The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization

A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy

(2016) Zachary W. Brenton et al.   GENETICS

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Dynamics of biomass partitioning, stem gene expression, cell wall biosynthesis, and sucrose accumulation during development ofSorghum bicolor

(2016) Brian McKinley et al.   PLANT JOURNAL

Transcriptome Profiling of Tiller Buds Provides New Insights into PhyB Regulation of Tillering and Indeterminate Growth in Sorghum

(2016) Tesfamichael H. Kebrom et al.   PLANT PHYSIOLOGY

Improving photosynthesis and crop productivity by accelerating recovery from photoprotection

(2016) Johannes Kromdijk et al.   SCIENCE

A survey of the sorghum transcriptome using single-molecule long reads

(2016) Salah E. Abdel-Ghany et al.   Nature Communications

Harnessing Diversity in Wheat to Enhance Grain Yield, Climate Resilience, Disease and Insect Pest Resistance and Nutrition Through Conventional and Modern Breeding Approaches

(2016) Suchismita Mondal et al.   Frontiers in Plant Science

A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy

(2016) Zachary W. Brenton et al.   GENETICS

Identification of Dw1, a Regulator of Sorghum Stem Internode Length

(2016) Josie Hilley et al.   PLoS One

Repeat DNA in genome organization and stability

(2015) Jan Padeken et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Determinants of nucleosome positioning and their influence on plant gene expression

(2015) Ming-Jung Liu et al.   GENOME RESEARCH

Agrochemical control of plant water use using engineered abscisic acid receptors

(2015) Sang-Youl Park et al.   NATURE

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

(2015) Robert VanBuren et al.   NATURE

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

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

The effects of chromatin organization on variation in mutation rates in the genome

(2015) Kateryna D. Makova et al.   NATURE REVIEWS GENETICS

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Redesigning photosynthesis to sustainably meet global food and bioenergy demand

(2015) Donald R. Ort et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RIG: Recalibration and Interrelation of Genomic Sequence Data with the GATK

(2015) Ryan F. McCormick et al.   G3-Genes Genomes Genetics

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation

(2015) Frank Technow et al.   PLoS One

A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

(2014) Nadia Shakoor et al.   BMC PLANT BIOLOGY

Energy Sorghum--a genetic model for the design of C4 grass bioenergy crops

(2014) J. Mullet et al.   JOURNAL OF EXPERIMENTAL BOTANY

Involvement of YODA and mitogen activated protein kinase 6 in Arabidopsis post-embryogenic root development through auxin up-regulation and cell division plane orientation

(2014) Veronika Smékalová et al.   NEW PHYTOLOGIST

The protein kinase TOUSLED facilitates RNAi inArabidopsis

(2014) Mohammad Nazim Uddin et al.   NUCLEIC ACIDS RESEARCH

Insights into the Maize Pan-Genome and Pan-Transcriptome

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

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

Resolution of Genetic Map Expansion Caused by Excess Heterozygosity in Plant Recombinant Inbred Populations

(2014) Sandra K. Truong et al.   G3-Genes Genomes Genetics

Expanding and Vetting Gene Annotations through Transcriptome and Methylome Sequencing

(2014) Andrew Olson et al.   Plant Genome

Repetitive Sequences in Plant Nuclear DNA: Types, Distribution, Evolution and Function

(2014) Shweta Mehrotra et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Plant Genome Engineering with Sequence-Specific Nucleases

(2013) Daniel F. Voytas   Annual Review of Plant Biology

Digital genotyping of sorghum -- a diverse plant species with a large repeat-rich genome

(2013) Daryl T Morishige et al.   BMC GENOMICS

Moderation of Arabidopsis Root Stemness by CLAVATA1 and ARABIDOPSIS CRINKLY4 Receptor Kinase Complexes

(2013) Yvonne Stahl et al.   CURRENT BIOLOGY

Regulation of floral patterning and organ identity by Arabidopsis ERECTA-family receptor kinase genes

(2013) Shannon M. Bemis et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-Wide Prediction of Nucleosome Occupancy in Maize Reveals Plant Chromatin Structural Features at Genes and Other Elements at Multiple Scales

(2013) J. A. Fincher et al.   PLANT PHYSIOLOGY

Extensive Variation in the Density and Distribution of DNA Polymorphism in Sorghum Genomes

(2013) Joseph Evans et al.   PLoS One

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

(2013) Emma S. Mace et al.   Nature Communications

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

(2012) Gengyun Zhang et al.   NATURE BIOTECHNOLOGY

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

(2012) G. P. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid

(2011) Diana V Dugas et al.   BMC GENOMICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

Impact of chromatin structure on sequence variability in the human genome

(2011) Michael Y Tolstorukov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide atlas of transcription during maize development

(2011) Rajandeep S. Sekhon et al.   PLANT JOURNAL

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum

(2011) R. L. Murphy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)

(2011) Lei-Ying Zheng et al.   GENOME BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

A dynamic gene expression atlas covering the entire life cycle of rice

(2009) Lei Wang et al.   PLANT JOURNAL

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH

The plant WNK gene family and regulation of flowering time inArabidopsis

(2008) Y. Wang et al.   PLANT BIOLOGY

Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites

(2008) S. Sasaki et al.   SCIENCE

Predicting Human Nucleosome Occupancy from Primary Sequence

(2008) Shobhit Gupta et al.   PLoS Computational Biology