Transcriptomics in the RNA-seq era

PA McGettigan - Current opinion in chemical biology, 2013 - Elsevier
The transcriptomics field has developed rapidly with the advent of next-generation
sequencing technologies. RNA-seq has now displaced microarrays as the preferred method …

[HTML][HTML] Anvi'o: an advanced analysis and visualization platform for 'omics data

AM Eren, ÖC Esen, C Quince, JH Vineis, HG Morrison… - PeerJ, 2015 - peerj.com
Advances in high-throughput sequencing and 'omics technologies are revolutionizing
studies of naturally occurring microbial communities. Comprehensive investigations of …

Separating homeologs by phasing in the tetraploid wheat transcriptome

KV Krasileva, V Buffalo, P Bailey, S Pearce, S Ayling… - Genome Biology, 2013 - Springer
Background The high level of identity among duplicated homoeologous genomes in
tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly …

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

LK Johnson, H Alexander, CT Brown - Gigascience, 2019 - academic.oup.com
Background De novo transcriptome assemblies are required prior to analyzing RNA
sequencing data from a species without an existing reference genome or transcriptome …

SLIMM: species level identification of microorganisms from metagenomes

TH Dadi, BY Renard, LH Wieler, T Semmler, K Reinert - PeerJ, 2017 - peerj.com
Identification and quantification of microorganisms is a significant step in studying the alpha
and beta diversities within and between microbial communities respectively. Both …

Dynamic read mapping and online consensus calling for better variant detection

K Břinda, V Boeva, G Kucherov - arXiv preprint arXiv:1605.09070, 2016 - arxiv.org
Variant detection from high-throughput sequencing data is an essential step in identification
of alleles involved in complex diseases and cancer. To deal with these massive data …

Transcriptome assembly and visualization for RNA-sequencing data

KM Nip - 2023 - open.library.ubc.ca
Since its introduction, RNA-sequencing has allowed us to interrogate the transcriptome of an
organism, thereby advancing our understanding of cell biology and diseases. Typically, raw …

Fusarium circinatum–host interaction: ecological and molecular aspects of the pathogenic and endophytic association

L Hernández Escribano - 2019 - oa.upm.es
Fusarium circinatum Nirenberg & O'Donnell es el agente causante de la enfermedad del
chancro resinoso del pino, reconocida como una de las enfermedades de coníferas más …

Optimizing Parameters for High-quality Metagenomic Assembly

A Kumar - 2015 - rave.ohiolink.edu
De novo assembly of metagenomic sequence data presents us with various computational
challenges in assembling short DNA fragments into larger sequences. An efficient assembly …

Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome

LS Wu, CL Ganote, TG Doak, W Barnett… - Proceedings of the …, 2015 - dl.acm.org
Today's genomics technologies generate more sequence data than ever before possible,
and at substantially lower costs, serving researchers across biological disciplines in …