iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease

Ziheng Duan; Yi Dai; Ahyeon Hwang; Cheyu Lee; Kaichi Xie; Chutong Xiao; Min Xu; Matthew J. Girgenti; Jing Zhang

doi:10.1371/journal.pcbi.1011444

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Open Access

Peer-reviewed

Research Article

iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease

Ziheng Duan,

Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

Affiliation Department of Computer Science, University of California, Irvine, California, United States of America
⨯
Yi Dai,

Roles Data curation

Affiliation Department of Computer Science, University of California, Irvine, California, United States of America
⨯
Ahyeon Hwang,

Roles Data curation, Validation

Affiliation Department of Computer Science, University of California, Irvine, California, United States of America

https://orcid.org/0000-0002-4686-3077

⨯
Cheyu Lee,

Roles Writing – review & editing

Affiliation Department of Computer Science, University of California, Irvine, California, United States of America
⨯
Kaichi Xie,

Roles Methodology, Software

Affiliation Department of Computer Science, University of California, Davis, California, United States of America
⨯
Chutong Xiao,

Roles Methodology, Software

Affiliation Department of Computer Science, University of California, Irvine, California, United States of America
⨯
Min Xu,

Roles Supervision

Affiliation Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
⨯
Matthew J. Girgenti ,

Roles Supervision

* E-mail: matthew.girgenti@yale.edu (MJG); zhang.jing@uci.edu (JZ)

Affiliations Department of Psychiatry, School of Medicine, Yale University, New Haven, Connecticut, United States of America, Clinical Neurosciences Division, National Center for PTSD, U.S. Department of Veterans Affairs, West Haven, Connecticut, United States of America
⨯
Jing Zhang

Roles Funding acquisition, Investigation, Project administration, Resources, Supervision, Writing – original draft, Writing – review & editing

* E-mail: matthew.girgenti@yale.edu (MJG); zhang.jing@uci.edu (JZ)

Affiliation Department of Computer Science, University of California, Irvine, California, United States of America

https://orcid.org/0000-0002-5970-0509

⨯

iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease

Ziheng Duan,
Yi Dai,
Ahyeon Hwang,
Cheyu Lee,
Kaichi Xie,
Chutong Xiao,
Min Xu,
Matthew J. Girgenti,
Jing Zhang

Published: September 11, 2023
https://doi.org/10.1371/journal.pcbi.1011444

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