trajectory inference

A knock-in Six2Cre line reveals transient interstitial potential in nephron progenitors

The paper generates a knock-in Six2Cre mouse line to study nephron progenitor potential, finding a transient contribution to the renal interstitium around embryonic day 11.

Regenerative base editing enables deep lineage recording

This paper introduces a regenerative molecular recording system called hypercascade that enables deep lineage reconstruction by maintaining a constant mutation rate over time.

Topological Entropy Correlates with the Predictive Power of Multiplexed Ensemble Reservoir Computing

This paper introduces DynML, a dynamical systems framework for modeling biological time series, showing that reservoir topological entropy correlates with predictive power.

Detection of Somatic Point Mutations Directly from Spatial Transcriptomics Enables in vivo Spatiotemporal Lineage Tracing

SpaceTracer detects somatic SNVs from spatial transcriptomics data to enable lineage tracing in human tissues, revealing tumor progression and immune cell migration.

Integration of fear learning and fear expression across the dorsoventral axis of the hippocampus

This study investigates how fear learning and expression are integrated across the dorsoventral axis of the hippocampus using single-unit recordings.

A modular transcript enrichment strategy for scalable, atlas-aligned, and clonotype-resolved single-cell transcriptomics

The paper introduces TRTL, a modular method for targeted single-cell transcriptomics that enables scalable, atlas-aligned, and clonotype-resolved analysis of user-defined transcript panels.

Cell-Intrinsic Vulnerability and Immune Activation Cooperate to Drive Degeneration in a Mitochondrial Complex I Deficiency Model of Optic Neuropathy

This study investigates how mitochondrial dysfunction and immune activation contribute to retinal ganglion cell degeneration in optic neuropathy using transgenic models.

TREM2 agonist antibody rebuilds the resident synovial macrophage lining barrier in rheumatoid arthritis

This study shows that a TREM2 agonist antibody rebuilds the synovial macrophage lining barrier in RA by shifting macrophage states toward a barrier-like phenotype.

Lifespan Development of EEG Alpha and Aperiodic Component Sources is Shaped by the Connectome and Axonal Delays

The paper introduces {xi}-Net, a generative model of cortical activity that estimates EEG components and connectivity across lifespan using rsEEG data.

ABCA7 deficiency exacerbates glutamate excitotoxicity in Alzheimer's disease mice -- a new pharmacological target for Glu-related neurotoxicity

This paper investigates how ABCA7 deficiency worsens glutamate excitotoxicity in Alzheimer's disease mice, identifying ABCA7 as a potential pharmacological target for Glu-related neurotoxicity.

A robust human airway organoid platform enables scalable expansion and trajectory mapping of pulmonary neuroendocrine cells

This paper develops a human airway organoid platform to expand and map the differentiation trajectories of pulmonary neuroendocrine cells.

The transcription factor TCF21 is necessary for adoption of cell fates by Foxd1+ stromal progenitors during kidney development

This study uses scRNA-seq to show that Tcf21 is essential for Foxd1+ stromal progenitor differentiation during kidney development, with loss of Tcf21 causing stromal subpopulation depletion and emergence of Emcn-expressing cells.

Closed-loop imitation learning reveals muscle-centric and latent-goal codes in primate sensorimotor cortex

This paper develops a closed-loop muscle-level model of primate grasping using imitation learning and neural recordings, revealing muscle-centric and latent-goal codes in sensorimotor cortex.

Maternal Obesity Reprograms Differentiation Trajectories of Fetal Hematopoietic Stem and Progenitor Cells Through Altered Inflammatory Signaling

This study shows maternal obesity disrupts fetal bone marrow hematopoiesis by altering HSPC maturation, reprogramming lineage trajectories, and inducing inflammatory bias in a nonhuman primate model.

Geometric Fragility in Alzheimer's Disease: Probing the Loss of Hippocampal Hierarchical Abstraction via Contrastive Point Cloud Modeling

This study uses contrastive point cloud modeling to show that Alzheimer's disease involves a loss of hippocampal hierarchical abstraction, revealing a linear geometric degradation correlated with cognitive decline.

