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

An evo-devo perspective on root genetic variation in cereals

(2017) Silvio Salvi   JOURNAL OF EXPERIMENTAL BOTANY

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

(2017) Thomas Mock et al.   NATURE

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

(2016) Candice N. Hirsch et al.   PLANT CELL

Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads

(2016) Jiaqiang Dong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

(2015) Matthew Pendleton et al.   NATURE METHODS

Gramene 2016: comparative plant genomics and pathway resources

(2015) Marcela K. Tello-Ruiz et al.   NUCLEIC ACIDS RESEARCH

Nonsyntenic Genes Drive Highly Dynamic Complementation of Gene Expression in Maize Hybrids

(2014) A. Paschold et al.   PLANT CELL

Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes

(2014) MeiYee Law et al.   PLANT PHYSIOLOGY

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

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

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

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

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

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Accessing complex crop genomes with next-generation sequencing

(2012) David Edwards et al.   THEORETICAL AND APPLIED GENETICS

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

Screening synteny blocks in pairwise genome comparisons through integer programming

(2011) Haibao Tang et al.   BMC BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm

(2011) A. J. Waters et al.   PLANT CELL

B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize

(2011) S. R. Eichten et al.   PLANT PHYSIOLOGY

Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm

(2011) M. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Germin-like proteins (GLPs) in cereal genomes: gene clustering and dynamic roles in plant defence

(2010) James Breen et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

(2010) R. A. Swanson-Wagner et al.   GENOME RESEARCH

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

(2009) Carol Soderlund et al.   PLoS Genetics

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE