Combined population transcriptomic and genomic analysis reveals cis-regulatory differentiation of non-coding RNAs in maize

A multi-tissue atlas of regulatory variants in cattle

(2022) Shuli Liu et al.   NATURE GENETICS

Natural Variation in Crops: Realized Understanding, Continuing Promise

(2021) Yameng Liang et al.   Annual Review of Plant Biology

Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

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From “Dark Matter” to “Star”: Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs

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The parent-of-origin lncRNA MISSEN regulates rice endosperm development

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Functional Long Non-coding RNAs Evolve from Junk Transcripts

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Where Are the Disease-Associated eQTLs?

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Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding

(2020) Qiuyue Chen et al.   Molecular Plant

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Evolutionary dynamics of linc RNA transcription in nine citrus species

(2019) Lili Ke et al.   PLANT JOURNAL

Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement

(2019) Ning Yang et al.   NATURE GENETICS

Genome-wide analyses reveal the role of noncoding variation in complex traits during rice domestication

(2019) X. M. Zheng et al.   Science Advances

Genome-wide Analysis of Transcriptional Variability in a Large Maize-Teosinte Population

(2018) Xufeng Wang et al.   Molecular Plant

Wheat miR9678 Affects Seed Germination by Generating Phased siRNAs and Modulating Abscisic Acid/Gibberellin Signaling

(2018) Guanghui Guo et al.   PLANT CELL

lncRNAs in Plant and Animal Sexual Reproduction

(2018) Agnieszka A. Golicz et al.   TRENDS IN PLANT SCIENCE

New lncRNA annotation reveals extensive functional divergence of the transcriptome in maize

(2018) Linqian Han et al.   Journal of Integrative Plant Biology

Kernel size‐related genes revealed by an integrated eQTL analysis during early maize kernel development

(2018) Junling Pang et al.   PLANT JOURNAL

Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation

(2018) Peter Kindgren et al.   Nature Communications

The Long Intergenic Noncoding RNA (LincRNA) Landscape of the Soybean Genome

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ZmCCT9enhances maize adaptation to higher latitudes

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Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations

(2017) Sarah Kim-Hellmuth et al.   Nature Communications

Construction of the third-generation Zea mays haplotype map

(2017) Robert Bukowski et al.   GigaScience

Genotype Imputation with Millions of Reference Samples

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Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens

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Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

(2016) Marta Melé et al.   GENOME RESEARCH

Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings

(2016) Xianglan Wang et al.   NATURE GENETICS

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

(2016) Igor Ulitsky   NATURE REVIEWS GENETICS

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

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(2016) Danelle K. Seymour et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lessons from Domestication: Targeting Cis -Regulatory Elements for Crop Improvement

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Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits

(2015) Huan Wang et al.   PLANT JOURNAL

The human transcriptome across tissues and individuals

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Genome Wide Association Studies Using a New Nonparametric Model Reveal the Genetic Architecture of 17 Agronomic Traits in an Enlarged Maize Association Panel

(2014) Ning Yang et al.   PLoS Genetics

The Role of cis Regulatory Evolution in Maize Domestication

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Genetic and Epigenetic Regulation of Human lincRNA Gene Expression

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Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

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RNA sequencing reveals the complex regulatory network in the maize kernel

(2013) Junjie Fu et al.   Nature Communications

Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants

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Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels

(2012) Hui Li et al.   NATURE GENETICS

Comparative population genomics of maize domestication and improvement

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Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

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Genome-Wide Association Studies Identified Three Independent Polymorphisms Associated with α-Tocopherol Content in Maize Kernels

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(2011) Anthony Studer et al.   NATURE GENETICS

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

(2011) Jeffrey B. Endelman   Plant Genome

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Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize

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Understanding mechanisms underlying human gene expression variation with RNA sequencing

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Constructing genomic maps of positive selection in humans: Where do we go from here?

(2009) J. M. Akey   GENOME RESEARCH

The Werner Syndrome Protein Binds Replication Fork and Holliday Junction DNAs as an Oligomer

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