trajectory inference

Distributed state-dependent neural ensembles across sleep stages

The paper identifies distributed neural ensembles across sleep stages in mice, revealing state-dependent firing patterns and temporal organization across multiple timescales.

Advancing Cardiac Tissue Engineering: Melt Electrowriting Conductive Polymer-Hydrogel Scaffolds

This paper develops conductive polymer-hydrogel scaffolds for cardiac tissue engineering using melt electrowriting, showing that gold coating supports better contractile activity than other conductivity methods.

Topology-Based Query Framework for Longitudinal Omics Trajectories

LongOmicsTraj provides a topology-based framework to represent and query longitudinal omics trajectories, identifying corticosteroid response genes with temporal patterns across treatment groups.

Cellfoundry: a GPU-accelerated, multi-physics ABM framework for cellular microenvironment and organoid-scale studies

Cellfoundry is a GPU-accelerated agent-based modeling framework for simulating cellular microenvironments, enabling the study of complex interactions between cells, extracellular matrix, and biochemical signals.

FluoroFate: A generalisable platform for time-resolved single-cell analysis of cell fate enables quantification of cell death dynamics

FluoroFate enables time-resolved single-cell analysis of cell fate by quantifying cell death dynamics using live-cell imaging and new biosensors.

Population-specific transcriptional-state remodeling of cortical and hypothalamic neurons in Alzheimer's disease

The paper identifies population-specific transcriptional changes in neurons across Alzheimer's disease models and human samples, revealing molecular remodeling not captured by population representation alone.

Promotion of Structured Motor Program Diversity Through Since-last-state Memory in Drosophila Larvae

The paper uses HSMM to analyze Drosophila larval locomotor activity, showing how memory of recent states promotes motor program diversity through adaptive competition between CPG modules.

Visualizing Reaction Pathways via Reciprocal Space Kinetic Decomposition

The paper introduces a method to decompose time-resolved crystallography data in reciprocal space to extract weak transient structural states from noisy datasets.

Cross-Cohort Optimal Transport Maps Macrophage Plasticity and Competing Routes to Inflammation and Fibrosis in Human Atherosclerotic Plaques

The paper develops a computational framework using optimal transport to analyze macrophage state transitions in atherosclerosis, identifying origin-dependent plasticity mechanisms and shared regulatory circuits in inflammation and fibrosis.

TipQUANT: A robust algorithm for quantitative analysis of spatiotemporally dynamic activities in tip-growing cells

TipQUANT quantifies spatiotemporal dynamics of fluorescent molecules in tip-growing cells, improving analysis efficiency and accuracy.

Coarse-grained models for simulations of double-stranded nucleic acids for mixed protein-nucleic acid condensates

The paper develops coarse-grained models for simulating double-stranded RNA and DNA in the CALVADOS framework to study their behavior in protein-nucleic acid condensates.

Cytoskeletal-nuclear control of alveolar fibroblast identity directs lung regeneration

This study shows that mechanical-nuclear signaling in alveolar fibroblasts influences lung regeneration by modulating transcriptional identity and epithelial repair after injury.

PASTRI: Resolving Stage-Specific Cell-State Dynamics from Annotated Cell Lineage Trees

PASTRI infers stage-specific cell-state transition rates from annotated cell lineages, revealing rate-limiting steps and attractor states in development and disease.

Psychedelics Align Brain Activity with Context

This study shows psilocybin reorganizes brain activity into context-sensitive patterns linked to subjective experience and mindset changes.

Functional connectivity scaffolds the emergence of the visual word form area

The paper shows that functional connectivity patterns in reading circuitry precede and predict the emergence of the visual word form area in children with dyslexia after reading intervention.

HIF-1α integrates metabolic and immunoregulatory programs in RORγt⁺ regulatory T cells during intestinal inflammation

This study identifies HIF-1α as a regulator of metabolic and immunoregulatory programs in RORγt⁺ Tregs during intestinal inflammation, showing its role in maintaining suppressive function and limiting inflammation.

Developmental Trajectories of Dynamic Brain Network Organization and Their Alteration in Tourette Syndrome

This study examines how brain network organization develops in typically developing children and those with Tourette Syndrome, finding altered network flexibility and stability in TS patients.

Moving through everyday life: distinct developmental timescales for head-rotation magnitude and rotation efficiency in infancy

The paper analyzes head movement data from infants to show that rotational magnitude increases and rotational efficiency improves over the first year of life.

Physically Grounded Generative Modeling of All-Atom Biomolecular Dynamics

BioKinema generates physically accurate all-atom biomolecular trajectories at lower computational cost than traditional MD simulations, enabling dynamic analysis of protein and protein-ligand systems.

Unique CD8+ T Cell Populations Expand during ART and Predict Delayed HIV-1 Rebound

The paper identifies a unique CD8+ T cell population that expands during ART and predicts delayed HIV-1 rebound.

Recovering directional brain networks under temporal undersampling: an application to schizophrenia

This paper introduces a method to estimate directed causal brain networks from fMRI data, showing it detects more group-differentiating edges in schizophrenia compared to existing methods.

Discrete Inverse Rendering: Biological Image Analysis with Integer Programming

The paper introduces a discrete inverse rendering framework using integer programming to solve multiple biological image analysis tasks by jointly optimizing discrete decisions across time and space.

Inference of lineage hierarchies, growth and drug response mechanisms in cancer cell populations without tracking

This study introduces a method to infer lineage hierarchies and drug response mechanisms in cancer cell populations without single-cell tracking, demonstrating its effectiveness through simulations and experiments.

Human Osteochondral Granular Extracellular Matrix (gECM) Hydrogels Drive Tissue-Specific Composition and Mechanics

This study develops human-derived granular extracellular matrix hydrogels for osteochondral repair, showing distinct biochemical and mechanical properties between cartilage and bone gECM.

Terminator-dependent facilitated recycling of RNA polymerase III couples transcriptional activation and chromatin remodeling in vivo

The paper shows that transcription terminators facilitate RNA polymerase III recycling, enhancing chromatin transcription and linking transcriptional activation with chromatin remodeling in vivo.

Hoverfly responses to looming stimuli depend on elevation and speed

This study shows that hoverflies respond more strongly to looming stimuli approaching from below at intermediate speeds, matching the sensitivity of ventral descending neurons.

Tuning viscoelasticity of dynamic covalent hydrogels for human tissue modeling

This study develops a tunable DCC hydrogel platform to control viscoelastic properties for 3D human tissue modeling.

Characterizing developmental changes in infant habituation using functional change point detection

This study uses functional change point detection to analyze infant fNIRS data and finds earlier habituation timing in older infants.

Hydrophilic Polydopamine (hPDA) Fueled Bioglue Enhances Tissue Adhesion and Promotes Healing of Avascular Meniscus Tears

This paper introduces a hydrophilic polydopamine (hPDA) bioglue that enhances tissue adhesion and promotes healing of avascular meniscus tears by improving mechanical properties and tissue integration.

MuSpAn: A Toolbox for Multiscale Spatial Analysis

MuSpAn, a Python library of over 100 spatial methods, quantifies multiscale tissue organisation and maps cancer-associated fibroblast subtypes to distinct immune niches in mouse colorectal tumours.