RNA sequencing: the teenage years

R Stark, M Grzelak, J Hadfield - Nature Reviews Genetics, 2019 - nature.com
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …

Single-cell RNA-seq technologies and related computational data analysis

G Chen, B Ning, T Shi - Frontiers in genetics, 2019 - frontiersin.org
Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene
expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A …

Dynamic genome evolution in a model fern

DB Marchant, G Chen, S Cai, F Chen, P Schafran… - Nature Plants, 2022 - nature.com
The large size and complexity of most fern genomes have hampered efforts to elucidate
fundamental aspects of fern biology and land plant evolution through genome-enabled …

Patient-derived organoids model treatment response of metastatic gastrointestinal cancers

G Vlachogiannis, S Hedayat, A Vatsiou, Y Jamin… - Science, 2018 - science.org
Patient-derived organoids (PDOs) have recently emerged as robust preclinical models;
however, their potential to predict clinical outcomes in patients has remained unclear. We …

High-fiber diet mitigates maternal obesity-induced cognitive and social dysfunction in the offspring via gut-brain axis

X Liu, X Li, B Xia, X Jin, Q Zou, Z Zeng, W Zhao, S Yan… - Cell metabolism, 2021 - cell.com
Maternal obesity has been reported to be related to neurodevelopmental disorders in the
offspring. However, the underlying mechanisms and effective interventions remain unclear …

Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis

LA Corchete, EA Rojas, D Alonso-López… - Scientific reports, 2020 - nature.com
RNA-seq is currently considered the most powerful, robust and adaptable technique for
measuring gene expression and transcription activation at genome-wide level. As the …

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

M Pertea, D Kim, GM Pertea, JT Leek, SL Salzberg - Nature protocols, 2016 - nature.com
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 …

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

L Chen, Q Qiu, YU Jiang, K Wang, Z Lin, Z Li, F Bibi… - Science, 2019 - science.org
INTRODUCTION The ruminants are one of the most successful mammalian lineages,
exhibiting extensive morphological and ecological diversity and containing several key …

GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet

Y Wang, X Wang, S Sun, C Jin, J Su, J Wei… - Nature …, 2022 - nature.com
Genetic and environmental factors collectively determine plant growth and yield. In the past
20 years, genome-wide association studies (GWAS) have been conducted on crops to …

variancePartition: interpreting drivers of variation in complex gene expression studies

GE Hoffman, EE Schadt - BMC bioinformatics, 2016 - Springer
Background As large-scale studies of gene expression with multiple sources of biological
and technical variation become widely adopted, characterizing these drivers of variation …