Artificial intelligence approaches to human-microbiome protein–protein interactions

DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes

(2021) Wang Liu-Wei et al.   BIOINFORMATICS

Protein Interaction Interface Region Prediction by Geometric Deep Learning

(2021) Bowen Dai et al.   BIOINFORMATICS

Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

(2021) Isabel Moreno-Indias et al.   Frontiers in Microbiology

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

Robust and accurate prediction of protein–protein interactions by exploiting evolutionary information

(2021) Yang Li et al.   Scientific Reports

HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry

(2020) Emine Guven-Maiorov et al.   JOURNAL OF MOLECULAR BIOLOGY

Energy‐based Graph Convolutional Networks for Scoring Protein Docking Models

(2020) Yue Cao et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A framework towards data analytics on host–pathogen protein–protein interactions

(2020) Huaming Chen et al.   Journal of Ambient Intelligence and Humanized Computing

Learning Context-aware Structural Representations to Predict Antigen and Antibody Binding Interfaces

(2020) Srivamshi Pittala et al.   BIOINFORMATICS

TaxoNN: Ensemble of Neural Networks on Stratified Microbiome Data for Disease Prediction

(2020) Divya Sharma et al.   BIOINFORMATICS

Microbiome analyses of blood and tissues suggest cancer diagnostic approach

(2020) Gregory D. Poore et al.   NATURE

The role of the gut microbiome in the development of schizophrenia

(2020) John R. Kelly et al.   SCHIZOPHRENIA RESEARCH

Microbiome in Colorectal Cancer: How to Get from Meta-omics to Mechanism?

(2020) Dominik Ternes et al.   TRENDS IN MICROBIOLOGY

DeepMicro: deep representation learning for disease prediction based on microbiome data

(2020) Min Oh et al.   Scientific Reports

IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data

(2020) Mohammad Arifur Rahman et al.   BIOINFORMATICS

APEX2S: A two‐layer machine learning model for discovery of host‐pathogen protein‐protein interactions on cloud‐based multiomics data

(2020) Huaming Chen et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

Evolution of sequence-based bioinformatics tools for protein-protein interaction prediction

(2020) Mst. Shamima Khatun et al.   CURRENT GENOMICS

Comprehensive host-pathogen protein-protein interaction network analysis

(2020) Babak Khorsand et al.   BMC BIOINFORMATICS

The BioGRID database: A comprehensive biomedical resource of curated protein, genetic and chemical interactions

(2020) Rose Oughtred et al.   PROTEIN SCIENCE

The diverse roles of RIP kinases in host-pathogen interactions

(2020) Vik Ven Eng et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Machine learning techniques for sequence-based prediction of viral–host interactions between SARS-CoV-2 and human proteins

(2020) Lopamudra Dey et al.   Biomedical Journal

Introduction to host microbiome symbiosis in health and disease

(2020) Florent Malard et al.   Mucosal Immunology

HVIDB: a comprehensive database for human–virus protein–protein interactions

(2020) Xiaodi Yang et al.   BRIEFINGS IN BIOINFORMATICS

Gut microbiome and its role in obesity and insulin resistance

(2019) Clare J. Lee et al.   Annals of the New York Academy of Sciences

Machine-Learning-Based Predictor of Human–Bacteria Protein–Protein Interactions by Incorporating Comprehensive Host-Network Properties

(2019) Xianyi Lian et al.   JOURNAL OF PROTEOME RESEARCH

Multifaceted protein–protein interaction prediction based on Siamese residual RCNN

(2019) Muhao Chen et al.   BIOINFORMATICS

MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks

(2019) Chieh Lo et al.   BMC BIOINFORMATICS

Predicting Drug–Target Interaction Using a Novel Graph Neural Network with 3D Structure-Embedded Graph Representation

(2019) Jaechang Lim et al.   Journal of Chemical Information and Modeling

Dynamic Graph CNN for Learning on Point Clouds

(2019) Yue Wang et al.   ACM TRANSACTIONS ON GRAPHICS

Protein Docking Model Evaluation by 3D Deep Convolutional Neural Networks

(2019) Xiao Wang et al.   BIOINFORMATICS

Oncoviruses Can Drive Cancer by Rewiring Signaling Pathways Through Interface Mimicry

