scRNA-seq

Order Matters: Ambient RNA correction confounds doublet detection in single-cell RNA sequencing

This study shows that ambient RNA correction can reduce doublet detection accuracy and recommends detecting doublets before correction, except when using CellBender.

MCT4-Associated Lactate Export Defines Myeloid Metabolic Reprogramming during Head and Neck Cancer Progression

The paper identifies increased MCT4-associated lactate export in myeloid cells during HNSCC progression using single-cell RNA-sequencing and metabolic flux analysis.

RiboTRAP-seq identifies spatially distinct functions for the anterior and posterior intestine in immune and metabolic regulation in C. elegans

Heterogeneity of HCMV-Specific CD8+ T Cells is Established Early in Infection, Clonally Encoded, and Stable Over Time

The paper tracks CMV-specific CD8+ T cells over time to show that clonal diversity and phenotypes are established early and remain stable during chronic infection.

Sex chromosome and gonadal regulation of cardiac myofibroblast activation decoupled using mechanically tunable hydrogels and the Four Core Genotypes model

This study decouples the effects of sex chromosomes and gonadal sex on cardiac myofibroblast activation using FCG mice and hydrogel cultures, revealing sex-specific gene and protein expression patterns.

Evolution of SARS-CoV-2 reshapes upper airway immunity in children

This study uses single-cell transcriptomics to show that SARS-CoV-2 variants reshape pediatric upper-airway immunity differently from adults.

Behavior-coupled single-cell transcriptomics reveals trafficking protein-dependent regulation of tumor cell migration

This study introduces BC-seq, a method linking migratory behavior to transcriptomics in cancer cells, identifying molecular programs associated with aggressive migration and a predictive gene signature for metastasis.

ZBTB7B is a Master Regulator of Salivary Acinar Cell Function

The paper identifies ZBTB7B as a master regulator of salivary acinar cell function through transcriptional and regulatory analyses in human and mouse salivary glands.

Evolutionary diversification of shared brain and nerve cord neuronal populations in Drosophila melanogaster

The paper identifies serial homology between neuronal populations in the Drosophila melanogaster brain and ventral nerve cord using lineage reporters, single-cell transcriptomics, and a connectome.

Single-cell profiling of physically interacting immune cells using image-guided sorting

The paper uses image-guided sorting to distinguish physically interacting T cell-monocyte pairs from coincidental doublets in tuberculosis patients, revealing distinct transcriptional signatures of contact.

Cross-Platform Evaluation of a Tumor-Budding-Associated Gene Signature in Colorectal Cancer.

The paper evaluates a tumor-budding-associated gene signature across bulk and single-cell RNA-seq data, finding stronger co-expression in single-cell data.

MOFI reveals dynamic multi-omics coordination during cell fate progression

MOFI reconstructs continuous cell fate transitions from paired multi-omics snapshots across time, revealing coordinated changes in transcriptomic, chromatin, and protein layers.

Local and distal signals drive cell-type-specific leaf responses during shade avoidance

The paper identifies how local and distal signals regulate cell-type-specific leaf responses to Far-Red light, revealing distinct transcriptional programs for differential and unidirectional growth.

scRIPT: a rapid, high-coverage single-cell lineage-tracing method applied to the hematoendothelial differentiation of embryonic stem cells

scRIPT is a single-cell lineage-tracing method that improves coverage and reliability in differentiation protocols by integrating rapid barcoding, sorting, and sequencing with quality control.

Biopsy-aware phylogenetic reconstruction from longitudinal single-cell copy number profiles

This paper introduces biopsy-guided methods for phylogenetic reconstruction from longitudinal single-cell copy number profiles, showing improved accuracy over pooled methods in simulated data and demonstrating feasibility in patient-derived data.

SCN1A haploinsufficiency disrupts neural progenitor networks and accelerates neurogenesis in human Dravet syndrome forebrain assembloids

This study shows that SCN1A haploinsufficiency disrupts neural progenitor networks and accelerates neurogenesis in human Dravet syndrome forebrain assembloids, leading to altered corticogenesis and circuit hyperexcitability.

