Fatemeh Sharifi

Computer Science, Bioinformatics, Metagenomics

Indiana University Bloomington

Research and Projects



MyRT: Identification and Classification of ReverseTranscriptases in Bacterial Genomes and Metagenomes



MyDGR: A web-server for identification and characterization of diversity-generating retroelements.

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A package for functional annotation for metagenomes

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A MATLAB package for performance visualization and optimization of ranking classifiers.

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Protein cold adaptation

Role of physico-chemical parameters in adaptation of proteins to low temperatures

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The Application of Protein-Protein Interaction network in subcellular location prediction.

Research Projects

• Performed different analyses on RNA-Seq, NGS, and metagenomics datasets.

• Built a pipeline for identification and classification of reverse transcriptases in bacterial genomes and metagenomes (myRT)

• Created a web server for identification and characterization of DGR systems (myDGR).

• Constructed a pipeline for functional annotation of metagenomics datasets (Fun4me).

• Contributed in building a MATLAB package for facilitating ranking classification (PROPER).

• Analyzed and visualized protein-protein interaction networks and protein subcellular location using different methods and tools.

• Extracted different physio-chemical parameters of proteins, and performed statistical tests on the parameters.

• Developed a comprehensive pipeline for genomic analysis (Boston Children's Hospital).

• Built a dashboard for real-time analysis of aggregated patient data (Boston Children's Hospital).

• Upgraded several genomics analysis tools (Boston Children's Hospital).

Course Projects

Machine Learning: Kaggle: Prudential Life Insurance Assessment (Python)

Databases: Designing a Bank Database (SQL)

Machine Learning: Impact of Dimention Reduction on KNN Classifier (MATLAB)

Data Structures and Algorithms: Implementing Page Editor (C)

Numerical Analysis: Implementing Different Numerical Methods (Maple)

Principles of Software Design: Designing a Hospital Information System

Information Systems Developement Methodology: Data Mining With K-means (MATLAB)

Artificial Intelligence: Image Processing (C#)

Principles of Operating Systems: Implementing Time scheduling algorithms in MATLAB