Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

Tying the knot: occurrence and possible significance of gene fusions in plant metabolism and beyond

(2017) Jillian M Hagel et al.   JOURNAL OF EXPERIMENTAL BOTANY

Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome

(2017) Xiaoxian Liu et al.   Molecular Ecology Resources

Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq

(2017) Ruolin Liu et al.   PLoS Computational Biology

Switchgrass SBP-box transcription factors PvSPL1 and 2 function redundantly to initiate side tillers and affect biomass yield of energy crop

(2016) Zhenying Wu et al.   Biotechnology for Biofuels

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

(2016) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis

(2016) Raphaël Méheust et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

(2016) Bo Wang et al.   Nature Communications

Analyses of Long Non-Coding RNA and mRNA profiling using RNA sequencing during the pre-implantation phases in pig endometrium

(2016) Yueying Wang et al.   Scientific Reports

The WRKY transcription factor family and senescence in switchgrass

(2015) Charles I. Rinerson et al.   BMC GENOMICS

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

GREENC: a Wiki-based database of plant lncRNAs

(2015) Andreu Paytuví Gallart et al.   NUCLEIC ACIDS RESEARCH

Long noncoding RNA transcriptome of plants

(2015) Jun Liu et al.   PLANT BIOTECHNOLOGY JOURNAL

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

(2015) Sean P. Gordon et al.   PLoS One

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

PNRD: a plant non-coding RNA database

(2014) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The rise of operon-like gene clusters in plants

(2014) Svetlana Boycheva et al.   TRENDS IN PLANT SCIENCE

Advances in biotechnology and genomics of switchgrass

(2013) Madhugiri Nageswara-Rao et al.   Biotechnology for Biofuels

Gene clustering in plant specialized metabolism

(2013) Hans-Wilhelm Nützmann et al.   CURRENT OPINION IN BIOTECHNOLOGY

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatumL.)

(2013) Ji-Yi Zhang et al.   PLANT JOURNAL

Characterization of the human ESC transcriptome by hybrid sequencing

(2013) K. F. Au et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long noncoding RNAs in development and disease of the central nervous system

(2013) Shi-Yan Ng et al.   TRENDS IN GENETICS

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

PBSIM: PacBio reads simulator—toward accurate genome assembly

(2012) Yukiteru Ono et al.   BIOINFORMATICS

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

(2012) M. Frenkel-Morgenstern et al.   GENOME RESEARCH

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

(2012) Mark F Rogers et al.   GENOME BIOLOGY

An optimized protocol for forensic application of the PreCR™ Repair Mix to multiplex STR amplification of UV-damaged DNA

(2011) Toni M. Diegoli et al.   Forensic Science International-Genetics

The Switchgrass Genome: Tools and Strategies

(2011) Michael D. Casler et al.   Plant Genome

The feasibility of switchgrass for biofuel production

(2011) Rob Mitchell et al.   Biofuels-UK

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Biosolutions to the energy problem

(2009) Arnold L. Demain   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Managing and enhancing switchgrass as a bioenergy feedstock

(2008) Rob Mitchell et al.   Biofuels Bioproducts & Biorefining-Biofpr

Switchgrass for bioethanol and other value-added applications: A review

(2008) Deepak R. Keshwani et al.   BIORESOURCE TECHNOLOGY

Genome-wide analyses of alternative splicing in plants: Opportunities and challenges

(2008) W. B. Barbazuk et al.   GENOME RESEARCH

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

How biotech can transform biofuels

(2008) Lee R Lynd et al.   NATURE BIOTECHNOLOGY