMATERIALS

Plant cell-made protein antigens for induction of Oral tolerance

(2019) Henry Daniell et al.   BIOTECHNOLOGY ADVANCES

The LsVe1L allele provides a molecular marker for resistance to Verticillium dahliae race 1 in lettuce

(2019) Patrik Inderbitzin et al.   BMC PLANT BIOLOGY

Characterization of four polymorphic genes controlling red leaf color in lettuce that have undergone disruptive selection since domestication

(2019) Wenqing Su et al.   PLANT BIOTECHNOLOGY JOURNAL

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Integrated mRNA, microRNA transcriptome and degradome analyses provide insights into stamen development in moso bamboo

(2019) Zhanchao Cheng et al.   PLANT AND CELL PHYSIOLOGY

PmiREN: a comprehensive encyclopedia of plant miRNAs

(2019) Zhonglong Guo et al.   NUCLEIC ACIDS RESEARCH

PlantRegMap: charting functional regulatory maps in plants

(2019) Feng Tian et al.   NUCLEIC ACIDS RESEARCH

The grain yield modulator miR156 regulates seed dormancy through the gibberellin pathway in rice

(2019) Chunbo Miao et al.   Nature Communications

MicroRNA miR396, GRF transcription factors and GIF co-regulators: a conserved plant growth regulatory module with potential for breeding and biotechnology

(2019) Daniela Liebsch et al.   CURRENT OPINION IN PLANT BIOLOGY

Overexpression of microRNA408 enhances photosynthesis, growth, and seed yield in diverse plants

(2018) Jiawei Pan et al.   Journal of Integrative Plant Biology

psRNATarget: a plant small RNA target analysis server (2017 release)

(2018) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data

(2018) Michael J. Axtell et al.   PLANT CELL

LCM-seq reveals the crucial role of LsSOC1 in heat-promoted bolting of lettuce (Lactuca sativa L.)

(2018) Zijing Chen et al.   PLANT JOURNAL

Inflorescence Development and the Role of LsFT in Regulating Bolting in Lettuce (Lactuca sativa L.)

(2018) Zijing Chen et al.   Frontiers in Plant Science

Metabolomic Evaluation of the Quality of Leaf Lettuce Grown in Practical Plant Factory to Capture Metabolite Signature

(2018) Yoshio Tamura et al.   Frontiers in Plant Science

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs

(2018) Saima Shahid et al.   NATURE

Systemic control of legume susceptibility to rhizobial infection by a mobile microRNA

(2018) Daniela Tsikou et al.   SCIENCE

miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants

(2018) Zheng Kuang et al.   BIOINFORMATICS

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Role of miRNAs in development and disease: Lessons learnt from small organisms

(2017) Swati Chandra et al.   LIFE SCIENCES

Mapping genome-wide transcription-factor binding sites using DAP-seq

(2017) Anna Bartlett et al.   Nature Protocols

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

MiR408 Regulates Grain Yield and Photosynthesis via a Phytocyanin Protein

(2017) Jin-Ping Zhang et al.   PLANT PHYSIOLOGY

RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis

(2017) Lei Zhang et al.   Nature Communications

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

(2017) Sebastian Reyes-Chin-Wo et al.   Nature Communications

miRNAFold: a web server for fast miRNA precursor prediction in genomes

(2016) Christophe Tav et al.   NUCLEIC ACIDS RESEARCH

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

(2016) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

The tae-miR408-mediated Control of TaTOC1 Gene Transcription Is Required for the Regulation of Heading Time in Wheat (Triticum aestivum L.)

(2016) Xiang Yu Zhao et al.   PLANT PHYSIOLOGY

DELAY OF GERMINATION1(DOG1) regulates both seed dormancy and flowering time through microRNA pathways

(2016) Heqiang Huo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.)

(2013) CHUNHUA YANG et al.   PLANT CELL AND ENVIRONMENT

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis Argonaute10 Specifically Sequesters miR166/165 to Regulate Shoot Apical Meristem Development

(2011) Hongliang Zhu et al.   CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

miR156-Regulated SPL Transcription Factors Define an Endogenous Flowering Pathway in Arabidopsis thaliana

(2009) Jia-Wei Wang et al.   CELL

The Sequential Action of miR156 and miR172 Regulates Developmental Timing in Arabidopsis

(2009) Gang Wu et al.   CELL

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

(2009) Marcelo A German et al.   Nature Protocols

Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana

(2009) Leonardo Alves-Junior et al.   NUCLEIC ACIDS RESEARCH

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS