Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis)

Achieving Plant Genome Editing While Bypassing Tissue Culture

(2020) Xiang Ji et al.   TRENDS IN PLANT SCIENCE

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

(2020) T. Rhyker Ranallo-Benavidez et al.   Nature Communications

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

(2020) Michael Abrouk et al.   Nature Communications

The genome of broomcorn millet

(2019) Changsong Zou et al.   Nature Communications

ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes

(2019) Anna E. J. Yssel et al.   Genes

Distinguishing friends, foes, and freeloaders in giant genomes

(2018) Jeffrey L Bennetzen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The causes and consequences of subgenome dominance in hybrids and recent polyploids

(2018) Kevin A. Bird et al.   NEW PHYTOLOGIST

MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes

(2018) Juan Manuel Crescente et al.   BMC BIOINFORMATICS

Rapid and user-friendly open-source CRISPR/Cas9 system for single- or multi-site editing of tomato genome

(2018) Nan Hu et al.   Horticulture Research

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

(2017) Ming-Cheng Luo et al.   NATURE

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

(2017) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

(2017) Michiel Van Bel et al.   NUCLEIC ACIDS RESEARCH

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives

(2016) Gautier Sarah et al.   Molecular Ecology Resources

A splice acceptor site mutation in TaGW2-A1 increases thousand grain weight in tetraploid and hexaploid wheat through wider and longer grains

(2016) James Simmonds et al.   THEORETICAL AND APPLIED GENETICS

Are We on the Right Track: Can Our Understanding of Abscission in Model Systems Promote or Derail Making Improvements in Less Studied Crops?

(2016) Sara E. Patterson et al.   Frontiers in Plant Science

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Monocot fossils suitable for molecular dating analyses

(2015) William J. D. Iles et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots

(2014) Yuannian Jiao et al.   PLANT CELL

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

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

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

Fine-Mapping and Identification of a Candidate Gene Underlying the d2 Dwarfing Phenotype in Pearl Millet, Cenchrus americanus (L.) Morrone

(2013) Rajiv K. Parvathaneni et al.   G3-Genes Genomes Genetics

High-Throughput Discovery of Mutations in Tef Semi-Dwarfing Genes by Next-Generation Sequencing Analysis

(2012) Q. Zhu et al.   GENETICS

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

Parallel domestication of the Shattering1 genes in cereals

(2012) Zhongwei Lin et al.   NATURE GENETICS

ORCAE: online resource for community annotation of eukaryotes

(2012) Lieven Sterck et al.   NATURE METHODS

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets

(2011) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Plant regeneration from stem segment-derived friable callus of “Fonio” (Digitaria exilis (L.) Stapf.)

(2010) Valentine O. Ntui et al.   SCIENTIA HORTICULTURAE

FONIO MILLET ( DIGITARIA EXILIS) RESPONSE TO N, P AND K FERTILIZERS UNDER VARYING CLIMATIC CONDITIONS IN WEST AFRICA

(2009) J. GIGOU et al.   EXPERIMENTAL AGRICULTURE

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes

(2009) M. Rho et al.   NUCLEIC ACIDS RESEARCH

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS