RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73

Ws-2Introgression in a Proportion ofArabidopsis thaliana Col-0Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification: Table 1

(2016) Mon-Ray Shao et al.   PLANT CELL

A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants: Table 1

(2016) Joy Bergelson et al.   PLANT CELL

Dissecting the molecular signatures of apical cell-type shoot meristems from two ancient land plant lineages

(2015) Margaret H. Frank et al.   NEW PHYTOLOGIST

Genome Sequencing of Arabidopsisabp1-5Reveals Second-Site Mutations That May Affect Phenotypes

(2015) Tara A. Enders et al.   PLANT CELL

LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms

(2015) Daniel Money et al.   G3-Genes Genomes Genetics

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

(2015) Irina Makarevitch et al.   PLoS Genetics

Thenaked endospermGenes Encode Duplicate INDETERMINATE Domain Transcription Factors Required for Maize Endosperm Cell Patterning and Differentiation

(2015) Gibum Yi et al.   PLANT PHYSIOLOGY

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize

(2015) Malachy T. Campbell et al.   PLoS One

Transcriptomic complexity in young maize primary roots in response to low water potentials

(2014) Nina Opitz et al.   BMC GENOMICS

Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice

(2014) Lin Wang et al.   NATURE BIOTECHNOLOGY

Insights into the Maize Pan-Genome and Pan-Transcriptome

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

Transcriptomic Analyses Indicate That Maize Ligule Development Recapitulates Gene Expression Patterns That Occur during Lateral Organ Initiation

(2014) Robyn Johnston et al.   PLANT CELL

Genome-Wide Analysis of Alternative Splicing in Zea mays: Landscape and Genetic Regulation

(2014) S. R. Thatcher et al.   PLANT CELL

Dynamic Transcriptome Landscape of Maize Embryo and Endosperm Development

(2014) Jian Chen et al.   PLANT PHYSIOLOGY

Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays

(2014) Rajandeep S. Sekhon et al.   PLoS One

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing

(2014) Jeffrey A. Martin et al.   Scientific Reports

The Role of cis Regulatory Evolution in Maize Domestication

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

Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17

(2013) Claude Urbany et al.   BMC PLANT BIOLOGY

Regulatory modules controlling maize inflorescence architecture

(2013) A. L. Eveland et al.   GENOME RESEARCH

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

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

(2013) M. Regulski et al.   GENOME RESEARCH

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

(2013) S. R. Eichten et al.   PLANT CELL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Unraveling the KNOTTED1 regulatory network in maize meristems

(2012) N. Bolduc et al.   GENES & DEVELOPMENT

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

(2012) A. Paschold et al.   GENOME RESEARCH

Maize HapMap2 identifies extant variation from a genome in flux

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

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq

(2012) A. Kakumanu et al.   PLANT PHYSIOLOGY

Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)

(2012) Sanzhen Liu et al.   PLoS One

Genes Identified by Visible Mutant Phenotypes Show Increased Bias toward One of Two Subgenomes of Maize

(2011) James C. Schnable et al.   PLoS One

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82

(2010) W. J. Haun et al.   PLANT PHYSIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE