Curriculum Vitae (CV)

University of California, San Francisco

PhD, Pharmaceutical Sciences and Pharmacogenomics (PSPG)

Fall Rotation: Pollard Lab

Winter Rotation: Shokat Lab

Department of Life Science Engineering | University of Tehran

M.Sc. Nano-biomimetics

Thesis title: "Gene regulatory network from single cell expression and DNA repair phenotype datasets"

School of Biology, College of Science | University of Tehran

B.Sc. Cellular & Molecular Biology

Thesis title: "Assessing how microRNA target genes are related using gene ontology analysis"

Gilbert Lab and Multi-Omics Tech Center | Arc Institute

Title: Senior Research Associate

Title: Research Associate II

Projects:

• Development of a CRISPR screen analysis python toolkit, ScreenPro2.
  Website | GitHub
• Multi-omics approach to study epi-{genome,transcriptome} crosstalk in Acute Myeloid Leukemia (AML)
  GitHub | Preprint | Blog Post
• Engineering higher-order combinatorial perturbation platforms for functional genomics.
  Preprint

Department of Biomedical Informatics (DBMI) | Harvard Medical School

Zitnik Lab | Artificial Intelligence for Medicine and Science

Title: Volunteer Researcher | Supervisor: Dr. Marinka Zitnik

Project: Defining new generalizable data loaders and tasks in artificial intelligence research on therapeutics

• Wrote new data loader module for knowledge graphs in Therapeutics Data Commons (TDC).
• Extended Precision Medicine Knowledge Graph (PrimeKG) by including OMIM gene and phenotypes entries.

Summer Institute in Biomedical Informatics (SIBMI)

Title: Post-bac Fellow @Zak Lab | Mentor: Dr. Hadi Amiri

Project: Biological similarities among rare disease patients at Undiagnosed Diseases Network (UDN)

• Clustered patients with undiagnosed disease using textual information in referral letters and EHR data.
• Built automated patient phenotyping workflow using NLP representation learning techniques.

Department of Life Science Engineering | University of Tehran

Goliaei and Mehrnejad Labs

Title: Master Student

Project:

• Conceptualization of multi-omics single cell assays using nano-biomimetic oligo probes for enzymatic activity detection.
  Thesis Slides
• Implemented single-cell analysis workflow and graph search algorithms to study gene regulatory networks.
  GitHub

University of California, San Francisco (UCSF)

Gilbert Lab

Title: Scientific Research Assistant II

Projects:

• Helped develop and publish a novel software for large-scale data integration in cancer research, called CanDI (Cancer Data Integrator).
• Implemented deep learning models for functional genomics research, e.g. Cancer-Cell-Encoder.

Goodarzi Lab

Title: Junior Specialist II

Projects:

• Performed bulk and single cell RNA-seq data analysis of in-vitro or in-vivo drug and gene perturbation studies.
• Implemented analytic workflow for RNA expression, stability, splicing, and m⁶A methylation analysis.
• Collaborated in NGS data analysis with laboratories in UCSF, Rockefeller, Yale, Georgetown, Cedars-Sinai Medical Center, Dana-Farber Cancer Institute, and Northwestern.

Broad Institute of Harvard and MIT

Cancer Cell Line Encyclopedia (CCLE) Project

Title: Volunteer Researcher | Adviser: Dr. Mahmoud Ghandi

Project:

• Integrated and assessed co-expression patterns of microRNAs and target genes across cancer cell lines.

Stem Cell Technology Research Center, Ltd. & University of Tehran

Arefian Lab

Title: Volunteer Researcher

Project:

• Studied microRNA regulation of target gene expression in Glioblastoma cancer cells and patients.

Publications:

• Arab A*, Ge A*, Dai R*, et al., A multiomics approach reveals RNA dynamics promotes cellular sensitivity to DNA hypomethylation, Scientific Reports (2024) | doi: 10.1038/s41598-024-77314-9
  * equal contribution first authors
• Hsiung CC, Wilson CM, Sambold NA, Dai R, Chen Q, Misiukiewicz S, Arab A, et al., Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics, Nature Biotechnology (2024) | doi: 10.1038/s41587-024-02224-0
  
