CHH DNA methylation increases at 24‐ PHAS loci depend on 24‐nt phased small interfering RNAs in maize meiotic anthers

Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize

(2020) Chong Teng et al.   Nature Communications

24-nt reproductive phasiRNAs are broadly present in angiosperms

(2019) Rui Xia et al.   Nature Communications

OUP accepted manuscript

(2018)   BIOINFORMATICS

Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon

(2018) Li Liu et al.   BMC GENOMICS

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture

(2018) Zhaoxue Han et al.   GENETICS

Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots

(2018) Atul Kakrana et al.   GENOME RESEARCH

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

(2018) Saleh Tamim et al.   NEW PHYTOLOGIST

Biogenesis and regulatory hierarchy of phased small interfering RNAs in plants

(2018) Pingchuan Deng et al.   PLANT BIOTECHNOLOGY JOURNAL

EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum

(2018) Seijiro Ono et al.   PLoS Genetics

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture

(2018) Zhaoxue Han et al.   GENETICS

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

Grass phasiRNAs and male fertility

(2017) Yang Yu et al.   Science China-Life Sciences

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

(2016) Guo-Ling Nan et al.   DEVELOPMENT

Identification of phasiRNAs and their drought- responsiveness inPopulus trichocarpa

(2016) Peng Shuai et al.   FEBS LETTERS

Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways

(2016) Qili Fei et al.   JOURNAL OF EXPERIMENTAL BOTANY

PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice

(2016) Yourong Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis

(2016) Stefanie Dukowic-Schulze et al.   Frontiers in Plant Science

Extensive Families of miRNAs andPHASLoci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants

(2015) Rui Xia et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

(2015) Mark A Urich et al.   Nature Protocols

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2015) Jixian Zhai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis

(2015) F. Mohn et al.   SCIENCE

piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production

(2015) B. W. Han et al.   SCIENCE

Genetic Perturbation of the Maize Methylome

(2014) Qing Li et al.   PLANT CELL

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

(2013) Siwaret Arikit et al.   CURRENT OPINION IN PLANT BIOLOGY

Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state

(2013) A. Le Thomas et al.   GENES & DEVELOPMENT

Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize

(2013) M. Zhang et al.   GENOME RESEARCH

PIWI-interacting RNAs: from generation to transgenerational epigenetics

(2013) Maartje J. Luteijn et al.   NATURE REVIEWS GENETICS

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development

(2012) Xianwei Song et al.   PLANT JOURNAL

Roles of DICER-LIKE and ARGONAUTE Proteins in TAS-Derived Small Interfering RNA-Triggered DNA Methylation

(2012) L. Wu et al.   PLANT PHYSIOLOGY

‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes

(2012) Matthew D. Schultz et al.   TRENDS IN GENETICS

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis

(2011) Xianwei Song et al.   PLANT JOURNAL

Emergence and patterning of the five cell types of the Zea mays anther locule

(2010) Timothy Kelliher et al.   DEVELOPMENTAL BIOLOGY

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

(2009) C. Johnson et al.   GENOME RESEARCH

Distinct extremely abundant siRNAs associated with cosuppression in petunia

(2009) E. De Paoli et al.   RNA

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

(2009) Ben Langmead et al.   GENOME BIOLOGY