Fatemeh Sharifi

Computer Science, Bioinformatics, Metagenomics

Indiana University Bloomington

About me

I'm a Computer Science Ph.D. candidate at Indiana University, and a Research Assistant working on Metagenomics projects in Prof. Yuzhen Ye's lab. I have been working with a lot of bioinformatics datasets and tools since 2012. Not only bioinformatics, I’m also interested in Data Science and Machine Learning. In Summer 2019, I got the opportunity to do a Bioinformatics/Genomics internship at Boston Children's hospital. I enjoy working with Python, R, Perl, MySQL, AWK, bash script, bioinformatics tools, PHP, and Linux servers.

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.



Indiana University

Research Assistant (Jan 2016- present)

Developing pipelines for microbiome studies.

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Boston Children's Hospital

Bioinformatics/Genomics Student Co-op (May 2019- Aug 2019)

Developed a comprehensive pipeline for genomic analysis. Built a dashboard for real-time analysis of aggregated patient data. Upgraded several genomics analysis tools.


Indiana University

Associate Instructor (Auguest 2015- Dec 2015)

I519: Introduction to Bioinformatics

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Fatemeh Sharifi, and Yuzhen Ye. Identification and Classification of Reverse Transcriptases in Bacterial Genomes and Metagenomes, bioRxiv, 2021. (Link)

Fatemeh Sharifi, and Yuzhen Ye. MyDGR: a server for identification and characterization of diversity-generating retroelements, Nucleic Acids Research, 2019. (Link)

Fatemeh Sharifi, and Yuzhen Ye. From gene annotation to function prediction for metagenomics. Protein Function Prediction. Humana Press, New York, NY, 2017. (Link)

Samad Jahandideh,Fatemeh Sharifi, Lukasz Jaroszewski, and Adam Godzik. PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB. Source code for biology and medicine, 2015. ( Link)

Soheila Shokrollahzade, Fatemeh Sharifi, Akbar Vaseghi, Maryam Faridounnia, and Samad Jahandideh. Protein cold adaptation: Role of physico-chemical parameters in adaptation of proteins to low temperatures. Journal of theoretical biology, 2015. ( Link)

Programming Skills

Python, R, Bash script, Bioinformatics tools, AWK, PHP, MATLAB, MySQL, LaTeX, Linux servers, and UNIX command lines