trajectory inference

Automated generation of personalized trajectories of aging phenotypes with DyViA-GAN

The paper develops DyViA-GAN to predict personalized aging phenotype trajectories using longitudinal data, showing its potential in healthspan research.

Unveiling a missing component of the atypical type IV secretion system required for natural transformation of Helicobacter pylori

The paper identifies a missing component of the ComB T4SS in H. pylori essential for DNA uptake, showing it is a hexameric ATPase interacting with ComB4.

Diversity in transcriptomics without cell types

The paper introduces scDIV, a robust diversity measure for single-cell and spatial transcriptomics data that is insensitive to clustering parameters and evaluates its application in developmental datasets.

Generating whole-brain neural activity and behavior through unified latent dynamics

This paper introduces NEBULA, a framework that models whole-brain neural activity and behavior in C. elegans, identifying shared dynamics for prediction and intervention.

Movement strategies reveal the success of mammals in urban areas

The paper examines movement strategies of three mammal species across an urbanisation gradient, finding distinct behavioural adaptations that correlate with urban success.

An immunocompetent model of MCPyV-driven Merkel cell carcinoma reveals tumor evolution under immune selection

This study shows that MCPyV-driven tumors evolve immune-evasive traits under immune pressure, favoring sT over LTT expression, using a mouse model of Merkel cell carcinoma.

Learning proteomic disease trajectories with flow matching

This paper introduces proteome velocity, a framework using flow matching to infer continuous proteome trajectories from proteomics data, showing its application in mouse sepsis and clinical COVID-19.

TRACR: an anterograde transneuronal tracing system for genetic access across synapses and longitudinal circuit analysis

TRACR is a transneuronal tracing system that uses synthetic Notch technology to label postsynaptic neurons and analyze circuit connectivity in the mouse visual system.

SPARC Reveals Distinct Osteoclastogenesis-Associated Malignant States in Metastatic Osteosarcoma

SPARC improves trajectory inference by jointly modeling state progression and transitions between conditions, revealing osteoclastogenesis-associated malignant states in osteosarcoma metastasis.

Somatic mutation inference from single-cell transcriptomics: A survey in the esophagus

This study evaluates SComatic's ability to detect somatic mutations in normal esophageal tissue using scRNA-seq, highlighting technical challenges and methodological improvements.

Macro evolutionary patterns do not predict micro evolutionary trajectories

The paper develops a modeling framework to explore phytoplankton evolutionary trajectories under climate change, showing it captures evolved phenotypes not predicted by traditional models.

HIV superinfection reveals sequential reservoir reactivation and immune-driven rebound dynamics

This paper studies HIV superinfection to show how immune responses shape rebound dynamics and reservoir reactivation during treatment interruption.

Data-driven oscillatory network modeling with condition-dependent coupling laws: Identifying directed neural interactions in working memory attention dynamics

The paper introduces a data-driven framework to model oscillatory neural networks with condition-dependent coupling laws, identifying directed pathways in working memory attention dynamics using MEG data.

Distinct roles of neuronal phenotypes during neurofeedback adaptation

The paper investigates single-neuron dynamics during neurofeedback adaptation in rhesus macaques, finding that inhibitory interneurons are more active and engaged in learning compared to excitatory pyramidal neurons.

Learning complex temporal dependencies via local synaptic plasticity

This paper investigates temporal predictive coding (tPC) as a framework for learning temporal dependencies in recurrent neural networks, showing its equivalence to BPTT variants and its ability to handle complex tasks with local plasticity.

scJET: Full-gene Space Single-cell Expression Generation with Patch-based Transformer Modeling

scJET generates full-gene single-cell expression matrices using a patch-based Transformer model, preserving global and local transcriptomic features.

Hemodynamic Signals Reshape Biological Inference in Widefield Calcium Imaging

This study shows hemodynamic correction significantly alters biological interpretations of cortical dynamics in calcium imaging by reducing global connectivity and changing network structure.

Generative AI Models Reveal Dynamic Views of Aging (DyViA) Phenotypes in Healthy Individuals

DyViA uses generative AI to create personalized aging trajectory models for femoral neck BMD, showing dynamic progression from 66 to 89 years.

Characterizing dynamic tissue architectures by identifying cell-type-specific spatiotemporal gene programs with stGP

This paper introduces stGP, a statistical framework to identify cell-type-specific spatiotemporal gene programs, revealing how gene programs are influenced by time and spatial structure in tissues.

A Porcine Model of Intervertebral Disc Injury Recapitulates Human Discogenic Pain via Notochordal Cell Loss and Pain-inducing Nucleus Pulposus Cell Emergence

This study develops a porcine model of intervertebral disc injury that mimics human discogenic pain through notochordal cell loss and nucleus pulposus cell emergence, validated by MRI, biobehavioral testing, and single-cell transcriptomics.

The Virtual Child Brain: Modeling Neuromaturational Trajectories

The paper develops a computational model to study human brain maturation by analyzing functional MRI data and simulating neural network dynamics.

BLASE: Bulk Linkage Analysis for Single Cell Experiments - Teasing Out the Secrets of Bulk Transcriptomics with Trajectory Analysis

BLASE uses scRNA-seq references to analyze bulk RNA-seq data, identifying trajectory progress and correcting developmental differences in differential expression analysis.

Growth and patterning in vertebrate limb developmentA timescale perspective on skeletal specification

This paper introduces a computational framework to model limb skeletal patterning in mice and axolotls by integrating growth, gene regulation, and signaling spread, showing varying contributions of these factors across limb regions.

Topological data analysis captures complex behavioral dynamics during naturalistic social interaction between domestic ferrets

This study uses Temporal Mapper to analyze postural dynamics during naturalistic social interaction in ferrets, finding more complex and consistent state transitions during social activity.

SupeRJump: Determining normal and leukemic differentiation fate through semi-supervised jump diffusion modeling

SupeRJump identifies differentiation fate and discontinuous transitions in leukemia using a semi-supervised jump diffusion model applied to scRNA-seq data.

Linking transcriptome to cell behavior in real time uncovers molecular fate-asymmetry and a quiescence cycle among adult neural stem cells

This study links transcriptomic data with real-time cell behavior to uncover molecular fate asymmetry and a quiescence cycle in adult neural stem cells.

Astrocyte-to-microglia purinergic signaling mediates synaptic shielding and promotes neuronal activity

The paper identifies astrocyte-to-microglia purinergic signaling as a mechanism converting neuronal hypoactivity into synapse-selective microglial regulation of circuit activity.

Glia mediate brain-wide activity and sleep behavior during sickness through an adrenergic-glutamatergic axis

This study identifies glia as key coordinators of sickness-induced sleep behavior through an adrenergic-glutamatergic axis in Drosophila.

Mechanochemical Feedback between Cell Shape and Intracellular Mechanics Revealed by a Finite-Element Framework

The paper develops a finite-element framework to simulate mechanochemical feedback in cell shape and mechanics, revealing new insights into cell migration, neutrophil protrusion, and dendritic spine remodeling.

Single-molecule m6A profiling reveals position-dependent mRNA regulation and non-canonical roles for Ythdf2 in early embryogenesis

The paper uses single-molecule m6A profiling to study mRNA regulation during zebrafish MZT, finding m6A's role in mRNA decay and poly(A) tail dynamics.