Natural variation for gene expression responses to abiotic stress in maize

Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4grass

(2016) John T. Lovell et al.   GENOME RESEARCH

Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences

(2015) Michael Freeling et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability

(2015) Michael V. Mickelbart et al.   NATURE REVIEWS GENETICS

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

Extensivecis-Regulatory Variation Robust to Environmental Perturbation inArabidopsis

(2014) Francisco A. Cubillos et al.   PLANT CELL

The Role of cis Regulatory Evolution in Maize Domestication

(2014) Zachary H. Lemmon et al.   PLoS Genetics

Molecular mechanisms of the plant heat stress response

(2013) Ai-Li Qu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Cold Signaling and Cold Response in Plants

(2013) Kenji Miura et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Physiological, Biochemical, and Molecular Mechanisms of Heat Stress Tolerance in Plants

(2013) Mirza Hasanuzzaman et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genome-Wide Analysis of ZmDREB Genes and Their Association with Natural Variation in Drought Tolerance at Seedling Stage of Zea mays L

(2013) Shengxue Liu et al.   PLoS Genetics

Mendelian and Non-Mendelian Regulation of Gene Expression in Maize

(2013) Lin Li et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

AP2/ERF family transcription factors in plant abiotic stress responses

(2011) Junya Mizoi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Genome-wide expression quantitative trait loci (eQTL) analysis in maize

(2011) Beth Holloway et al.   BMC GENOMICS

Binding affinities and interactions among different heat shock element types and heat shock factors in rice (Oryza sativa L.)

(2011) Dheeraj Mittal et al.   FEBS Journal

Role of DREBs in regulation of abiotic stress responses in plants

(2011) C. Lata et al.   JOURNAL OF EXPERIMENTAL BOTANY

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ABA perception and signalling

(2010) Agepati S. Raghavendra et al.   TRENDS IN PLANT SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Cold stress tolerance mechanisms in plants. A review

(2009) Sudesh Kumar Yadav   Agronomy for Sustainable Development

Paternal Dominance of Trans-eQTL Influences Gene Expression Patterns in Maize Hybrids

(2009) R. A. Swanson-Wagner et al.   SCIENCE

Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis

(2008) Robert M Stupar et al.   BMC PLANT BIOLOGY

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

(2008) A. Yilmaz et al.   PLANT PHYSIOLOGY