bulk RNA-seq

A CRISPR/Cas9 screen reveals convergent dysregulation of neurological pathways within and across glycosylation pathways

The paper uses CRISPR/Cas9 to knockdown glycosylation genes in zebrafish, revealing shared neurological dysregulation across CDG classes through RNA sequencing and behavioral assays.

TMEM55B downregulation promotes neurodegeneration in Alzheimer disease models.

The paper shows TMEM55B downregulation contributes to neurodegeneration in Alzheimer's disease models by impairing lysosomal transport and autophagy.

Direct reprogramming of human monocytes generates blue light- and leptin-responsive ipRGC-like neurons

This study directly reprograms human monocytes into ipRGC-like neurons and identifies factors that enable this conversion.

A polysynaptic hypothalamuspelvic-ganglion circuit regulates prostate tumor growth via WNT3A

The paper identifies a polysynaptic hypothalamus-pelvic-ganglion circuit that promotes prostate tumor growth through WNT3A signaling in mice.

mobileRNA: a tool for efficient analysis of mobile RNA molecules in multiple genomes.

The paper introduces mobileRNA, an R package that efficiently identifies mobile RNA molecules in grafted plants using merged genome alignment and simulated datasets.

Aldosterone drives HSD2 neuron activity and molecular remodeling of synaptic function to promote sodium appetite

The paper shows aldosterone enhances synaptic transmission in HSD2 neurons through SV2C, driving sodium appetite.

Two potent, functionally redundant MazF toxins inactivate the 16S rRNA anti-Shine-Dalgarno sequence and are differentially expressed in Mycobacterium tuberculosis

This study identifies two MazF toxins in Mycobacterium tuberculosis that target the 16S rRNA anti-Shine-Dalgarno sequence, showing differential expression under stress conditions.

Integrative reanalysis of public intracellular and vaccine-challenge transcriptomes, informed by single-cell and metabolomic atlases, refines antigen prioritisation for next-generation veterinary Brucella vaccines

The paper reanalyzes public transcriptomic and metabolomic data to prioritize antigens for improved Brucella vaccines by integrating single-cell and metabolomic atlases.

Crystalline silica exposure causes latent biomechanical abnormalities along the cardiopulmonary axis

This study shows that a single crystalline silica exposure causes subclinical cardiopulmonary abnormalities in mice, with sex-dependent effects on lung mechanics and transcriptomic responses.

Novel retinoic acid receptor-related orphan receptor gamma inverse agonist enhances checkpoint blockade in hepatocellular carcinoma: a preclinical mouse study

This study shows that inhibiting RORgamma enhances PD-L1 blockade efficacy in HCC by reducing neutrophil recruitment and increasing PD-L1 expression.

Serpin A3 is Increased in Cerebral Amyloid Angiopathy and ARIA

The paper investigates Serpin A3 expression in cerebral amyloid angiopathy and Alzheimer's disease using single-nucleus transcriptomics and microscopy, finding increased Serpin A3 in affected tissues.

The U6 snRNA capping enzyme Amus/MePCE is required for the stability of U6atac and the processing of introns with features of both major and minor classes

The paper identifies a role for Amus/MePCE in stabilizing U6atac and shows that some minor introns require both major and minor splicing pathways for processing.

Selenium-enriched rapeseed extract synergizes with chemotherapy drug cisplatin in inhibiting proliferation and promoting apoptosis of colorectal cancer cells

This study shows that selenium-enriched rapeseed extract enhances cisplatin's anti-cancer effects on colorectal cancer cells without harming normal cells.

corrdeconv corrects deconvolution's misreading of disease cell states as abundance, overturning benchmarks and outperforming every published deconvolution method

corrdeconv corrects deconvolution errors by addressing misread disease cell states as abundance, outperforming existing methods and reducing refuted effects.

RNA-sequencing of butyrate-treated human lymphoblastoid cell lines shows dysregulated genes of multiple disease-related pathways

This study uses RNA-seq to analyze the transcriptomic effects of butyrate on human lymphoblastoid cell lines, identifying dysregulated genes in multiple disease-related pathways.

METTL3-mediated m6A modification alleviates skeletal muscle atrophy in ALS by regulating ACSL1-dependent triglyceride metabolism

This study identifies METTL3-mediated m6A modification as a regulator of triglyceride metabolism in ALS skeletal muscle, alleviating atrophy through ACSL1 expression.

Phylogenomic screening reveals idsA2 loss conferring nitroimidazole cross-resistance in Mycobacterium tuberculosis

A length- and mutation-load-corrected homoplasy screen of 1,813 MDR-TB genomes flags idsA2; its loss raises pretomanid MIC fourfold, delamanid and ethambutol twofold, via isoprenoid flux redirection.

COGNITIVE HETEROGENEITY AND AGING: AN AGE-INDEPENDENT CILIARY GENE PROGRAM TRACKS COGNITIVE RESILIENCE IN MICE

This study identifies a ciliary gene program linked to cognitive resilience in mice, independent of age, by integrating behavioral data with transcriptomic profiling.

Brain microvascular endothelial cell dysfunction during Plasmodium infection does not result from astrocyte-derived wingless-related integration site (Wnt)7a deficiency

This study investigates whether astrocyte-derived Wnt7a deficiency contributes to BMEC dysfunction during Plasmodium infection, finding no protective effect of Wnt7a overexpression on cerebral malaria outcomes.

Pan-pediatric brain tumor microRNA networks define immune microenvironment states and responses to CAR T-cell therapy

This study identifies miRNA programs in pediatric brain tumors linked to immune states and CAR T-cell therapy responses, highlighting miR-149 as a potential regulator.

Different, same, or arrhythmic: an empirically informed benchmark of differential rhythmicity methods

The paper benchmarks 12 differential rhythmicity methods using synthetic RNA-seq data to guide method selection for time series analysis.

Dissecting cellular and molecular networks of aging and senescence in the human hippocampus

This study identifies spatially resolved aging and senescence signatures in the human hippocampus using multi-omics approaches, revealing cell-type and sex-specific gene expression changes.

Loss of Farnesoid X Receptor Signaling Promotes Choroidal Neovascularization in Mice

This study shows that loss of FXR signaling in mice promotes choroidal neovascularization, fibrosis, and vascular leakage, suggesting FXR as a therapeutic target for nAMD.

OmniRE-seq: A Dual-Method Framework for Decoding RNA Editing Dynamics in Disease and Therapy

OmniRE-seq quantifies RNA editing across bulk and single-cell data, identifying disease-related patterns and therapeutic targets in multiple models.

Coordination of cell cycle and hematopoietic differentiation by a HoxA9/Myc/Cdk6 feedback loop

This study identifies a HoxA9/Myc/Cdk6 feedback loop that coordinates cell cycle and hematopoietic differentiation through transcriptional and post-translational mechanisms.

Convergent evolution of animal photosymbiosis through co-option of ancestral endodermal programs

This study shows that photosymbiosis in different animals uses ancestral endodermal programs and lineage-specific innovations, revealing a general cellular principle for complex symbiosis evolution.

Multi-omics Profiling Reveals an NF-κB-Driven Anti-apoptotic Network Underlying Resistance to Oncolytic VSV in Prostate Cancer Cells

This study identifies an NF-κB-driven anti-apoptotic network in PC3 prostate cancer cells that contributes to resistance against oncolytic VSV, suggesting combination therapies may enhance virotherapy efficacy.

Reference-free isoform discovery links unannotated RNA processing to disease risk

Torino, a reference-free framework for isoform discovery, identifies RNA processing patterns linked to disease risk by analyzing read coverage variation across species and disease states.

Transcriptomic and lipidomic profiles reveal higher thermal adaptability in a tropical versus a temperate isolate of Chromera velia

This study compares transcriptomic and lipidomic responses of two Chromera velia isolates from different thermal environments to elevated temperatures, finding that the tropical isolate shows greater thermal adaptability.

ICOS blockade alleviates immune suppression in breast tumor microenvironment

This study shows that blocking ICOS reduces immune suppression in breast tumors by altering Treg and CD8 T cell dynamics, enhancing anti-tumor immunity.