diffusion model

Precise Generation of Conformational Ensembles for Intrinsically Disordered Proteins via Fine-tuned Diffusion Models

This paper introduces IDPFold, a diffusion model that generates conformational ensembles for intrinsically disordered proteins directly from sequences, without requiring MSA or experimental data.

RiboDiffusion: Tertiary Structure-based RNA Inverse Folding with Generative Diffusion Models

RiboDiffusion generates RNA sequences from 3D structures using a diffusion model, outperforming baselines in sequence recovery and showing consistent performance across RNA types and lengths.

Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models

This study introduces ProteinReDiff, a diffusion-based model for redesigning ligand-binding proteins using sequence and ligand SMILES inputs, showing effectiveness in affinity and structural preservation.

Changes in growth, lanthanide binding, and gene expression in Pseudomonas alloputida KT2440 in response to light and heavy lanthanides

This study investigates how light and heavy lanthanides affect growth, lanthanide binding, and gene expression in Pseudomonas alloputida KT2440, revealing differential responses and a dimmer switch mechanism for lanthanide-dependent enzymes.

Cross-modal influence of odorant stimulation on sound localization revealed by EEG and diffusion modeling

This study uses EEG and diffusion modeling to show odorant stimulation biases sound localization, with effects strongest when sound location is ambiguous.

Guided Diffusion for molecular generation with interaction prompt

This paper introduces InterDiff, a diffusion model guided by atomic interactions to generate molecules with desired ligand-protein interactions, showing improved or comparable binding modes to known drugs.

AMP-Diffusion: Integrating Latent Diffusion with Protein Language Models for Antimicrobial Peptide Generation

AMP-Diffusion generates functional antimicrobial peptides using a latent diffusion model integrated with the ESM-2 protein language model, showing alignment with experimentally validated AMPs in pseudo-perplexity and physicochemical properties.

DiffTopo: Fold exploration using coarse grained protein topology representations

This paper introduces DiffTopo, a diffusion model for generating novel protein folds by exploring designable topology space efficiently.

DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements

DNA-Diffusion uses diffusion models to generate cell type-specific regulatory DNA sequences that modulate chromatin accessibility and gene expression.

PPML-Omics: a Privacy-Preserving federated Machine Learning method protects patients' privacy in omic data

PPML-Omics is a privacy-preserving federated learning method that balances privacy protection and model utility across three omic data tasks.

PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking

PackDock predicts accurate protein-ligand complex conformations using a diffusion model for side-chain packing, validated through multiple docking experiments.

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

DiffModeler uses diffusion models to accurately model protein complex structures from low-resolution cryo-EM maps, achieving high TM-Scores across various resolutions.

Multi-condensate state as a functional strategy to optimize the cell signaling output

The paper demonstrates that multiple biomolecular condensates can optimize cell signaling output by maximizing actin polymerization through an optimal number of condensates.

Cytochrome P450 Enzyme Design by Constraining Catalytic Pocket in Diffusion model

The paper designs artificial cytochrome P450 enzymes by applying a 'three-point fixation' model derived from structural and evolutionary analysis, resulting in enzymes with enhanced catalytic activity.

Baikal: Unpaired Denoising of Fluorescence Microscopy Images using Diffusion Models

Baikal improves fluorescence microscopy image denoising using diffusion models without requiring paired noisy and clean images.

Spontaneous breaking of symmetry in overlapping cell instance segmentation using diffusion models

This paper introduces a diffusion model-based method for instance segmentation that spontaneously breaks symmetry, allowing overlapping labels in cell instance segmentation.

Attenuation of the CpG Island Methylator Phenotype and lack of WNT signaling activation restrains Kras mutant intestinal neoplasia

This study compares Kras and Braf mutant intestinal neoplasia in mice, showing Kras mutations lead to less aggressive serrated lesions with reduced WNT signaling activation and attenuated DNA methylation changes compared to Braf mutations.

TopoDiff: Improving Protein Backbone Generationwith Topology-aware Latent Encoding

TopoDiff improves protein backbone generation by using a topology-aware latent encoding to enhance controllability and coverage of generated structures.

Alignment of spatial transcriptomics data using diffeomorphic metric mapping

This paper introduces STalign, a method for aligning spatial transcriptomics data using diffeomorphic metric mapping, improving alignment accuracy over affine methods.

A Pose-Informed De-Noising Diffusion Model for Adult Naturalistic EEG Signals

This paper introduces a denoising diffusion model for EEG signals that uses pose coordinates to improve denoising performance and maintain spatial dependencies.

Multimodal generation of astrocyte by integrating single-cell multi-omics data via deep learning

The paper introduces ACGDC, a deep learning model that generates synthetic single-cell multi-omics samples to aid in brain disease research.

Gene expression shifts in Emperor penguin adaptation to the extreme Antarctic environment

This study compares gene expression in Emperor and King penguins to identify adaptations to extreme Antarctic environments, finding key roles for muscle and liver in metabolism and regulatory shifts in the brain.

mb-PHENIX: Diffusion and Supervised Uniform Manifold Approximation for denoising microbiota data

mb-PHENIX denoises microbiota data by combining diffusion and supervised UMAP, improving differential abundance analysis in sparse and noisy count matrices.

Boosting performance of generative diffusion model for molecular docking by training on artificial binding pockets

This paper introduces a generative diffusion model for molecular docking trained on artificial binding pockets, showing improved performance over existing methods.

FrameDiPT: SE(3) Diffusion Model for Protein Structure Inpainting

FrameDiPT is a diffusion model for protein structure inpainting that recovers masked sections using sequence and structural context, achieving comparable accuracy to existing models with limited data.

Diffusion in a quantized vector space generates non-idealized protein structures and predicts conformational distributions

Video Diffusion models for the apoptosis forcasting

This paper introduces a video diffusion model for early apoptosis prediction by considering cell-cell interactions and spatial-temporal dynamics, achieving high accuracy and low error rates.

Illuminating protein space with a programmable generative model

This paper introduces Chroma, a generative model for proteins that can sample novel structures and sequences, conditioned on desired properties and functions.

Synthetic Echocardiograms Generation Using Diffusion Models

This paper introduces a video diffusion model for generating synthetic echocardiograms with higher resolution and fewer artifacts than existing methods.

Amalga: Designable Protein Backbone Generation with Folding and Inverse Folding Guidance

Amalga improves protein backbone designability by using folding and inverse folding guidance to generate more designable structures.