trajectory inference

Sniffing Shapes Dopamine Signals for Reward Prediction

The paper shows that sniffing rhythm temporally organizes information flow between the olfactory tubercle and dopamine neurons during odor-guided learning, shaping predictive coding in reinforcement learning.

Spatial Single-Cell Proteomics Reveals Molecular Trajectories Of Tangle-Bearing Neurons In Alzheimer's Disease

The paper uses spatial single-cell proteomics to analyze tangle-bearing neurons in Alzheimer's disease, revealing a continuum of proteomic changes associated with tau pathology.

In silico model of axonal pathfinding during spinal cord regeneration in zebrafish larvae

The paper develops an agent-based model to simulate axonal growth during zebrafish spinal cord regeneration and shows it aligns with experimental imaging data.

Deep profiling of lupus nephritis kidneys reveals dynamic changes in myeloid cells associated with disease progression

This study uses single-cell RNA-sequencing and spatial transcriptomics to analyze myeloid cell dynamics in lupus nephritis, showing shifts in immune responses linked to disease progression.

Predicting Pain Using a Data-Driven Agent-Based Model of the Bilateral Central Amygdala

The paper develops a 3D agent-based model of the bilateral central amygdala to predict pain outcomes by integrating neuronal data from CGRPR and PKCδ cells.

High-throughput, organ-scale 3D tubule tracking using TubuleMAP

The paper introduces TubuleMAP, a semi-automated 3D tubule tracking pipeline for analyzing tubular networks, achieving high throughput and accuracy in reconstructing kidney and testis tubules.

Detailed single-cell mapping of the transcriptional response to a virus infection driven by copy-back viral genomes

The paper uses single-cell RNA-sequencing to study how copy-back viral genomes drive host cell responses during Sendai virus infection, revealing dynamic transcriptional changes over time.

Quantitative live imaging reveals PRICKLE1 controls junctional neural tube morphogenesis independent of Planar Cell Polarity

The paper uses live imaging to show PRICKLE1 controls neural tube morphogenesis through actomyosin-driven processes independent of planar cell polarity.

MMH: A multimodal dataset of whole-body kinematics, bilateral ground reaction forces, and lower-limb surface electromyography signals during load lifting and lowering

The paper introduces the MMH dataset, which includes kinematic, force, and sEMG data from load lifting and lowering tasks to support musculoskeletal modeling and ergonomic risk assessment.

Non-destructive transcriptomics via vesicular export

This paper introduces NTVE, a non-destructive transcriptomics method using vesicular export to monitor RNA dynamics in living cells over time.

Polycomb shapes active chromatin and promoter bivalency during ovarian reserve formation and activation

The paper shows Polycomb complexes regulate active chromatin remodeling during ovarian reserve formation and oocyte growth, establishing quiescence and future promoter states through distinct H3K27ac and H3K4me3 dynamics.

Transcriptional regulators predicted to drive macrophage dysregulation during impaired wound healing in diabetic mice

This study identifies transcriptional regulators driving macrophage state transitions in diabetic wound healing using scRNA-seq and computational methods.

Autonomous multimodal agents enable transparent, spatiotemporal reconstruction of immune dynamics in pancreatic cancer progression

The paper introduces an agentic computational framework to reconstruct immune dynamics in pancreatic cancer using H&E histology, identifying three temporally ordered immune-stromal states in mouse models.

scSketch: Interactive Sketch-based Trajectory Exploration and Pathway-Aware Analysis of Single-Cell Data

scSketch allows interactive trajectory sketching and pathway-aware analysis of single-cell data, revealing infection-associated gradients in human oral keratinocytes.

MECP2 Mutations Rewire Human ESC Fate and Bias Cortical Lineage Commitment

This study shows MECP2 mutations alter human ESC fate and bias cortical lineage commitment by affecting ZFP42 and EMX1 expression.

Charting developmental trajectories of dynamic brain networks during emotional face processing

The paper uses DyNeMo to analyze MEG data from children and adults during emotional face processing, revealing distinct developmental trajectories in brain network activation and connectivity.

Spheroid Assembly in Microwells of Defined Geometry for Quantitative Assessment of Aggregation Kinetics and Shape Engineering

This study develops a geometry-controlled platform to analyze and modulate spheroid compaction kinetics and shape engineering using microwells and computational modeling.

Booster vaccination improves the durability of antibody-secreting plasma cells

This study shows that booster vaccination enhances plasma cell durability by shifting their fate toward long-lived states rather than just increasing numbers.

Nuclear Factor I genes drive chondrogenic cell-fate commitment

The paper maps chondrogenic cell-fate trajectories in hiPSCs using scRNA-seq and scATAC-seq, identifying NFIA and NFIB as key regulators driving chondrogenic commitment.

HMCVelo: A Deterministic Model for Hydroxymethylation Velocity in Single Cells

HMCVelo computes hydroxymethylation velocity in single cells using a deterministic ODE model, outperforming RNA velocity in trajectory inference for murine cortical cells.

Dissecting the coordinated progression of cell states in spatial transcriptomics with CoPro

CoPro identifies spatially coordinated gene expression programs across tissues, revealing distinct cellular states and their interactions in colon, brain, liver, and kidney.

DECODING BRAIN DYNAMICS VIA CROSS-NETWORK NON-LINEAR TRAJECTORIES

The paper introduces CNTC to analyze nonlinear developmental trajectories across brain networks using fMRI data from infants, finding linear and selective nonlinear effects across systems.

PathPinpointR: Predicting the progression of sc-RNAseq samples through reference trajectories.

PathPinpointR predicts scRNA-seq sample positions along reference trajectories using switching-gene events to assign pseudo-time values.

Cell fate specification during respiratory development requires ARID1A-containing canonical BAF complex activity

The paper shows that the ARID1A-containing BAF complex is essential for lung development, proximal-distal axis specification, and cell fate acquisition during respiratory development.

Inferring norepinephrine dynamics from partial observations reveals the temporal structure of elevations during arousal

The paper develops methods to infer norepinephrine dynamics from partial observations, revealing temporal patterns during arousal.

PALINCODE: Recording cell lineage with ternary palindromic CRISPR bits

PALINCODE uses ternary CRISPR bits to record cell lineage in the genome, enabling high-density lineage trees and in vivo clonal evolution analysis.

Mapping breast cancer lineage in radiation and immunotherapy using the REMAP mouse

The paper introduces REMAP, a mouse model for tracking breast cancer lineage, and shows how treatment affects tumor evolution and immune response.

Longitudinal per-lesion in vivo imaging reveals allele-dependent resistance evolution in EGFR-mutant lung cancer

This study uses longitudinal in vivo imaging to show how different EGFR mutations affect resistance evolution in lung cancer lesions under therapy.

Dysfunction of the episodic memory network in the Alzheimer's disease cascade

This study examines how episodic memory network dysfunction relates to AD biomarkers, neurodegeneration, and cognition using longitudinal fMRI data from the DZNE study.

Temporal Profiling of Upper-Layer Neurons Reveals Changes in the Molecular Landscape Upon Maternal Immune Activation

This study maps the molecular changes in murine upper-layer cortical neurons during development and shows how maternal immune activation disrupts this process through post-transcriptional and signaling mechanisms.