CV

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General Information

Full Name Mohammaderfan Farhadieh
Label Molecular Biologist and Bioinformatician
Email erfan.m.farhadieh99@gmail.com
Personal Website https://mefarhadieh.github.io
Languages English (fluent), Persian (native)
Summary A passionate biologist with a keen interest in multimodal data who is dedicated to solving complex challenges and advancing research through innovative approaches

Education

  • 2022
    M.S. in Cell and Molecular Biology
    University of Isfahan, Isfahan, Iran
    • GPA:19.08/20 (4/4)
    • First among 10
    • Thesis -> Identification of differential transcripts usage in the Alzheimer’s disease brain cells based on single cell RNA sequencing data
  • 2020
    B.S. in Animal Biology
    University of Isfahan, Isfahan, Iran
    • GPA:18.48/20 (3.95/4)
    • First among 30

Experience

  • Apr2023-Present
    Research Assistant
    Developmental Biology Lab, University of Isfahan, Iran
    • Analyzing single cell RNA-Seq profiles of dopaminergic neurons subpopulation during floor plate development to identify key lncRNAs controlling differentiation processes
    • Analyzing single cell RNA-Seq, RNA-Seq, ATAC-Seq, and DNA methylation data of Parkinson diseases
  • Apr2023-Present
    Research Assistant
    NeuroTRACT Association, University of Tehran Medical Science, Iran
    • Analyzing multi-module data of Alzheimer’s disease cohorts with machine learning approaches to identify potential biomarkers
      • Polygenic score based on SNPs
      • miRNA expression in CSF and Plasma
      • Proteins concentrations in CSF and Plasma
  • Sep2021-Jan2023
    Research Assistant / Graduate Student
    Molecular Biology Lab, University of Isfahan, Iran
    • Analyzed NGS data of post-mortem brain to detect alternative splicing and gene expression alterations in Alzheimer’s disease at the cell level
    • Designed an approach to reduce failed exon junctions calling in scRNA-seq data and memory consumption
  • Feb2019-Oct2019
    Research Assistant
    Cellular Neuroscience Lab, Shahid Beheshti University of Medical Science, Iran
    • Determined cell linage by flow cytometry, and conducted primary cell culture and RNA isolation to examine stem cell therapy effects on neurodegeneration
    • Rat handling, setting up lab equipment, and maintaining a safe lab environment
  • Sep2018-Feb2019
    Research Assistant
    Gastrointestinal Disorders Research Center, Shahid Beheshti University of Medical Science, Iran
    • Conducted RNA isolation and mammalian cell culture techniques including MTT, migration, and invasion assay to reveal miR-298 role in colon cancer
    • Setting up lab equipment, and maintaining a safe lab environment
  • Sep2018-Sep2020
    Chief Editor
    Jahesh scientific-specialized biology journal, University of Isfahan, Iran
    • Jahesh is a student journal that publishes only formal scientific review articles written by students in Persian
      • Ensure all articles meet the journal’s standards and guidelines
      • Assign submitted manuscripts to appropriate reviewers
      • Manage the layout and formatting of the journal
  • Summer 2018
    Summer Intern
    Royan Institute, Iran
    • Conducted mammalian cell culture techniques
    • Investigating the effect of mitogens on cell growth

Skills

  • Bioinformatics and Programming
    • Programming language (R, Python, Bash, shinyapps, jupyter notebook, HTML)
    • Frameworks (Git, Docker, High performance computing in the cloud, Google Colab)
    • Pipeline managements (NextFlow)
    • Alignment (STAR, HISAT2, Salmon, Kallisto, Cufflinks)
    • Splicing analysis (rMATS, maser, LeafCutter, SICILIAN, SpliZ, SpliceAI)
    • Single-cell RNA-Seq data analysis (Seurat, SingleCellExperiment, Scanpy, scvi-tools, Monocle, Palantir, SCENIC)
    • Spatial transcriptomics analysis (Squidpy, spaGCN)
    • DNA Methylation (Minfi, RnBeads, MethyAnalysis)
    • Variant calling and analysis ( GATK, SAMtools, picard, bcftools, VCFtools, Plink, ANNOVAR, IGV)
    • ATAC-Seq data analysis (MACS2, Signac)
    • Networks and pathway analysis (WGCNA, hdWGCNA, Cytoscape, clusterProfiler, ssGSEA, CellChat)
    • Machine learning and deap learning (Scikit-learn, TensorFlow)
  • Wet lab
    • Cell culture
    • RNA extraction
    • PCR
    • Flow cytometry
    • Western Blot
    • Animal model handling
  • Content creation
    • Adobe Photoshop, Adobe Illustrator, Adobe InDesign, BioRender, Freeform

Honors and Awards

  • 2023
    • 1st rank at MSc. Cell and Molecular Biology University of Isfahan (2020 class)
  • 2020
    • 1st rank at BSc. Animal Biology University of Isfahan (2016 class)
  • 2019
    • Students’ Publications Award

Academic Interests

  • Bioinformatics and Multimodal Data Analysis
    • Single Cell Data (scRNA-Seq, scATAC-Seq)
    • RNA splicing and processing analysis with RNA-Seq based data
    • Peak calling
    • Variant calling
    • DNA methylation
    • Quantitative Trait Locus (QTL) analysis
    • Spatial transcriptomics
    • Application of machine learning and deep learning algorithms to bioinformatics
  • Molecular Pathology of Multifactorial Diseases
    • Gene regulatory network behind multifactorial diseases
    • Signaling pathways behind multifactorial diseases
    • Cell-cell comunication behind multifactorial diseases
    • Perturbation model generation
    • Cheap screaning
    • Cheap treatments