Cross Study Regulator Activity Analysis Reveals Convergent Programs in alpha Synuclein PFF Models of Parkinson Disease

The paper analyzes regulator activity across mouse PFF Parkinson disease models and human PD data, identifying shared transcriptional programs in dopaminergic identity, protein homeostasis, and inflammation.

Molecular anatomy of the entorhinal cortex

This study creates a molecular atlas of the mouse entorhinal cortex using snRNAseq and compares it to macaque data, revealing conserved molecular patterns and gradients in neuron subtypes.

Beyond the gene: contextualizing novel isoforms through pathway analysis in long-read single-cell RNA sequencing

The paper develops a computational framework to contextualize novel isoforms identified through long-read single-cell RNA sequencing by integrating pathway analysis with expression-based neighborhoods.

NOTCH-driven oscillations control cell fate decisions during intestinal homeostasis

The paper shows that NOTCH-driven Hes1 oscillations with different periods control cell fate decisions in intestinal stem cells, influencing secretory and absorptive lineage commitment.

Title: Unilateral loss of tyrosine hydroxylase in adult midbrain dopaminergic neurons reveals reduction to neuregulin1 in rat model of acute dopaminergic dysfunction

This study creates a rat model of adult dopamine loss by knocking out tyrosine hydroxylase and identifies early transcriptional changes, including reduced neuregulin1, in dopaminergic neurons and surrounding cells.

Transcriptomic and phenotypic characterization of Alzheimer's disease risk genes in neurons and astrocytes highlights shared and cell type specific cellular mechanisms

The paper uses single-cell transcriptomics and phenotypic analysis of gene knockouts in hiPSC-derived neurons and astrocytes to identify cell-type specific and shared mechanisms of Alzheimer's disease risk genes.

Human Choroid Plexus Organoids Progress to Postnatal-like Maturation and Reveal a Closing Window of Developmental Plasticity

This study uses single-cell RNA sequencing to track the maturation of human choroid plexus organoids and identifies a stage-dependent window of developmental plasticity.

scMTG reconstructs single-cell temporal dynamics with Markov transition generators

scMTG reconstructs single-cell temporal dynamics from unpaired time-series data by learning cell representations and transitions, outperforming existing methods in interpolation and transition matrix inference.

Progerin disrupts intestinal epithelial homeostasis by impairing mitochondrial metabolism and absorptive enterocyte maturation

A Single-Cell Atlas of PVOD Across the Lifespan Reveals Cellular and Molecular Therapeutic Targets

The paper constructs a single-cell atlas of PVOD across the lifespan, identifying endothelial dysfunction and molecular pathways as key drivers of the disease with potential therapeutic targets.

From Closed-Set Annotation to In-Context Discovery: Biologically Grounded LLMs for Cellular Profiling

CellScribe is a generative framework that unifies cell identity and state by using a language model to generate cell type annotations and meta-program profiles, outperforming baselines and identifying new cell types through in-context learning.

Early-onset spontaneous murine mammary tumors show increased lymphocyte representation and reduced MHC antigen presentation

This study shows that introducing the PWK/PhJ genetic background in HER2/neu-driven breast cancer mice leads to earlier tumor onset, increased immune cell presence, and reduced MHC antigen presentation.

Neuronal and vascular genome-maintenance states organize opposing multicellular architectures in the aging brain

The paper maps DNA damage response states in aging mouse brains, revealing opposing neuronal and vascular spatial patterns linked to genome maintenance.

Cerebral microthrombi promote focal Cav-1-dependent blood-brain barrier impairment, triggering neuroinflammation and neuronal damage after traumatic brain injury

This study identifies cerebral microthrombi as focal sites of Cav-1-dependent BBB dysfunction after TBI, linking microvascular thrombosis to neuronal damage through transcytosis.