The how and why of lncRNA function: an innate immune perspective

EK Robinson, S Covarrubias, S Carpenter - Biochimica et Biophysica Acta …, 2020 - Elsevier
Next-generation sequencing has provided a more complete picture of the composition of the
human transcriptome indicating that much of the “blueprint” is a vastness of poorly …

[PDF][PDF] A simple guide to de novo transcriptome assembly and annotation

V Raghavan, L Kraft, F Mesny… - Briefings in …, 2022 - academic.oup.com
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 …

1000 spider silkomes: Linking sequences to silk physical properties

K Arakawa, N Kono, AD Malay, A Tateishi, N Ifuku… - Science …, 2022 - science.org
Spider silks are among the toughest known materials and thus provide models for
renewable, biodegradable, and sustainable biopolymers. However, the entirety of their …

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 …

Genomes of subaerial Zygnematophyceae provide insights into land plant evolution

S Cheng, W Xian, Y Fu, B Marin, J Keller, T Wu, W Sun… - Cell, 2019 - cell.com
The transition to a terrestrial environment, termed terrestrialization, is generally regarded as
a pivotal event in the evolution and diversification of the land plant flora that changed the …

Interpretation of differential gene expression results of RNA-seq data: review and integration

A McDermaid, B Monier, J Zhao, B Liu… - Briefings in …, 2019 - academic.oup.com
Differential gene expression (DGE) analysis is one of the most common applications of RNA-
sequencing (RNA-seq) data. This process allows for the elucidation of differentially …

De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers

M Hölzer, M Marz - Gigascience, 2019 - academic.oup.com
Background In recent years, massively parallel complementary DNA sequencing (RNA
sequencing [RNA-Seq]) has emerged as a fast, cost-effective, and robust technology to …

–Omic and electronic health record big data analytics for precision medicine

PY Wu, CW Cheng, CD Kaddi… - IEEE Transactions …, 2016 - ieeexplore.ieee.org
Objective: Rapid advances of high-throughput technologies and wide adoption of electronic
health records (EHRs) have led to fast accumulation of–omic and EHR data. These …

Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce

T Wei, R Van Treuren, X Liu, Z Zhang, J Chen, Y Liu… - Nature Genetics, 2021 - nature.com
Lettuce (Lactuca sativa) is an important vegetable crop worldwide. Cultivated lettuce is
believed to be domesticated from L. serriola; however, its origins and domestication history …

Long noncoding RNA discovery in cardiovascular disease: decoding form to function

T Sallam, J Sandhu, P Tontonoz - Circulation research, 2018 - Am Heart Assoc
Despite significant improvements during the past 3 decades, cardiovascular disease
remains a leading worldwide health epidemic. The recent identification of a fascinating …