trajectory inference

STAVelo: deciphering spatiotemporal cellular dynamics via spatial RNA velocity inference from spatial transcriptomics data

STAVelo infers RNA velocity from spatial transcriptomics data to capture spatiotemporal cellular dynamics across multiple species and tissues.

A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

Division-resolved inference of flow and trajectories in proliferating cell populations

DRIFT infers division-resolved cellular dynamics from population measurements, recovering accurate state progression and redistribution in proliferating cell populations.

Spatial mitochondrial lineage tracing uncovers a premetastatic niche and microenvironment programmed fate switching in osteosarcoma

The paper uses spatial and single-cell transcriptomics with mitochondrial lineage tracing to uncover fate switching and premetastatic niche formation in osteosarcoma.

Flexible 3D multimodal organoid interface reveals functional subnetworks and coordinated circuit activity in cortical organoids

This paper introduces INFORM, a multimodal interface for cortical organoids that enables long-term recordings and modulation of neural activity, revealing functional subnetworks and inhibitory signaling.

Multi-Trajectory Pseudotime Inference via Permutation Factorizations

Factorizing multiple monotone pseudotimes into one shared donor permutation plus cluster-specific warps (HiP-BIND) yields Alzheimer's donor orderings agreeing better with Braak, ADNC and CERAD staging than single-trajectory B-BIND.

Connectomics by Sequencing Reveals Self-Organizing Principles of Neuronal Networks in Cerebral Organoids

The paper develops COSCO to map neuronal connectivity in cerebral organoids and shows self-organizing network motifs and disease-related topological changes.

Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets

Mastodon is a software platform for analyzing large-scale lineage-tracing microscopy datasets, enabling manual and automated cell tracking and lineage analysis in complex 3D geometries.

Engineering developmental transitions during human neurulation through modular integration of multimodal spatial cues

This paper introduces MoSAIC, a platform that integrates spatial cues to guide human neurulation in vitro, enabling the study of developmental transitions through controlled mechanical and chemical perturbations.

Distinct Progression Paths Underlie the Diversity of Pancreatic Papillary Cystic Neoplasms

The paper identifies distinct progression paths in pancreatic papillary cystic neoplasms using integrated transcriptomics and histology, enabling phenotype-specific prediction of high-grade dysplasia.

A piece-wise linear recurrent neural network identifies generalizable dynamics from neural activity during decision-making in rodents

This study uses a piecewise linear recurrent neural network to identify generalizable latent dynamics in neural activity during decision-making in rodents, showing faster rotational dynamics for impulsive choices.

Longitudinal imaging of single cells in opaque tissue with cell chirp ultrasound

This paper introduces cell chirp ultrasound to image single cells in opaque tissues, showing it can track rare cell populations over time with high specificity and sensitivity.

A First-in-Class, Brain-Penetrant Small Molecule Inhibitor of the NOS1AP-Tau Interaction Rescues Tau Pathology In Vivo and Improves Cognition

CAPTOR-1, a small molecule inhibitor of NOS1AP-tau interaction, reduces tau pathology and improves cognition in AD models.

Identifiable inverse optimal transport for single-cell state transitions

This paper introduces UOT-IOT, an inverse optimal transport framework for single-cell state transitions, showing improved identifiability and performance over existing methods.

CardamomOT: a mechanistic optimal transport-based framework for gene regulatory network inference, trajectory reconstruction and generative modeling

CardamomOT improves gene regulatory network inference and trajectory reconstruction by integrating mechanistic models with optimal transport, using exact time labels and reducing hyperparameters.

Inhibition of mucin-type O-glycosylation impairs melanogenesis, melanoma growth, and metastatic capacity

This study shows that inhibiting O-glycosylation in melanoma cells reduces melanin production and immune evasion, slowing tumor growth and metastasis in mice.

Lifespan Trajectories of Resting State Bipolar EEG Power

The paper derives lifespan trajectories of resting state bipolar EEG power from a large sample, finding age-related decreases followed by divergent patterns and sex-specific inter-frequency correlations.

PWK genetic background reprograms heterochromatin and malignant epithelial states in Neu-driven mammary tumors

The paper shows that the PWK genetic background alters transcriptional programs, heterochromatin organization, and malignant epithelial state trajectories in NeuT mammary tumors.

A two-step organoid screen identifies transient p53 activation as a senolytic strategy for radiation-induced salivary gland dysfunction

The paper identifies Nutlin3a as a senolytic compound that reduces radiation-induced salivary gland dysfunction by transiently activating p53 in a two-step organoid screening approach.

Predicting recovery trajectories and injury severity following partial crush spinal cord injury in mice

This paper predicts recovery trajectories and injury severity after partial crush spinal cord injury in mice using behavioral data and statistical modeling.

One Circuit, Many Flow Fields: Mechanistic Models of Single-Trial Neural Dynamics

The paper introduces a mechanistic model to infer control parameters of neural circuits from single-trial activity, showing how internal states shape dynamics across trials.

Pseudotime trajectory analysis reveals divergent rod photoreceptor states during dark adaptation

The paper analyzes single-cell RNA-seq data to reveal two divergent rod photoreceptor states during dark adaptation using pseudotime trajectory inference.

The Par complex regulates apical-basal cell polarity through modulation of FAK signaling homeostasis

This study shows that the Par complex regulates cell polarity and differentiation by modulating FAK signaling through the AKT-FURIN-LEFTY pathway in mouse embryonic stem cells.

Creation of a High-Resolution, Continually Evolvable Lineage Tracer

The paper introduces SCRIBBLE, a lineage tracing tool that enables high-resolution, multigenerational lineage tracking in embryonic mouse retina.

Embedding wear assessment in musculoskeletal simulation: A proof-of-concept application to total hip arthroplasty

This paper presents a computational framework for embedding wear estimation in musculoskeletal simulations, demonstrating its feasibility in total hip arthroplasty.

Automated inference of respiratory and syringeal biomechanical trajectories from birdsong acoustics

This paper introduces VIBE, a tool that automatically infers biomechanical control parameters from birdsong acoustics, validated against empirical measurements and neural data.

Decoding brain anatomy from neuronal neighborhoods with MYCEL

The paper introduces MYCEL, a graph neural network that improves decoding of brain anatomy from neuronal neighborhoods by learning local pooling, outperforming fixed aggregation on multiple datasets.

Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis

Prime-editing lineage trees for 16 mouse embryos (E7.5 to E10.0, >1.4 million cells) quantify fate restriction timing, progenitor numbers and lineage relationships, and are reproducible across replicate embryos.

Molecular Transducers of Physical Activity Consortium (MoTrPAC): Initial Insights into the Dynamic Human Responses to Exercise

The paper presents initial findings from the MoTrPAC consortium, showing that acute and chronic exercise induce distinct physiological and molecular responses, with chronic training improving key health metrics.

Deep Lineage: Single-Cell Lineage Tracing and Fate Inference Using Deep Learning

Deep Lineage uses deep learning to analyze time-series single-cell RNA-sequencing with lineage-tracing data to predict cell fate and gene expression profiles more accurately than existing methods.