Machine Learning Bioinformatics Scientist

Behzad Damirchi

US Permanent Resident ******.********@*****.***

Irvine, California 814-***-****

BIOINFORMATICS SCIENTIST

Bioinformatics Scientist with 4+ years of experience developing scalable data analysis solutions, applying statistical analysis and machine learning models in clinical and translational oncology. Proven track record in cross-functional therapeutic development and translational research, leveraging advanced analytical tools to drive impactful results. Experienced in analyzing high-dimensional multi-omics datasets from both solid tumors and hematologic malignancies. Proficient in designing reproducible computational workflows, building interactive visualization tools, and collaborating with research, clinical, manufacturing, analytical and process development teams to translate complex data into actionable insights. SKILLS

Bioinformatics Analysis:

Multimodal Single Cell Sequencing: 10x Genomics Cell Ranger, QC, doublet detection, ambient RNA correction, normalization, clustering, PCA, tSNE, UMAP, PaCMAP, integration, DE analysis, gene set scoring, pseudotime, and automated cell type annotation using Seurat, scRepertoire, Harmony, VISION, scATOMIC, as well as many other R packages and Python libraries

TCR/BCR Repertoire Analysis: MiXCR, TRUST4, RTCR, MIGEC, Immunarch, Divo, and PowerTCR (diversity analysis, clonotype abundance, clustering, and visualization).

Bulk RNA Sequencing: STAR, featureCounts, HTSeq, DEXSeq, Salmon, RSEM, DESeq2, Gene Set Enrichment Analysis (GSEA), Gene Set Scoring/Variation Analysis (GSSA/GSVA), DRAGEN RNA Pipeline. Visualization/data exploration: PCA, cell type deconvolution, Volcano/MA plots, customizable heatmaps, and other publication-ready visualizations.

Whole Exome Sequencing: DRAGEN Enrichment and GATK pipelines; BWA, Picard, HaplotypeCaller, Mutect2, SnpEff, SnpSift, Sequenza, VarScan2, SpecHLA (HLA LOH), Nirvana annotation engine. ATAC-seq, ChIP-seq, Cut & Tag: Bowtie, Trimmomatic, Cutadapt, Samtools, Bedtools, Homer, MEME, STREME, IGV (peak calling, annotation, motif analysis, transcription factor binding, visualization). Targeted DNA Sequencing: Amplican (analysis of on-/off-target gene editing), CRISPResso2. Machine Learning, Predictive Modeling:

Proficient in applying statistical analysis, and machine learning predictive and explanatory models: Linear/Logistic Regression, SVM, KNN, Regularization, Random Forest regressor/classifier, XGBoost, feature selection, etc. Programming:

• Linux HPC (Slurm), AWS (EC2, batch, S3), and Illumina Connected Analytics (DRAGEN)

• Python, R, Bash

• Snakemake and Nextflow

• GitHub, Conda, Docker toolkit

EMPLOYMENT & EDUCATION

Bioinformatics Scientist I, Iovance Biotherapeutics Aug 2022-Aug 2025

Developed random forest, SVM and regression machine learning models on predicting the outcome of Tumor Infiltrating Lymphocytes (TIL) therapy and feature selection using comprehensive cross-functional datasets from multiple sources

(Manufacturing, Clinical and Translational datasets), identifying the key predictors in Melanoma.

Developed multiple analysis workflows and Snakemake pipelines for bulk RNA/TCR-seq, single-cell RNA/TCR-seq, WES and Targeted DNA-seq experiments to effectively monitor the analysis progress, significantly reducing the computation time and human error in NGS data analysis.

Developed UMI-aware bulk TCR-seq and Targeted DNA-seq analysis workflows (Nextflow) in Illumina Connected Analytics (ICA) platform enabling seamless process from sequencer raw files to tertiary analysis results in production.

Performed comprehensive single cell analysis in Melanoma, Lung and Endometrial tumor samples, annotated cell types, identified tumor reactive clones and tracked them in the Tumor Infiltrating Lymphocytes (TIL) manufacturing product.

Enabled enterprise-level cross-functional data analysis and visualization dashboards in Spotfire.

Analyzed bulk RNA-seq and TCR-seq of actual manufacturing process deviations and failure modes, and identified the differentially expressed genes and corresponding enriched pathways in each condition, along with TCR repertoire profiling for comparability analysis.

Provided bioinformatics support across research, translational, analytical, and process development teams.

Managed two summer interns, providing guidance on project design, data analysis, and professional development.

Contributed to patent applications, IND submissions, BLA information requests, and post-approval commitments. Postdoctoral fellow, City of Hope Medical Center July 2021-August 2022

Analyzed bulk RNA-seq data of over 2000 Acute Lymphoblastic Leukemia (ALL) patient samples focusing on cancer subtyping using gene expression profile, fusion, mutation and copy number variation (CNV).

