trajectory inference

Fixation-evoked potentials reveal neural signatures of hierarchical value-integration during decision-making

This study uses EEG and eye-tracking with a computational model to identify neural signatures of value-integration during decision-making under naturalistic conditions.

NeuroGate: waveform translation between brain

NeuroGate translates neural waveforms between brain regions using a framework that outperforms baselines across multiple modalities and datasets.

Allele-Resolved Hybrid Embryos Reveal the Fates of Regulatory Divergence

The paper tracks regulatory divergence in hybrid embryos of Ciona species, showing how allelic differences are maintained or remodeled in lineage-specific ways and how GRN hierarchy influences allelic divergence.

Sharp and smooth state transitions during resting state brain dynamics

The paper analyzes resting-state fMRI data to determine whether brain state transitions are discrete or continuous, finding structured and heterogeneous transitions that depend on anatomical regions.

Divergent amyloid trajectories distinguish normal aging from Alzheimer's disease progression

This paper models Alzheimer's disease progression as a deviation from aging using longitudinal amyloid PET data and a self-supervised trajectory-learning framework, revealing distinct trajectories in early-stage aging and AD.

Longitudinal single-cell and spatial transcriptomics reveals intratumor heterogeneity, therapeutic response, and comparative value of canine marginal zone lymphoma

V-TRACE: End-to-end temporal inference and annotation ofanimal behaviors from video

V-TRACE provides an end-to-end platform for automated animal behavior analysis from video, achieving high accuracy and throughput across species and contexts.

From Geometry to Hierarchy: Charting the Dominant Modes of Human Cortical Function Through Development

This study shows that the development of long-range cortical connections leads to the emergence of hierarchical functional modes in the human cortex, shifting from geometrically driven patterns to sensory-association organization.

Lifelong Invertebrate Chordate Central Nervous System Regeneration is Driven by a Migrating Pool of Conserved Neural Stem Cells Program

This study identifies a conserved neural stem cell pool driving continuous CNS regeneration in Botryllus schlosseri, showing aging disrupts this process.

The enigmatic bone reduction pattern of thalidomide embryopathy is set by sequential exit from the sensitive window

The paper analyzes thalidomide-affected limbs to determine the sequential bone reduction pattern, identifying two co-reduction rules and a maturation wave mechanism.

Flexible reorientation of conserved neural dynamics underlies grasp control

The paper reanalyzes neural recordings from rhesus monkeys during grasping tasks and finds that a flexible dynamical model applies to grasp control, showing conserved rotational frequencies and reoriented state-space planes.

The Principal Component Life Trajectory (PCLT): Mapping Sex-Specific Physiological Change Across the Human Lifespan

The paper introduces PCLT to map sex-specific physiological changes across the lifespan using NHANES data, identifying five phases and linking them to health outcomes.

Mammalian spermatogenesis at single-cell resolution downstream of genetic perturbations in meiotic double-strand break repair

Single-nucleus RNA+ATAC profiling of 32 mice shows asymmetric PRDM9 binding drives asynapsis, pachytene cell loss, aneuploidy and multi-megabase crossover redistribution, tuned by a chromosome 15 locus.

Age-associated B cells (ABCs) develop from a CNS-localized progenitor pool into a pro-inflammatory phenotype after stroke

The paper identifies age-associated B cells (ABCs) in the CNS that develop from a localized progenitor pool and contribute to impaired post-stroke recovery in mice.

Reference-guided pseudotime inference across species and biological contexts

Cavebear improves pseudotime inference by using reference species time-series data to guide ordering of cells in query species or conditions without time labels.

CoTRA: a comprehensive R/Shiny framework for transparent bulk and single-cell RNA-seq analysis

CoTRA provides an R/Shiny framework for bulk and single-cell RNA-seq analysis, offering integrated workflows and reproducibility across 49 criteria.

An RGS5-positive fibroblast to WNT-like epithelial TGFB axis in colorectal liver metastasis, replicated in an independent paired cohort

Three-dimensional Virtual Adult Cardiomyocyte Transcriptomics

This paper introduces 3D-VirtualCM, a method to reconstruct full cardiomyocyte transcriptomes from spatial transcriptomic sections, revealing spatial and transcriptional heterogeneity in infarcted mouse hearts.

Neural subspace reorganization reflects value-based decision making

The paper shows how value-based decisions reorganize neural subspaces in LPFC by rotating and expanding chosen option representations.

Prepatterned Tissue Stiffness Gradient Controls Organ shape and size

This study shows how prepatterned tissue stiffness gradients control organ shape and size through mechanosensing and Wnt5a signaling in sweat glands.

Overcoming artificial structures in resolution-enhanced Hi-C data by signal decomposition and multi-scale attention

This paper introduces SHARP, a method to enhance Hi-C data resolution while avoiding artificial structures by decomposing signals and using multi-scale attention.

Transition Intermediates Encode Ligand Efficacy at the μ-Opioid Receptor-Gi Protein Complex

The paper uses computational and experimental methods to identify transition intermediates in the μ-opioid receptor-Gi protein complex that encode ligand efficacy.

High-frequency oscillations reveal progressive recruitment of remote cortex into the epileptic network in a mouse model of focal cortical dysplasia type II

The paper tracks how high-frequency oscillations evolve in a mouse model of focal cortical dysplasia type II, showing contralateral cortex recruitment into the epileptic network over time.

Tracking propagating cortical activity in MEG/EEG with a bilinear state-space model

This paper introduces a bilinear state-space model to track cortical traveling waves in MEG/EEG data, showing improved accuracy over traditional methods in simulations and empirical recordings.

Reconstructing signaling histories of single cells via perturbation screens and transfer learning

The paper develops a framework combining perturbation screens and transfer learning to reconstruct signaling histories in cells and optimize differentiation protocols.

Early life stress alters lifespan trajectories of amygdala development: a cross-species model of amygdala burnout

The paper proposes the amygdala burnout hypothesis, showing early-life stress leads to initial amygdala volume increases in adolescence followed by reductions in older age across rodents and humans.

Structured Connectivity Across Multiple Drosophila Mushroom Bodies

The paper identifies structured connectivity patterns in Drosophila mushroom bodies across multiple connectomes, showing reproducible pathways that prioritize food-related sensory information.

Coupled transcriptomic divergence establishes a human-specific synaptic glial precursor state

The paper identifies a human-specific synaptic glial precursor state by analyzing single-cell differentiation trajectories across multiple species and shows its role in human cortical evolution.

Computer vision-aided locomotor behavioral analysis identifies therapeutic motor signatures in a mouse model of Huntington disease

The paper introduces a computer vision framework to analyze fine motor behaviors in HD mice, identifying disease-specific motor signatures and a scoring system to assess therapeutic effects.

A physics-informed hybrid deep learning model for spatiotemporal rice disease prediction using multi-source data

The paper introduces a physics-informed hybrid deep learning model for spatiotemporal rice disease prediction, improving accuracy and interpretability using multi-source data.