Author ORCID Identifier
https://orcid.org/0009-0000-2034-8336
Date of Award
8-31-2026
Document Type
Open Access Thesis
Degree Name
Master of Biological Science (MBioSci)
Department
Biology
First Advisor
Shailja Pathania
Second Advisor
Augustin Luna
Third Advisor
Alexey Veraksa
Abstract
Cancer cell lines are essential resources for connecting genomic and molecular features with drug response and identifying biomarkers. Therefore, large-scale cancer cell line resources have been growing, but this introduces challenges such as data standardization, consistent annotation, matching identifiers, cross-database integration, and a reproducible computational framework. CellMiner Cross Database (CellMinerCDB) integrates pharmacogenomic datasets from multiple resources and provides a standardized analysis of cell lines across datasets. This thesis examines cancer cell line cross-databases and their importance in pharmacogenomics, with a particular focus on CellMinerCDB. As part of this work, I developed an R package for the gCSI (Genentech Cell Line Screening Initiative) dataset using the rcellminer reusable framework and integrated it into CellMinerCDB. This project standardized and organized gCSI mRNA expression and drug activity data in a structure compatible with CellMinerCDB. I also contributed to cross-referencing between CellMinerCDB and external resources to improve the tool's consistency. Together, this work contributed to CellMinerCDB with new dataset integration and data standardization, which aim to increase the accessibility of large-scale pharmacogenomic data for biomarker discovery, drug response analysis, and cancer research.
Recommended Citation
Kinali, Meric, "Data Curation and Integration for Cancer Cell Line Pharmacogenomics Analysis" (2026). Graduate Masters Theses. 971.
https://scholarworks.umb.edu/masters_theses/971
Included in
Bioinformatics Commons, Biotechnology Commons, Cancer Biology Commons, Computational Biology Commons, Integrative Biology Commons, Molecular Genetics Commons, Pharmacology Commons
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