ppi-networks

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a-r-j /graphein

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Star1.1k

Protein Graph Library

python bioinformatics deep-learning structural-biology protein-data-bank protein-structure computational-biology pytorch protein drug-discovery rna interactome protein-design interactomics geometric-deep-learning ppi-networks graph-neural-networks pytorch-geometric gene-regulatory-networks dgl

UpdatedMar 3, 2025
Jupyter Notebook

LirongWu /MAPE-PPI

Star255

Code for ICLR 2024 (Spotlight) paper "MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding"

vocabulary protein-protein-interaction codebook ppi-networks protein-embedding protein-representation-learning microenvironment masked-modeling

UpdatedJun 20, 2024
Python

evanpeikon /Amilioride_Drug_MOA

Star24

Uncovering Amiloride's Mechanisms of Action in Multiple Myeloma: A Bioinformatics Approach

rna-seq wgcna ppi-networks functional-enrichment-analysis drug-drug-interaction

UpdatedJan 31, 2025
Jupyter Notebook

pulimeng /CancerOmicsNet

Star17

A Graph Neural Network Model for prediction of the effectiveness of a drug on a given cancer cell lines

systems-biology cancer-genomics drug-discovery ppi-networks graph-neural-network

UpdatedApr 3, 2023
Python

chao1224 /SGNN-EBM

Star13

Structured Multi-task Learning for Molecular Property Prediction, AISTATS'22 (https://proceedings.mlr.press/v151/liu22e.html)

string molecule knowledge-graph chembl energy-based-model ppi-networks multitask-learning chembl-string

UpdatedJul 6, 2022
Python

evanpeikon /SmallSeqFlow

Star11

SmallSeqFlow: A streamlined, notebook-based bulk RNA-seq analysis pipeline optimized for small-sample studies with modular extensions.

rna-seq transcriptomics ppi-networks functional-enrichment-analysis coexpression-network

UpdatedFeb 23, 2025
Jupyter Notebook

pievos101 /Ensemble-GNN

Star11

Ensemble learning with graph neural networks for disease module discovery and classification

ensemble-learning ppi-networks graph-neural-networks

UpdatedNov 5, 2023
Python

THinnerichs /DTI-VOODOO

Star9

A PPI network driven approach to drug-target-interaction prediction using deep graph learning methods.

ontologies ppi-networks graph-neural-networks dti-prediction

UpdatedNov 4, 2021
TeX

paulmorio /protclus

Star9

Python 3 library implementing a number of topological clustering techniques used on protein-protein interaction networks.

clustering ppi-networks

UpdatedNov 29, 2020
Python

ylaboratory /ETNA

Star9

Embeddings to Network Alignment - align biological networks between two species

computational-biology network-alignment bioinformatics-tool ppi-networks protein-protein-interaction-network

UpdatedSep 8, 2023
Python

SaniyaKhullar /NetREm

Star6

Network Regression Embeddings reveal cell-type Transcription Factor coordination for target gene (TG) regulation

transcription-factors protein-interaction network-regularization gene-expression-profiles transcriptional-regulatory-network single-cell-analysis ppi-networks network-lasso multiomics-data gene-regulatory-network-inference bioinformatics-software transcription-factor-coordination regularization-embeddings regression-embeddings predictor-interactions network-guided-regression regression-with-prior-knowledge network-based-inference netrem

UpdatedMay 18, 2024
Jupyter Notebook

c3biolab /struct_ppi_pred

Star2

This study presents a deep learning-based framework for predicting PPIs between human and gut bacterial proteins using structural data.

bioinformatics deep-learning protein-structure attention-mechanism protein-protein-interaction ppi-networks

UpdatedFeb 13, 2025
Python

Barabasi-Lab /NonCoding

Star2

Codes for the paper entitled: Non-Coding RNAs Improve the Predictive Power of Network Medicine

network ncrna ppi-networks disease-modules ncrna-protein-interactions network-medicine netsci

UpdatedOct 11, 2023
HTML

aGalhoz /wppi

Star1

Gene prioritisation tool using a weighted network methodology based on Gene Ontology and Human Phenotype Ontology annotations to infer closely related genes to given genes of interest.

gene-ontology gene-prioritization random-walk-with-restart ppi-networks human-phenotype-ontology omnipath

UpdatedNov 2, 2022
R

pulimeng /Biology-Network-Reduction

Star1

Graph representation for system biology networks and the reduction of them for machine learning purposes

systemsbiology ppi-networks

UpdatedApr 11, 2023
Python

ylaboratory /splitpea

Star1

A tool for calculating PPI network rewiring due to alternative splicing

bioinformatics cancer protein-protein-interaction ppi-networks splicing

UpdatedJan 15, 2024
Jupyter Notebook

giuliapalmaa /PPI-Networks-Clustering

Star1

New implementation of the Girvan-Newman edge-betweenness' algorithm and study of the clustering structure through modularity. Based on "A MapReduce-Based Parallel Clustering Algorithm for Large Protein-Protein Interaction Networks", by Liu and others

clustering modularity ppi-networks edge-betweenness