Data Web Developer

Elnaz Mirzaei Mehrabad CV Jan-****

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Education

PhD in Computing, Data Management and Analysis Jan. 2018- Present University of Utah, U.S.

GPA: 3.94 (out of 4.0)

Selected Courses: Data Mining, Scientific Visualization, Data Science for Bioengineers, Computational Topology, Deep Learning, Clustering

Master of Science in Computer Science, Bioinformatics Sep. 2012-Sep. 2014 Shahid Beheshti University, Tehran, Iran

Thesis: “Predicting protein sub-cellular localization with personal recommendation based on bipartite networks” Selected Course: Combinatorial Algorithms in Bioinformatics, Theory of Graph Algorithms, Computational Geometry and Advance Mathematical Software

Bachelor of Science in Computer Science Sep. 2008-Jun. 2012 Kharazmi University, Tehran, Iran

Selected Courses: Discrete Mathematics, Probability and Statistics, Data Structure and Algorithms, Numerical Analysis, Numerical Linear Algebra, Artificial Intelligence and Neural Network Fields of Interest

Data Mining, Cancer Genomics, Data Visualization, Machine Learning, Recommender Systems Professional Experiences

Graduate Researcher at Spike Lab, in Huntsman Cancer Institute, under supervision Sep. 2017-Present of Prof. Benjamin Spike.

- Data Imputation, de-noising and Normalization on Single cell RNAseq data

- Single cell RNAseq pipeline (10X data, BAM files, Fastq files, RSEM, …)

- Seurat package

- Monocle

- Clustering (k-means, KNN, DBSCAN, HAC, …)

- Dimension Reduction (PCA, tSNE, UMAP)

- Matrix Factorization (SVD, NMF)

- Optimal Number of feature identification

- Velocity

- Cell Cycle Analysis

- Differentially expressed genes

- D3 and Plotly used for an online 3D interactive Visualization tool : https://uofuhealth.utah.edu/huntsman/labs/spike/d3.php

- Lung tissue data [Bulk and single cell data] Tumor vs. Control

-Breast Cancer Tissue data [single cell data] Developmental stages Graduate Researcher at the Bioinformatic research team at Institute for Research in Jan. 2014-Feb. 2017 Fundamental Sciences (IPM) under supervision of Prof. Changiz Eslahchi.

- Working with data bases such as Gene Ontology, UniProt and SwissProt

- Recommender Systems

Elnaz Mirzaei Mehrabad

Address: 236 University Village, Salt Lake City, UT, USA Birthday: 19 August 1990

Phone Number: 385-***-****

E-mail: *.*******.*@*****.***

GitHub: https://github.com/elnazmirzaei

Google Scholar: https://scholar.google.com/citations?user=QgluZSQAAAAJ&hl=en Elnaz Mirzaei Mehrabad CV Jan-2021

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- Improving sub-cellular location prediction using a graph-based recommender system called NBI

- C++ and C# used for the package generation

- Cross Validation

- Recall, Precision and F-measure analysis

Game Developer at Simulator Developer, Tehran, Iran Summer 2012 3D Modeling using 3D Max

Web Developer at Barad, Tehran, Iran Summer 2010

Designing and developing websites using HTML, CSS and JavaScript Computer Skills

Programming: R, Python, C/C++

Bioinformatic Datasets: GO, Geo, UniPort, STRING, TCGA, FireBrowse, HESc, EScells, Mefs Cloud Computing: Cancer Genomics Cloud Seven Bridges Web Application Development: D3, Plotly

Python Libraries: Numpy, Scipy, Pandas, Scikit-learn, Scikit-image, TensorFlow, Keras, Mapper, Matplotlib R Libraries: ggplot2, rgl, glmnet, tidyverse, devtools, roxygen2, dplyr, stringr, Seurat, reticulate, cowplot, MASS, fitdistrplus, mixtools, NMF, Monocle2, and, … Web Developing: JavaScript, HTML, CSS

Operating Systems: Windows, Linux

Other Softwares: SRA toolkit, Cytoscape, WinBUGS, Visual Studio, Microsoft Office, Notepad++, Adobe Photoshop

Teaching Experience

Teaching Mentorship (TM) for Data Mining course. Lecturer: Dr. Jeff Phillips Fall 2020 Teaching Mentorship (TM) for Algorithm course. Lecturer: Dr. Hari Sundar Spring 2019 Publications

1. Mehrabad, Elnaz Mirzaei, Reza Hassanzadeh, and Changiz Eslahchi. "PMLPR: A novel method for predicting subcellular localization based on recommender systems." Scientific reports 8, no. 1 (2018): 12006. 2. Giraddi RR, Chung CY, Heinz RE, Balcioglu O, Novotny M, Trejo CL, Dravis C, Hagos BM, Mehrabad EM, Rodewald LW, Hwang JY. Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development. Cell reports. 2018 Aug 7;24(6):1653-66.

3. Zewdu, Rediet, et al. "An NKX2-1/ERK/WNT feedback loop modulates gastric identity and response to targeted therapy in lung adenocarcinoma." bioRxiv (2020). 4. Balcioglu, Ozlen, et al. "CRIPTO antagonist ALK4 L75A-Fc inhibits breast cancer cell plasticity and adaptation to stress." Breast Cancer Research 22.1 (2020): 1-14. Presentations

1. Elnaz Mirzaei Mehrabad, University of Utah, Huntsman Cancer Institute, United States of America Title: “Recommender Systems for Gene Expression Recovery in scRNA-seq Data” PEARC 19, Chicago, US 2. Elnaz Mirzaei Mehrabad, University of Utah, Huntsman Cancer Institute, United States of America Title: “Matrix Factorization for Gene Expression Recovery in scRNA-seq Data” TAPIA 20,Virtual, US 3. Elnaz Mirzaei Mehrabad, University of Utah, Huntsman Cancer Institute, United States of America Title: “Matrix Factorization for zero inflation problem in scRNA-seq and sparse data sets in medical biology” GHC 20,Virtual, US

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