Learning the Structural Vocabulary of a Network

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions

(2016) Jie Tan et al.   mSystems

MassExodus: modeling evolving networks in harsh environments

(2015) Saket Navlakha et al.   DATA MINING AND KNOWLEDGE DISCOVERY

Deep learning

(2015) Yann LeCun et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles

(2015) Minseung Kim et al.   PLoS Computational Biology

Topological properties of robust biological and computational networks

(2014) S. Navlakha et al.   Journal of the Royal Society Interface

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization

(2013) Jimin Song et al.   PLoS Computational Biology

Global network alignment using multiscale spectral signatures

(2012) R. Patro et al.   BIOINFORMATICS

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

(2012) Geoffrey Hinton et al.   IEEE SIGNAL PROCESSING MAGAZINE

Complex-valued autoencoders

(2012) Pierre Baldi et al.   NEURAL NETWORKS

Systemic risk in banking ecosystems

(2011) Andrew G. Haldane et al.   NATURE

Mitigation of malicious attacks on networks

(2011) C. M. Schneider et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network Archaeology: Uncovering Ancient Networks from Present-Day Interactions

(2011) Saket Navlakha et al.   PLoS Computational Biology

Catastrophic cascade of failures in interdependent networks

(2010) Sergey V. Buldyrev et al.   NATURE

Network medicine: a network-based approach to human disease

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

Trade-Offs Between Efficiency and Robustness in Bacterial Metabolic Networks Are Associated with Niche Breadth

(2009) Melissa J. Morine et al.   JOURNAL OF MOLECULAR EVOLUTION

The evolution of modularity in bacterial metabolic networks

(2008) A. Kreimer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality

(2008) Elena Zotenko et al.   PLoS Computational Biology