differential expression

Predictive consequences of alternative representations of metabolic measurements: A controlled synthetic study of categories, longitudinal information and transition preservation

The paper evaluates predictive performance of different metabolic measurement representations in synthetic data, finding that some representations outperform others in specific scenarios.

Single-cell RNA-seq of amniotic fluid provides unique insight into fetal development

This study uses scRNA-seq on amniotic fluid to create a cell atlas of healthy fetal cells, revealing gestational age-related changes in cell composition and gene expression.

Genomic and phenotypic adaptation tunes an endangered California plant to the fog that climate change and wind energy will reshape

This study identifies genomic adaptations in an endangered California plant to coastal fog, revealing candidate genes and potential impacts of wind farms on gene flow.

Parkinson's disease genetic risk converges on Lewy body pathology-associated microglial states

The paper identifies microglial states associated with Parkinson's disease genetic risk and Lewy body pathology using single-cell profiling and integrates data with AMP PD.

Viral subversion of the host ubiquitin proteasome system is broadly sensed by the NLRP1 inflammasome

The paper identifies viral E3 ligase activity as a conserved trigger of NLRP1 inflammasome activation, expanding effector-triggered immunity against viral pathogens.

Acetylation of NDUFA13 at K7 Senses OXPHOS Dysfunction to Disrupt Prohibitin Scaffolds and Drive Cristae Remodelling in Heart Failure

This study identifies NDUFA13-K7 acetylation as a sensor linking OXPHOS dysfunction to cristae remodelling and metabolic changes in heart failure.

Transcriptomic profiling of normal and glaucomatous trabecular meshwork cells in a tissue-like soft ECM environment

The paper identifies 588 differentially expressed genes in glaucomatous versus normal trabecular meshwork cells cultured in a soft ECM environment, revealing three disease-related programs.

A new bioinformatic analysis highlights a subpopulation of mitochondria with highly methylated DNA present in oocytes, early embryos and blood.

The paper identifies a subpopulation of highly methylated mtDNA in oocytes, embryos, and blood using single-read methylation analysis, revealing functional heterogeneity among mitochondria.

RAP2.6 negatively regulates Arabidopsis submergence tolerance through GSNOR1-dependent redox and hormonal signaling

This study identifies RAP2.6 as a negative regulator of submergence tolerance in Arabidopsis, showing its interaction with GSNOR1-dependent redox and hormonal signaling.

MXene Protein Corona Interfaces for Molecular Profiling of Alzheimers Disease

This study uses MXene nanosheets to capture Alzheimer's disease-associated plasma protein signatures, revealing disease-specific proteomic changes and potential biomarkers.

Dosage-sensitive RBFOX2 autoregulation promotes cardiomyocyte differentiation by maturing the transcriptome

This study shows that RBFOX2 autoregulation is critical for cardiomyocyte differentiation by maturing the transcriptome, and its disruption leads to congenital heart disease.

Personalised prediction of anomalous bone regeneration in multiple myeloma patients

This study develops computational models to predict bone regeneration in multiple myeloma patients using patient data and genomics, showing rapid strengthening not fully explained by known mechanisms.

The interplay between cortical tracking and functional connectivity in musicians and non-musicians listening to speech and music

This study finds that musicians show enhanced cortical tracking and functional connectivity during speech and music listening, along with better rhythmic abilities, suggesting domain-general auditory processing advantages.

Core Coefficient quantifies transcription-factor functional dominance for therapeutic target selection

The paper introduces the Core Coefficient (CC) to quantify transcription factor functional dominance in regulatory networks, showing it can predict therapeutic target shifts in disease progression.

Temporal phosphoproteomic programmes set a redox-gated rheostat on neutrophil phagocytosis

This paper identifies a redox-gated phagocytic rheostat in neutrophils by analyzing phosphoproteomic and functional responses to bacterial exposure.

Screening and evaluation of medicine food homology herbal combinations for ameliorating chemotherapy induced ovarian aging under an integrated multi-strategy framework

This paper identifies Astragalus ginseng as a candidate herb pair for ameliorating chemotherapy-induced ovarian aging using a multi-strategy framework combining single-cell transcriptomics, chemical profiling, and molecular modeling.

Multi-scale spatial transcriptomic atlas of the whole mouse spinal cord

The paper creates a spatial transcriptomic atlas of the whole mouse spinal cord, revealing multi-scale cellular organization and gene-expression patterns across different regions.

Transcriptional differences between repeatedly recultured and freshly induced embryogenic calli reveal candidate developmental regulators

The paper compares gene expression in freshly induced and repeatedly subcultured peanut embryogenic calli to identify candidate developmental regulators.

Out-of-balance Growth Enables Cost-free Synthesis of the Flagellum and Other Proteins in a Single Bacterium

The paper shows that single-cell growth rates increase with flagellar gene activity, contradicting bulk measurements, and attributes this to inherited growth factors.

Reconstruction of the human nigrostriatal pathway in vitro reveals target-dependent dopamine neuron maturation

The paper introduces a human stem cell-based model of the nigrostriatal pathway that mimics in vivo connectivity and reveals target-dependent dopamine neuron maturation.

Neonatal T cell maternal microchimerism is common and associates with early pregnancy SARS2 vaccination

The paper finds that early pregnancy SARS2 vaccination is associated with increased detection of T cell maternal microchimerism in cord blood.

Long-read sequencing reveals telomere inheritance patterns from human trios

The paper uses long-read sequencing to analyze telomere inheritance patterns in human trios, finding parent-of-origin effects and heritable influences on telomere length.

Loss of Ferroptosis-suppressors Accelerates Breast Cancer Recurrence by Promoting Dormancy Exit

This study identifies PNPLA2, GOT1, and GPX4 as ferroptosis-suppressors whose loss accelerates breast cancer recurrence by promoting dormancy exit and enhancing ferroptosis resistance in dormant cells.

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system

The paper identifies two rodent-specific transposable element subfamilies that function as cell-type-specific enhancers in the mouse immune system, contributing to cell identity and gene regulation.

Integrated Transcriptomic and Structural Prioritization of Sulforaphane Targets in Neurodegeneration: A Multi-Dataset In Silico Study

This study identifies potential neurodegeneration targets of sulforaphane using computational methods across multiple datasets.

Sodium butyrate inhibits the proliferation of temozolomide-resistant glioblastoma (A172) and lung adenocarcinoma (A549) cells and biphasically regulates EGFR expression

Divergent transcriptional responses of conserved cellular machinery to warming and phosphorus limitation in freshwater phytoplankton

The paper examines how four freshwater phytoplankton species respond transcriptionally to warming and phosphorus limitation, finding divergent responses even within phyla.

Glutamine-derived NADH fuels lactate production to maximize ATP yield under oxygen consumption constraints in head and neck cancer

The regulator of G protein signaling RGS9 supports insulin secretion in male mouse islets

This study shows RGS9 supports glucose-stimulated insulin secretion in male mouse islets by dampening inhibitory signaling through Gi/o.

VIPER-seq: Protein-mediated small RNA enrichment enhances plant virus detection at low viral abundance

VIPER-seq improves virus detection in plants by enriching viral small RNAs using protein-mediated methods, showing better sensitivity in low-titre infections.