trajectory inference

ShapeSpaceExplorer: Analysis of morphological transitions in migrating cells using similarity-based shape space mapping

ShapeSpaceExplorer analyzes morphological transitions in migrating cells using a shape difference measure to visualize and quantify shape changes during migration.

Linking Brain and Behavior States in Zebrafish Larvae Locomotion using Hidden Markov Models

This study uses Hidden Markov Models to link neural activity and behavior in zebrafish larvae, revealing state-based correlations between swimming patterns and circuit activation.

Phylodynamics of Somatic Evolution: A Likelihood-Based Approach for Cellular Reproduction

This paper introduces a likelihood-based framework for modeling somatic evolution by linking mutations to discrete cell division events, demonstrating its application on simulated and hematopoietic stem cell data.

NetMD: Unsupervised Synchronization of Molecular Dynamics Trajectories via Graph Embedding and Time Warping

NetMD synchronizes and analyzes molecular dynamics trajectories using graph embedding and time warping to reveal shared dynamics and deviations across conditions.

Informed, scalable and unified transport couplings for single-cell alignment and downstream inference with scBIOT

scBIOT introduces a biologically informed optimal transport framework for single-cell alignment, enabling scalable analysis and downstream biological inference across multiple tasks.

Progenitor Diversity and Architecture of the Human Ganglionic Eminences Shaping the Basal Ganglia

The paper identifies distinct progenitor populations in human ganglionic eminences, their gene regulatory networks, and lineage trajectories using single-nucleus transcriptomics and spatial transcriptomics.

Organoid Profiler: Automated, high-throughput and quantitative morphological characterization uncovers conserved longitudinal developmental kinetics in microfluidics-engineered organoids

The paper introduces Organoid Profiler, a deep-phenotyping pipeline that quantitatively characterizes microfluidics-engineered organoids, revealing conserved developmental kinetics and improved viability and homogeneity.

3D reconstruction of spatial transcriptomics with spatial pattern enhanced graph convolutional neural network

This paper introduces Spa3D, a method that reconstructs 3D spatial structures from 2D spatial transcriptomics data, improving spatial domain identification, cell-cell communication analysis, and developmental trajectory modeling.

Tracing the neural trajectories of evidence accumulation and motor preparation processes during voluntary decisions

This study examines neural processes during voluntary decisions, finding evidence accumulation and motor preparation dynamics similar to perceptual decisions.

Title: KymoTip: High-throughput Characterization of Tip-growth Dynamics in Plant Cells

KymoTip is a tool for analyzing live imaging data of plant cell tip growth, enabling accurate quantification of cell dynamics and intracellular events despite fluctuations in position and shape.

Validating molecular target-enriched fMRI for disentangling drug effects on dopamine

The paper validates the REACT method for isolating dopamine-specific effects of methylphenidate on brain function using fMRI and PET data.

In vivo tracking of CAR-T cells in tumors via nanobubble-based contrastenhanced ultrasound

This paper demonstrates a method to track CAR-T cells in vivo using nanobubble-based contrast-enhanced ultrasound, showing effective visualization in both tumor-bearing and non-tumor-bearing mice.

Behavioral Imitation with Artificial Neural Networks Leads to Personalized Models of Brain Dynamics During Videogame Play

This paper uses imitation learning with ANNs to model individual brain dynamics during videogame play, finding that subject-specific models better predict brain activity than generic ones.

Integrating Machine Learning with Musculoskeletal Simulation Improves OpenCap Video-Based Dynamics Estimation

This paper develops a hybrid machine learning and musculoskeletal simulation framework to improve dynamics estimation from smartphone video during walking, achieving lower error rates than simulation-only or ML-only approaches.

How human-derived brain organoids are built differently from brain organoids derived of genetically-close relatives: A multi-scale hypothesis

The paper proposes a multiscale hypothesis to explain structural differences in brain organoids derived from human versus genetically close non-human primate stem cells, linking chromatin reorganization to delayed cell fate transitions.

