diffusion model

Dynamical modelling of proliferative-invasive plasticity and IFN-gamma signaling in melanoma reveals mechanisms of PD-L1 expression heterogeneity

This study uses dynamical modeling to uncover how IFN-gamma signaling and proliferative-invasive transitions shape PD-L1 expression heterogeneity in melanoma, with experimental validation in cell lines and datasets.

Energy Guided Diffusion for Generating Neurally Exciting Images

This paper introduces Energy Guided Diffusion (EGG) to generate neurally exciting images, outperforming gradient ascent in generalization and efficiency for macaque V4 models.

End-to-end protein-ligand complex structure generation with diffusion-based generative models

This paper introduces a diffusion-based generative model for end-to-end protein-ligand complex structure generation without relying on existing protein structures.

De novo protein backbone generation based on diffusion with structured priors and adversarial training

SCUBA-D generates high-quality protein backbones from noisy initial structures using diffusion with structured priors and adversarial training.

Privacy-Preserving Statistical Analysis of Genomic Data using Compressive Mechanism with Haar Wavelet Transform

This paper introduces two privacy-preserving methods for genomic data analysis using compressive mechanisms and Haar wavelet transforms, achieving differential privacy with high utility.

Spatiotemporal modeling reveals geometric dependence of AMPAR dynamics on dendritic spine morphology

This paper develops a spatiotemporal model to study how dendritic spine geometry influences AMPAR dynamics during long-term potentiation, finding non-monotonic relationships between spine volume and AMPAR changes.

Sensitivity of diffusion-tensor and correlated diffusion imaging to white-matter microstructural abnormalities: application in COVID-19

This study compares diffusion MRI methods to detect white-matter changes in COVID-19 patients, finding correlated diffusion imaging is most sensitive to microstructural abnormalities.

Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture

The paper develops a stochastic model of histone dynamics at the replication fork, showing that differential diffusivity explains histone inheritance patterns and predicts epigenomic patterns observed in experiments.

Asymmetric expression of homoeologous genes in wheat roots modulates the early phase of iron-deficiency signalling

This study examines the transcriptional response of wheat roots to iron deficiency at early stages, identifying dynamic gene expression and homoeologous gene expression patterns.

Analog of the Hutchinson equation in biophysical neurodynamics: from the Morris-Lecar model to a delay differential equation

The paper derives a delay differential equation analog of the Hutchinson equation from the Morris-Lecar model, showing it reproduces neuronal dynamics with delay-induced changes in excitability types.

Computational Enhanced Hi-C data reveals the function of structural geometry in genomic regulation

The paper develops CTG, a diffusion-based method to improve Hi-C data reliability and reveal structural genomic regulation.

Differential geometry methods for constructing manifold-targeted recurrent neural networks.

This paper introduces a method using differential geometry to construct recurrent neural networks with dynamics targeted to a specific manifold, improving the design of task-solving neural dynamics.

Cross-attractor repertoire provides new perspective on structure-function relationship in the brain

This paper introduces a novel dynamical systems framework to analyze cross-attractor coordination in the brain and its relation to functional connectivity and energy costs.

Diffusion on PCA-UMAP manifold captures a well-balance of local, global, and continuum structures to denoise single-cell RNA sequencing data

The paper introduces sc-PHENIX, an imputation method for scRNA-seq data that addresses over-smoothing issues in diffusion-based approaches by using PCA-UMAP initialization.

Network communication models narrow the gap between the modular organization of structural and functional brain networks

The paper shows that adding models of indirect neural communication to structural brain networks better aligns their modular organization with functional systems.

Transcriptional response of individual Hawaiian Culex quinquefasciatus mosquitoes to the avian malaria parasite Plasmodium relictum

This study examines the transcriptional response of Hawaiian Culex quinquefasciatus mosquitoes to Plasmodium relictum infection, identifying gene expression changes at different stages of the parasite life cycle.

The transcriptomic signature of physiological trade-offs caused by larval overcrowding in Drosophila melanogaster

This study examines the transcriptomic effects of larval overcrowding in Drosophila melanogaster, identifying differentially expressed genes and enriched pathways under varying crowding conditions.

Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures

This paper introduces a diffusion-based generative model for designing and optimizing antigen-specific antibodies by jointly modeling CDR sequences and structures.

isomiRs-specific differential expression is the rule, not the exception: Are we missing hundreds of species in microRNA analysis?

The paper shows isomiRs significantly affect differential expression analysis and highlights the need to consider them instead of relying solely on reference miRNA sequences.

The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour

This study uses molecular dynamics simulations to show that the fatty acid binding site in the SARS-CoV-2 spike protein influences distant functional regions and variant behavior.

How far to build it before they come? Analyzing the use of the Field of Dreams hypothesis in bull kelp restoration

The paper evaluates the effectiveness of partial restoration strategies for bull kelp forests using a dynamical model, finding that initial conditions matter more than prolonged efforts.

Efficient Differentially Private Methods for a Transmission Disequilibrium Test in Genome Wide Association Studies

The paper introduces efficient differentially private methods for a transmission disequilibrium test in genome-wide association studies, showing significant speed improvements over existing methods.

ANDOR and beyond: dynamically switchable logic gates as modules for flexible information processing

The paper introduces dynamically switchable biochemical logic gates that perform different logical operations based on network dynamics, demonstrating their efficiency and resilience in computational tasks.

Crosstalk with keratinocytes causes GNAQ oncogene specificity in melanoma

The paper shows that epidermal crosstalk impairs GNAQQ209L-expressing melanocytes, explaining GNAQ oncogene specificity in cutaneous melanoma.

Computing the Riemannian curvature of image patch and single-cell RNA sequencing data manifolds using extrinsic differential geometry

The paper estimates Riemannian curvature of image and scRNA-seq data manifolds using extrinsic differential geometry, revealing curvature in scRNA-seq datasets.

A two-stage diffusion modeling approach to the compelled-response task

The paper introduces a two-stage diffusion model to explain decision-making in the compelled-response task, predicting response times and choices without assuming cross-trial variability.

Privacy-preserving quality control of neuroimaging datasets in federated environments

The paper introduces decentralized quality control tools for neuroimaging data in federated environments, showing promising results in visualization and outlier detection while preserving privacy.

Spatial heterogeneity enhance robustness of large multi-species ecosystems

This paper shows that spatial heterogeneity increases ecosystem robustness by allowing stability beyond previously identified limits, while excessive fragmentation reduces stability.

Nonlinear delay differential equations and their application to modeling biological network motifs

This paper applies delay differential equations to model biological network motifs, finding simplifications and insights into dynamics with delays.

Modelling Human Gait using a Nonlinear Differential Equation

The paper models human gait using a nonlinear differential equation based on 3D visualization of center of mass movement during walking or running.