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Master’s Thesis Defense
Thesis Committee Members: Dr. Guanglan Zhang (Advisor), Dr. Lou Chitkushev (first reader) and Dr. Derin Keskin (second reader)
Monday, May 13th, 2024 10:00am EST 1010 Commonwealth Ave, Room 122
For those unable to attend in person, the thesis defense will be available through Zoom – http://www.bu.edu/metit/edu-technology/zoom-web-conferencing/
Select “Computer Science” from the drop down menu.
As MHC binding is considered the most selective step in T cell recognition, many existing bioinformatics systems focus on modeling this step to predict MHC binders. However, modeling MHC binding alone is insufficient for accurate immunogenicity predictions, often resulting in false positives. With the recent technological advancements, large amounts of mass spectrometry (MS)-identified MHC class I ligands became available to the public, making it possible to incorporate information from antigen processing steps before MHC binding. We collected >5,000 binding peptides and >4,000 eluted ligands for H2-Dᵇ, and>5,000 binding peptides and >5,000 eluted ligands for H2-Kᵇ. The thermostability assessment of MHC peptide binding evaluates the strength and duration of the interaction between the peptide and the MHC molecule under varying temperatures. Our collaborators at the Dana-Farber Cancer Institute performed temperature gradient experiments to investigate the stability of peptide-MHC complexes for H2-Dᵇ and H2-Kᵇ alleles under three temperature conditions, 37°C, 50°C, and 70°C, using the MS technique. We ended up with over 3,000 H2-Dᵇ binding peptides and over 5,000 H2-Kᵇ binding peptides. The data enable us to perform a comprehensive thermostability analysis of MHC binding.
In this thesis project, we developed a computational system for identifying T-cell epitopes in C57BL/6 mice by integrating relevant contributing factors, such as the antigen processing steps before MHC binding and thermostability, with the MHC binding predictions. Utilizing deep learning methods, we first trained and rigorously validated the binding prediction models using naturally eluted H2-Kᵇ and H2-Dᵇ ligands collected from public resources. Then, we built Thermostability models using proprietary data generated by our collaborators. We compared the performance of our models with that of NetMHCPan-4.1, an online prediction tool validated by many benchmark studies to be one of the most accurate predictors. Our integrated model, combining the binding and the Thermostability models, exhibited superior predictive capabilities using an external validation dataset, surpassing the overall performance of the NetMHCPan-4.1 model. We consolidated the models into a user-friendly web-based application named PREDBL6 to facilitate accurate predictions of immunogenic peptides that stably bind H2b molecules and stimulate immune responses in C57BL/6 mice. To our knowledge, this is the first online T cell epitope prediction system that simulates MHC binding and considers other antigen processing steps and thermostability in a model organism.
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To search for Australian and International theses: Click on Advanced Search, Books & Libraries. Select Thesis in the Format field, and tick the Australian content box. Enter your terms in the search box and click search. Trove contains all of the thesis records that were previously accessible via the now discontinued Australasian Digital Theses ...
Student thesis: Doctoral Thesis. File. A critical analysis of the sustainability performance in the retail food service outlet sector of South East Queensland. Author: Grigalius, S., 18 Jun 2018. ... Bond University Research Portal data protection policy. About web accessibility.
With a focus on niche areas of research excellence, Bond's research profile has grown rapidly over the last decade. Our research supports the needs of our local community and extends to benefit the national and international community more broadly. Our research portfolio supports a broad spectrum of Higher Degree Research student projects and ...
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Full draft. Final thesis. Approved on: Jun 23, 2023. Edition: 2.7. Last updated: Dec 15, 2023. Bond University - Australia's #1 university for student experience. Our accelerated bachelor''s and master's degrees allow you to graduate earlier.
This thesis is submitted to Bond University in fulfilment of the requirements of the degree of Doctor of Philosophy. This thesis represents my own original work towards this research degree and contains no material that has previously been submitted for a degree or a dip-loma at this University or any other institution, except where due acknow-
This thesis is submitted to Bond University in fulfilment of the requirements of the degree of Doctor of Philosophy. This thesis represents my own original work towards this research degree and contains no material that has previously been submitted for a degree or a diploma
Student thesis: Doctoral Thesis. File. Artificial Neural Networks: A Financial Tool As Applied in the Australian Market Author: Tan, C., 8 Feb 1997. Supervisor: Carmichael, J. (External person) (Supervisor) & Tsoi, A. C. (External person) (Supervisor) ... Bond University Research Portal data protection policy.
This thesis is submitted to Bond University in fulfilment of the requirements of the degree of Doctor of Philosophy. This thesis represents my own original work towards this research degree and contains no material that has been submitted for a degree or diploma at this
Bond University - Australia's #1 university for student experience. Our accelerated bachelor''s and master's degrees allow you to graduate earlier. ... research in the form of a poster and presentation at the 4th Year poster session and submit a copy of the completed thesis for examination. Subject details Type: Honours Subject: Code ...
Dissertations & Theses Full Text (ProQuest) can also be searched directly.The link to the database is also available from the Electronic Resources A-Z list.. Bond University theses are also indexed in Library Search, and they can be browsed as a list directly from the University's research portal. << Previous: Audiovisual & multimedia
Student thesis: Doctoral Thesis. File. Critical analysis of the law surrounding "one punch" killings Author: Burgess, C., 8 Oct 2016. Supervisor: Mackenzie, G. (Supervisor) & Levy, K. (Supervisor) ... Bond University Research Portal data protection policy. About web accessibility.
Bond University - Australia's #1 university for student experience. Our accelerated bachelor''s and master's degrees allow you to graduate earlier. ... The thesis poster session is on Friday of week 10. SLOs included. Understand, apply and evaluate basic research methods in psychology, including research design, data analysis and ...
A Collaboration Framework of Selecting Software Components Based on Behavioural Compatibility with User Requirements. Author: Wang, L., 3 Jun 2006 Supervisor: Krishnan, P. (Supervisor)
This thesis is submitted to Bond University in fulfilment of the requirements of the degree of Doctor of Philosophy by Research. I declare that the research presented within this thesis is a product of my own original ideas and work and contains no material which has previously been submitted for a degree
In the spirit of reconciliation, Bond University acknowledges the Kombumerri people, the traditional Owners and Custodians of the land on which the university now stands. We pay respect to Elders past, present and emerging.
Master's Thesis Defense. Zitian Zhen, a MET MSHI degree candidate defends his thesis entitled: "In Silico Prediction of C57BL/6 Mouse T-cell Epitopes: Enhancing Immunogenicity Assessment with PREDBL6" Thesis Committee Members: Dr. Guanglan Zhang (Advisor), Dr. Lou Chitkushev (first reader) and Dr. Derin Keskin (second reader) Monday, May ...
This thesis is submitted to Bond University in fulfilment of the requirements of the degree of Doctor of Philosophy. This thesis represents my own original work towards this research degree and contains no material that has previously been submitted for a degree or diploma at this University or any
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Bond University - Australia's #1 university for student experience. Our accelerated bachelor''s and master's degrees allow you to graduate earlier. ... Design Thesis Studio is the final studio project in the Masters sequence and represents a synthesis of comprehensive architectural understanding. This studio-based subject shall focus upon ...