[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 …

Foodomics: A new approach in food quality and safety

P Balkir, K Kemahlioglu, U Yucel - Trends in Food Science & Technology, 2021 - Elsevier
Background. The progress in the analytical methods in food science and technology brought
about a novel and modern approach concerning human health and food quality and safety …

[HTML][HTML] Regulation of vitamin C accumulation for improved tomato fruit quality and alleviation of abiotic stress

I Mellidou, A Koukounaras, S Kostas, E Patelou… - Genes, 2021 - mdpi.com
Ascorbic acid (AsA) is an essential multifaceted phytonutrient for both the human diet and
plant growth. Optimum levels of AsA accumulation combined with balanced redox …

scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured

T Sun, D Song, WV Li, JJ Li - Genome biology, 2021 - Springer
A pressing challenge in single-cell transcriptomics is to benchmark experimental protocols
and computational methods. A solution is to use computational simulators, but existing …

Hypergraph geometry reflects higher-order dynamics in protein interaction networks

KA Murgas, E Saucan, R Sandhu - Scientific Reports, 2022 - nature.com
Protein interactions form a complex dynamic molecular system that shapes cell phenotype
and function; in this regard, network analysis is a powerful tool for studying the dynamics of …

Transcriptomic and metabolomic approaches deepen our knowledge of plant–endophyte interactions

X Chen, M Sun, S Chong, J Si, L Wu - Frontiers in Plant Science, 2022 - frontiersin.org
In natural systems, plant–symbiont–pathogen interactions play important roles in mitigating
abiotic and biotic stresses in plants. Symbionts have their own special recognition ways, but …

RNA sequencing and its applications in cancer and rare diseases

S Ergin, N Kherad, M Alagoz - Molecular Biology Reports, 2022 - Springer
With the invention of RNA sequencing over a decade ago, diagnosis and identification of the
gene-related diseases entered a new phase that enabled more accurate analysis of the …

Recommendations for statistical reporting in cardiovascular medicine: a special report from the American Heart Association

AD Althouse, JE Below, BL Claggett, NJ Cox… - Circulation, 2021 - ahajournals.org
Statistical analyses are a crucial component of the biomedical research process and are
necessary to draw inferences from biomedical research data. The application of sound …

bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling

IW Vock, MD Simon - Rna, 2023 - rnajournal.cshlp.org
Differential expression analysis of RNA sequencing (RNA-seq) data can identify changes in
cellular RNA levels, but provides limited information about the kinetic mechanisms …

Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

FB Machado, KC Moharana, F Almeida‐Silva… - The Plant …, 2020 - Wiley Online Library
SUMMARY Soybean (Glycine max [L.] Merr.) is a major crop in animal feed and human
nutrition, mainly for its rich protein and oil contents. The remarkable rise in soybean …