(2019) Emine Guven-Maiorov et al.   Frontiers in Oncology

Performance of rotation forest ensemble classifier and feature extractor in predicting protein interactions using amino acid sequences

(2019) Alhadi Bustamam et al.   BMC GENOMICS

Interplay between host and pathogen: immune defense and beyond

(2019) Eun-Kyeong Jo   EXPERIMENTAL AND MOLECULAR MEDICINE

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

(2019) P. Gainza et al.   NATURE METHODS

BIPSPI: a method for the prediction of Partner-Specific Protein-Protein Interfaces

(2018) Ruben Sanchez-Garcia et al.   BIOINFORMATICS

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions

(2018) Takanori Hayashi et al.   BMC BIOINFORMATICS

Interactome INSIDER: a structural interactome browser for genomic studies

(2018) Michael J Meyer et al.   NATURE METHODS

Gut microbiota associations with common diseases and prescription medications in a population-based cohort

(2018) Matthew A. Jackson et al.   Nature Communications

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

Using Two-dimensional Principal Component Analysis and Rotation Forest for Prediction of Protein-Protein Interactions

(2018) Lei Wang et al.   Scientific Reports

The gut microbiome: Relationships with disease and opportunities for therapy

(2018) Juliana Durack et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Geometric Deep Learning: Going beyond Euclidean data

(2017) Michael M. Bronstein et al.   IEEE SIGNAL PROCESSING MAGAZINE

Prediction of Host–Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer

(2017) Emine Guven-Maiorov et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural host-microbiota interaction networks

(2017) Emine Guven-Maiorov et al.   PLoS Computational Biology

Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins

(2017) Farideh Halakou et al.   Scientific Reports

Pathogen mimicry of host protein-protein interfaces modulates immunity

(2016) Emine Guven-Maiorov et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences

(2015) Nan Xiao et al.   BIOINFORMATICS

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

(2015) Thom Vreven et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational approaches for prediction of pathogen-host protein-protein interactions

(2015) Esmaeil Nourani et al.   Frontiers in Microbiology

The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets

(2015) Takaya Saito et al.   PLoS One

Improving B-cell epitope prediction and its application to global antibody-antigen docking

(2014) Konrad Krawczyk et al.   BIOINFORMATICS

A review ofin silicoapproaches for analysis and prediction of HIV-1-human protein–protein interactions

(2014) Sanghamitra Bandyopadhyay et al.   BRIEFINGS IN BIOINFORMATICS

VirusMentha: a new resource for virus-host protein interactions

(2014) Alberto Calderone et al.   NUCLEIC ACIDS RESEARCH

PRISM: a web server and repository for prediction of protein–protein interactions and modeling their 3D complexes

(2014) Alper Baspinar et al.   NUCLEIC ACIDS RESEARCH

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data

(2014) Thibaut Guirimand et al.   NUCLEIC ACIDS RESEARCH

Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions

(2014) Engin Cukuroglu et al.   PLoS One

The Human Microbiome: From Symbiosis to Pathogenesis

(2013) Emiley A. Eloe-Fadrosh et al.   Annual Review of Medicine

PHISTO: pathogen–host interaction search tool

(2013) Saliha Durmuş Tekir et al.   BIOINFORMATICS

INstruct: a database of high-quality 3D structurally resolved protein interactome networks

(2013) Michael J. Meyer et al.   BIOINFORMATICS

Exploiting Conformational Ensembles in Modeling Protein–Protein Interactions on the Proteome Scale

(2013) Guray Kuzu et al.   JOURNAL OF PROTEOME RESEARCH

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

SAbDab: the structural antibody database

(2013) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

PAIRpred: Partner-specific prediction of interacting residues from sequence and structure

(2013) Fayyaz ul Amir Afsar Minhas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Human Microbiome: Our Second Genome

(2012) Elizabeth A. Grice et al.   Annual Review of Genomics and Human Genetics

Computational analysis of interactomes: Current and future perspectives for bioinformatics approaches to model the host–pathogen interaction space

(2012) Roland Arnold et al.   METHODS

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

HCVpro: Hepatitis C virus protein interaction database

(2011) Samuel K. Kwofie et al.   INFECTION GENETICS AND EVOLUTION

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM

(2011) Nurcan Tuncbag et al.   Nature Protocols

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

Structural principles within the human-virus protein-protein interaction network

(2011) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH