J. Zhai

发表

A comprehensive online database for exploring ~20,000 public Arabidopsis RNA-Seq libraries

Li Feng, Hong Zhang, Fei Zhang, 2019, bioRxiv.

An Online Database for Exploring Over 2,000 Arabidopsis Small RNA Libraries1[OPEN]

Li Feng, Yan Zhao, Blake C Meyers, 2019, Plant Physiology.

Multiple RNA recognition patterns during microRNA biogenesis in plants

Blake C Meyers, Javier F. Palatnik, Jixian Zhai, 2013, Genome research.

sRNAanno --- a database repository of uniformly-annotated small RNAs in plants

J. Zhai, B. Meyers, Chengjie Chen, 2019, bioRxiv.

Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis

J. Li, S. Jacobsen, Li Feng, 2018, Proceedings of the National Academy of Sciences.

A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis

I. Henderson, S. Jacobsen, J. Zhai, 2015, Cell.

Short-read sequencing technologies for transcriptional analyses.

J. Zhai, B. Meyers, J. Zeng, 2009, Annual review of plant biology.

The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses

Alvaro J. González, Shelby L. Bidwell, B. Roe, 2011, Nature.

Plant MicroRNAs Display Differential 3′ Truncation and Tailing Modifications That Are ARGONAUTE1 Dependent and Conserved Across Species[W]

Xuemei Chen, Manoj Pillay, Blake C. Meyers, 2013, Plant Cell.

Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis.

Matteo Pellegrini, Veit Schubert, Suhua Feng, 2014, Molecular cell.

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs.

Gary Stacey, Pamela J Green, Blake C Meyers, 2011, Genes & development.

MCIBox: A Toolkit for Single-molecule Multi-way Chromatin Interaction Visualization and Micro-Domains Identification

Dariusz M Plewczynski, M. Fullwood, Meizhen Zheng, 2022, bioRxiv.

Widespread Long-range Cis-Regulatory Elements in the Maize Genome

Robert J. Schmitz, Nathan M. Springer, Alexandre P. Marand, 2019, Nature Plants.

A Phytophthora Effector Suppresses Trans-Kingdom RNAi to Promote Disease Susceptibility.

Li Feng, J. Zhai, Xuemei Chen, 2019, Cell host & microbe.

The Cornucopia of Small RNAs in Plant Genomes

J. Zhai, B. Meyers, J. Zeng, 2008, Rice.

Deep Sequencing from hen 1 Mutants to Identify Small RNA 3 0 Modifications

J. Zhai, B. Meyers, J. ZHAI, 2013 .

Single-nucleus full-length RNA profiling in plants incorporates isoform information to facilitate cell type identification

Hong Zhang, Jinbu Jia, J. Zhai, 2020, bioRxiv.

Comprehensive Investigation of MicroRNAs Enhanced by Analysis of Sequence Variants, Expression Patterns, ARGONAUTE Loading, and Target Cleavage1[W][OA]

J. Zhai, B. Meyers, P. Green, 2013, Plant Physiology.

Identification of microRNAs and their mRNA targets during soybean nodule development: functional analysis of the role of miR393j-3p in soybean nodulation.

G. Stacey, M. Hossain, J. Zhai, 2015, The New phytologist.

Coordination of MicroRNAs, PhasiRNAs, and NB‐LRR Genes in Response to a Plant Pathogen: Insights from Analyses of a Set of Soybean Rps Gene Near‐Isogenic Lines

J. Zhai, B. Meyers, J. Thimmapuram, 2015, The plant genome.

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes[W]

H. Nguyen, G. Stacey, T. Musket, 2014, Plant Cell.

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

T. Mockler, J. Zhai, B. Meyers, 2013, Genome Biology.

An atlas of plant full-length RNA reveals tissue-specific and monocots–dicots conserved regulation of poly(A) tail length

Hong Zhang, Jinbu Jia, J. Zhai, 2022, Nature Plants.

Induced Mutation in GmCOP1b Enhances the Performance of Soybean under Dense Planting Conditions

T. Zhao, J. Zhai, Jun Liu, 2022, International journal of molecular sciences.

The Dynamic Kaleidoscope of RNA Biology in Plants1

J. Zhai, M. Seki, J. Bailey-Serres, 2020, Plant Physiology.

Plant Public RNA‐seq Database: a comprehensive online database for expression analysis of ~45 000 plant public RNA‐Seq libraries

Hong Zhang, J. Zhai, Yanping Long, 2022, Plant biotechnology journal.

