To Embed or Not: Network Embedding as a Paradigm in Computational Biology

The latent geometry of the human protein interaction network

(2018) Gregorio Alanis-Lobato et al.   BIOINFORMATICS

deepNF: deep network fusion for protein function prediction

(2018) Vladimir Gligorijević et al.   BIOINFORMATICS

Modeling polypharmacy side effects with graph convolutional networks

(2018) Marinka Zitnik et al.   BIOINFORMATICS

Identification of drug-target interaction by a random walk with restart method on an interactome network

(2018) Ingoo Lee et al.   BMC BIOINFORMATICS

Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches

(2018) Gamal Crichton et al.   BMC BIOINFORMATICS

A Comprehensive Survey of Graph Embedding: Problems, Techniques and Applications

(2018) HongYun Cai et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Network structure from rich but noisy data

(2018) M. E. J. Newman   Nature Physics

Deep learning improves prediction of drug–drug and drug–food interactions

(2018) Jae Yong Ryu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

(2018) Rafael Gómez-Bombarelli et al.   ACS Central Science

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

Learning network representations

(2017) Luis G. Moyano   European Physical Journal-Special Topics

Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction

(2017) Connor W. Coley et al.   Journal of Chemical Information and Modeling

Deep-Learning-Based Drug–Target Interaction Prediction

(2017) Ming Wen et al.   JOURNAL OF PROTEOME RESEARCH

Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions

(2017) Kyuho Han et al.   NATURE BIOTECHNOLOGY

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

Opportunities and challenges in phenotypic drug discovery: an industry perspective

(2017) John G. Moffat et al.   NATURE REVIEWS DRUG DISCOVERY

A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

(2017) Yunan Luo et al.   Nature Communications

Machine learning meets complex networks via coalescent embedding in the hyperbolic space

(2017) Alessandro Muscoloni et al.   Nature Communications

Vicus: Exploiting local structures to improve network-based analysis of biological data

(2017) Bo Wang et al.   PLoS Computational Biology

Predicting MicroRNA-Disease Associations Using Network Topological Similarity Based on DeepWalk

(2017) Guanghui Li et al.   IEEE Access

Low Data Drug Discovery with One-Shot Learning

(2017) Han Altae-Tran et al.   ACS Central Science

A probabilistic approach for collective similarity-based drug–drug interaction prediction

(2016) Dhanya Sridhar et al.   BIOINFORMATICS

Fifty years of graph matching, network alignment and network comparison

(2016) Frank Emmert-Streib et al.   INFORMATION SCIENCES

Molecular graph convolutions: moving beyond fingerprints

(2016) Steven Kearnes et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

In silico methods for drug repurposing and pharmacology

(2016) Rachel A. Hodos et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation

(2015) V. Vijayan et al.   BIOINFORMATICS

The rising tide of polypharmacy and drug-drug interactions: population database analysis 1995–2010

(2015) Bruce Guthrie et al.   BMC Medicine

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Network geometry inference using common neighbors

(2015) Fragkiskos Papadopoulos et al.   PHYSICAL REVIEW E

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

Drug target prioritization by perturbed gene expression and network information

(2015) Zerrin Isik et al.   Scientific Reports

Detection of gene communities in multi-networks reveals cancer drivers

(2015) Laura Cantini et al.   Scientific Reports

A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome

(2015) Susan Dina Ghiassian et al.   PLoS Computational Biology

MAGNA: Maximizing Accuracy in Global Network Alignment

(2014) Vikram Saraph et al.   BIOINFORMATICS

A comparison of algorithms for the pairwise alignment of biological networks

(2014) Connor Clark et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

SPINAL: scalable protein interaction network alignment

(2013) Ahmet E. Aladağ et al.   BIOINFORMATICS

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding

(2013) Carlo Vittorio Cannistraci et al.   BIOINFORMATICS

Predicting drug-target interactions using restricted Boltzmann machines

(2013) Yuhao Wang et al.   BIOINFORMATICS

Exploitation of genetic interaction network topology for the prediction of epistatic behavior

(2013) Gregorio Alanis-Lobato et al.   GENOMICS

Network deconvolution as a general method to distinguish direct dependencies in networks

(2013) Soheil Feizi et al.   NATURE BIOTECHNOLOGY

Going the Distance for Protein Function Prediction: A New Distance Metric for Protein Interaction Networks

(2013) Mengfei Cao et al.   PLoS One

Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization

(2012) M. Gonen   BIOINFORMATICS

A survey of two-dimensional graph layout techniques for information visualisation

(2012) Helen Gibson et al.   Information Visualization

Uncovering the hidden geometry behind metabolic networks

(2012) M. Ángeles Serrano et al.   Molecular BioSystems

Drug–target interaction prediction by random walk on the heterogeneous network

(2012) Xing Chen et al.   Molecular BioSystems

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Combining Drug and Gene Similarity Measures for Drug-Target Elucidation

(2011) Liat Perlman et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Harnessing synthetic lethal interactions in anticancer drug discovery

(2011) Denise A. Chan et al.   NATURE REVIEWS DRUG DISCOVERY

Multilevel Compression of Random Walks on Networks Reveals Hierarchical Organization in Large Integrated Systems

(2011) Martin Rosvall et al.   PLoS One

Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework

(2010) Y. Yamanishi et al.   BIOINFORMATICS

Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data

(2010) Z.-H. You et al.   BIOINFORMATICS

Manifold Learning in Protein Interactomes

(2010) Elisabetta Marras et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Spatial networks

(2010) Marc Barthélemy   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Network analyses in systems pharmacology

(2009) S. I. Berger et al.   BIOINFORMATICS

Community detection in graphs

(2009) Santo Fortunato   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Geometric De-noising of Protein-Protein Interaction Networks

(2009) Oleksii Kuchaiev et al.   PLoS Computational Biology

Fitting a geometric graph to a protein–protein interaction network

(2008) Desmond J. Higham et al.   BIOINFORMATICS

Increasing the reliability of protein interactomes

(2008) Hon Nian Chua et al.   DRUG DISCOVERY TODAY

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Global alignment of multiple protein interaction networks with application to functional orthology detection

(2008) R. Singh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA