trajectory inference

Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions

TCOF1 dosage is limiting for transitional human neural crest cells; its enhancers buffer promoter output against MYC fluctuations rather than amplifying it, a pattern seen across 14 dosage-sensitive promoters.

Longitudinal Subject Pairing in Cross-Sectional Neonatal Data Reveals Asynchronous Structural and Functional Brain Maturation

The paper uses a longitudinal subject-pairing framework on cross-sectional neonatal data to reveal asynchronous structural and functional brain maturation, finding a functional maturation lag of about five days relative to structural development.

mmVelo: A deep generative model for estimating cell state-dependent dynamics across multiple modalities

mmVelo estimates cell state-dependent dynamics across multiple modalities using deep generative modeling, validated on mouse and human data.

PhenoStream: A Cyberinfrastructure for Automated and AI-Based Crop Trait Extraction from Aerial Imagery

PhenoStream automates crop trait extraction from aerial imagery, enabling high-throughput phenotyping with reduced latency and manual effort.

scLANTERN: High-Throughput Retrospective Lineage Tracing via Full-Length Single-Cell Transcriptomics and Expressed Repeat Variation

This paper introduces scLANTERN, a method using full-length single-cell transcriptomics and expressed repeat variation to enable high-throughput retrospective lineage tracing in cancer.

MT-LLE: Multi-Task Locally Linear Embedding for Interpretable Disease Modeling from Longitudinal Omics Data

This paper introduces MT-LLE, a multi-task manifold learning method that improves disease modeling from longitudinal omics data by integrating clinical labels and temporal progression, achieving better clinical structure and progression forecasting than standard methods.

Multimodal temporal modeling of behavioral reorganization across threat learning and extinction in rats

The paper models behavioral reorganization in rats during threat learning and extinction using hidden Markov models, showing shifts in behavioral configurations over time.

NuclearIDTracker resolves intestinal cell identity and lineage dynamics through nuclear phenotypic signatures

NuclearIDTracker uses nuclear phenotypic signatures to classify intestinal cell types and track lineage dynamics without fluorescent reporters.

Inference of self-limiting neutrophil swarming dynamics using Bayesian physics-informed neural networks

The paper develops a Bayesian physics-informed neural network to model neutrophil swarming dynamics in human and murine cells, revealing species-specific differences in recruitment and self-limitation.

Reconstruction of epithelial transcriptional trajectories reveals heterogeneous progression and early therapy-resistance programs in high-grade serous carcinomaprecursors

This study reconstructs transcriptional trajectories of Fallopian-tube epithelium to show STICs occupy diverse positions along a progression continuum and exhibit variable PARPi resistance signatures.

Granule cells reorient cortical trajectories to separate contexts

In mice learning two tasks, cerebellar granule cells kept the low-rank geometry of premotor cortical output within each task but rotated their population trajectories apart between tasks, while cortex generalized.

Interpretable Forecasting of Kidney Cancer Progression via Generative AI and Symbolic Reasoning

This paper uses generative and symbolic AI to forecast kidney cancer progression from cross-sectional data, providing interpretable models and molecular insights.

Sensory experience drives glutamate spillover, presynaptic LTP and functional connectome remodeling in the barrel cortex

The paper shows that sensory experience increases glutamate release and strengthens synaptic connections in the barrel cortex, leading to changes in the functional connectome.

DPF3a couples H3K36me2-dependent chromatin remodeling to genome architecture during myogenesis

This study identifies DPF3a as a chromatin remodeler that regulates myogenesis through three-dimensional genome organization rather than local chromatin accessibility.

Connectome-constrained modeling identifies neurons and synapses that sustain spontaneous activity in Drosophila

The paper uses a connectome-constrained model to identify neurons and synapses sustaining spontaneous activity in Drosophila.

Transcriptomic Analysis Identifies Transient Mesendodermal State and Lineage Divergence in Human Pluripotent Stem Cell Differentiation

Information Flow and Traveling Waves show distinct cortical trajectories

The paper introduces DIFF, a method to map directed information flow in cortical networks, and shows it reveals distinct trajectories from traveling waves in simulations and electrophysiological recordings.

Single-cell roadmap of bovine oogenesis and somatic niche interactions during fetal ovarian development

This study creates a single-cell RNA-seq atlas of bovine fetal ovarian development, identifying cell populations and developmental stages, and showing parallels with human fetal ovaries.

The Internal Structure of Seizures Reflects Animal-Specific Trajectories of Disease Progression and Circadian Modulation in Epileptic Mice

The paper analyzes seizure dynamics in epileptic mice, finding structured, animal-specific trajectories and circadian modulation in seizure microstructure.

Brachyury expression levels predict lineage potential and axis-forming ability of in vitro derived neuromesodermal progenitors

The paper identifies two thresholds of Brachyury expression in NMPs that determine lineage potential and axis-forming ability in vitro.

Cross-Regional Trajectory Analysis Reveals Distinct Temporal Progression of Shared Proteomic Programs in Alzheimer's Disease

The paper analyzes proteomic trajectories in Alzheimer's disease to show distinct temporal progression of shared molecular programs across brain regions.

A pharmacokinetics-informed ODE extrapolates long-term fenofibrate transcriptomic responses

The paper develops a pharmacokinetics-informed ODE model to extrapolate long-term transcriptomic responses to fenofibrate in rats, achieving high correlation and low error compared to baselines.

Microenvironment-informed inference of transcriptional progression geometry

BIOCURRENT infers donor-specific pseudotime geometry in transcriptomic data by modeling gene expression with microenvironmental context and latent pseudotime, revealing condition- and donor-specific distortions in progression intervals.

A Cytokine Receptor Signaling Atlas Reveals How STAT Mosaics Fine-Tune T Cell Function

A fully orthogonal IL-2 receptor platform isolates 36 cytokine receptors in T cells; receptor-specific STAT combinations specify distinct fates, and STAT3-dominant programs give curative antitumor responses.

Mechanochemical modeling of exercise-induced skeletal muscle hypertrophy

This paper develops a multiscale computational model to predict skeletal muscle hypertrophy by integrating mechanical and biochemical stimuli, showing how exercise protocols affect muscle growth and shape.

Stimulation of rodent and human beta-cell proliferation using synthetic modified mRNAs encoding cell cycle regulators

This study uses synthetic modified mRNAs to stimulate beta-cell proliferation in rodents and humans, showing temporary activation of cell cycle pathways without sustained proliferation.

Time-resolved operator archetypes characterize dynamical sensitivity during cell-state transitions

This paper introduces scJDO, a framework for analyzing dynamical sensitivity during cell-state transitions, and applies it to iPSC reprogramming to distinguish productive from diverted fates.

Pseudotime analysis of 2,106 brains across nine regions reveals conserved immune, neuronal, and myelin regulatory programs in Alzheimer's disease

The paper uses pseudotime analysis on bulk RNA-seq data from Alzheimer's disease brains to identify conserved and region-specific molecular programs across nine brain regions.

A unified multiscale modelling framework to explore the brain excitatory-inhibitory balance: application to multiple sclerosis

The paper presents a multiscale brain modelling framework combining DCM and TVB to study excitatory-inhibitory balance in multiple sclerosis, finding altered connectivity patterns and their association with clinical and behavioural outcomes.

Postnatal Pax7-expressing limb cells are multipotent and generate non-myogenic lineages that persist into adulthood.

This study shows that postnatal Pax7+ cells in limb muscles are multipotent, generating non-myogenic lineages like fibro-adipogenic progenitors that persist into adulthood and respond to injury.