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Resume / CV

Ziynet Nesibe Kesimoglu – Research Assistant and PhD student at Department of Computer Science and Engineering at University of North Texas. Interested in computational biology, data science, machine learning/deep learning. Skilled in programming especially in R, python, Java, and C. Passionate about research with strong combination of programming skills, statistics, and mathematics. Now, improving computational tools integrating high-throughput biological datasets (Multiomics Integration), inferring gene regulatory networks, and mainly leveraging graph representation learning, machine learning/deep learning, mathematics, and statistics to solve open problems and to decipher underlying biological mechanisms in complex diseases, especially in cancer.

Google Scholar: here 

Linkedin: https://www.linkedin.com/in/ziynetnesibe

Orcid: https://orcid.org/0000-0001-8592-4365

Twitter: https://twitter.com/ziynet_

Work Experience

  • Aug 2017-Present (US): Research Assistant at Bozdag lab (Marquette University and University of North Texas consecutively) developing computational tools integrating multiple types of high-dimensional biological datasets to solve open problems in bioinformatics with novel approaches and using skills in programming, machine learning/deep learning (especially graph representation learning and geometric deep learning), statistics, parallel processing, data mining, and mathematics.
  • Feb 2013-Jul 2016 (Turkey): Researcher in Cryptology department of TUBITAK (agency for the management, funding, and conduct of research in Turkey) and designed the cryptographic protocol and architecture for projects by providing the encryption and integrity services and analyzing them against possible risks and vulnerabilities. 

Education

  • PhD in Computer Science: 2017-Present – University of North Texas – (transferred from Marquette University along with supervisor)
  • PhD in Computer Science and Engineering (Not completed): 2014–2017 Sabanci University
  • MS in Computer Engineering: 2012-2014 Fatih University Computer Engineering

Thesis title: “Securing Paper Based Exam Evaluation on the Cloud”

  • BS in Math (Double Major): 2010-2013 Fatih University Mathematics
  • BS in Computer Engineering: 2008-2012 Fatih University Computer Engineering

Interests

  • Machine Learning/Deep Learning
  • Data Science, Data Preprocessing, Data Analysis, Data Evaluation including relevant Statistics and Mathematics
  • Graph Representation Learning, Graph Neural Networks, Graph Convolutional Neural Networks, Graph Attention Networks
  • Multiomics (multiple high dimensional datatypes) integration
  • Computational Biology, Bioinformatics
  • Natural Language Processing
  • Cryptology, Cryptographic Protocols, Public Key Cryptography, Data Confidentiality, Data Integration

Publication & Presentation

  • SUPREME: a cancer subtype prediction methodology integrating multiple biological datatypes using graph convolutional neural networks – Ziynet Nesibe Kesimoglu & Serdar Bozdag
    • Paper @ Preprint version on BioRxiv (Paper link)
    • Talk @ OxML (Oxford Machine Learning) Summer School 2022 – Unconference Track
    • Talk and Poster Presentation @ 2022 ISMB (Intelligent Systems for Molecular Biology) – MLCSB COSI
    • Invited Talk @ BH-BINGEN Technical University in Germany – Bits & Chips Seminar Series
    • Talk @ 2021 ACM-BCB (ACM Conference on Bioinformatics, Computational Biology, and Health Informatics)
    • Poster Presentation @ 2017 Forward Thinking Poster Session/Colloquy
  • The Impact of Pre-Operative Healthcare Utilization on Complications, Readmissions, and Post-Operative Healthcare Utilization Following Total Joint Arthroplasty? – Collaboration with physicians from Medical College of Wisconsin
  • Do in-hospital Rothman Index scores predict postdischarge adverse events and discharge location after total knee arthroplasty? –Collaboration with physicians from Medical College of Wisconsin
    • Paper @ 2021 The Journal of Arthroplasty (Paper link)
  • CRINET: Inferring competing endogenous RNA (ceRNA) interactions in cancer – Ziynet Nesibe Kesimoglu & Serdar Bozdag
    • Paper @ 2021 PLOS ONE (Paper link)
    • Talk and Poster Presentation @ 2020 ISMB (Intelligent Systems for Molecular Biology) – iRNA COSI
    • Poster Presentation @ 2019 RSGDREAM (RECOMB/ISCB Conference on Regulatory and Systems Genomics with DREAM)
    • Poster Presentation @ 2019 A Celebration of Research – Marquette University Arts and Science Poster Session
    • Poster Presentation @ 2019 GLBIO (The Great Lakes Bioinformatics)
    • Poster Presentation @ 2018 Forward Thinking Poster Session/Colloquy
  • Deep Integration of genotypic features in cancer for phenotype prediction – Ziynet Nesibe Kesimoglu
    • Poster Presentation @ 2019 Forward Thinking Poster Session/Colloquy
  • Secure Database in Cloud Computing – CryptDB revisited -Ziynet Nesibe Dayioglu (Kesimoglu), Mehmet Sabir Kiraz, Fatih Birinci, and Ihsan Haluk Akin
    • Paper @ 2014 IJISS (International Journal of Information Security Science)
      • Z.N. Dayioglu, M.S. Kiraz, F. Birinci, I.H. Akin. “Secure Database in Cloud Computing – CryptDB revisited.” International Journal of Information Security Science 3.1 (2014): 129-147.
    • Paper @ 2013 ISC Turkey (The 6th International Conference on Information Security and Cryptology)
      • Z.N. Dayioglu, M.S. Kiraz, F. Birinci, I.H. Akin. ”Secure Database in Cloud Computing: CryptDB Revisited”, In Proceedings of the 6th International Conference on Information Security and Cryptology, ISCTurkey 2013, Ankara, Turkey, pp. 94-104, 20-21 September 2013. ISBN:978-605-86904-1-7.

Honors & Awards

  • 2022 Grace Hopper Celebration of Women in Computing – in Person: a distinguished award limited to 8 of 1500+ students of the University of North Texas
  • 2022 Oxford Machine Learning (OxML) 2022 Summer School Attendance
  • 2022 BioDiscovery Institute (BDI) Summer Research Assistantship Funding
  • 2021 and 2020 Grace Hopper Celebration of Women in Computing: a distinguished award limited to only 20/30 of 1500+ students of the University of North Texas
  • 2020, 2019, and 2018 CSSRFP (Computational Sciences Summer Research Fellows Program) Summer Research Fundings
  • 2019 NMDSI (Northwestern Mutual Data Science Institute) Summer Research Award
  • Best Poster Award at 2018 Forward Thinking Poster Session/Colloquy
  • TUBITAK Scholarship for Undergraduate Students to Support Graduate Education
  • OSYM High-Performance Scholarship (top-ranking (270th in quantitative section) at the national university entrance exam of Turkey among 1.5M participants) 

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