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Farid Rashidi |
I am a predoctoral fellow at the National Cancer Institute (NCI) working in Cancer Data Science Laboratory (CDSL) under supervision of Dr. Cenk Sahinalp. I am also a Ph.D. student studying Computer Science at the Indiana University Bloomington (IUB) since 2017. My main research focus is on Tumor Heterogeneity and Cancer Evolution using Single-cell sequencing data. I completed my Master’s thesis at the Sharif University of Technology where I worked on learning of Alternative Splicing problem, jointly supervised by Dr. Abolfazl Motahari and Dr. Hamid Rabiee. I received my Bachelor’s degree from Amirkabir University of Technology (Tehran Polytechnic) in Iran.
Publications
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Studying the history of tumor evolution from single-cell sequencing data by exploring the space of binary matrices bioRxiv Full text |
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PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem Bioinformatics ISMB 2020 Proceedings Full text Supplementary Code Presentation |
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PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data Genome Research Full text Supplementary Code Presentation |
Software
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PhISCS-BnB: a fast tool for reconstructing the perfect tumor phylogeny using single-cell data via branch and bound algorithm Code Publication Star Fork |
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PhISCS: a tool for sub-perfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data, with later being an optional Code Publication Star Fork |
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Kaggle Solutions: a searchable list of almost all available solutions and ideas shared by top performers in the past Kaggle competitions Webpage Code Star Fork |