Investigated the transcription factor binding site of various PAX5 protein mutants as one of the oncogenes in B-ALL and comparison between them investigating differential binding regions and motif discovery analysis.

Investigated exon-level and splicing events to find patterns within each leukemia subtype, revealing the role of novel junctions on subtypes’ subgroups.

Closely collaborated and consulted with wet lab teams to investigate, test and optimize bioinformatics tools and packages to meet their needs.

Computational biology Intern, New Equilibrium Biosciences May 2020

Conformational study and modeling of intrinsically disordered proteins (IDPs). Ph.D. in Mechanical Engineering, The Pennsylvania State University– NASA funded project 2016-2021

Developed Ultra High Strength Lightweight computational model for deep space explorations from atomistic modeling to manufacturing in a highly collaborative project. M.Sc. in Mechanical Engineering, Sharif University of Technology 2011-2014

Atomic-scale modeling and simulation of multiple drug carrier candidates’ penetration into lipid bilayer membrane. B.Sc. in Mechanical Engineering, K. N. Toosi University of Technology 2007-2011 SELECTED PUBLICATIONS/CONFERENCES

1. Zhang, Y., Moore, K.N., Jazaeri, A.A., Fang, J., Patel, I., Yuhas, A., Innamarato, P., Gilbert, N., Dean, J.W., Damirchi, B. and Yglesias, J., (2025). Feasibility of Manufacturing and Antitumor Activity of TIL for Advanced Endometrial Cancers. International Journal of Molecular Sciences, 26(15), p.7151. 2. Patrick Innamarato*, Joe Dean*, Mohammed Alkhouli, Marcus Machin, Nathan Gilbert, Sadie Johnson, Gerard Sapena, Nino Mtchedlidze, Behzad Damirchi, Robyn Oldham, Andrew Yuhas, Judy Fang, Jamie Blauvelt, Shari Pilon-Thomas, Rongsu Qi, Hequn Yin, Sean Hall. (2025) IOV-5001, autologous tumor-infiltrating lymphocytes armored with inducible membrane-tethered IL-12, shows enhanced antitumor efficacy with an improved cellular state. American Association for Cancer Research (AACR). Chicago IL (Poster).

3. Judy Fang, Ilabahen Patel, Patrick Innamarato, Nathan Gilbert, Joe Dean, Behzad Damirchi, Joe Yglesias, Rongsu Qi, Michelle R. Simpson-Abelson, Erwin Cammaart, Hequn Yin, Yongliang Zhang. (2024) Manufacture and Functional Characterization of Tumor-Infiltrating Lymphocyte Product from Endometrial Tumors. International Gynecologic Cancer Society (IGCS). Dublin, Ireland (Poster).

4. Joe Dean, Theresa Medina, Amod Sarnaik, Jason Chesney, Mike Cusnir, Joe Yglesias, Behzad Damirchi, Mark Ozeck, Kranthi Kunkalla, Brian Gastman, Rana Fiaz, Giri Sulur, Hequn Yin, Rongsu Qi. (2024) Multimodal single-cell sequencing analysis reveals putative tumor-reactive population in Lifileucel TIL products. Society for Immunotherapy of Cancer

(SITC). Houston TX (Oral and Poster).

5. Taghi Khani, A., Kumar, A., Sanchez Ortiz, A., Radecki, K.C., Aramburo, S., Lee, S.J., Hu, Z., Damirchi, B., Lorenson, M.Y., Wu, X. and Gu, Z., 2023. Isoform-specific knockdown of long and intermediate prolactin receptors interferes with evolution of B-cell neoplasms. Communications biology, 6(1), p.295. 6. Jia, Z., Hu, Z., Damirchi, B., Han, T. T., & Gu, Z. (2022). Characterization of PAX5 mutations in B-progenitor acute lymphoblastic leukemia. Blood, 140(Supplement 1), 1001-1002. 7. Hu, Z., Jia, Z., Damirchi, B., & Gu, Z. (2022). Multi-Omics Signature of B-Cell Acute Lymphoblastic Leukemia Subtypes. Blood, 140(Supplement 1), 5902-5904.

8. Sarnaik, A., Chesney, J., Medina, T., Hamid, O., Thomas, S., Wermke, M., Gontcharova, V., Damirchi, B., Dean, J., Mastellar, E. and Wu, X., 2023, February. Response to Lifileucel Tumor-Infiltrating Lymphocyte (TIL) Cell Therapy after ICI Resistance Regardless of Definition: An Analysis of the C-144-01 Trial in Patients with Advanced Melanoma. In 2023 Tandem Meetings Transplantation & Cellular Therapy Meetings of ASTCT and CIBMTR. Tandem Meetings.

Contact this candidate