Plant Public RNA‐seq Database: a comprehensive online database for expression analysis of ~45 000 plant public RNA‐Seq libraries

Hong Zhang, J. Zhai, Yanping Long, 2022, bioRxiv.

Genome-wide characterization of nascent RNA processing in plants.

J. Zhai, Yanping Long, Yuwei Qin, 2022, Current opinion in plant biology.

Deep sequencing from hen1 mutants to identify small RNA 3' modifications.

J. Zhai, B. Meyers, 2012, Cold Spring Harbor symposia on quantitative biology.

MTHFD1 controls DNA methylation in Arabidopsis

Christopher J. Hale, Shawn Cokus, S. Jacobsen, 2016, Nature Communications.

controls DNA methylation in Arabidopsis.

Christopher J. Hale, Shawn Cokus, S. Jacobsen, 2016 .

Plant Intron Splicing Efficiency Database (PISE): exploring splicing of ∼1,650,000 introns in Arabidopsis, maize, rice and soybean from ∼57,000 public RNA-seq libraries

Hong Zhang, Jinbu Jia, J. Zhai, 2022, bioRxiv.

MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize

J. Fernandes, V. Walbot, J. Zhai, 2017, Development.

Regulation of DNA Methylation During Plant Endosperm Development

J. Zhai, M. Xi, Dongdong Lu, 2022, Frontiers in Genetics.

The Ca2+/calmodulin2‐binding transcription factor TGA3 elevates LCD expression and H2S production to bolster Cr6+ tolerance in Arabidopsis

J. Zhai, Hua Li, Yanping Long, 2017, The Plant journal : for cell and molecular biology.

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

V. Walbot, J. Zhai, B. Meyers, 2015, Proceedings of the National Academy of Sciences.

sRNAanno—a database repository of uniformly annotated small RNAs in plants

J. Zhai, B. Meyers, Chengjie Chen, 2021, Horticulture Research.

MicroRNA482/2118, a miRNA superfamily essential for both disease resistance and plant development.

J. Zhai, Chengjie Chen, Rui Xia, 2021, The New phytologist.

Distinct extremely abundant siRNAs associated with cosuppression in petunia.

J. Zhai, B. Meyers, R. Jorgensen, 2009, RNA.

Roles of small RNAs in soybean defense against Phytophthora sojae infection.

J. Zhai, B. Meyers, Lei Gao, 2014, The Plant journal : for cell and molecular biology.

MicroRNA Processing: Battle of the Bulge

Blake C. Meyers, Jixian Zhai, J. Zhai, 2010, Current Biology.

FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants

Hong Zhang, Jinbu Jia, J. Zhai, 2021, Genome biology.

Safeguard DCL2-Dependent 22-nt siRNA generation by DCL1.

Li Feng, J. Zhai, Bosheng Li, 2022, Biochemical and biophysical research communications.

Soybean DICER-LIKE2 Regulates Seed Coat Color via Production of Primary 22-Nucleotide Small Interfering RNAs from Long Inverted Repeats

Bin Liu, Li Feng, Jinbu Jia, 2020, Plant Cell.

Cis-directed cleavage and nonstoichiometric abundances of 21-nucleotide reproductive phased small interfering RNAs in grasses.

J. Zhai, B. Meyers, Qifa Zhang, 2018, The New phytologist.

Cis-directed cleavage and nonstoichiometric abundances of 21-nt reproductive phasiRNAs in grasses

J. Zhai, B. Meyers, Qifa Zhang, 2018, bioRxiv.

Cis-directed cleavage and nonstoichiometric abundances of 21-nt reproductive phasiRNAs in grasses

J. Zhai, B. Meyers, Qifa Zhang, 2018, bioRxiv.

Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection.

T. Joshi, Dong Xu, G. Stacey, 2016, Plant biotechnology journal.

Distinct and Cooperative Activities of HESO1 and URT1 Nucleotidyl Transferases in MicroRNA Turnover in Arabidopsis

Xuemei Chen, Blake C. Meyers, Bin Tu, 2015, PLoS genetics.

Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing.

J. Zhai, B. Meyers, Stacey A. Simon, 2014, Methods.

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

Samuel E. Fox, T. Mockler, J. Zhai, 2013, Genome Biology.

Biogenesis and function of rice small RNAs from non-coding RNA precursors.

J. Zhai, B. Meyers, S. Arikit, 2013, Current opinion in plant biology.

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis.

Lijia Ma, Xiu-Jie Wang, B. Liu, 2012, The Plant journal : for cell and molecular biology.

siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis

J. Zhai, B. Meyers, H. Vaucheret, 2010, Nucleic acids research.

The Arabidopsis Nucleotidyl Transferase HESO1 Uridylates Unmethylated Small RNAs to Trigger Their Degradation

Xuemei Chen, Blake C. Meyers, Jixian Zhai, 2012, Current Biology.

Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants

Hong Zhang, Jinbu Jia, J. Zhai, 2020, Nature Plants.

Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants

Hong Zhang, Jinbu Jia, J. Zhai, 2020, Nature Plants.

Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation

S. Jacobsen, J. Zhai, S. Feng, 2021, Science.

SDG714, a Histone H3K9 Methyltransferase, Is Involved in Tos17 DNA Methylation and Transposition in Rice[W]

J. Zhai, Q. Qian, Yong Ding, 2007, The Plant Cell Online.

Conservation and divergence in eukaryotic DNA methylation

J. Zhai, B. Meyers, Tzuu-fen Lee, 2010, Proceedings of the National Academy of Sciences.

Plant 22-nt siRNAs mediate translational repression and stress adaptation

Hong Zhang, Li Feng, J. Zhai, 2020, Nature.

Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice

Zhike Lu, J. Zhai, B. Meyers, 2014, Proceedings of the National Academy of Sciences.

Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage[W][OA]

Sai Guna Ranjan Gurazada, J. Zhai, B. Meyers, 2011, Plant Cell.

FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing

Jinbu Jia, J. Zhai, Yanping Long, 2021, Nature Protocols.

The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis

S. Jacobsen, J. Zhai, S. Bischof, 2020, Nature Communications.

RNA-directed DNA methylation involves co-transcriptional small RNA-guided slicing of Pol V transcripts in Arabidopsis

J. Chory, Jonathan Hetzel, S. Jacobsen, 2017, Nature Plants.

Small RNA-Directed Epigenetic Natural Variation in Arabidopsis thaliana

B. Liu, J. Zhai, B. Meyers, 2008, PLoS genetics.

CG gene body DNA methylation changes and evolution of duplicated genes in cassava

S. Jacobsen, J. Zhai, J. Carrington, 2015, Proceedings of the National Academy of Sciences.

Substrate deformation regulates DRM2-mediated DNA methylation in plants

Sarah M. Leichter, Q. Cui, J. Zhai, 2020, Science Advances.

Landes Highlights

Sai Guna Ranjan Gurazada, J. Zhai, B. Meyers, 2012, RNA Biology.

Efficient transformation and artificial miRNA gene silencing in Lemna minor.

R. Martienssen, J. Zhai, B. Meyers, 2015, Plant biology.

Multiple RNA recognition patterns during microRNA biogenesis in Material Supplemental

J. Boisbouvier, J. Zhai, B. Meyers, 2014 .

Solitary fibrous tumor of the abdominal wall re-surfacing as unilateral pleural effusion and mass: A case report and review of the literature

J. Zhai, Carrie D. Chun, Xiaogang Bi, 2017, Respiratory medicine case reports.

ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis

J. Zhai, B. Meyers, Lei Gao, 2017, PLoS biology.

Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates.

J. Zhai, B. Meyers, N. Bologna, 2013, Methods.

Highly efficient gene silencing using perfect complementary artificial miRNA targeting AP1 or heteromeric artificial miRNA targeting AP1 and CAL genes

J. Zhai, Jung-Youn Lee, Wonkeun Park, 2009, Plant Cell Reports.

ROR1/RPA2A, a Putative Replication Protein A2, Functions in Epigenetic Gene Silencing and in Regulation of Meristem Development in Arabidopsis[W]

J. Zhai, Xuhui Hong, Xiaofeng Cao, 2005, The Plant Cell Online.

Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions.

