Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop

Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop

(2019) Glaucia Mendes Souza et al.   GigaScience

CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses

(2018) Pedro S. T. Russo et al.   BMC BIOINFORMATICS

A mosaic monoploid reference sequence for the highly complex genome of sugarcane

(2018) Olivier Garsmeur et al.   Nature Communications

The Challenge of Analyzing the Sugarcane Genome

(2018) Prathima P. Thirugnanasambandam et al.   Frontiers in Plant Science

Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations

(2018) Maria Lucia C. Vieira et al.   Frontiers in Genetics

The transcriptional landscape of polyploid wheat

(2018) R. H. Ramírez-González et al.   SCIENCE

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

(2018) Jisen Zhang et al.   NATURE GENETICS

Analysis of three sugarcane homo/homeologous regions suggests independent polyploidization events of Saccharum officinarum and Saccharum spontaneum

(2017) Mariane de Mendonça Vilela et al.   Genome Biology and Evolution

TSSPlant: a new tool for prediction of plant Pol II promoters

(2017) Ilham A. Shahmuradov et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Ryan F. McCormick et al.   PLANT JOURNAL

Brazilian sugarcane ethanol as an expandable green alternative to crude oil use

(2017) Deepak Jaiswal et al.   Nature Climate Change

The role of bioenergy in a climate-changing world

(2017) Glaucia Mendes Souza et al.   Environmental Development

Ethylene-induced transcriptional and hormonal responses at the onset of sugarcane ripening

(2017) Camila P. Cunha et al.   Scientific Reports

Reconciling food security and bioenergy: priorities for action

(2016) Keith L. Kline et al.   Global Change Biology Bioenergy

missMDA: A Package for Handling Missing Values in Multivariate Data Analysis

(2016) Julie Josse et al.   Journal of Statistical Software

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences

(2016) Elisabeth Veeckman et al.   PLANT CELL

Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane

(2016) Savio Siqueira Ferreira et al.   PLANT MOLECULAR BIOLOGY

Expression partitioning of homeologs and tandem duplications contribute to salt tolerance in wheat (Triticum aestivum L.)

(2016) Yumei Zhang et al.   Scientific Reports

The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads

(2016) Jeremy R. Shearman et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)

(2015) Zhenshan Liu et al.   BMC PLANT BIOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Large-Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content

(2015) Renato Vicentini et al.   PLoS One

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes

(2014) Fengming Han et al.   BMC GENOMICS

Building the sugarcane genome for biotechnology and identifying evolutionary trends

(2014) Nathalia de Setta et al.   BMC GENOMICS

Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates

(2014) C. Kim et al.   PLANT CELL

De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties

(2014) Claudio Benicio Cardoso-Silva et al.   PLoS One

Full-Length Enriched cDNA Libraries and ORFeome Analysis of Sugarcane Hybrid and Ancestor Genotypes

(2014) Milton Yutaka Nishiyama et al.   PLoS One

Haplotype analysis of sucrose synthase gene family in three Saccharum species

(2013) Jisen Zhang et al.   BMC GENOMICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

MotifSuite: workflow for probabilistic motif detection and assessment

(2012) M. Claeys et al.   BIOINFORMATICS

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

(2012) Douglas S Domingues et al.   BMC GENOMICS

A Systems Biology View of Responses to Lignin Biosynthesis Perturbations in Arabidopsis

(2012) R. Vanholme et al.   PLANT CELL

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum

(2011) James C Nelson et al.   BMC GENOMICS

Sugarcane improvement: how far can we go?

(2011) Maximiller Dal-Bianco et al.   CURRENT OPINION IN BIOTECHNOLOGY

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

A Novel Isoform of Sucrose Synthase Is Targeted to the Cell Wall during Secondary Cell Wall Synthesis in Cotton Fiber

(2011) Elizabeth Brill et al.   PLANT PHYSIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

The Genetics of Lignin Biosynthesis: Connecting Genotype to Phenotype

(2010) Nicholas D. Bonawitz et al.   Annual Review of Genetics

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

(2010) Jianping Wang et al.   BMC GENOMICS

Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content

(2010) Alessandro J. Waclawovsky et al.   PLANT BIOTECHNOLOGY JOURNAL

Modulation of sugar metabolism by an INDETERMINATE DOMAIN transcription factor contributes to photoperiodic flowering in Arabidopsis

(2010) Pil Joon Seo et al.   PLANT JOURNAL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom

(2009) Zhanyou Xu et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Sugarcane genes associated with sucrose content

(2009) Flavia S Papini-Terzi et al.   BMC GENOMICS

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways

(2009) R. Rawat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sucrose synthase affects carbon partitioning to increase cellulose production and altered cell wall ultrastructure

(2009) H. D. Coleman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The sustainability of ethanol production from sugarcane

(2008) José Goldemberg et al.   ENERGY POLICY

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence

(2008) Osamu Gotoh   NUCLEIC ACIDS RESEARCH

Sucrose Synthase Is Associated with the Cell Wall of Tobacco Pollen Tubes

(2008) D. Persia et al.   PLANT PHYSIOLOGY

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

(2008) A. Yilmaz et al.   PLANT PHYSIOLOGY

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY