Fatemeh Sharifi
Computer Science, Bioinformatics, MetagenomicsIndiana University Bloomington
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.
MyRT: Identification and Classification of ReverseTranscriptases in Bacterial Genomes and Metagenomes
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.
Developing pipelines for microbiome studies.
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Developed a comprehensive pipeline for genomic analysis. Built a dashboard for real-time analysis of aggregated patient data. Upgraded several genomics analysis tools.
I519: Introduction to Bioinformatics
Read moreFatemeh 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)