• Arshadi AK, Salem M, Karner H, Garcia K, Arab A, et al., Functional microRNA-Targeting Drug Discovery by Graph-Based Deep Learning, Patterns (2024) | doi: 10.1016/j.patter.2023.100909
• Richter M, …, Arab A, et al., Inhibition of muscarinic receptor signaling protects human enteric inhibitory neurons against platin chemotherapy toxicity, bioRxiv (2023) | doi: 10.1101/2023.03.08.531806
• Majd H, Amin S, Ghazizadeh Z, ..., Arab A, et al., Deriving Schwann cells from hPSCs enables disease modeling and drug discovery for diabetic peripheral neuropathy, Cell Stem Cell (2023) | doi: 10.1016/j.stem.2023.04.006.
• Xiao J, Sharma U, Arab A, et al., Propagated circulating tumor cells uncovers the role of NFκB and COP1 in metastasis, Cancers (2023) | doi: 10.1038/s41467-022-29587-9.
• Furuya H, Sasaki Y, Chen R, ..., Arab A, et al., PAI-1 is a potential transcriptional silencer that supports bladder cancer cell activity, Nature Scientific Reports (2022) | doi: 10.1038/s41598-022-16518-3.
• Yogodzinski C, Arab A, et al., A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy, Genome Medicine (2021) | doi: 10.1186/s13073-021-00987-8.
• Zhu X, Chudnovskiy A, Baudrier L, ..., Arab A, et al., Functional Genomics In Vivo Reveal Metabolic Dependencies of Pancreatic Cancer Cells, Cell Metabolism (2020) | doi: 10.1016/j.cmet.2020.10.017.
• Tabibkhooei A, Izadpanahi M, Arab A, et al., Profiling of novel circulating microRNAs as a non-invasive biomarker in diagnosis and follow-up of high and low-grade gliomas, Clinical Neurology and Neurosurgery (2020) | doi: 10.1016/j.clineuro.2019.105652.

Conferences:

• Arab A, O'loughlin T, Jost M, Youngblut N, Li N, Gilbert LA, A path toward development of FunGI – Functional Genomics Interpreter, Poster Presentation, Biological Data Science Conference, Cold Spring Harbor Laboratory (2024)
• Arab A, Gilbert L, Integrative systems biology approach reveals RNA dynamics that promote cellular sensitivity to DNA hypomethylation as potential to design new combination therapy strategies, Poster Presentation, Bay Area RNA Club 2023, UCSF, San Francisco (2023)
• Arab A, Gilbert L, A multiomics approach identifies genes potentially regulated through RNA m⁶A methylation and promote cellular sensitivity to DNA hypomethylation, Poster Presentation, 1st NYC RNA Symposium 2023, The Rockefeller University, NYC (2023)
• Arab A, Goliaei S, Mehrnejad F, Demonstration of cellular dynamic behavior in response to DNA damage through gene regulatory network analysis of single-cell resolution DNA repair phenotype and gene expression multi-omics dataset, Poster Presentation, 1st International and 10th National Iranian Conference on Bioinformatics, Kish, Iran, (2022)
• Arab A, Gheidari F, Arabi F, Arefian E, Predicting an application of miR-190b: Apoptotic enhancement effects on glioblastoma multiform, Poster Presentation, the 3rd Iranian Conference on Systems Biology, Tehran, Iran, (2018)

Teaching:

• Mentored rotation student Meri Okorie, Analysis of pooled RNA-seq dataset for drug screening, Goodarzi Lab, UCSF – Winter 2022
• Mentored high school student Sonakshi Bhalla, Implement a WES analytic pipeline, Goodarzi Lab, UCSF – Winter 2022
• Content designer and lecturer, “Bioinformatics for All, RNA-seq data analysis”, Goodarzi Lab, UCSF – Summer 2022
• Bootcamp designer and lecturer, “Introduction to RNA-seq data analysis”, Gilbert Lab, UCSF – Summer 2020
• Teaching Assistant for Molecular Genetics, University of Tehran – Spring 2019
• Teaching Assistant for Mathematics I, University of Tehran – Fall 2014

Honors and Awards:

• Awardee, JXTX + CSHL Biological Data Science 2024, The JXTX Foundation – 2024.
• Funded Post-bac Fellow, Summer Institute in Biomedical Informatics (SIBMI), Harvard Medical School – 2019.
• 2^nd team at Startup Weekend, 2^nd Young Scientists Festival, University of Tehran – 2018.
• Awarded student journal of science, Iranian National Student Journals Festival – 2016; 2017.
  - DeNA issue 14 – Roles: Editor-in-chief and layout design
  - DeNA issue 10 – Roles: Secretory, interviewer, and layout design
  
• Awarded for the Best Innovative Idea, Domestic Festival at University of Tehran – 2016.
  Title: “A development roadmap of scientific student associations”
• 2nd team, Hamnet Entrepreneurship Event, Isfahan branch of National Foundation of Elites – 2015.
• Honored to join high School for the Gifted, National Organization for Development of Exceptional Talents (Sampad) – 2009.

Volunteer Activities and Hobbies:

• Secretory, Editor-in-Chief, or author at DeNA, Student Journal of Biology, University of Tehran
  - Arab A, Pursue problem-solving biology: What I’ve learned at Harvard, DeNA 22 (2020)
  - Arab A, Interview with Dr. Mohsen Khosravi M.D., Ph.D., “The Inception of being a Researcher”, DeNA 15 (2016)
  - Jadidi M, Arab A, CRISPR Gene Therapy System: Novel Tools to Treat Complex Diseases, DeNA 15, (2016)
  - Arab A, Interview with Dr. Hani Goodarzi Ph.D., “Todays Scientists Social Status”, DeNA 10 (2014)
• Member of Student Association of Biology, University of Tehran – June 2014 - June 2017
• Basketball – player at high school and university college teams, Kong-Fu Toa, Mountain Bike