GRAVITY: Dynamic gene regulatory network-enhanced RNA velocity modeling for trajectory inference and biological discovery

GRAVITY improves RNA velocity modeling by integrating gene regulatory networks, enabling accurate trajectory inference and discovery of terminal cell states in embryonic brain development.

A spatial-temporal atlas of human islet pathophysiology identifies a size-dependent trajectory from compensation to decompensation

This study identifies a size-dependent trajectory of islet remodeling in T2D, showing medium and large islets correlate with glycemic failure while small islets show compensatory responses.

The Impact of Visual Perturbations on Balance Control during Walking

This study examines how different visual perturbations affect balance control during walking, finding that specific perturbations alter foot placement and center of mass trajectories in humans.

Targeting Modulated Vascular Smooth Muscle Cells in Atherosclerosis via FAP-Directed Immunotherapy

Single-cell and spatial maps of human coronary arteries identify FAP as a marker of SMC-derived modulated cells; an anti-FAP BiTE reduced plaque burden in mouse models.

Impact of Aging on Theta-Phase Gamma-Amplitude Coupling During Learning: A Multivariate Analysis

This study uses multivariate PAC analysis to show that older adults have reduced theta-gamma coupling during learning, suggesting impaired working memory function.

Dynamical Aβ-Tau-Neurodegeneration Model Predicts Alzheimer's Disease Mechanisms and Biomarker Progression

The paper introduces a dynamical ATN model to simulate and predict the spatiotemporal progression of Aβ, tau, and neurodegeneration in Alzheimer's disease using multimodal imaging data.

Modeling 3D Mesoscaled Neuronal Complexity through Learning-based Dynamic Morphometric Convolution

This paper introduces a convolution framework for neuronal morphology reconstruction, showing improved performance on mesoscaled neuronal datasets.

Epithelial-mesenchymal transition couples with cell cycle arrest at various stages

The paper shows that EMT paths are influenced by cell cycle phase coupling and highlights the limitations of low-dimensional representations in capturing transition dynamics.

Co-delivery of human adipose derived stromal cells and endothelial colony forming cells in cell-assembled decellularized adipose tissue scaffolds for applications in soft tissue regeneration

This study develops cell-assembled decellularized adipose tissue scaffolds for co-delivering ASCs and ECFCs to enhance soft tissue regeneration, showing improved ECFC retention and vascular regeneration.

The endoderm cell trajectory of urochordate Styela clava reveals the dual developmental origin and evolution of digestive tract

This study uses single-cell RNA sequencing to trace endoderm cell trajectories in Styela clava, revealing dual origins of the digestive tract and conserved regulatory programs across chordates.

Single Cell Proteomics in the Developing Human Brain

This study develops a single-cell proteomics workflow to analyze the developing human brain, revealing transcriptome-proteome discordance and identifying molecular vulnerabilities in neurodevelopmental disorders.

Deep learning predicts tissue outcomes in retinal organoids

This paper uses deep learning to predict tissue outcomes in retinal organoids before they are visually discernible, improving understanding of developmental trajectories.

Single Cell RNA-seq analysis reveals the connection between the miR-124-3p/NEAT1 axis and Erlotinib Drug Resistance in Non Small Cell Lung Cancer

The paper uses scRNA-seq to analyze Erlotinib resistance in NSCLC, identifying a dynamic miR-124-3p/NEAT1 axis involved in resistance evolution.

Multiplexed, scalable analog recording of gene regulation dynamics over weeks using intracellular protein tapes

This paper introduces CytoTape, a tool for continuous, multiplexed recording of gene regulation dynamics over weeks at single-cell resolution, and demonstrates its use in measuring transcription factor activities.

SpatialDINO: A Self-Supervised 3D Vision Transformer that enables Segmentation and Tracking in Crowded Cellular Environments

SpatialDINO enables automated segmentation and tracking of crowded cellular objects using self-supervised 3D vision transformers without manual annotations or retraining.