Peptidomics

R Hellinger, A Sigurdsson, W Wu… - Nature Reviews …, 2023 - nature.com
Peptides are biopolymers, typically consisting of 2–50 amino acids. They are biologically
produced by the cellular ribosomal machinery or by non-ribosomal enzymes and …

Challenges and best practices in omics benchmarking

TG Brooks, NF Lahens, A Mrčela, GR Grant - Nature Reviews Genetics, 2024 - nature.com
Technological advances enabling massively parallel measurement of biological features—
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …

Plasma proteomic profiles predict future dementia in healthy adults

Y Guo, J You, Y Zhang, WS Liu, YY Huang, YR Zhang… - Nature Aging, 2024 - nature.com
The advent of proteomics offers an unprecedented opportunity to predict dementia onset.
We examined this in data from 52,645 adults without dementia in the UK Biobank, with 1,417 …

Defining dysbiosis for a cluster of chronic diseases

LJ Wilkins, M Monga, AW Miller - Scientific reports, 2019 - nature.com
The prevalence of many chronic diseases has increased over the last decades. It has been
postulated that dysbiosis driven by environmental factors such as antibiotic use is shifting …

miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems

F Kern, T Fehlmann, J Solomon, L Schwed… - Nucleic acids …, 2020 - academic.oup.com
Gene set enrichment analysis has become one of the most frequently used applications in
molecular biology research. Originally developed for gene sets, the same statistical …

Brassica carinata genome characterization clarifies U's triangle model of evolution and polyploidy in Brassica

X Song, Y Wei, D Xiao, K Gong, P Sun, Y Ren… - Plant …, 2021 - academic.oup.com
Ethiopian mustard (Brassica carinata) in the Brassicaceae family possesses many excellent
agronomic traits. Here, the high-quality genome sequence of B. carinata is reported …

MultipleTesting. com: A tool for life science researchers for multiple hypothesis testing correction

O Menyhart, B Weltz, B Győrffy - PloS one, 2021 - journals.plos.org
Scientists from nearly all disciplines face the problem of simultaneously evaluating many
hypotheses. Conducting multiple comparisons increases the likelihood that a non-negligible …

Essential guidelines for computational method benchmarking

LM Weber, W Saelens, R Cannoodt, C Soneson… - Genome biology, 2019 - Springer
In computational biology and other sciences, researchers are frequently faced with a choice
between several computational methods for performing data analyses. Benchmarking …

An atlas of genetic correlations and genetically informed associations linking psychiatric and immune-related phenotypes

DS Tylee, YK Lee, FR Wendt, GA Pathak… - JAMA …, 2022 - jamanetwork.com
Importance Certain psychiatric and immune-related disorders are reciprocal risk factors.
However, the nature of these associations is unclear. Objective To characterize the …

Toward a gold standard for benchmarking gene set enrichment analysis

L Geistlinger, G Csaba, M Santarelli… - Briefings in …, 2021 - academic.oup.com
Motivation Although gene set enrichment analysis has become an integral part of high-
throughput gene expression data analysis, the assessment of enrichment methods remains …