From hairballs to hypotheses–biological insights from microbial networks

L Röttjers, K Faust - FEMS microbiology reviews, 2018 - academic.oup.com
Microbial networks are an increasingly popular tool to investigate microbial community
structure, as they integrate multiple types of information and may represent systems-level …

Venn diagrams in bioinformatics

A Jia, L Xu, Y Wang - Briefings in bioinformatics, 2021 - academic.oup.com
Venn diagrams are widely used tools for graphical depiction of the unions, intersections and
distinctions among multiple datasets, and a large number of programs have been developed …

Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

ZJ Cao, G Gao - Nature Biotechnology, 2022 - nature.com
Despite the emergence of experimental methods for simultaneous measurement of multiple
omics modalities in single cells, most single-cell datasets include only one modality. A major …

Undulating changes in human plasma proteome profiles across the lifespan

B Lehallier, D Gate, N Schaum, T Nanasi, SE Lee… - Nature medicine, 2019 - nature.com
Aging is a predominant risk factor for several chronic diseases that limit healthspan.
Mechanisms of aging are thus increasingly recognized as potential therapeutic targets …

The transcriptional landscape of Arabidopsis thaliana pattern-triggered immunity

M Bjornson, P Pimprikar, T Nürnberger, C Zipfel - Nature plants, 2021 - nature.com
Plants tailor their metabolism to environmental conditions, in part through the recognition of
a wide array of self and non-self molecules. In particular, the perception of microbial or plant …

[HTML][HTML] In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age

NAP Lieberman, V Peddu, H Xie, L Shrestha… - PLoS …, 2020 - journals.plos.org
Despite limited genomic diversity, severe acute respiratory syndrome coronavirus 2 (SARS-
CoV-2) has shown a wide range of clinical manifestations in different patient populations …

Multi-trait analysis for genome-wide association study of five psychiatric disorders

Y Wu, H Cao, A Baranova, H Huang, S Li, L Cai… - Translational …, 2020 - nature.com
We conducted a cross-trait meta-analysis of genome-wide association study on
schizophrenia (SCZ)(n= 65,967), bipolar disorder (BD)(n= 41,653), autism spectrum …

An atlas of cortical circular RNA expression in Alzheimer disease brains demonstrates clinical and pathological associations

U Dube, JL Del-Aguila, Z Li, JP Budde, S Jiang… - Nature …, 2019 - nature.com
Parietal cortex RNA-sequencing (RNA-seq) data were generated from individuals with and
without Alzheimer disease (AD; n control= 13; n AD= 83) from the Knight Alzheimer Disease …

Cell type-specific transcriptomics reveals that mutant huntingtin leads to mitochondrial RNA release and neuronal innate immune activation

H Lee, RJ Fenster, SS Pineda, WS Gibbs… - Neuron, 2020 - cell.com
The mechanisms by which mutant huntingtin (mHTT) leads to neuronal cell death in
Huntington's disease (HD) are not fully understood. To gain new molecular insights, we …

Brain cell type specific gene expression and co-expression network architectures

AT McKenzie, M Wang, ME Hauberg, JF Fullard… - Scientific reports, 2018 - nature.com
Elucidating brain cell type specific gene expression patterns is critical towards a better
understanding of how cell-cell communications may influence brain functions and …