Quantitative Full-length transcriptome analysis by nanopore sequencing with Error-Aware UMI mapping

The paper introduces UMImap, a pipeline for accurate UMI identification and error correction in nanopore sequencing, enabling reliable full-length transcriptome analysis and discovery of novel isoforms.

Modelling Discrete States and Long-Term Dynamics in Functional Brain Networks

This paper introduces DyNeStE, a model that combines recurrent neural networks with Bayesian inference to capture long-term dynamics in brain networks while maintaining interpretability, outperforming HMMs in simulations and resting-state MEG data.

Secondary Growth and Exodermal Barriers Shape Local Root Hydraulics: Modeling Insights in Tomato

The paper models how secondary growth and exodermal barriers affect root hydraulics in tomato, showing exodermal suberin has little effect with a lignin cap and secondary growth is crucial for maintaining axial conductance.

Label-Free All-Electrical Tracking of Individual and Collective Cell Migration on a Megapixel CMOS Capacitance Sensor

This paper introduces a CMOS capacitance sensor array for label-free tracking of cell migration and tissue dynamics, demonstrating single-cell segmentation and multicellular spheroid analysis.

TimeFlow 2: an unsupervised cell lineage detection method for flow cytometry data

TimeFlow 2 infers cell lineages from flow cytometry data without prior knowledge, outperforming existing methods on benchmark datasets.

Love-thy-neighbor: Neural networks for tracking and lineage tracing in budding yeast

The paper introduces neural networks for tracking and lineage tracing in budding yeast, achieving robust performance on new and existing datasets.

Learning decouples accuracy and reaction time for rapid decisions in a transitive inference task

This study applies a drift diffusion model to analyze decision-making dynamics in a transitive inference task, showing stable reaction times despite improved accuracy during learning.

Intravital Two-Photon Imaging of Touch Sensory Axon Morphology in Mouse Skin

This study introduces an in vivo two-photon imaging method to visualize LTMR axon morphology in mouse skin during development and in adults, enabling longitudinal analysis of sensory circuit structure and function.

Generative Reconstruction of Unobserved Cellular Dynamics using Single-Cell Transcriptomic Trajectories

GRAIL reconstructs intermediate cellular states between two developmental stages using a combination of LSH-based cell selection, latent space interpolation, and GAN-based gene expression generation.

Neural Dynamics Underlying Repeated Learning of Visual Image Sequences

This study examines how repetitive learning affects two ERP components associated with recognition memory, finding that the parietal old/new effect changes with repetition while the frontal effect remains stable.

Investigating the mechanisms underlying saccade generation in the frontal eye fields using multi-site microstimulation

This study investigates how population activity in the frontal eye field (FEF) is integrated to generate saccadic eye movements using multi-site microstimulation in monkeys.

Geometry-preserving vector field reconstruction of high-dimensional cell-state dynamics using ddHodge

The paper introduces ddHodge, a method for reconstructing vector fields from scRNA-seq data to analyze cell-state dynamics, revealing gene expression follows a gradient system during mouse embryogenesis.

Dose-dependent NFI regulation of progenitor lifespan and output underlying human neocortical malformation

This study shows that NFI proteins regulate radial glial progenitor lifespan and output in a dose-dependent manner, affecting neocortical development and causing malformations in human cerebral organoids and mouse models.

Integrative Analysis of Spatial Transcriptome and Connectome by SpaCon

SpaCon integrates spatial transcriptomics and connectomics to reveal gene-connectivity coupling in the cortico-thalamic circuit and improves connectivity prediction from gene expression.

An Atlas of Extrachromosomal DNA Structures Illuminates Its Evolution and Biogenesis in Cancer

The paper maps ecDNA structures in glioblastoma using long-read sequencing and ecLego3, revealing structural variation, evolutionary dynamics, and transcriptional links to tumor adaptation.