Li Feng, Jinbu Jia, J. Zhai, 2021, The Plant cell.

A comprehensive online database for exploring ∼20,000 public Arabidopsis RNA-Seq libraries.

Hong Zhang, Fei Zhang, Li Feng, 2020, Molecular plant.

Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

Hong Zhang, Jinbu Jia, J. Zhai, 2021, Genome biology.

DNA methylome of the 20-gigabase Norway spruce genome

S. Jacobsen, J. Zhai, S. Feng, 2016, Proceedings of the National Academy of Sciences.

Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae

J. Zhai, B. Meyers, N. Donofrio, 2013, BMC Genomics.

The antagonistic MYB paralogs RH1 and RH2 govern anthocyanin leaf markings in Medicago truncatula

N. Young, J. Zhai, Zhixi Tian, 2020, The New phytologist.

RNA-directed DNA methylation involves co-transcriptional small-RNA-guided slicing of polymerase V transcripts in Arabidopsis

J. Chory, Jonathan Hetzel, S. Jacobsen, 2018, Nature Plants.

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

Hong Zhang, Jinbu Jia, J. Zhai, 2023, Nature Plants.

Mutations in the Type II Protein Arginine Methyltransferase AtPRMT5 Result in Pleiotropic Developmental Defects in Arabidopsis1[C][OA]

J. Zhai, Xiaofeng Cao, Y. Pei, 2007, Plant Physiology.

Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens.

Li Feng, J. Zhai, Rui Xia, 2021, Annual Review of Phytopathology.

miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis

R. Martienssen, J. Zhai, B. Meyers, 2014, Nature.

The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis

S. Jacobsen, J. Zhai, S. Bischof, 2020, Nature Communications.

Single-molecule targeted accessibility and methylation sequencing of centromeres, telomeres and rDNAs in Arabidopsis

J. Zhai, Tong Li, Bo Liu, 2023, Nature Plants.

Distinct and in in

J. Zhai, B. Meyers, Xuemei Chen, 2015 .

RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats

Sai Guna Ranjan Gurazada, J. Zhai, B. Meyers, 2012, Epigenetics.

Comparative single-nucleus RNA-seq analysis captures shared and distinct responses to beneficial and pathogenic microbes in roots

J. Zhai, Zhijian Liu, Yanping Long, 2023, bioRxiv.

A SYBR Gold-based Label-free in vitro Dicing Assay.

J. Zhai, S. Feng, Jiamu Du, 2022, Bio-protocol.

Coordination of MicroRNAs, PhasiRNAs, and NB‐LRR Genes in Response to a Plant Pathogen: Insights from Analyses of a Set of Soybean Rps Gene Near‐Isogenic Lines

J. Zhai, B. Meyers, J. Thimmapuram, 2015, The plant genome.

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis.

Lijia Ma, Xiu-Jie Wang, B. Liu, 2012, The Plant journal : for cell and molecular biology.

Genome sequencing and analysis of the model grass Brachypodium distachyon

Sai Guna Ranjan Gurazada, Henry D. Priest, Samuel E. Fox, 2010, Nature.

Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago

J. Zhai, Wen Dong, Zhijian Liu, 2023, Nature Plants.

TO IDENTIFY SMALL RNA 3' MODIFICATIONS

J. Zhai, 2013 .

Characteristics and processing of Pol IV-dependent transcripts in Arabidopsis.

J. Zhai, Yanping Long, Xinyuan Chen, 2017, Journal of genetics and genomics = Yi chuan xue bao.

The chromatin will never forget

J. Zhai, Yiming Yu, 2020, Nature Plants.

Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

Jeff H. Chang, Henry D. Priest, D. Inzé, 2009 .

An atlas of plant full-length RNA reveals tissue-specific and evolutionarily-conserved regulation of poly(A) tail length

Jinbu Jia, J. Zhai, Bo Liu, 2022, bioRxiv.

Genome evolution and initial breeding of the Triticeae grass Leymus chinensis dominating the Eurasian Steppe

J. Zhai, Xiaofeng Cao, Yanan Chang, 2023, Proceedings of the National Academy of Sciences of the United States of America.

Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5

Jinbu Jia, J. Zhai, Xiaofeng Cao, 2024, Proceedings of the National Academy of Sciences of the United States of America.