Topic
Gene expression research, explained
29 open-access gene expression studies, each with a flashcard deck and a quiz.
- How do microRNAs recognize their targets?
Sites with as little as seven base pairs matching the miRNA 5′ end can confer regulation; such 5′-dominant sites are common in conserved 3′ UTRs.
- Why do identical cells make different amounts of mRNA?
Mammalian genes switch rarely between ON and OFF, so intrinsically random transcriptional bursts create large cell-to-cell mRNA differences.
- Cataloging mammalian circular RNAs
Thousands of mammalian circRNAs arise by back-splicing and can be quantified across ENCODE cell types.
- MYB transcription-factor families in plants
Rice and Arabidopsis encode large MYB families dominated by R2R3 types with distinct expression patterns.
- What marks definitive endoderm progenitors in hESCs?
Single-cell RNA-seq separates definitive endoderm progenitors and links metabolism/hypoxia to DE differentiation.
- FLI1 circRNA FECR1 drives metastasis
Exonic circular RNA FECR1 binds the FLI1 promoter and epigenetically activates FLI1 in breast cancer.
- Where does cells minimize expression noise?
Yeast minimizes protein-expression noise preferentially for essential genes and protein-complex subunits, supporting that noise is generally harmful.
- Vascularized brain organoids tracked with scRNA-seq
Human cortical vOrganoids kept for >200 days show cortical cell types, vessel-like structure, synapses, and scRNA-seq neurogenesis/vessel programs; grafts form functional human–mouse vessels in mouse S1 cortex.
- CDK2 anchors an immune/ceRNA prognosis model in LUAD
Across GEO/TCGA analyses, CDK2 is upregulated with strong LUAD survival association and is embedded in immune, Nomogram, ceRNA, and drug-IC50 networks.
- A single-cell atlas refines colorectal cancer subtypes
Across ~487,829 cells from diverse CRC samples and cohorts, tumors show CMS-related programs plus immune/stromal continua; high CAF and C1Q+ TAM content track poorer outcomes and may simplify prognosis beyond bulk CMS alone.
- Do SNPs prove exonic splicing enhancers are real?
Human polymorphism patterns validate computationally predicted ESEs and show splicing constrains exon evolution.
- Multi-tissue networks behind obesity biology
Adipose–hypothalamus coexpression subnetworks, including circadian genes, associate with obesity-related biology beyond single-tissue views.
- What cell programs mark ischemic cardiomyopathy?
snRNA-seq of ~100k cardiac nuclei showed fewer cardiomyocytes and more specialized endothelial states in ICM, overlapping other end-stage cardiomyopathy programs.
- Pea aphid miRNAs and plasticity
Pea aphids encode dozens of miRNAs whose expression tracks phenotypic plasticity.
- Atlantic cod heat-shock gene responses
Heat shock elevates cortisol and rewires chaperone and stress-gene expression in Atlantic cod tissues.
- Are there molecular subtypes of Alzheimer brains?
Brain multi-omics integration found four multimodal AD profiles, including severe Knight-C4 with worse cognition and heavy molecular dysregulation.
- Which follicle genes differ in high- vs low-laying hens?
RNA-seq of 18 follicle libraries from 10 high-laying Lohmann Brown and 10 low-laying Jilin Black hens found 236/544/386 DEGs at LWF/SYF/LYF stages, 13 genes shared across stages, and KEGG hits including neuroactive ligand–receptor and cAMP signaling.
- Can topology find real cell types across scales?
HiDeF finds structures that persist across resolutions: it recovered 89/136 mouse cell types (Jaccard >0.5), proposed 273 cell-type communities from 100,605 cells, and linked SARS-CoV-2 Nsp13 to TLE/WNT proteins.
- Can a neural net sort DNA from the nanopore’s raw current?
SquiggleNet, a ResNet-style 1D CNN, classifies Oxford Nanopore reads from ~1 s of raw current faster than DNA translocates, beating base-calling-plus-alignment and exceeding 90% accuracy on human vs bacterial DNA.
- How does fish liver gene expression change under confinement stress?
Microarrays track the time course of gilthead sea bream liver transcriptional responses after confinement stress linked to cortisol biology.
- Can single-cell plus bulk RNA-seq predict LUAD survival?
From 8,170 lung cells and TCGA LUAD bulk data, a six-gene score (CP, GOLM1, CYP4B1, DAPK2, NFIX, FHL2) stratified survival (1-/3-/5-year AUC 0.67/0.67/0.64) and tracked TP53, TMB, and PD-L1.
- Can single-cell RNA clocks tell how old your immune system is?
sc-ImmuAging clocks trained on 1,081 healthy adults’ PBMCs showed monocyte age acceleration in COVID-19 that eased with recovery, and CD8+ T-cell rejuvenation after BCG mainly in people with high baseline interferon genes.
- Do miRNAs plus cytokines flag deadly COVID-19?
In 166 hospitalized COVID-19 patients, combining 171 microRNAomes with 25 cytokines discriminated severe disease better than either alone; CCL20, IL6, IL10, and miR-451a were key fatality correlates.
- What do co-fermenting yeasts express together?
In balanced continuous co-culture, L. thermotolerans contributes ~24% of anaerobic reads vs ~8% aerobically.
- Simple baselines beat cell foundation models on Perturb-seq
Benchmarking scGPT and scFoundation against baselines finds that training-set mean and basic ML with biological features outperform the foundation models on post-perturbation expression prediction.
- High-mito filters can discard living cancer cell states
Across ~441k cells from 134 patients, malignant cells often exceed 15% mitochondrial RNA without stress-death signatures and show metabolic programs relevant to therapy.
- Do human and cattle transcriptomes match?
Across 10,830 human and 4,866 cattle RNA-seq samples (20 tissues, 17,315 orthologs), expression, cis-eQTLs, and co-expression were generally conserved, and GWAS heritability sat more in conserved than diverged genes.
- Is ITGAL a gastric-cancer immune biomarker?
ITGAL mRNA is higher in 408 GC vs 211 normal samples (AUC 0.798), tracks CD8/macrophage infiltrates and PD1, and worse OS on KM plotter (HR 1.25 and 1.47) across 1,065 tumors.
- What’s new about pegunigalsidase alfa for Fabry?
This review covers plant-cell PEGylated α-Gal A ERT: Gb3 clearance, phase 3 programs, and BALANCE eGFR slope difference −0.36 mL/min/1.73 m²/year vs agalsidase beta within non-inferiority bounds.