Global investigation of the co-evolution ofMIRNAgenes and microRNA targets during soybean domestication

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

Evolutionary Patterns and Coevolutionary Consequences ofMIRNAGenes and MicroRNA Targets Triggered by Multiple Mechanisms of Genomic Duplications in Soybean

(2015) Meixia Zhao et al.   PLANT CELL

Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae

(2015) Lisa M. Smith et al.   PLANT JOURNAL

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

(2015) Meixia Zhao et al.   Plant Genome

Genetic, evolutionary and plant breeding insights from the domestication of maize

(2015) Sarah Hake et al.   eLife

Genetic controls on starch amylose content in wheat and rice grains

(2014) PARVIZ FASAHAT et al.   JOURNAL OF GENETICS

Global Coevolution of Human MicroRNAs and Their Target Genes

(2014) Shahar Barbash et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

5′ isomiR variation is of functional and evolutionary importance

(2014) Geok Chin Tan et al.   NUCLEIC ACIDS RESEARCH

Soybean miR172c Targets the Repressive AP2 Transcription Factor NNC1 to ActivateENOD40Expression and Regulate Nodule Initiation

(2014) Youning Wang et al.   PLANT CELL

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

(2014) Siwaret Arikit et al.   PLANT CELL

Global Dissection of Alternative Splicing in Paleopolyploid Soybean

(2014) Yanting Shen et al.   PLANT CELL

Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record

(2014) D. Q. Fuller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Current perspectives and the future of domestication studies

(2014) G. Larson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biosynthesis, regulation, and domestication of bitterness in cucumber

(2014) Y. Shang et al.   SCIENCE

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

(2013) Ying-hui Li et al.   BMC GENOMICS

Conserved Proteins Are Fragile

(2013) Raquel Assis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching

(2013) Yu-Chan Zhang et al.   NATURE BIOTECHNOLOGY

A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)

(2013) Guanqing Jia et al.   NATURE GENETICS

A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity

(2013) Jianjian Qi et al.   NATURE GENETICS

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

Birth and expression evolution of mammalian microRNA genes

(2012) J. Meunier et al.   GENOME RESEARCH

Analyses of aGlycine maxDegradome Library Identify microRNA Targets and MicroRNAs that Trigger Secondary SiRNA Biogenesis

(2012) Zheng Hu et al.   Journal of Integrative Plant Biology

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops

(2012) Rachel S. Meyer et al.   NEW PHYTOLOGIST

Pericentromeric Effects Shape the Patterns of Divergence, Retention, and Expression of Duplicated Genes in the Paleopolyploid Soybean

(2012) J. Du et al.   PLANT CELL

Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean

(2012) Z. Tian et al.   PLANT CELL

Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication

(2012) M. Abrouk et al.   PLANT CELL

Preceramic maize from Paredones and Huaca Prieta, Peru

(2012) A. Grobman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

(2012) G. P. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

(2011) Qing-Xin Song et al.   BMC PLANT BIOLOGY

Epigenetic regulation of transposable element derived human gene promoters

(2011) Ahsan Huda et al.   GENE

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

(2011) J. Zhai et al.   GENES & DEVELOPMENT

Selection Fine-Tunes the Expression of MicroRNA Target Genes in Arabidopsis thaliana

(2011) S. Takuno et al.   MOLECULAR BIOLOGY AND EVOLUTION

Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes

(2011) L. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data

(2010) Li Guo et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

High-throughput degradome sequencing can be used to gain insights into microRNA precursor metabolism

(2010) Y. Meng et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice

(2010) Yongqing Jiao et al.   NATURE GENETICS

OsSPL14 promotes panicle branching and higher grain productivity in rice

(2010) Kotaro Miura et al.   NATURE GENETICS

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

MicroRNA Gene Evolution inArabidopsis lyrataandArabidopsis thaliana

(2010) Noah Fahlgren et al.   PLANT CELL

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

Signatures of Purifying and Local Positive Selection in Human miRNAs

(2009) Hélène Quach et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

(2009) Z. Tian 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

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

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

Chromodomains direct integration of retrotransposons to heterochromatin

(2008) X. Gao et al.   GENOME RESEARCH

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

The birth and death of microRNA genes in Drosophila

(2008) Jian Lu et al.   NATURE GENETICS

Sequence Variation of MicroRNAs and Their Binding Sites in Arabidopsis

(2008) I. M. Ehrenreich et al.   PLANT PHYSIOLOGY

Evolution of Arabidopsis thaliana microRNAs from random sequences

(2008) F. Fenselau de Felippes et al.   RNA

Evolution of plant microRNAs and their targets

(2008) Michael J. Axtell et al.   TRENDS IN PLANT SCIENCE