differential expression

MAST1 is neuron-specific regulator of mitochondrial trafficking and abundance in human brain tissue

This study identifies MAST1 as a neuron-specific regulator of mitochondrial trafficking and abundance, linking its mutations to neuronal mitochondrial dysfunction and microcephaly.

Pneumocystis phosphoglucomutase links glucose-phosphate metabolism to β-1,3-glucan synthesis and cell-wall integrity

This study shows that Pgm2 in Pneumocystis links glucose-phosphate metabolism to β-1,3-glucan synthesis and cell-wall integrity, making it a potential antifungal target.

BCL10 Gain-of-Function Impairs Germinal Center Participation by Naive B Cells and Cooperates with BCL6 to Drive Extrafollicular Diffuse Large B-Cell Lymphoma

This study shows BCL10 gain-of-function mutations prevent naive B cells from entering germinal centers and cooperate with BCL6 to cause extrafollicular diffuse large B-cell lymphoma.

Use of Integrative Proteomic Analysis to Uncover Shared Molecular Signatures Across Distinct Forms of Hydrocephalus

This study identifies shared and etiology-specific proteomic signatures across hydrocephalus subtypes using cross-study proteomic analysis of CSF.

Sex differences in cell type-specific transcriptional programs and GPCR signaling in the human subgenual anterior cingulate cortex

The paper identifies sex-specific transcriptional differences in specific cell types of the human subgenual anterior cingulate cortex and links them to GPCR signaling differences in mice.

Temporal Variability in Brain Connectivity for Estimating Two-Year Clinical Severity in Mild Cognitive Impairment

The paper examines if temporal variability in brain connectivity improves prediction of two-year clinical severity in mild cognitive impairment compared to static connectivity measures.

Epigenetic reprogramming by promoter hypomethylation is linked to aberrant gene expression and transcriptomic plasticity in colorectal cancer

The paper identifies promoter hypomethylation as a driver of transcriptomic plasticity and aberrant gene expression in colorectal cancer, linking it to distinct cell states and metastatic behavior.

SPECHTacle: An Efficient Detection and Visualization of Cell Specific Regulation in Single Cell-Based Experiments Using a Novel Combinatorial Computational Tool

SPECHTacle efficiently identifies and visualizes cell-specific regulatory changes in single-cell experiments using optimal transport and entropy analysis.

Temperature alters Culex tarsalis West Nile virus vector competence, tissue bottlenecks, and transcriptional responses

This study shows that temperature affects Culex tarsalis vector competence, tissue bottlenecks, and gene expression in response to West Nile virus infection.

Classifying tumors from broad category to hierarchical molecular subtype: an interpretable hierarchical framework for precision oncology

This paper introduces HHRM, a hierarchical model for tumor subtype classification, achieving high accuracy in pan-cancer and breast cancer subtyping with interpretable biomarker identification.

A Kernel-Spectral Index for Single-Neuron Input-Output Complexity

The paper introduces the Spectral Complexity Index (SCI), a white-box measure of single-neuron computational complexity that outperforms existing methods in efficiency and interpretability.

A Urinary Metabolomic Signature Associated with Small Intestinal Bacterial Overgrowth in Children with Short Bowel Syndrome

The paper identifies a urinary metabolomic signature linked to small intestinal bacterial overgrowth in children with short bowel syndrome using gas chromatography/mass spectrometry.

Metformin lowers HMGA1a and RBM3 protein in breast cancer cells, and its effect on ESR1 splicing depends on cell density and exposure time

This paper investigates how metformin affects ESR1 splicing in breast cancer cells, finding that its effect depends on cell density and exposure time, and that HMGA1a is unlikely to be the splicing factor responsible.

Receptor-proximal phosphoform organization precedes β2 integrin activation

The paper quantifies phosphoform organization near β2 integrins and shows that signaling alters phosphosites while preserving spatial organization of proteins.

A Bias Correction Method for Substructure Estimation with Small Reference Sample Sizes

The paper evaluates how small reference sample sizes affect substructure estimation and proposes bias corrections for improved accuracy.

