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

Intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maize

(2018) Nannan Liu et al.   BMC PLANT BIOLOGY

From signals to stem cells and back again

(2018) Denis Janocha et al.   CURRENT OPINION IN PLANT BIOLOGY

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

High-resolution comparative analysis of great ape genomes

(2018) Zev N. Kronenberg et al.   SCIENCE

Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

(2018) Karl A. G. Kremling et al.   NATURE

The maize W22 genome provides a foundation for functional genomics and transposon biology

(2018) Nathan M. Springer et al.   NATURE GENETICS

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

(2018) Silong Sun et al.   NATURE GENETICS

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Signaling in Early Maize Kernel Development

(2017) Nicolas M. Doll et al.   Molecular Plant

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

RNA-guided Cas9 as an in vivo desired-target mutator in maize

(2017) Chuxi Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Contributions of Zea mays subspecies mexicana haplotypes to modern maize

(2017) Ning Yang et al.   Nature Communications

CLAVATA-WUSCHEL signaling in the shoot meristem

(2016) Marc Somssich et al.   DEVELOPMENT

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Multi-environment QTL analysis of grain morphology traits and fine mapping of a kernel-width QTL in Zheng58 × SK maize population

(2016) Mohammad Sharif Raihan et al.   THEORETICAL AND APPLIED GENETICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Plant stem cell maintenance by transcriptional cross-regulation of related receptor kinases

(2015) Z. L. Nimchuk et al.   DEVELOPMENT

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

(2015) Robert VanBuren et al.   NATURE

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Genome-wide dissection of the maize ear genetic architecture using multiple populations

(2015) Yingjie Xiao et al.   NEW PHYTOLOGIST

Genome-wide recombination dynamics are associated with phenotypic variation in maize

(2015) Qingchun Pan et al.   NEW PHYTOLOGIST

High-resolution genetic mapping of maize pan-genome sequence anchors

(2015) Fei Lu et al.   Nature Communications

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

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

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Structural variations in plant genomes

(2014) R. K. Saxena et al.   Briefings in Functional Genomics

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

(2014) W. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

P-MITE: a database for plant miniature inverted-repeat transposable elements

(2013) Jiongjiong Chen et al.   NUCLEIC ACIDS RESEARCH

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Matthew B Hufford et al.   NATURE GENETICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes

(2011) Torsten Wenke et al.   PLANT CELL

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

(2011) Martin W. Ganal et al.   PLoS One

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

(2010) Xiaohong Yang et al.   MOLECULAR BREEDING

Genetic signals of origin, spread, and introgression in a large sample of maize landraces

(2010) J. van Heerwaarden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity in enoyl-acyl carrier protein reductases

(2009) R. P. Massengo-Tiassé et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS