HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases

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HOODS : finding context-specific neighborhoods of proteins, chemicals and diseases. / Palleja, Albert; Jensen, Lars J.

In: PeerJ, Vol. 3, e1057, 2015, p. 1-10.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Palleja, A & Jensen, LJ 2015, 'HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases', PeerJ, vol. 3, e1057, pp. 1-10. https://doi.org/10.7717/peerj.1057

APA

Palleja, A., & Jensen, L. J. (2015). HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases. PeerJ, 3, 1-10. [e1057]. https://doi.org/10.7717/peerj.1057

Vancouver

Palleja A, Jensen LJ. HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases. PeerJ. 2015;3:1-10. e1057. https://doi.org/10.7717/peerj.1057

Author

Palleja, Albert ; Jensen, Lars J. / HOODS : finding context-specific neighborhoods of proteins, chemicals and diseases. In: PeerJ. 2015 ; Vol. 3. pp. 1-10.

Bibtex

@article{4a9c85f33530446a9c0d877f893c9c90,
title = "HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases",
abstract = "Clustering algorithms are often used to find groups relevant in a specific context; however, they are not informed about this context. We present a simple algorithm, HOODS, which identifies context-specific neighborhoods of entities from a similarity matrix and a list of entities specifying the context. We illustrate its applicability by finding disease-specific neighborhoods of functionally associated proteins, kinase-specific neighborhoods of structurally similar inhibitors, and physiological-system-specific neighborhoods of interconnected diseases. HOODS can be used via a simple interface at http://hoods.jensenlab.org, from where the source code can also be downloaded.",
author = "Albert Palleja and Jensen, {Lars J}",
year = "2015",
doi = "10.7717/peerj.1057",
language = "English",
volume = "3",
pages = "1--10",
journal = "PeerJ",
issn = "2167-8359",
publisher = "PeerJ",

}

RIS

TY - JOUR

T1 - HOODS

T2 - finding context-specific neighborhoods of proteins, chemicals and diseases

AU - Palleja, Albert

AU - Jensen, Lars J

PY - 2015

Y1 - 2015

N2 - Clustering algorithms are often used to find groups relevant in a specific context; however, they are not informed about this context. We present a simple algorithm, HOODS, which identifies context-specific neighborhoods of entities from a similarity matrix and a list of entities specifying the context. We illustrate its applicability by finding disease-specific neighborhoods of functionally associated proteins, kinase-specific neighborhoods of structurally similar inhibitors, and physiological-system-specific neighborhoods of interconnected diseases. HOODS can be used via a simple interface at http://hoods.jensenlab.org, from where the source code can also be downloaded.

AB - Clustering algorithms are often used to find groups relevant in a specific context; however, they are not informed about this context. We present a simple algorithm, HOODS, which identifies context-specific neighborhoods of entities from a similarity matrix and a list of entities specifying the context. We illustrate its applicability by finding disease-specific neighborhoods of functionally associated proteins, kinase-specific neighborhoods of structurally similar inhibitors, and physiological-system-specific neighborhoods of interconnected diseases. HOODS can be used via a simple interface at http://hoods.jensenlab.org, from where the source code can also be downloaded.

U2 - 10.7717/peerj.1057

DO - 10.7717/peerj.1057

M3 - Journal article

C2 - 26157625

VL - 3

SP - 1

EP - 10

JO - PeerJ

JF - PeerJ

SN - 2167-8359

M1 - e1057

ER -

ID: 150709290