trajectory inference

Drift-diffusion dynamics of hippocampal replay

This paper develops a computational framework to model hippocampal replay dynamics using drift-diffusion processes, revealing insights into replay speed, randomness, and preplay events in rat hippocampal recordings.

Folate deficiency disrupts key metabolic transitions within the developing neural ectoderm

This study uses a deep-learning model to analyze scRNA-seq data and identifies how folate deficiency disrupts metabolic transitions in developing mouse neural ectoderm, leading to morphological defects.

Time-resolved single-cell state tracing exposes bidirectional state dynamics during differentiation

The paper uses single-cell state tracing to show bidirectional differentiation dynamics and rare transcriptome conversions across lineage boundaries in both in vivo and in vitro settings.

Noninvasive tomography of tumor progression via dynamical changes of T-cells in surrounding microenvironment

This paper develops a framework to noninvasively assess tumor progression by analyzing T-cell distribution changes in the microenvironment.

Deconvolution of the mechanisms of T cell drug response in multiple myeloma induction therapy

This study investigates the molecular effects of RVd therapy on T cells using TEA-seq, revealing how individual and sequential drug administration impacts T cell function and states.

Genetically inducible coordinators of cytokine signaling pathways for interrogating T cell motility

The paper develops CAMPs, genetically inducible receptors to control cytokine signaling in T cells, to study motility and signaling pathways without paracrine interference.

An integrated, transcript-resolution atlas of prostate cancer progression unmasks associations with oncogenic pathways

A transcript-resolution prostate cancer atlas, built by uniformly reprocessing public RNA-seq cohorts, links isoform switches in cancer genes to oncogenic pathway activity and some to CRPC survival.

A transcriptional continuum from clinically normal to lesional skin: Single-cell trajectory analysis of psoriasis

The paper identifies a transcriptional continuum from normal to lesional skin in psoriasis using single-cell RNA sequencing and trajectory analysis, revealing cell-type-specific state transitions.

StressNET: an adaptable deep-learning model for mechanical stress inference in tissues

StressNET infers intercellular mechanical stresses from tissue geometry using a Graph Neural Network, achieving state-of-the-art performance in zebrafish and Xenopus embryos.

Segment Any Plant (SAP): Foundation-Model Segmentation for Plant Time-Series Phenotyping

SAP provides a transferable, training-free framework for automated segmentation of plant time-series imagery across species and conditions.

A lifespan single-cell atlas of the human developing hippocampus benchmarks familial Alzheimer's disease brain organoids.

The paper constructs a lifespan single-cell atlas of the human developing hippocampus and benchmarks iPSC-derived brain organoids with a PSEN1 mutation linked to familial Alzheimer's disease.

Basolateral amygdala neurons await oscillatory recruitment into valence-relevant ensembles

The paper shows that specific BLA neurons are recruited by oscillatory states to drive valence-related behaviors.

Parvalbumin interneurons and dentate gyrus homeostatic dysregulation shape epileptogenesis in Angelman syndrome model mice

This study identifies parvalbumin interneurons and dentate gyrus remodeling as key factors in epileptogenesis in Angelman syndrome model mice.

Single-cell profiling reveals disruption of cell-cycle homeostasis following JDP2 depletion in colorectal epithelial cells

This study shows JDP2 depletion disrupts cell-cycle homeostasis in colorectal epithelial cells, increasing proliferation and altering transcriptional states.

Transcriptomic profiling identifies cellular and molecular transitions during Merkel cell regeneration

This study uses single-cell RNA sequencing to analyze Merkel cell regeneration in zebrafish, identifying molecular transitions and conserved features across species.

Sleep renormalizes learning-perturbed cortical dynamics to stabilize memory

The paper shows sleep reorganizes cortical dynamics after learning to stabilize memory by following wake-induced perturbations.

An extended Kalman filter for large-volume path positioning of aquatic animals within acoustic telemetry arrays

This paper introduces EK-TOA, an extended Kalman filter method for accurately tracking fine-scale movement of aquatic animals using acoustic telemetry data.

Joint inference of paired dynamical gene regulatory networks reveals distinct cell-state landscapes of neutrophil reprogramming

The paper introduces NetDes-Duo, a method to jointly infer gene regulatory networks from scRNA-seq data, revealing distinct cell-state landscapes in neutrophil reprogramming under different conditions.

Curved by Design: Applying Microfluidic Principles for Nonplanar and Planar Suspended Tissue Patterning to the Development of Bladder Models with Tunable Mechanics

The paper develops the STEAM platform for creating suspended 3D bladder models with tunable mechanics and spatial complexity.

An anti-Galectin-3 intrabody improves primary and memory response of antigen-specific CD8+ T cells during viral infection

This study shows that an anti-Galectin-3 intrabody enhances CD8+ T cell activation, proliferation, and memory formation during viral infection.

Interpretable spherical geometry of single-cell state transitions from dominant principal components

The paper introduces SPHERE-PCA, a method to interpret single-cell state transitions using spherical geometry, revealing structured patterns in developmental and disease datasets.

Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

OPA1-dependent mitochondrial remodeling coordinates TCR signaling and metabolic adaptation during iNKT cell differentiation

Characterizing Individual and Population-Level Heterogeneity in Infant BMI Trajectories Using Flexible and Functional Modeling Approaches

The paper models infant BMI trajectories using flexible methods to identify individual and population-level patterns, finding sex differences and associations with maternal gestational diabetes.

Engineering Stable Hydrogels with Polydisperse Yeast Exopolysaccharides for Embedding Cancer Spheroids

The paper develops a stable hydrogel using polydisperse yeast exopolysaccharides for embedding cancer spheroids, demonstrating improved consistency and long-term stability.

Tractography from Serial Optical Coherence Tomography: How and Why?

This paper develops a method for microscale white matter tractography using S-OCT and validates it on simulated and mouse brain data, showing improved ODF estimation and tractography performance.

H3-K27M mutation alters the dynamics of human hematopoietic stem cells and delays erythroid differentiation

This study shows that the H3-K27M mutation alters hematopoietic stem cell dynamics and erythroid differentiation, increasing blood cell numbers despite impaired maturation.

Comparison of cell-cycle gene expression dynamics and mRNA kinetics across mouse and human pluripotent systems

This study compares cell-cycle gene expression dynamics and mRNA kinetics across mouse and human pluripotent systems, revealing species-specific differences in transcriptional complexity and oscillatory control.

Whole-body 3D kinematics of freely behaving Drosophila

Seven high-speed cameras, a hybrid 2D/3D network and body-model inverse kinematics track 50 keypoints on freely moving flies; height and speed peak together at all running speeds.

Engineering phenotypic heterogeneity for functional organization in microbial populations

This paper introduces PROMETEO, a genetic-circuit framework that programs microbial population composition through asymmetric circuits, enabling functional organization and efficient biotransformation.