AIMC Topic: Transcriptome

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SpaCross deciphers spatial structures and corrects batch effects in multi-slice spatially resolved transcriptomics.

Communications biology
Spatially Resolved Transcriptomics (SRT) has revolutionized tissue architecture analysis by integrating gene expression with spatial coordinates. However, existing spatial domain identification methods struggle with unsupervised learning constraints,...

Integrated multi omics and machine learning reveal mitochondrial immunometabolic networks in sepsis associated encephalopathy.

Scientific reports
Sepsis-associated encephalopathy (SAE) is a major complication in intensive care units, characterized by diffuse brain dysfunction due to systemic inflammation. Despite advances in critical care medicine, SAE remains a key factor in poor patient outc...

Machine learning-based transcriptomic analysis identifies NAMPT and SAT1 as potential biomarkers and therapeutic targets in ferroptosis-associated rheumatoid arthritis.

PloS one
BACKGROUND: Rheumatoid arthritis (RA) is an autoimmune disease with chronic presentation, involving symmetric joints and systemic involvement. Ferroptosis is iron-dependent programmed cell death through lipid peroxide accumulation, implicated in infl...

BrainProt v3.0: An Integrative and Simplified Omics-Based Knowledge-Base About the Human Brain and Its Associated Diseases.

Journal of proteome research
The advancements in neuroscience research and omics technologies generate extensive data for brain-related diseases and disorders that are scattered across various manuscript repositories and databases, potentially hindering global initiatives to adv...

Multi-omics analysis of parthanatos related molecular subgroup and prognostic model development in stomach adenocarcinoma.

PloS one
Stomach adenocarcinoma (STAD), the most prevalent histological subtype of gastric cancer, exhibits high heterogeneity and poor prognosis, posing significant therapeutic challenges. Parthanatos, a distinct form of regulated cell death mediated by poly...

A specific gene expression program underlies antigen archiving by lymphatic endothelial cells in mammalian lymph nodes.

Nature communications
Lymph node (LN) lymphatic endothelial cells (LEC) actively acquire and archive foreign antigens. Here, we address questions of how LECs achieve durable antigen archiving and whether LECs with high levels of antigen express unique transcriptional prog...

Biomarker genes for model-based prediction of drought-stress perception levels in rice.

BMC plant biology
BACKGROUND: Drought is a global challenge that severely restricts crop yields and threatens food security. Plants respond to drought stress by modulating gene expression before visible phenotypic changes occur. However, most studies of drought resist...

E2-regulated transcriptome complexity revealed by long-read direct RNA sequencing: from isoform discovery to truncated proteins.

RNA biology
Oestrogen receptor alpha (ERα)-positive (ER+) breast cancers are driven by the binding of 17β-oestradiol (E2) to ERα, which transcriptionally regulates target genes. Although microarrays and conventional RNA sequencing have identified E2 target genes...

Integrative analysis identifies FERMT3 as a key regulator of metabolic reprogramming in keloid scarring and metabolic syndrome.

Functional & integrative genomics
 Keloid scarring and Metabolic Syndrome (MS) are distinct conditions marked by chronic inflammation and tissue dysregulation, suggesting shared pathogenic mechanisms. Identifying common regulatory genes could unveil novel therapeutic targets. Methods...