trajectory inference

Neural representation of action grammar structure in primate frontal cortex

The paper investigates how primate frontal cortex represents action grammar structure during novel problem-solving tasks and identifies preSMA as a key region for encoding grammatical properties.

Uncovering Dynamic Neural Information Flow with Continuous-Time Weighted Dynamic Bayesian Networks

This paper introduces CTwDBN to model dynamic neural information flow and shows it captures long-term temporal fluctuations in cortical networks.

Microbiopsy of living mouse brain for longitudinal molecular profiling

This paper introduces a minimally invasive microbiopsy technique for longitudinal molecular profiling of the living mouse brain, enabling transcriptomic and epigenomic analyses without sacrificing the animal.

Bayesian data driven modelling of kinetochore dynamics: space-time organisation of the human metaphase plate

The paper uses Bayesian inference to analyze kinetochore dynamics in human cells, identifying spatial and temporal organization patterns during mitosis.

SigDyn: single-cell mutational signature dynamics

SigDyn analyzes single-cell mutational signature dynamics to uncover tumor evolution and heterogeneity, revealing therapeutic insights in invasive ductal carcinoma and laryngeal squamous cell carcinoma.

Fast Adversarial Generation of Molecular Dynamics Trajectories with Kinetic Fidelity

This paper introduces a GAN-based method to generate molecular dynamics trajectories with kinetic fidelity, enabling efficient sampling of rare events in complex systems.

Modelling multicellular coordination by bridging cell-cell communication and intracellular regulation through multilayer networks

ReCoN models multicellular coordination by integrating cell-cell communication and intracellular regulation to predict cellular responses to perturbations.

Temporal tissue dynamics from a spatial snapshot

OSDR estimates dynamic cell population changes from a single tissue sample using spatial proteomics, revealing tumor microenvironment dynamics and predicting treatment responses in breast cancer.

Single-cell mitochondrial lineage tracing decodes fate decision and spatial clonal architecture in human hematopoietic organoids

This study uses mitochondrial variants as barcodes to track clonal dynamics and spatial organization in human hematopoietic organoids.

VAETracer: Mutation-Guided Lineage Reconstruction and Generational State Inference from scRNA-seq

VAETracer reconstructs cellular lineages and infers generational states from scRNA-seq data by analyzing mutation profiles, improving accuracy over noisy mutation signals.

Functional interrogation uncovers a critical role for a high-plasticity cell state in lung adenocarcinoma

In vivo lineage tracing and targeted ablation in autochthonous mouse lung adenocarcinoma establish the Slc4a11+ high-plasticity cell state as a bidirectional transition hub driving tumor progression and therapy resistance.

Energy Landscape Analysis Reveals Thalamic Modulation of Brain State Transitions During Movie Watching

This study uses energy landscape modeling on fMRI data to identify brain states and their transitions during movie watching, revealing thalamic modulation of neural dynamics.

4D multimodal wound healing atlas reveals organ-level controls of repair phase transitions

The paper presents OWHA, a 4D multimodal atlas of wound healing in mice, revealing a conserved Basal IV/SEMA3C circuit that coordinates repair, and shows its disruption in diabetic wounds.

Transcriptomic profiling of human γδ T cells reveals non-linear immune aging characterized by childhood transitions and relative stability in adulthood

This study maps the aging trajectories of human γδ T cells using single-cell transcriptomics, revealing non-linear aging with distinct childhood transitions and stability in adulthood.

An Asynchronous Production Line of Meiotic Prophase I in the Mouse Fetal Ovary

The paper challenges the notion of synchronous meiosis initiation in mouse fetal ovaries, showing asynchronous entry and progression from E12.5 to E16.5, supported by a predictive meiotic clock model.

The geometry of context-dependent biased decisions during learning

This study shows how reward context is encoded through geometric shifts in neural representations, enabling rapid decision adjustments during learning.

Organization of mouse prefrontal cortex subnetwork revealed by spatial single-cell multi-omic analysis of SPIDER-Seq

This study uses SPIDER-Seq to create a spatial multi-omic atlas of mouse prefrontal cortex, revealing modular organization and neural transmission mechanisms.

Mapping Brain Growth and Sex Differences Across Prenatal to Postnatal Development

This study analyzes a large MRI dataset to model age-related brain volume changes and sex differences from prenatal to postnatal development.

Rhythms and Background (RnB): The Spectroscopy of Sleep Recordings

The paper introduces RnB, a wavelet-based method to separate rhythmic and arrhythmic components in sleep EEG data, improving time-domain analysis of NREM sleep oscillations.

Modeling predicts a biochemical feedback mechanism underlying astrocyte calcium refractory periods

The paper develops a computational model of astrocytic calcium signaling that predicts refractory periods through a feedback mechanism involving cPKC, validated with in vivo imaging data.

Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia

The paper uses consumer-resource models parametrized from monoculture exometabolite data to predict and design synthetic microbial consortia, revealing the importance of cross-feeding interactions and nonlinear dynamics.

Integrated Cross-Species Translation and Biophysical Multi-Scale Modeling Links Molecular Signatures and Locomotory Phenotypes in Spaceflight-Induced Sarcopenia

The paper identifies conserved molecular pathways in spaceflight-induced sarcopenia using cross-species analysis and develops a model linking transcriptional changes to locomotion deficits.

Spatiotemporal Regulatory Logics of Mouse Gastrulation

This study constructs a spatiotemporal regulatory framework for mouse gastrulation using multi-omic data and reveals mechanisms of lineage commitment and symmetry breaking.

Integrative scRNA-seq and spatial transcriptomics uncovers distinct macrophage-fibroblast cross-talk in human hip synovium between patients with femoroacetabular impingement and osteoarthritis

In hip osteoarthritis (OA) versus femoroacetabular impingement (FAI) synovium, inflammatory EREG+ lining fibroblasts expand and co-localize more with COL1A1+ fibrotic macrophages; FGF2-SDC4 is their top predicted interaction.

Single-cell RNA analysis reveals unexpected hemocyte plasticity and immune cell specialization in a Drosophila overgrowth model

The paper uses single-cell RNA sequencing to analyze hemocyte diversity in Drosophila overgrowth models, identifying new plasmatocyte subtypes and plasticity under chronic apoptotic signaling.

Molecular computation at equilibrium via programmable entropy

This paper introduces a thermodynamics-first approach to molecular computation using the TBN model, demonstrating systems that perform Boolean logic and concatemer synthesis.

Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent

The paper introduces veloAgent, a framework that integrates spatial information with RNA velocity to improve accuracy and scalability in analyzing spatially resolved cellular dynamics.

Aging redirects prior expectations from perception to action

This study shows aging changes how the brain uses prior expectations in decision-making, leading to stronger bias and reduced sensory precision, with neural changes in alpha and beta rhythms.

Ontogeny of the spinal cord dorsal horn

This paper investigates how the dorsal horn of the spinal cord develops, showing that neurons are diversified by time and spatial-molecular gradients, leading to the formation of laminae.

Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development