CV

Education

• PhD in Computer Science and Engineering, Yildiz Technical University, 2017
• MS in Computer Science and Software Engineering, Qazvin Islamic Azad University, 2012
• BS in Computer Science and Software Engineering, Khoy Islamic Azad University, 2009

Work experience

• Postdoctoral Researcher, Department of Medical & Molecular Genetics, Indiana University School of Medicine, 2022–Present
• Assistant Professor, Istanbul Aydın University, Department of Software Engineering, 2018–2024

Skills

• Bioinformatics
• Machine Learning and Metaheuristic Algorithms
• Optimization Methods
• Programming: R, MATLAB, C, C++, Python

Publications

DiCE: differential centrality-ensemble analysis based on gene expression profiles and protein–protein interaction network

Elnaz Pashaei, Sheng Liu, Kailing Li, et al. (2025). "DiCE: differential centrality-ensemble analysis based on gene expression profiles and protein–protein interaction network." Nucleic Acids Research.

Binary Hiking Optimization for Gene Selection: Insights from HNSCC RNA-Seq Data

Pashaei, E., Pashaei, E., Mirjalili, S. (2025). "Binary Hiking Optimization for Gene Selection." Expert Systems with Applications.

Biomarker Identification for Alzheimer’s Disease Using a Multi-Filter Gene Selection Approach

Pashaei, E., Pashaei, E., Aydin, N. (2025). "Biomarker Identification for Alzheimer’s Disease Using a Multi-Filter Gene Selection Approach." IJMS.

CDHu40: a novel marker gene set of neuroendocrine prostate cancer

Liu, S., Nam, H.S., Zeng, Z., Deng, X., Pashaei, E., et al. (2024). "CDHu40: a novel marker gene set of neuroendocrine prostate cancer." Briefings in Bioinformatics.

Meta-analysis of miRNA Expression Profiles for Prostate Cancer Recurrence following Radical Prostatectomy

Elnaz Pashaei, Elham Pashaei, Maryam Ahmady, Mustafa Ozen, Nizamettin Aydin (2017). "Meta-analysis of miRNA Expression Profiles for Prostate Cancer Recurrence following Radical Prostatectomy." PLoS ONE.

Invited Talks

• 12th Edition of International Conference on Neurology and Brain Disorders, Orlando, FL, USA, Oct 20–22, 2025 (Invited)
• 5th Global Summit on Artificial Intelligence (5th GSAI 2025), Virtual Conference, Oct 09–10, 2025 (Invited)
• International Meet on Neuroscience and Brain Disorders (NEUROMEET2025), Chicago, USA, Dec 04–05, 2025 (Invited)
• 15th Annual World Congress of Neurotalk (NT), Stockholm, Sweden, June 18–20, 2025 (Invited)

Teaching

• SEN 437 – Machine Learning, Istanbul Aydın University
• SEN 426 – Bioinformatics Algorithms, Istanbul Aydın University
• MAT 317 – Probability and Statistics, Istanbul Aydın University
• EEE 244 – Computer Programming I (C Language), Istanbul Aydın University
• SEN 431 – Data Mining, Istanbul Aydın University
• SEN 263/232 – Database Management System (MS SQL/PLSQL), Istanbul Aydın University
• SEN 225 – Data Structures and Algorithms, Istanbul Aydın University
• SEN 424 – Genetic Algorithm, Istanbul Aydın University
• SEN 312 – Operation Research, Istanbul Aydın University
• SEN 521 – Optimization Methods, Istanbul Aydın University

Graduate Student Supervision

• Sayed Pedram Haeri Boroujeni, Master’s Thesis Supervisor, Istanbul Aydın University, Türkiye, 2021
  Thesis Title: “Data Clustering Using Swarm Intelligence”
• Niloufar Mehrabi, Master’s Thesis Supervisor, Istanbul Aydın University, Türkiye, 2021
  Thesis Title: “Feature Selection on Biological Data Using Swarm Intelligence Algorithm”

Service and leadership

• Editorial Board Member: PLOS One (2025)
• Editorial Review Board: Frontiers in Computational Neuroscience (2023)
• Guest Editor: Special Issue on Computational Neuroscience and Neural Networks (2024)
• Program Committee Member: CoSIT 2022, ITCCMA 2022, ICAETA 2021
• Reviewer for multiple scientific journals, including:
  • PLOS ONE
  • Frontiers in Computational Neuroscience
  • Artificial Intelligence in Medicine
  • Artificial Intelligence Review
  • BMC Bioinformatics
  • BMC Medical Informatics and Decision Making
  • Cancers
  • Computers in Biology and Medicine
  • Engineering Applications of Artificial Intelligence
  • Frontiers in Physiology
  • Genes
  • IEEE Access
  • IEEE Internet of Things Journal
  • IEEE Transactions on Cybernetics
  • IEEE Transactions on Evolutionary Computation
  • IEEE Transactions on Knowledge and Data Engineering
  • International Journal of Molecular Sciences
  • Journal of Cancer Research and Clinical Oncology
  • Journal of Medical Systems
  • Knowledge and Information Systems
  • Scientific Reports
  • Swarm and Evolutionary Computation
  • Statistical Methods in Medical Research