trajectory inference

Mechanistic interpretation of biological tissue growth experiments with a computational model

This paper presents a computational model to simulate tissue growth by integrating geometry, mechanics, and stochastic processes, demonstrating its application to 3D-printed scaffolds and bone formation in cortical pores.

Opening the Black Box of Neural Computation from Neural Recordings with Gain-Modulated Linear Dynamical System

This paper introduces a method to infer neural computation mechanisms from recordings by decomposing dynamics into gain and connectivity components, revealing coexisting selection mechanisms in decision-making tasks.

Integrated multi-modal data analysis for computational modeling of healthy and location-dependent myocardial infarction conditions in porcine hearts

The paper develops porcine ventricular digital twins using multi-modal data to study myocardial infarction effects on cardiac function and ECG patterns.

Constrained Diffusion as a Paradigm for Evolution

This paper introduces DiffEvol, a constrained diffusion framework to model evolution, and applies it to SARS-CoV-2 data to reconstruct fitness trends and vaccine-induced phase transitions.

Reconstitution of the Spinal Cord Injury Microenvironment in Adult Neural Stem Cell-Derived Organoids

This paper introduces neuroids, a modular organoid system that mimics the adult spinal cord injury microenvironment to study NSC differentiation and gliogenic bias.

High-Fidelity Long-term Whole-embryo Lineage and Fate Reconstruction by Iterative Tracking with Error Correction

ITEC reconstructs high-fidelity cell lineages and fate maps of embryos with over 99.7% accuracy using iterative tracking and error correction.

Dynamic shifts in brain criticality support cognitive processing

This study examines how critical dynamics in the hippocampus shift during learning and sleep to support cognitive functions.

The Developmental Trajectory of the Social Brain: A Movie-Based Exploration from childhood to adolescence

This study examines the developmental trajectories of social cognition networks in children and adolescents using movie-based functional connectivity analysis.

Mid-infrared chemical imaging of living cells enabled by plasmonic metasurfaces

This paper introduces a method for mid-infrared chemical imaging of living cells using plasmonic metasurfaces, enabling non-destructive, label-free imaging with sub-cellular resolution.

ProAR: Probabilistic Autoregressive Modeling for Molecular Dynamics

ProAR generates molecular dynamics trajectories with reduced error and improved conformational accuracy compared to existing methods.

Integrated single-cell and spatial transcriptomic analysis of T cell exhaustion and immunometabolic remodeling in HPV-positive oropharyngeal squamous cell carcinoma

This study integrates single-cell and spatial transcriptomics to uncover mechanisms of immune checkpoint resistance in HPV-positive oropharyngeal cancer, identifying a KMT2D-KLF7-PD-L1 axis as a therapeutic target.

Addressing complex autofluorescence signatures in solid tissue samples to enhance full spectrum flow cytometry of non-immune cells.

This paper optimizes full spectrum flow cytometry for analyzing non-immune cells in solid tissues by addressing autofluorescence and improving subpopulation resolution.

Benchmarking zero-shot single-cell foundation model embeddings for cellular dynamics reconstruction

This study benchmarks zero-shot single-cell foundation model embeddings for cellular dynamics reconstruction and finds they underperform a traditional HVG baseline in capturing complex temporal patterns.

Monocytes are biological sensors of aging and frailty in humans

This study shows that monocyte behaviors can predict aging and frailty in humans using single-cell analysis and a deep learning model.

Temporal Mechanisms of T-Cell Fate Decisions under Immune Checkpoint Blockade Resolved by CanonicalTockySeq

This paper introduces CanonicalTockySeq to analyze T-cell fate decisions over time in immunotherapy, showing that effective treatment correlates with reduced antigen engagement and exhaustion signaling.

An alternative patterning mechanism for vertebrate tooth complexity

This study identifies an alternative epithelial patterning mechanism for vertebrate tooth complexity in squamates, showing that cusp formation does not rely on enamel knots but on a broad signaling field.

High-resolution retrospective single cell lineage tracing with mutable homopolymers

RETrace2 enables high-resolution retrospective lineage tracing and cell-type identification using mutable homopolymers, achieving resolution below five cell divisions in microsatellite-unstable organisms.

Decoding Living Systems: Reassessing Crop Model Frontiers via Biological Dynamics and Optimized Phenotype

This paper develops an inverse engineering framework to optimize crop phenotypes by integrating sensitivity analysis, genetic algorithms, and similarity analysis to identify adaptive strategies and breeding candidates.

Decoupling Lineage and Intrinsic Information in Single-Cell Lineage Tracing Data with Deep Disentangled Representation Learning

DeepTracing disentangles lineage and intrinsic cellular variation in single-cell lineage tracing data, outperforming existing methods in clustering, phylogenetic recovery, and tumor-type classification.

Accelerated Discovery of Cell Migration Regulators Using Label-Free Deep Learning-Based Automated Tracking

This paper introduces DeepBIT, a deep learning method for automated cell migration tracking, enabling high-throughput analysis of cancer cell motility under various conditions and identifying new regulators of migration.

Volumetric Bioprinting of Bone-like Mineralizing Hydrogel Constructs in the Presence of High Cell Densities and Mineral Precursors

This study combines volumetric bioprinting with mineralization to create high-density cell-laden hydrogel constructs with bone-like properties.

Distinct beta burst motifs exhibit opposing error relationships during motor adaptation

Comparative human embryo-mapping reveals neural bias of neuromesodermal progenitors in stem cell axial elongation models

The paper maps scRNA-seq from stem cell-based axial organoids to a human embryo, revealing three origins of axial development and the neural bias of neuromesodermal progenitors.

A transition-prone brain state precedes spontaneous behavioral switching

The paper identifies a whole-brain transition-prone state that predicts spontaneous behavioral switches in mice using functional ultrasound imaging and optogenetics.

The chromatin remodeling complex PRC2 safeguards cell fate in alveolar epithelial type 2 cells

This study shows that PRC2 maintains AT2 cell fate in the adult lung by preventing transitions to ABI and basal-like states, both in vitro and in vivo.

Performance of the 10X Genomics Flex Single-Cell Sequencing Assay and its Application to Overcome Challenges in Clinical Trial Samples

The paper compares scRNA-seq protocols for clinical trial samples, finding that GEM-X Flex with chop-fix outperforms standard protocols and snRNA-seq in fixed tissue and FFPE blocks.

HIF-1α+ CD4 T cells coordinate a tissue resident immune cell network in the lung

This study identifies HIF-1α+ CD4 T cells as key coordinators of a tissue-resident immune network in the lung during infection and cancer.

Unbiased Quantification of Persistent Postural and Motor Deficits Following Spinal Cord Injury in Mice

This study quantifies persistent postural and motor deficits after spinal cord injury in mice using unbiased, high-speed video tracking and machine learning.

PAVR: High-Resolution Cellular Imaging via a Physics-Aware Volumetric Reconstruction Framework

PAVR enables high-resolution volumetric imaging of cells using a physics-aware framework trained on simulated data, demonstrating applications in tracking subcellular structures and analyzing cardiac cell dynamics.

A latent space thermodynamic model of cell differentiation

This paper introduces scLSD, a thermodynamics-inspired model for cell differentiation that reconstructs differentiation trajectories and predicts fate commitment, outperforming existing methods.