bulk RNA-seq

SPACE-Tag Enables High-Throughput Spatial Chromatin Profiling With CUT&Tag

The paper introduces SPACE-Tag, a spatial CUT&Tag method for chromatin profiling, and applies it to the mouse brain to reveal age-related chromatin and transcriptome changes.

Identification of Kinome Biomarkers and Therapeutic Rescue in cGMP-Linked Retinal Degeneration

This study identifies kinome biomarkers and shows therapeutic rescue in cGMP-linked retinal degeneration using LP-CN03 in mouse models.

Fatty Acid Synthase Binds Cellular mRNAs and its Depletion Reduces Translational Efficiency

This study identifies FASN's RNA binding sites and shows its depletion reduces translational efficiency of associated mRNAs.

Epidermal Langerhans Cells Act as Neuroimmune Regulators of Pain and Itch

This study identifies Langerhans cells as immune-derived amplifiers of cutaneous sensory signaling and identifies semaphorin 7A as a mediator of LC-induced itch potentiation.

Multi-omics integration reveals candidate genes and molecular mechanisms associated with resistance to sugarcane smut

The paper integrates association mapping and transcriptomics to identify candidate genes and molecular mechanisms associated with sugarcane resistance to smut.

From Fill to Freeze: Redesigning homeRNA to Enable Robust Sampling and Scalable Downstream Processing Workflows for Remote Blood Transcriptomics

This paper validates the redesigned homeRNA platform's robustness to remote study stresses, showing it maintains RNA quality under varied conditions and storage times.

Mutant Isocitrate Dehydrogenase 1 Alters Extracellular Vesicle Secretion and Cargo Composition in Cellular Models

This study shows mutant IDH1 increases sEV secretion and alters their cargo composition in glioma and chondrosarcoma cells, with D2HG packaged into sEVs and cell-type-specific cargo remodeling.

Learning interpretable compositional features associated with continuous covariates

This paper introduces IsoVita, a framework for learning interpretable compositional features from continuous covariates, showing improved detection of temporal isoform variation in human brain RNA-seq data.

CD300f is required for efficient lipid handling during cuprizone-induced demyelination

This study shows CD300f is essential for microglial lipid handling and remyelination during demyelination, with deficits in lipid metabolism and motor coordination in its absence.

Concussion decreases brain signal variability

This study shows that concussion reduces BOLD signal variability in specific brain networks, linking it to symptom severity and cognitive decline.

TailEnrich enables discovery of dysregulated genes through disease sample enrichment testing

TailEnrich identifies dysregulated genes in patient subsets by testing expression distribution tails, outperforming DESeq2 and edgeR in simulated data and uncovering novel genes in Alzheimer's disease.

Satellite cell glucocorticoid receptor restrains myogenic commitment without mediating the effects of therapeutic glucocorticoids on muscle repair

This study shows that satellite cell glucocorticoid receptor (GR) maintains quiescence but does not mediate therapeutic GC effects on muscle repair, highlighting the importance of treatment timing and context.

Secondary growth in the tomato stem is suppressed by the flowering regulators FUL2 and STM3

This study identifies FUL2 and STM3 as repressors of secondary growth in tomato stems, showing their role in limiting xylem accumulation during stem development.

Starve, stress, and mate: Activation of the CCAAT-Binding complex overrides sterility of mating-type heterozygous Candida albicans

The paper identifies the CCAAT-binding complex (CBC) as a key regulator that overrides genetic sterility in Candida albicans by integrating environmental stress signals to enable mating.

Metabolites cross the membrane, the transcriptome does not follow: co-localization is required for the cyanobacterial response to a yeast partner

This study shows that cyanobacteria respond to yeast partners only when co-localized, not just through metabolite exchange.

Integrative Multiomics Analysis of the Angiogenesis-EMT Interface in Head and Neck Squamous Cell Carcinoma

This study identifies coordinated angiogenesis-EMT gene programs in OSCC using multi-omic analysis and validates candidate genes through external datasets and protein-level confirmation.

Isoform diversity as a complementary dimension of gene expression

The paper shows isoform diversity is a distinct dimension of gene expression, complementary to gene-level abundance, and changes with age and tissue-specific processes.

CauloBrowser 2.0: an AI powered update

CauloBrowser 2.0 updates the systems-biology database for Caulobacter crescentus with AI-powered tools for querying and visualizing experimental data.

MOCHI enables systematic identification of candidate independent intronic transcriptional signals from short-read RNA-seq data

MOCHI identifies candidate independent intronic transcripts from short-read RNA-seq data, revealing novel transcripts associated with cancer survival.

Deep transcriptomic analysis of molecular mediators of complex traits in heterogeneous stock (HS) rats

This paper expands the RatGTEx resource with transcriptome-wide associations across 3,160 RNA-seq samples, identifying 7,473 gene-trait links and 144,876 QTLs for 22,599 genes.

Shared additive- and variance-associated genetic architecture of cardiac structure and function

The paper identifies shared and distinct genetic architectures for cardiac structure and function using UK Biobank data, revealing common variants influencing multiple chambers and phenotypic variability.

Systematic comparison of gliflozins identifies a selective anti-calcifying effect of canagliflozin beyond canonical SGLT2 inhibition

This study compares gliflozins and finds canagliflozin uniquely reduces vascular calcification through mechanisms beyond SGLT2 inhibition, affecting VSMC metabolism and calcification.

High piRNA abundance is a hallmark of evolutionarily persistent piRNA-producing loci.

The paper identifies high piRNA abundance as a key feature of evolutionarily persistent piRNA-producing loci across mouse and primate species.

Optogenetic induction of TAD boundary pairing promotes gene activity

This study uses OptoTet to manipulate TAD boundaries and shows that boundary pairing enhances gene activity for ERRFI1 but not MYC.

Plumage diversity without differential expression of pigmentation genes in a rapid avian radiation

The paper investigates plumage diversity in Capuchino Seedeaters by analyzing gene expression and variants, finding that pigmentation differences arise from regulatory changes rather than differential gene expression.

Signatures for conserved phenolic-based acclimation responses to UV in a unicellular algal sister of land plants

The paper exposes zygnematophyte algae to UV irradiance and identifies conserved molecular responses, including lipid droplets and phenolic compounds, suggesting a shared UV acclimation mechanism with land plants.

Ribosomal Remodeling and Translational Suppression in the Post-Arrest Heart

This study investigates how cardiac arrest affects myocardial ribosome biology and protein synthesis in pigs and mice, finding increased ribosomal transcripts with ischemic burden and suppressed ribosome activity post-arrest.

Preferential Isoform Usage and Isoform Switching in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Profile

The paper identifies subgroup-specific isoform usage and switching in SLE patients with distinct autoantibody profiles, highlighting their functional relevance in autoimmune pathogenesis.

Establishing an ex vivo platform for molecular profiling of skin structural cells using frozen human skin biopsies

This study establishes a scalable ex vivo platform using frozen human skin biopsies to study inflammatory responses in skin structural cells.

Arrest-associated transcriptional programmes outweigh apoptosis-associated programmes in treatment-naive pancreatic ductal adenocarcinoma

The paper examines the balance between apoptosis and arrest-associated transcriptional programs in untreated PDAC, finding a consistent bias toward arrest programs.