RNA-seq Falls Short for TCR Repertoire Recovery, Review Finds
A review of matched-sample benchmarking studies finds standard RNA-seq recovers only 3–5% of TCR clonotypes identified by dedicated TCR-seq.
Tag: RNA-Seq
Tumor microbes, immune cells and metabolites track CEA levels in colorectal cancer
A multi-omics study of 63 colorectal tumors links higher bacterial richness, specific anaerobic taxa, myeloid immune infiltration and the metabolite ...
Plant Hormone Treatment Keeps Harvested Kiwifruit Firm for Longer
A new BMC Plant Biology study shows that thidiazuron treatment kept harvested kiwifruit at 27.72 newtons of firmness after 20 ...
Gene expression tests for non-coding variants compared in neurodevelopmental disorders
A Genome Medicine study finds differential expression outperforms allele-specific analysis for most genes, while CRISPR allele labeling enables sensitive targeted ...
TabNet brings interpretable attention to miRNA classification, but classical models still lead
A leakage-controlled benchmark of TabNet and eight baselines on cervical cancer and Alzheimer's disease miRNA datasets finds a shared accuracy ...
How RNA-seq quantification choices reshape eQTL, colocalization and TWAS results
A Nature Genetics analysis of GTEx tissues and seven phenotypes shows that annotation and quantification method choices substantially alter eQTL ...
Wheat study links carbohydrate metabolism genes to yield under low nitrogen
A multi-omics study of 191 wheat accessions associated a sucrose-synthase gene and carbohydrate metabolism with yield stability and low-nitrogen tolerance.
lncRNA decay hypothesis cannot be tested with current half-life coverage
A new analysis finds that only a small fraction of annotated long non-coding RNAs have measured half-lives, leaving the proposed ...
Lactic Acid Bacteria Reprogram and Displace Mastitis-Associated Staphylococcus aureus Biofilms
An in vitro study shows that three lactic acid bacterial strains from human milk and infant feeding tubes can colonize ...
Ancient Liverwort Study Reveals No Universal Cell-Death Program Across Stresses
A cross-stress transcriptomic reanalysis of Marchantia polymorpha shows that regulated cell-death-associated genes are recruited selectively within context-dependent stress-response networks, with ...
Cold-exposed frog livers rewire metabolism toward glucose production and fat storage
A five-day cold exposure at 5 °C triggers hyperglycemia and a coordinated transcriptional shift in the Xenopus laevis liver toward ...
JuxtaBAM flags mismatched samples in joint multi-omic datasets
JuxtaBAM uses variants discovered within joint epigenomic and transcriptomic datasets to flag possible sample mismatches and duplications without requiring predefined ...
CRISPR Editing Route, Not Just Target Genes, Reshapes CHO Cell Lines
A systematic comparison shows that sequential and multiplex CRISPR/Cas9 workflows produce CHO cell lines with the same nine hydrolase knockouts ...
Tiny miR-15a-5p emerges as central switch in ovarian cancer angiogenesis network
An integrated miRNA–mRNA network study in ovarian cancer places miR-15a-5p at the center of an angiogenic module and highlights epithelial ...
Fungi Rewire Their Sugar Metabolism in Surprising Ways to Germinate
A comparative study of five Sordariomycete fungi reveals that spore germination is driven by flexible, redundant mannitol and trehalose networks ...
Bacteria Hiding Inside Tumors May Shape Epstein-Barr Virus Activity in Nasopharyngeal Cancer
A paired biopsy study finds that nasopharyngeal carcinoma tissue harbors distinct bacterial communities linked to Epstein-Barr virus activity and immune ...
A Single Botched Splice May Explain a Deadly Yellow-Leaf Soybean Mutant
Fine mapping of a soybean yellow-leaf lethal mutant has narrowed the cause to a 165-kilobase region on chromosome 10, where ...
Massive Cell-by-Cell Map Reveals the Cerebellum’s Hidden Role in Alzheimer’s Disease
A single-nucleus multiome atlas of over 100,000 brain cells reveals disease-linked regulatory programs and potentially causal genetic variants in the ...
Scientists Urge Caution Before Using MGMT to Guide Treatment of Rare Childhood Brain Cancer
A new correspondence in Acta Neuropathologica warns that technical artifacts in RNA sequencing data must be resolved before MGMT expression ...
Chagas Parasite Keeps Its Gene Expression Playbook Across Strains, Study Finds
A large-scale reanalysis of 86 RNA-seq libraries shows that the developmental gene expression programs of Trypanosoma cruzi are largely conserved ...
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