trajectory inference

Quantitative mapping of heterochrony to species-specific phenotypes

The paper maps heterochrony in zebrafish and medaka using single-cell genomics, revealing cell-level timing shifts that contribute to species-specific phenotypes.

Molecular basis of polyadenylated RNA fate determination in the nucleus

The paper identifies a nuclear mechanism that determines the fate of polyadenylated RNAs by distinguishing between functional and non-functional transcripts through the opposing actions of PAXT and TREX-2.

Density-based longitudinal neuron tracking in high-density electrophysiological recordings

DANT improves longitudinal neuron tracking in high-density electrophysiological recordings by combining density-based clustering and motion correction to increase match yield and reduce false negatives.

A single-cell transcriptome atlas of the barley root apical meristem uncovers conserved and divergent roles of HvWOX5

The paper creates a single-cell transcriptome atlas of barley root apical meristem, identifying 24 cell populations and showing HvWOX5's role in meristem organization and metaxylem patterning.

Inferring Cell Fate Trajectories in Time-Resolved Metabolic RNA Labeling data

The paper introduces FLOWSATATE, a trajectory inference method using time-resolved RNA labeling data to model cell fate dynamics and predict future states.

Single-cell map of the healthy human immune system across the lifespan reveals unique infant immune signatures

The paper maps the human immune system across the lifespan using scRNA-seq and snATAC-seq, revealing unique infant immune signatures and age-related changes in immune cell populations.

Temporally overlapping mechanisms diversify clonal B cell responses in vivo.

Single-cell RNA and BCR sequencing of infected mouse spleens shows class switching overlaps clonal expansion, GC-seeding clones also form plasmablasts, and SHM proceeds at constant rate.

Entanglement-governed protein networks enable mechanically adaptive artificial skin for transplantation-scale skin replacement

This paper develops a mechanically adaptive artificial skin using entanglement-mediated protein networks, showing improved toughness, regenerative compatibility, and wound healing in mice.

Short-Term Developmental Trajectories of Dorsal-Ventral Pathways and Their Relationships with First-Grade Learning

This study tracks brain development and learning in first graders, finding that white matter changes predict math learning but not reading.

Gonadal PIP-seq reveals genes involved in germ cell development and sexual differentiation in sea lamprey ( Petromyzon marinus )

The paper uses PIP-seq to analyze gonadal cell transcriptomes in sea lamprey, identifying gene expression patterns associated with germ cell development and sexual differentiation.

Predicting stress response trajectories: Differential contributions of limbic and prefrontal regions to cortisol and affective responses

This study identifies distinct stress response trajectories in humans by analyzing brain region predictors of cortisol and affective responses to psychosocial stress.

Dynamic Reversal of IT-PFC Information Flow Orchestrates Visual Categorization Under Perceptual Uncertainty

The paper investigates how information flow between the inferotemporal (IT) cortex and prefrontal cortex (PFC) changes with perceptual certainty, finding that feedback from PFC to IT dominates under uncertainty.

DyMoTree decodes early cell state transitions and drivers from single-cell transcriptomes using a tree-structured neural network

DyMoTree infers early cell fate transitions and drivers from single-cell transcriptomes using a tree-structured neural network, outperforming existing methods in resolving fate biases.

Fleeing is Believing: Adaptive behavior under social threat as an inference process

This paper models social defeat in mice as a POMDP to understand how adverse social experiences reshape decision-making and predict behavioral outcomes.

Revealing trajectories of multi-modal voxel-level changes in neurodegenerative diseases using latent event mapping

This paper introduces LEMING, a method to model voxel-level disease progression in neurodegenerative diseases, revealing new insights into acetylcholine receptor associations with amyloid and atrophy events.

A quantitative coordinate system for developmental dynamics

This paper introduces STERN, a framework that quantitatively compares developmental trajectories across embryos by learning spatiotemporal representations from 4D imaging data.

Developmental variation in dopamine neurobiology, neurocognitive functioning, and impulsivity shape substance use trajectories in youth

This study identifies four substance use trajectories in youth and links them to dopamine-related neurobiology, impulsivity, and inhibitory control during adolescence.

GeroEngine: Generative single-cell aging trajectories reveal a bidirectionally traversable identity core and direction-specific inflammatory remodeling

GeroEngine reveals aging trajectories show bidirectional identity recovery and direction-specific inflammation, suggesting homeostatic restoration over inflammation suppression.

DigiMus: a connectome-informed spiking framework for multi-region mouse neural-behavior modeling

DigiMus integrates connectome-derived structural priors into a spiking neural network framework for mouse neural-behavior modeling, showing improved performance in complex tasks.

Liquidity of gene co-expression trajectories across the lifespan highlights delayed maturation and the perinatal GABA switch in schizophrenia risk

The paper uses a novel 'liquidity' metric to analyze gene expression trajectories across lifespan, revealing delayed maturation and perinatal GABA switch in schizophrenia risk without detectable neuropathology.

Electron transport chain complex I and mitochondrial fusion regulate ROS for differentiation in Drosophila neural stem cells

This study shows that complex I and mitochondrial fusion regulate ROS levels, which in turn affect differentiation in Drosophila neuroblasts.

BiXformer: A Bidirectional Cross Attention Transformer for Disentangling Inter-Regional Neural Dynamics

BiXformer disentangles bidirectional neural communication by modeling causal and acausal streams, revealing temporally structured components in neural dynamics.

Dynamic network reconfigurations during task engagement following resting state in adolescent onset schizophrenia

This study uses energy landscape analysis on fMRI data to show that adolescent-onset schizophrenia exhibits altered brain state dynamics during task engagement compared to healthy controls.

Sciphy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.

SciPhy estimates time-scaled phylogenies and cell population parameters from sequential genetic lineage tracing data using a Bayesian framework, showing improved accuracy over existing methods.

Single-cell transcriptomics of heterogeneous patient-derived organoids reveals novel therapeutic targets in high-grade serous ovarian cancer

This study uses single-cell transcriptomics on patient-derived organoids to identify AGRIN as a regulator of metastatic competence in high-grade serous ovarian cancer.

Recreating the Native Airway Microenvironment Using Tissue-Specific Extracellular Matrix Bioinks for Proximal Airway Engineering

This paper develops a bioink using decellularized extracellular matrix to create functional airway structures, showing viability and mechanical properties similar to native airways.

Integrated mesenchymal and extracellular cues drive bioengineered liver tissue formation and function

This study develops bioengineered liver tissues using multiple cell types and synthetic hydrogels, showing improved structure, function, and maturation.

What can a neuron compute

The paper demonstrates that detailed models of rat pyramidal neurons can perform complex computational tasks using a novel algorithm, highlighting dendritic nonlinearities as key to high-order feature binding.

Single-nucleus multiomics unveils malignant cellular states, regulatory architectures and microenvironmental reorganization across the G-CIMP epigenomic transition in IDH-mutant glioma

The paper integrates single-nucleus RNA and ATAC sequencing to identify cellular states and regulatory networks associated with the G-CIMP epigenomic transition in IDH-mutant gliomas.

Interplay of pupil-linked arousal and cortical decision computations in mice

The paper examines the relationship between frontal cortical activity and pupil responses in mice during decision-making, finding that pupil-linked arousal tracks decision uncertainty and predicts future behavior adjustments.