プロフィール詳細

プロジェクトを作成

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Dr. Somayeh S.に依頼

Turkey

Omics Data Analysis | Bioinformatics Specialist | RNA-Seq, scRNA-Seq, WES, Metagenomics, WGCNA, Network Biology

プロフィール概要

Profile Summary I hold a Ph.D. in Chemical Engineering with a strong specialization in bioinformatics and multi-omics data analysis. Over the past three years, I have developed expertise in NGS workflows, multi-omics integration, and biological network analysis across cancer, transplant rejection, and microbiome studies. Core expertise includes: • Transcriptomics: Bulk and single-cell RNA sequencing (scRNA-seq), QC, integration, clustering, trajectory analysis, DEGs (DESeq2, edgeR), enrichment, and co-expression network construction (WGCNA). • Genomics: Whole exome sequencing (WES), CRAM/VCF handling, variant calling, SNP/indel analysis, and functional annotation. • Systems biology: Pathway enrichment, biomarker discovery, protein–protein interaction networks, community detection, and multi-dataset meta-analysis. • Microbiome & Metagenomics: 16S rRNA (QIIME2, DADA2, diversity analysis) and shotgun metagenomics (Kraken2, Bracken, Kneaddata, MetaPhlAn). • Drug discovery: Structure-based virtual screening, molecular docking (Schrödinger, PyRx), and FDA drug repurposing. I have developed modular and reusable pipelines using both R and Bash, with ongoing efforts to expand into Snakemake/Nextflow for workflow automation. My repositories are openly available on GitHub, reflecting my commitment to reproducibility and transparency. Sample Workflows (GitHub) • 🔬 TNBC scRNA-seq (GSE161529) – End-to-end single-cell RNA-seq analysis in triple-negative breast cancer (QC, integration, annotation, CNV via CopyKAT, CellChat trajectory).(https://github.com/somayehsarirchi/TNBC_scRNAseq_GSE161529) • 🐟 16S Analysis – Grass Carp (PRJNA1293113) – Microbiome diversity under dietary treatments. (https://github.com/somayehsarirchi/16S_Analysis_GrassCarp) • 🐠 Shotgun Metagenomics – Fish Gut (PRJNA1254096) – Taxonomic profiling and functional annotation. (https://github.com/somayehsarirchi/Shotgun-GutFish-PRJNA1254096) • 📊 Bioinformatics Templates – Modular pipelines for RNA-seq, VCF filtering, visualization (heatmaps, volcano plots).(https://github.com/somayehsarirchi/Bioinformatics-Templates) ________________________________________ DOI Citations (Zenodo) • Sarirchi, S. (2025). Bioinformatics Analysis Templates: RNA-seq, VCF Filtering, and Visualization Pipelines. (https://doi.org/10.5281/zenodo.16493302) • Sarirchi, S. (2025). Shotgun metagenomic profiling of fish gut microbiota (PRJNA1254096). (https://doi.org/10.5281/zenodo.16447049) • Sarirchi, S. (2025). 16S rRNA Gut Microbiome Analysis in Grass Carp. (https://doi.org/10.5281/zenodo.16493433) • Sarirchi, S. (2025). Triple-Negative Breast Cancer (TNBC) scRNA-seq Analysis — GSE161529. (https://doi.org/10.5281/zenodo.17127154) ________________________________________ Current Collaborations • Chronic kidney allograft rejection (Tehran University of Medical Science (TUMS)) – DEG analysis, WGCNA, and functional enrichment. • Cancer-related research (Shahid Beheshti University of Medical Sciences) – computational drug repurposing and resistance profiling. Services Offered • RNA-seq & scRNA-seq (end-to-end pipelines: QC → count matrix → DEGs → enrichment) • WES/Variant analysis (CRAM/VCF handling, variant calling, filtering, annotation) • Network biology (WGCNA, PPI networks, hub genes, enrichment prioritization) • Microbiome & metagenomics (16S and shotgun workflows, taxonomic and functional analysis) • Drug repurposing (molecular docking, network-based target prioritization)

専門分野

• ★ Bioinformatics
• ★ Systems Biology
• ★ Cancer Research
• ☆ Chemoinformatics
• ☆ Computational Biology
• ☆ Molecular Biology
• ☆ Omics
• ☆ Transcriptomics
• ☆ Data Analysis
• ☆ Gene & Protein Expression Analysis
• ☆ Structural Bioinformatics
• ☆ Biomolecular Engineering
• ☆ Protein/Enzyme Engineering
• ☆ R
• ☆ Drug Discovery
• ☆ Drug Target Identification
• ☆ Drug Design
• ☆ Medical Sciences
• ☆ Cancer Biology
• ☆ Carcinogenesis

