Advances and challenges in metatranscriptomic analysis
Sequencing-based analyses of microbiomes have traditionally focused on addressing the
question of community membership and profiling taxonomic abundance through amplicon …
question of community membership and profiling taxonomic abundance through amplicon …
A survey of best practices for RNA-seq data analysis
Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
Transcriptome assembly from long-read RNA-seq alignments with StringTie2
RNA sequencing using the latest single-molecule sequencing instruments produces reads
that are thousands of nucleotides long. The ability to assemble these long reads can greatly …
that are thousands of nucleotides long. The ability to assemble these long reads can greatly …
Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods
Background Accurate fusion transcript detection is essential for comprehensive
characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools …
characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools …
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
E Bushmanova, D Antipov, A Lapidus… - GigaScience, 2019 - academic.oup.com
Background The possibility of generating large RNA-sequencing datasets has led to
development of various reference-based and de novo transcriptome assemblers with their …
development of various reference-based and de novo transcriptome assemblers with their …
Discovery and engineering of colchicine alkaloid biosynthesis
RS Nett, W Lau, ES Sattely - Nature, 2020 - nature.com
Few complete pathways have been established for the biosynthesis of medicinal
compounds from plants. Accordingly, many plant-derived therapeutics are isolated directly …
compounds from plants. Accordingly, many plant-derived therapeutics are isolated directly …
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
High-throughput sequencing of mRNA (RNA-seq) has become the standard method for
measuring and comparing the levels of gene expression in a wide variety of species and …
measuring and comparing the levels of gene expression in a wide variety of species and …
A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors
DM Bryant, K Johnson, T DiTommaso, T Tickle… - Cell reports, 2017 - cell.com
Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly
regenerative and can replace entire limbs. The mechanisms underlying limb regeneration …
regenerative and can replace entire limbs. The mechanisms underlying limb regeneration …
Lipid exchanges drove the evolution of mutualism during plant terrestrialization
Symbiosis with arbuscular mycorrhizal fungi (AMF) improves plant nutrition in most land
plants, and its contribution to the colonization of land by plants has been hypothesized …
plants, and its contribution to the colonization of land by plants has been hypothesized …
[PDF][PDF] A simple guide to de novo transcriptome assembly and annotation
A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily
attainable proxy catalog of protein-coding genes when genome assembly is unnecessary …
attainable proxy catalog of protein-coding genes when genome assembly is unnecessary …