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Robust, Fair and Accessible: Algorithms for Enhancing Proteomics and Under-Studied Proteins in Network Biology

Yilmaz, Serhan
http://orcid.org/0000-0003-4669-9593
http://rave.ohiolink.edu/etdc/view?acc_num=case1688578767297045

Abstract Details

2023, Doctor of Philosophy, Case Western Reserve University, EECS - Computer and Information Sciences.
This dissertation presents a comprehensive approach to advancing proteomics and under-studied proteins in network biology, emphasizing the development of reliable algorithms, fair evaluation practices, and accessible computational tools. A key contribution of this work is the introduction of RoKAI, a novel algorithm that integrates multiple sources of functional information to infer kinase activity. By capturing coordinated changes in signaling pathways, RoKAI significantly improves kinase activity inference, facilitating the identification of dysregulated kinases in diseases. This enables deeper insights into cellular signaling networks, supporting targeted therapy development and expanding our understanding of disease mechanisms. To ensure fairness in algorithm evaluation, this research carefully examines potential biases arising from the under-representation of under-studied proteins and proposes strategies to mitigate these biases, promoting a more comprehensive evaluation and encouraging the discovery of novel findings. Additionally, this dissertation focuses on enhancing accessibility by developing user-friendly computational tools. The RoKAI web application provides a convenient and intuitive interface to perform RoKAI analysis. Moreover, RokaiXplorer web tool simplifies proteomic and phospho-proteomic data analysis for researchers without specialized expertise. It enables tasks such as normalization, statistical testing, pathway enrichment, provides interactive visualizations, while also offering researchers the ability to deploy their own data browsers, promoting the sharing of findings and fostering collaborations. Overall, this interdisciplinary research contributes to proteomics and network biology by providing robust algorithms, fair evaluation practices, and accessible tools. It lays the foundation for further advancements in the field, bringing us closer to uncovering new biomarkers and potential therapeutic targets in diseases like cancer, Alzheimer's, and Parkinson's.
Mehmet Koyutürk (Committee Chair)
Mark Chance (Committee Member)
Vincenzo Liberatore (Committee Member)
Kevin Xu (Committee Member)
Michael Lewicki (Committee Member)
156 p.
Bioinformatics; Biomedical Research; Computer Science
Computational models; Phospho-proteomics; Phosphorylation; Cellular signaling networks; Network propagation; Systems biology; Data mining; Web application; Online tool; Kinase activity inference; Graph algorithms; Fair Evaluation; Bias-awareness; Machine Learning; Link prediction; Network biology; Biomedical networks; RokaiXplorer; RoKAI; CoLiPE

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Citations

  • Yilmaz, S. (2023). Robust, Fair and Accessible: Algorithms for Enhancing Proteomics and Under-Studied Proteins in Network Biology [Doctoral dissertation, Case Western Reserve University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=case1688578767297045

    APA Style (7th edition)

  • Yilmaz, Serhan. Robust, Fair and Accessible: Algorithms for Enhancing Proteomics and Under-Studied Proteins in Network Biology. 2023. Case Western Reserve University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=case1688578767297045.

    MLA Style (8th edition)

  • Yilmaz, Serhan. "Robust, Fair and Accessible: Algorithms for Enhancing Proteomics and Under-Studied Proteins in Network Biology." Doctoral dissertation, Case Western Reserve University, 2023. http://rave.ohiolink.edu/etdc/view?acc_num=case1688578767297045

    Chicago Manual of Style (17th edition)

case1688578767297045
64
© 2023, all rights reserved.
This open access ETD is published by Case Western Reserve University School of Graduate Studies and OhioLINK.