Quayle Lab

Quayle Lab

Cancer Bioinformatics Research

Ronak Naeemaee


About Me

Hello! I’m Ronak Naeemaee, a dedicated biomedical researcher with extensive experience in biomarker discovery and translational research. My expertise lies in molecular biology, genetics, and bioinformatics. Currently, I am pursuing a PhD in Advanced Survival Analysis Tools for Cancer Biomarker Validation with a focus on developing innovative methods to enhance precision medicine in oncology. I have a strong academic and research background, aiming to contribute to personalized cancer treatment strategies through rigorous analysis and novel tool development.

Professional Experience

PhD Candidate | Sheffield Hallam University

September 2023 – Present

  • Engaged in a PhD project titled “Unlocking Precision Medicine: Advanced Survival Analysis Tools for Cancer Biomarker Validation” under the supervision of Dr. Lewis Quayle, Dr. Keith Harris, and Dr. Neil Cross.
  • Focused on developing a novel multivariate proportional hazards-based method to assess biomarker-survival relationships, integrating clinical variables for enhanced predictive accuracy in cancer research.
  • Aiming to produce an innovative R package and web portal for biomarker validation to make sophisticated analysis techniques accessible to researchers and clinicians, thereby contributing to more personalized and effective cancer treatment strategies.

Research Assistant | Cancer Institute, Hacettepe University

March 2020 – January 2024

  • Conducted research on identifying robust prognostic biomarkers for Proximal Colorectal cancer patients.
  • Designed, planned, conducted, and optimized various methodologies under the supervision of Assist. Prof. Secil Demirkol CANLI.
  • Successfully implemented survival analysis to identify significant biomarkers for colorectal cancer.

Graduate Student Research Assistant | Bilkent University - Dept. of Molecular Biology and Genetics

September 2020 – September 2023

  • Initiated and successfully completed a Master’s thesis project under the supervision of Prof. Dr. Ali Osmay Gure.
  • Explored the intersection of the nervous system in cancer development and progression.
  • Contributed to the understanding of biomedical sciences through rigorous research, analysis, and application of molecular biology techniques.

Teaching Assistant | Bilkent University - Dept. of Molecular Biology and Genetics

September 2020 – September 2023

  • Instructed the theoretical and practical aspects of the laboratory sessions for the course Biology I (MBG101).
  • Planned and coordinated lessons and laboratory sessions, facilitating a supportive learning environment for undergraduate students.

Research Assistant | Bilkent University - Dept. of Molecular Biology and Genetics

March 2022 – August 2022

  • Managed the bioinformatics phase of a project in collaboration with a research group in Iran, funded by The Scientific and Technological Research Institution of Turkey (TUBITAK).
  • Applied bioinformatics tools to analyze complex biological data.

Education

PhD in Cancer Bioinformatics

Sheffield Hallam University, 2023 – Present

  • Research Project: Unlocking Precision Medicine: Advanced Survival Analysis Tools for Cancer Biomarker Validation
  • Developing innovative survival analysis methods to assess biomarker-survival relationships, integrating clinical and demographic variables.

Master of Science in Molecular Biology and Genetics

Bilkent University, 2020 – 2023

  • Specialized in Biomedical Sciences
  • Thesis: Focused on prognostic and predictive biomarkers for colorectal cancer.

Bachelor of Science in Biomedical Sciences

Information not provided in the document. (If you have a Bachelor’s, please insert the relevant details here)

Skills

  • Research Techniques: Molecular Biology, Genetics, Biomarker Discovery, Survival Analysis
  • Bioinformatics: Data analysis pipelines, Statistical Analysis, Survival Regression, R Programming
  • Programming & Software Development: R, Python (for bioinformatics and statistical analysis), SPSS, Shiny (web application development)
  • Project Management: Research Planning, Data Collection, Team Collaboration, Software Development
  • Communication & Teaching: Experience in teaching, mentoring, and presenting complex scientific concepts to a variety of audiences.

Projects

1. PhD Project: Advanced Survival Analysis Tools for Cancer Biomarker Validation

  • Developing a novel multivariate proportional hazards method to improve the validation of cancer biomarkers using open-access datasets.
  • Aiming to create an R package and web application for comprehensive biomarker analysis, enabling researchers and clinicians to perform survival analysis without programming expertise.
  • Conducting extensive data analysis on the “big four” cancers (breast, prostate, lung, and colorectal) to enhance predictive accuracy through integration of clinical covariates.

2. Biomarker Discovery in Colorectal Cancer

Conducted a comprehensive study to identify robust prognostic biomarkers for colorectal cancer, resulting in the identification of significant genes through survival analysis techniques. The findings contributed to enhancing personalized treatment strategies in cancer therapy.

3. Nervous System Involvement in Cancer Progression

Explored the intersection between the nervous system and cancer development during my Master’s thesis project, which expanded the understanding of cancer progression at a molecular level.

4. Bioinformatics Analysis for Collaborative Project

Led the bioinformatics phase of a collaborative project funded by TUBITAK, applying data analysis methods to investigate complex biological datasets.

Currently Learning

  • Advanced survival analysis methods for cancer biomarker validation.
  • Statistical tools and methodologies to improve multivariate analysis in clinical oncology data.
  • Developing an R package and web application to make biomarker validation more accessible to the broader research community.

Achievements

  • Successfully initiated and progressed a comprehensive PhD project that targets critical gaps in cancer biomarker validation, with the potential to significantly influence personalized medicine strategies.
  • Demonstrated proficiency in biomarker discovery and survival analysis across multiple research projects, including colorectal cancer and nervous system involvement in cancer progression.
  • Developed a robust Cox regression-based methodology pipeline as part of my Master’s research, demonstrating my ability to contribute to the field of cancer bioinformatics.

Let’s Connect