[HTML][HTML] A guide to systems-level immunomics

L Bonaguro, J Schulte-Schrepping, T Ulas… - Nature …, 2022 - nature.com
The immune system is highly complex and distributed throughout an organism, with
hundreds to thousands of cell states existing in parallel with diverse molecular pathways …

Correlation and association analyses in microbiome study integrating multiomics in health and disease

Y Xia - Progress in molecular biology and translational …, 2020 - Elsevier
Correlation and association analyses are one of the most widely used statistical methods in
research fields, including microbiome and integrative multiomics studies. Correlation and …

Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap

J Reimand, R Isserlin, V Voisin, M Kucera… - Nature protocols, 2019 - nature.com
Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists
generated from genome-scale (omics) experiments. This method identifies biological …

Impaired mitochondrial oxidative phosphorylation limits the self-renewal of T cells exposed to persistent antigen

SA Vardhana, MA Hwee, M Berisa, DK Wells… - Nature …, 2020 - nature.com
The majority of tumor-infiltrating T cells exhibit a terminally exhausted phenotype, marked by
a loss of self-renewal capacity. How repetitive antigenic stimulation impairs T cell self …

Three differential expression analysis methods for RNA sequencing: limma, EdgeR, DESeq2

S Liu, Z Wang, R Zhu, F Wang, Y Cheng… - JoVE (Journal of Visualized …, 2021 - jove.com
RNA sequencing (RNA-seq) is one of the most widely used technologies in transcriptomics
as it can reveal the relationship between the genetic alteration and complex biological …

[HTML][HTML] Brain motor and fear circuits regulate leukocytes during acute stress

WC Poller, J Downey, AA Mooslechner, N Khan, L Li… - Nature, 2022 - nature.com
The nervous and immune systems are intricately linked. Although psychological stress is
known to modulate immune function, mechanistic pathways linking stress networks in the …

[PDF][PDF] Fusobacterium nucleatum promotes chemoresistance to colorectal cancer by modulating autophagy

TC Yu, F Guo, Y Yu, T Sun, D Ma, J Han, Y Qian… - Cell, 2017 - cell.com
Gut microbiota are linked to chronic inflammation and carcinogenesis. Chemotherapy failure
is the major cause of recurrence and poor prognosis in colorectal cancer patients. Here, we …

Haploinsufficiency leads to neurodegeneration in C9ORF72 ALS/FTD human induced motor neurons

Y Shi, S Lin, KA Staats, Y Li, WH Chang, ST Hung… - Nature medicine, 2018 - nature.com
An intronic GGGGCC repeat expansion in C9ORF72 is the most common cause of
amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), but the pathogenic …

[HTML][HTML] Normalization and microbial differential abundance strategies depend upon data characteristics

S Weiss, ZZ Xu, S Peddada, A Amir, K Bittinger… - Microbiome, 2017 - Springer
Background Data from 16S ribosomal RNA (rRNA) amplicon sequencing present
challenges to ecological and statistical interpretation. In particular, library sizes often vary …

[HTML][HTML] An essential role for the IL-2 receptor in Treg cell function

T Chinen, AK Kannan, AG Levine, X Fan, U Klein… - Nature …, 2016 - nature.com
Regulatory T cells (Treg cells), which have abundant expression of the interleukin 2 receptor
(IL-2R), are reliant on IL-2 produced by activated T cells. This feature indicates a key role for …