Orchestrating single-cell analysis with Bioconductor

RA Amezquita, ATL Lun, E Becht, VJ Carey… - Nature …, 2020 - nature.com
Recent technological advancements have enabled the profiling of a large number of
genome-wide features in individual cells. However, single-cell data present unique …

[PDF][PDF] ComBat-seq: batch effect adjustment for RNA-seq count data

Y Zhang, G Parmigiani… - NAR genomics and …, 2020 - academic.oup.com
The benefit of integrating batches of genomic data to increase statistical power is often
hindered by batch effects, or unwanted variation in data caused by differences in technical …

[HTML][HTML] pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components

F Marini, H Binder - BMC bioinformatics, 2019 - Springer
Background Principal component analysis (PCA) is frequently used in genomics
applications for quality assessment and exploratory analysis in high-dimensional data, such …

[HTML][HTML] Inhibition of colony stimulating factor 1 receptor corrects maternal inflammation-induced microglial and synaptic dysfunction and behavioral abnormalities

S Ikezu, H Yeh, JC Delpech, ME Woodbury… - Molecular …, 2021 - nature.com
Maternal immune activation (MIA) disrupts the central innate immune system during a critical
neurodevelopmental period. Microglia are primary innate immune cells in the brain although …

[HTML][HTML] Alternative empirical Bayes models for adjusting for batch effects in genomic studies

Y Zhang, DF Jenkins, S Manimaran, WE Johnson - BMC bioinformatics, 2018 - Springer
Background Combining genomic data sets from multiple studies is advantageous to
increase statistical power in studies where logistical considerations restrict sample size or …

Review of batch effects prevention, diagnostics, and correction approaches

J Čuklina, PGA Pedrioli, R Aebersold - Mass spectrometry data analysis in …, 2020 - Springer
Systematic technical variation in high-throughput studies consisting of the serial
measurement of large sample cohorts is known as batch effects. Batch effects reduce the …

Machine learning applied to whole‐blood RNA‐sequencing data uncovers distinct subsets of patients with systemic lupus erythematosus

WA Figgett, K Monaghan, M Ng… - Clinical & …, 2019 - Wiley Online Library
Objectives Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease
that is difficult to treat. There is currently no optimal stratification of patients with SLE, and …

Integrative analysis of omics big data

XT Yu, T Zeng - Computational Systems Biology: Methods and …, 2018 - Springer
The diversity and huge omics data take biology and biomedicine research and application
into a big data era, just like that popular in human society a decade ago. They are opening a …

Assessing Biomaterial‐Induced Stem Cell Lineage Fate by Machine Learning‐Based Artificial Intelligence

Y Zhou, X Ping, Y Guo, BC Heng, Y Wang… - Advanced …, 2023 - Wiley Online Library
Current functional assessment of biomaterial‐induced stem cell lineage fate in vitro mainly
relies on biomarker‐dependent methods with limited accuracy and efficiency. Here a …

[HTML][HTML] Increased longevity due to sexual activity in mole-rats is associated with transcriptional changes in the HPA stress axis

A Sahm, M Platzer, P Koch, Y Henning, M Bens… - Elife, 2021 - elifesciences.org
Sexual activity and/or reproduction are associated with a doubling of life expectancy in the
long-lived rodent genus Fukomys. To investigate the molecular mechanisms underlying this …