trajectory inference

CellVocal links spatial context to transcriptional dynamics by integrating spatial RNA velocity with cell-cell communication to attribute cell-state transitions to signalling modules and neighbouring cells.

This paper introduces PertVI, a deep generative model that disentangles treatment effects from cellular state and batch effects in single-cell perturbation data, revealing state-specific transcriptional responses.

The paper uses subcellular spatial transcriptomics to identify why some neurons in Alzheimer's disease accumulate tau while others resist it, finding differences in molecular programs and neuron-glia interactions.

The paper introduces a model to classify brain dynamics based on chronnectome complexity, showing high accuracy in distinguishing cognitive states and age-related changes.

This paper introduces scJDO2, a method to separate score and flow operators from single-cell time courses, evaluating their ability to identify unstable cells and bifurcations in hematopoiesis.

scDisentangle predicts single-cell transcriptional responses to perturbations by decomposing expression into residual components, outperforming existing methods in cytokine stimulation, infection, and genetic perturbations.

This study compares hidden Markov models (HMMs) and vector autoregressive (VAR) models in resting-state fMRI to determine if apparent state transitions reflect discrete dynamics or continuous activity, finding that VAR often outperforms HMMs in continuous cases.

This study identifies immune and antigen-presentation states associated with response to azacitidine and sabatolimab in MDS and CMML using single-cell RNA sequencing.

The paper introduces Live D-seq, a method for longitudinal, non-destructive single-cell RNA sequencing, and demonstrates its ability to track cellular dynamics over time.

GOTSurv models patient-specific disease progression from cross-sectional survival data, identifying heterogeneous risk strata and individualized progression trajectories without predefined risk cut-offs.

This study shows thalamic stereo-EEG can detect sleep stages N2 and N3 with high accuracy, comparable to scalp EEG, using machine learning classifiers.

LOTUS reconstructs continuous clonal fate dynamics using lineage-aware optimal transport, improving lineage consistency and fate prediction in single-cell data.

The paper predicts alcohol-use trajectories in adolescents and young adults by analyzing social context, social affective benefit, and fronto-striatal neural involvement over one year.

This paper introduces a phase decoder that reconstructs missing muscle activity from sparse EMG signals, achieving accurate phase estimation and muscle activation reconstruction in real-time.

The paper develops SiMPLeSENSE, a simulated-IMU pipeline that estimates knee joint contact forces using motion capture and EMG, validated against in vivo measurements with high accuracy.

This study shows that Csu pili in A. baumannii have opposing roles in early and late stages of chronic lung infection, reducing bacterial burden initially but promoting persistence later.

MUTUAL enables cross-modality analysis between transcriptome and chromatin by learning a shared RNA-ATAC space from multiome data without refitting.

The paper shows that somatic variants' transcriptomic impact depends on cellular context, not just sequence, using single-cell transcriptomics and new tools.

The paper generates organoid models of Barrett oesophagus and oesophageal adenocarcinoma to study disease progression and therapy response.

This paper develops a modular biofabrication strategy to create a vascularized skeletal muscle model by separately maturing muscle and vascular compartments and then assembling them.

The paper introduces bowside, a neural model for trajectory inference and gene regulatory network reconstruction in single-cell RNA sequencing data, showing it recovers known regulatory motifs in hematopoiesis and reprogramming.

This study shows that increased mitochondrial metabolism in Down syndrome iPSCs impairs neuroectoderm commitment by reducing ciliation, and this effect can be reversed by inhibiting mitochondrial calcium uptake.

The paper introduces ImmuneTwins, a digital twin framework that personalizes immune response models for individuals, improving prediction accuracy of immune trajectory changes.

This paper introduces Tau-CTFP, a model for forecasting regional tau PET abnormality onset in Alzheimer's disease using connectome-informed continuous-time first-passage modeling, achieving high precision and recall in predicting abnormality onset.

The paper introduces GTPase biosensors that report activity without blocking ligand interactions, revealing feedback mechanisms in Rac1 regulation.

This study shows that COG5 deficiency disrupts Golgi organization and affects neural progenitor fate during human brain development through altered trafficking and glycosylation.

This study decomposes gait cycles using a dynamic system framework to identify coordination patterns in human locomotion.

This paper describes a method to generate dense neuronal microcultures by combining fibroblast reprogramming with matrix remodeling in collagen microgels.

This study examines insula functional connectivity development across 562 individuals, showing spatially heterogeneous changes aligned with an antero-posterior axis.

JuloVelo improves RNA velocity and cell fate prediction by incorporating gene kinetics patterns, outperforming existing methods across multiple differentiation programs.