サービス

• Research
• Data & AI

Research Meta-Research, Scientific and Technical Research

Data & AI Statistical Analysis, Data Visualization, Data Mining, Data Cleaning, Data Processing

職務経験

Scientific Collaborator, Transcriptomic Biomarker Analysis in Kidney Transplant Rejection

Iranian Tissue Bank, Tehran University of Medical Sciences

10月 2024 - 現在

Bioinformatics Analyst, Colorectal Cancer Transcriptomics and Drug Repurposing

RIGLD, Shahid Beheshti Univ. of Medical Sciences

7月 2022 - 現在

学歴

PhD (Chemical Engineering)

Iran University of Science and Technology

- 2月 2020

MSc (Chemical Engineering/Biotechnology)

Sharif University of Technology

9月 2004 - 8月 2006

B.Sc (Chemical Engineering)

Islamic Azad University, Science and Research Branch

2月 1999 - 2月 2003

認定資格

• School of Oncology & Tumor Therapy Design

  International Institute of New Sciences

  12月 2023 - 現在

• Weighted Gene Coexpression Network Analysis

  Shahid Beheshti University of Medical Sciences

  5月 2023 - 現在

• Bioinformatics & Drug Design & Molecular Dynamics

  International Institute of New Sciences

  5月 2023 - 現在

• Whole Exome Sequencing

  Shahid Beheshti University of Medical Sciences

  4月 2023 - 現在

• Single Cell RNA Sequencing Analysis

  Shahid Beheshti University of Medical Sciences

  10月 2022 - 現在

• Biological Network Analysis

  Shahid Beheshti University of Medical Sciences

  10月 2022 - 現在

• Microarray Data Analysis

  Shahid Beheshti University of Medical Sciences

  10月 2022 - 現在

• RNASeq Meta Analysis

  Shahid Beheshti University of Medical Sciences

  9月 2022 - 現在

• Bulk RNA Sequencing Analysis

  Shahid Beheshti University of Medical Sciences

  9月 2022 - 現在

• Fundamentals of R

  Shahid Beheshti University of Medical Sciences

  8月 2022 - 現在

• Protein Design & Enzyme Engineering

  International Institute of New Sciences

  8月 2021 - 現在

出版物

JOURNAL ARTICLE

Somayeh Sarirchi, Masomeh Askari, Ebrahim Mirzaei, Leila Navapour, Mina Karimpour, Leili Rejali, Ehsan Nazemalhosseini-Mojarad, Stefania Nobili, Claudia Cava, Amir Sadeghi, et al. (2024). Integrative Bioinformatics Analysis: Unraveling Variant Signatures and Single-Nucleotide Polymorphism Markers Associated with 5-FU-Based Chemotherapy Resistance in Colorectal Cancer Patients . Journal of Gastrointestinal Cancer.

Somayeh Sarirchi, Soosan Rowshanzamir, Foad Mehri (2020). Effect of sulfated metal oxides on the performance and stability of sulfonated poly (ether ether ketone) nanocomposite proton exchange membrane for fuel cell applications . Reactive and Functional Polymers.

Somayeh Sarirchi, Soosan Rowshanzamir, Foad Mehri (2020). Simultaneous improvement of ionic conductivity and oxidative stability of sulfonated poly(ether ether ketone) nanocomposite proton exchange membrane for fuel cell application . International Journal of Energy Research.

Somayeh Sarirchi, S. Rowshanzamir (2017). An overview of organic/inorganic membranes based on sulfonated poly ether ether ketone for application in proton exchange membrane fuel cells . Journal of Renewable Energy and Environment.

Zahra Mossayebi, Taghiyeh Saririchi, Soosan Rowshanzamir, Mohammad Javad Parnian (2016). Investigation and optimization of physicochemical properties of sulfated zirconia/sulfonated poly (ether ether ketone) nanocomposite membranes for medium temperature proton exchange membrane fuel cells . International Journal of Hydrogen Energy.

Taghiyeh Saririchi, Reza Roosta Azad, Daryush Arabian, Asghar Molaie, Fahimeh Nemati (2012). On the optimization of sphalerite bioleaching; the inspection of intermittent irrigation, type of agglomeration, feed formulation and their interactions on the bioleaching of low-grade zinc sulfide ores . Chemical Engineering Journal.