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Open AccessJournal ArticleDOI

Human symptoms–disease network

TLDR
It is found that the symptom-based similarity of two diseases correlates strongly with the number of shared genetic associations and the extent to which their associated proteins interact.
Abstract
In the post-genomic era, the elucidation of the relationship between the molecular origins of diseases and their resulting phenotypes is a crucial task for medical research. Here, we use a large-scale biomedical literature database to construct a symptom-based human disease network and investigate the connection between clinical manifestations of diseases and their underlying molecular interactions. We find that the symptom-based similarity of two diseases correlates strongly with the number of shared genetic associations and the extent to which their associated proteins interact. Moreover, the diversity of the clinical manifestations of a disease can be related to the connectivity patterns of the underlying protein interaction network. The comprehensive, high-quality map of disease-symptom relations can further be used as a resource helping to address important questions in the field of systems medicine, for example, the identification of unexpected associations between diseases, disease etiology research or drug design.

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Journal Article

Interactome networks and human disease

TL;DR: Why interactome networks are important to consider in biology, how they can be mapped and integrated with each other, what global properties are starting to emerge from interactome network models, and how these properties may relate to human disease are detailed.
Journal ArticleDOI

Uncovering disease-disease relationships through the incomplete interactome

TL;DR: A network-based framework to identify the location of disease modules within the interactome and use the overlap between the modules to predict disease-disease relationships is presented and it is found that disease pairs with overlapping disease modules display significant molecular similarity, elevated coexpression of their associated genes, and similar symptoms and high comorbidity.
Journal ArticleDOI

Deep learning with word embeddings improves biomedical named entity recognition.

TL;DR: This work shows that a completely generic method based on deep learning and statistical word embeddings [called long short‐term memory network‐conditional random field (LSTM‐CRF)] outperforms state‐of‐the‐art entity‐specific NER tools, and often by a large margin.
Journal ArticleDOI

MicroRNAs and complex diseases: from experimental results to computational models.

TL;DR: Twenty state-of-the-art computational models of predicting miRNA-disease associations from different perspectives are reviewed, including five feasible and important research schemas, and future directions for further development of computational models are summarized.
Journal ArticleDOI

Transcription Factor NRF2 as a Therapeutic Target for Chronic Diseases: A Systems Medicine Approach

TL;DR: NRF2 represents one of the first targets fully embraced by classic and systems medicine approaches to facilitate both drug development and drug repurposing by focusing on a set of disease phenotypes that appear to be mechanistically linked.
References
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Journal ArticleDOI

Collective dynamics of small-world networks

TL;DR: Simple models of networks that can be tuned through this middle ground: regular networks ‘rewired’ to introduce increasing amounts of disorder are explored, finding that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs.
Book

Introduction to Algorithms

TL;DR: The updated new edition of the classic Introduction to Algorithms is intended primarily for use in undergraduate or graduate courses in algorithms or data structures and presents a rich variety of algorithms and covers them in considerable depth while making their design and analysis accessible to all levels of readers.
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Community structure in social and biological networks

TL;DR: This article proposes a method for detecting communities, built around the idea of using centrality indices to find community boundaries, and tests it on computer-generated and real-world graphs whose community structure is already known and finds that the method detects this known structure with high sensitivity and reliability.
Book

Networks: An Introduction

Mark Newman
TL;DR: This book brings together for the first time the most important breakthroughs in each of these fields and presents them in a coherent fashion, highlighting the strong interconnections between work in different areas.
Journal ArticleDOI

Database resources of the National Center for Biotechnology Information

TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
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