From smartphone to gene: Automated image-based phenotyping captures flowering diversity of common buckwheat

The paper uses smartphone imaging and automated analysis to phenotype flowering traits in buckwheat, identifying heritable traits and genomic regions associated with flowering patterns.

Differential Gene Expression and Functional Enrichment Analysis of Breast Tumor and Normal Tissue RNA-seq Data: A Reanalysis of GEO Dataset GSE210787

The paper reanalyzes RNA-seq data from breast tumor and normal tissues to identify differentially expressed genes and assess functional enrichment, finding 120 DEGs but no significant KEGG pathways after correction.

Altered Steroidogenesis in Response to Impaired Mitochondrial Protein Homeostasis

This study shows that mitochondrial proteostasis stress causes a biphasic cortisol response, with mild stress increasing and severe stress decreasing cortisol production, linking mitochondrial function to steroidogenesis in Parkinson's disease models.

A new Serratia taxon found in a trombidiform mite shows genomic evidence of host adaptation but is phylogenetically distinct from Serratia symbiotica

The paper identifies a new Serratia taxon in mites with genomic signs of host adaptation but phylogenetically distinct from S. symbiotica.

Vorinostat Can Reduce an Ongoing Fibrosis and Preserve Key Liver Metabolic Functions by Selectively Altering Mesenchymal Cell Differentiation

This study shows Vorinostat reduces ongoing liver fibrosis and preserves metabolic functions by altering mesenchymal cell differentiation in a human iPSC-derived model.

Unprecedented urban freshwater microviral survey highlights shift from sewage to river water communities

The paper surveys microviruses in urban freshwater environments, finding shifts in community composition from sewage to river water, with wastewater treatment plants acting as filters.

RubisCO-encoding methanotrophs elicit a coordinated transcriptional response to carbon dioxide limitation.

This paper shows that Methylococcus capsulatus uses CO2 for growth and activates a transcriptional response to CO2 limitation through the CbbR regulator.

Evaluating the Identifiability of Temporal Delay and Response Attenuation in Endometrial Decidualization

The paper evaluates the identifiability of temporal delay and response attenuation in endometrial decidualization using computational models and datasets, showing that distinguishing these mechanisms requires careful analysis.

A microstructural analysis of water intake patterns associated with light phase food and water restriction in male and female rats.

The paper examines how food and water intake patterns in rats change under light phase restrictions, finding that food access timing more strongly influences water intake than water access timing influences food intake.

MicrobeRT: A Framework and Suite of Fine-tuned Language Models for Genomic Sequences

MicrobeRT is a framework of fine-tuned language models for metagenomic analysis, achieving strong performance in taxonomic classification, antibiotic resistance detection, and pathogenicity assessment.

Aging activates latent enhancers that can be reversed withexercise

This study identifies age-acquired enhancers in mouse hearts and shows that exercise can reverse their activation.

Gut Stem Cell Secretome Therapy Promotes Durable Neuroprotection and Functional Recovery After Stroke

This study shows that intestinal epithelial stem cell secretome improves gut repair and cognitive outcomes after stroke in male rats but not in female rats, highlighting the need for sex-specific therapies.

Polygenic polymorphisms cooperate to drive expansion of HCMV adaptive NK cell and NK-like T cell populations

This study identifies genetic polymorphisms in NKG2C, CD16a, and HLA-E that influence NKG2C expression and ADCC capacity in HCMV-infected individuals.

Prediction of early Toxoplasma gondii infection during pregnancy combining host biomarkers and machine learning

This paper develops a machine learning model using serum biomarkers to predict early Toxoplasma gondii infection in pregnant sheep, achieving high accuracy and sensitivity for early diagnosis.

Interpretable Machine Learning Links Group-Specific Plasma Proteomics to Regional Structural Neuroimaging in Alzheimer's Disease

The paper identifies group-specific plasma proteomic signatures in Alzheimer's disease stages and links them to regional brain structural changes using machine learning and neuroimaging.