trajectory inference

An organismal view of newborn cell dynamics in mammalian aging

The paper uses TrackerSci to analyze newborn cell dynamics across 21 mouse tissues at different ages, showing how aging affects cell renewal and composition.

Reconstructing heterogeneous metabolic trajectories of E. coli diauxie via a dynamical Maximum Entropy Principle

This paper develops a dynamical maximum entropy framework to model single-cell metabolic states during E. coli diauxie, revealing co-consumption as a continuous rather than discrete phenomenon.

MORPHE: Bridging Image Generation and Spatial Omics for Tissue Synthesis

MORPHE synthesizes biologically faithful tissue architecture from spatial-omics data, enabling reconstruction and extension of tissue context beyond experimental limitations.

NeuRoDev resolves lifelong temporal and cellular variation in human cortical gene expression

NeuRoDev provides a computational resource to analyze human cortical gene expression across development, revealing temporal and cellular variation in neuronal and glial cells.

Cell-type-specific synaptic scaling mechanisms differentially contribute to associative learning

The paper shows that excitatory and inhibitory synaptic scaling mechanisms interact to shape memory specificity during associative learning.

Diurnal rhythms of choice: a novel state-dependent drift diffusion model uncovers time-dependent changes in rat decision making

This paper introduces a drift diffusion model with hidden Markov states to analyze time-dependent decision-making in rats, revealing daily fluctuations in performance linked to circadian rhythms.

Inferring Multi-Stage Pathway Progression Models from Tumor Phylogenies

PhyloStage infers multi-stage pathway-level cancer progression models from tumor phylogenies, aligning with known AML progression and stratifying NSCLC patients by tumor size.

Delay Differential Equation (DDE) Modeling of CAR-T Cellular Kinetics: Application to BCMA-Targeted (Ide-cel, Orva-cel) and CD19-Targeted (Liso-cel) Therapies

This paper develops a delay differential equation model for CAR-T cell kinetics, showing it better fits longitudinal data and supports delayed conversion from effector to memory cells.

The Regional Vulnerability Index (RVI) as a Neuroimaging-Based Biomarker for Autism: Associations with Likelihood, Cognition, and Longitudinal Social Outcomes

The paper develops and evaluates the Regional Vulnerability Index (RVI-ASD) as a neuroimaging biomarker for autism, showing its stability, heritability, and associations with cognition and social outcomes.

Epithelial cell fusion is required for tissue repair following UV-A irradiation

This study shows that cell fusion is essential for tissue repair after UV-A irradiation in fruit flies, generating multinucleated polyploid cells that depend on caspase activation.

The V-ATPase/ATG16L1 axis drives membrane remodeling during epithelial morphogenesis

The paper shows the V-ATPase/ATG16L1 axis is essential for de novo lumen formation during epithelial tube morphogenesis.

Resolving thyroid lineage cell trajectories merging into a dual endocrine gland in mammals

The paper uses single-cell transcriptomics to study thyroid lineage development in mice, identifying gene regulatory networks and lineage-specific processes that explain how thyroid and ultimobranchial cells merge into a dual endocrine organ.

A kinetics-based model of hematopoiesis reveals extrinsic regulation of skewed lineage output from stem cells

This study uses single-cell transplantation and mathematical modeling to show that lineage biases in hematopoiesis arise from extrinsic feedback and clonal competition, not intrinsic HSC properties.

SOFisher: Reinforcement Learning-Guided Experiment Designs for Spatial Omics

SOFisher improves spatial omics experiment design by using reinforcement learning to guide FOV selection, outperforming conventional methods in capturing relevant biological features.

Collagen Rope Trick: Cell-Laden Fibre Assembly at 1 Liquid Interfaces

This paper develops a liquid-liquid interfacial spinning method to create cell-laden, uniaxially aligned collagen fibres with mechanical properties comparable to tendon collagen and spider silk.

Hippocampal astrocytes contribute to encoding context-specific aversive stimuli to regulate fear-related behavior

This study shows that hippocampal astrocytes encode context-specific aversive stimuli to regulate fear-related behavior through Ca2+ activity preceding freezing responses.

Temporal Phosphoproteomic Network Reconstruction of Condition-Dependent EGFR Signaling Routes Through Unmeasured Proteins

The paper introduces TS-BFS-BS to reconstruct temporal phosphoproteomic networks by integrating time-course data with STRING priors, identifying signaling routes through unmeasured proteins.

Simultaneous brain-wide single-cell recording resolves spatiotemporal memory architecture

The paper introduces GLOBE, a brain-wide single-cell recording technology, and demonstrates its use in capturing Fos transcriptional activity across a mouse brain over time.

Human club cells derived from pluripotent stem cells reveal new insights into epithelial lineage plasticity through structural and functional validation

This study generates human club cells from pluripotent stem cells, revealing epithelial plasticity and new differentiation trajectories.

Internal state dynamically gates task-specific attractor dynamics in prefrontal cortex

The paper shows that motivational states modulate attractor dynamics in the medial prefrontal cortex during working memory tasks, revealing how internal states control neural dynamics and cognitive function.

An integrated protocol for multiplexed DNA FISH and protein detection in large tissue sections

The paper presents a protocol combining DNA FISH and multiplexed immunofluorescence to analyze gene and protein expression in large tissue sections at the single-cell level.

The Cxcl14 chemokine defines pioneer axon guidance and early circuit assembly in the inner ear

This study identifies Cxcl14 as a chemokine guiding pioneer axons in inner ear circuit formation and shows its role in axon navigation and mechanosensory behavior.

Spatial ciliary signaling regulates the dorsal/ventral regionalization of human brain organoids

Atomic elementary flux modes explain the steady state flow of metabolites in large-scale flux networks

The paper introduces atomic elementary flux modes (AEFMs) to efficiently analyze metabolic fluxes in large networks, showing they outperform traditional EFMs and reveal new insights into carbon and nitrogen metabolism in HepG2 cells.

Cell Trajectory Inference based on Optimal Transport and a mechanistic stochastic gene expression model

This paper introduces a method for cell trajectory inference using optimal transport with a mechanistic stochastic gene expression model, showing the Bursty model better captures gene dynamics than the Diffusive model.

A hierarchical computational motif unifies neural dynamics across the ventral visual stream

The paper identifies a common temporal motif in neural dynamics across the ventral visual stream and shows that current models fail to replicate these dynamics.

AI-Discovered Cognitive Models Reveal Novel Insights into Human and Animal Learning

This paper introduces DataDIVER, an automated method for discovering computational models from data, which reveals novel insights into human and animal learning.

Real-time label-free exploration of the dynamics and interactions of bacteriophages

This paper introduces a label-free method to monitor bacteriophage dynamics and interactions using caustics in conventional microscopy, demonstrating feasibility with three phage strains.

Trial-Level Sequence Modeling Reveals Hidden Dynamics of Dual-Task Interference

This paper uses trial-level sequence modeling of EEG to reveal shared and variable cognitive operations in dual-task interference, showing how individual strategies affect performance.

Static2Dynamic: Reconstructing videos of unobservable cellular, developmental, and disease processes

Static2Dynamic reconstructs unseen biological dynamics from static images, enabling simulation of cellular and developmental processes not directly observable.