Bioinformatics Scientist and Project Manager

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Curriculum Vitae

Naila Gulzar, M.Sc.

Email: *****.*******@*****.*** Phone: +1-860-***-****

Web profile: Google Scholar

Professional experience Research Technologies Branch/DIR/NIAID, National Institutes of Health Bioinformatics Scientist (Contractor)

• Analysis of multiple RNA-seq data sets on NIH high-performance computing systems - Helix/Biowulf using a variety of computational tools April. 2022 – Oct.,

2022

Research Associate (Staff) at the Department of Biochemistry and Molecular Medicine, The George Washington University (GW)

Product Manager of High-performance Integrated Virtual Environment (GW HIVE)

• Testing and benchmarking commonly used and highly requested bioinformatics tools for integration in the HIVE system and developing best practices for the HIVE platform

• Writing standard operating procedures (SOPs), providing hands-on HIVE demos, conducting HIVE workshops, and training MS students, interns, and collaborators on HIVE.

• Experience with Agile management software such as JIRA and Confluence

• Lead Scrums and Sprints for the HIVE platform team

• Updating security documentation for GW HIVE regarding system data confidentiality, integrity, and availability

• Contributed to proposal/grant/contract writings for research projects on HIVE Performed admin tasks for the purchase of hardware for the GW HIVE system and keeping track of expenses (travel, invoices, renewal of contracts) using the GW Concur platform Research projects

• Analysis of multiple RNA-seq data sets using a variety of computational tools

• Leading and managing collaboration projects with the External Quality Assurance Program Oversight Laboratory (EQAPOL), Duke University. Specifically for designing the workflows for analyses of NGS data from chronic HIV-1 patients to identify the subtypes, quasispecies, recombination events, and drug-resistance mutations and co-authored a paper

• Scientific and technical lead on collaboration projects with the researchers in vaccine analytical development at MERCK & Co.

• Optimized workflows for detecting adventitious elements in vaccines and the application of BioComputeObject, co-authored in paper

• Developed pipelines for metagenomics analysis of data from the healthy human gut, GutFeelingKnowledgebase, and co-authored a paper

• Contributed significantly to the manual curation of studies with differential expression in cancer in the BioXpress database and co-authored a paper Nov., 2014 – April,

2022

Research Trainee at Computational Chemistry and Biophysics Department, University of Maryland Baltimore County

• Performed molecular dynamic simulations to find out the effective allosteric sites of several HIV proteins for assisting therapeutic drug designs 2014

2

Research Assistant (volunteer) at Department of Pharmacology, University of Connecticut

• Performed protein purification; genomic isolation of DNA and RNA from tissues and blood samples; plasmid Isolation; and assisted in protein crystallization experiments 2013

Academic chronicle The George Washington University

Department of Biochemistry and Molecular Medicine

Courses taken:

1. Intro to Clinical Bioinformatics

2. Bioscience Big data statistics

2017 - 2020

University of Kashmir

Master of Sciences in Biochemistry

Major courses: Bioinformatics, Molecular Biology, Immunology, Cell biology, Intermediary Metabolism and Microbiology

2009 - 2011

University of Kashmir

Bachelor of Sciences in Biochemistry

Major courses: Biochemistry, Organic Chemistry, Inorganic Chemistry, Physical Chemistry, Zoology, and English (Prose, Poetry, and Writing)

2005 - 2008

Publications 1. Hora B#, Gulzar N#, Chen Y, Karagiannis K, Cai F, Su C, Smith K, Simonyan V, Shah SA, Ahmed M, Sanchez AM, Stone M, Cohen MS, Denny TN, Mazumder R, Gao F. Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing. mSphere. 2020 Oct 14; PMID: 33055255. #Co-first authors/equal contribution.

2. Charles H K, Desai H, Sylvetsky A C, LoTempio J, Ayanyan S, Carrie J, Crandall K, Fochtman B, Gasparyan L, Gulzar N, Howell P, Issa N, Krampis K, Mishra L, Morizono H, Pisegna J R, Rao S, Ren Y, Simonyan V, Smith K, VedBrat S, Yao M, Mazumder R. Baseline Human gut microbiota profile in healthy people and standard reporting template. Plos One. 2019 Sep 11. PMID: 31509535

3. Gulzar N, Dingerdissen H, Yan C, Mazumder R. Impact of Nonsynonymous Single-Nucleotide Variations on Post- Translational Modification Sites in Human Proteins. Methods Mol Biol. 2017; 1558:159-190. doi: 10.1007/978-1- 4939-6783-4_8. PMID: 28150238. Book chapter.

4. Simonyan V, Chumakov K, Dingerdissen H, Faison W, Goldweber S, Golikov A, Gulzar N, Karagiannis K, Vinh Nguyen Lam P, Maudru T, Muravitskaja O, Osipova E, Pan Y, Pschenichov A, Rostovtsev A, Santana-Quintero L, Smith K, Thompson EE, Tkachenko V, Torcivia-Rodriguez J, Voskanian A, Wan Q, Wang J, Wu TJ, Wilson C, Mazumder R. High- performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis. Database (Oxford). 2016 Mar 17. PMID: 26989153. 5. Wan Q, Dingerdissen H, Fan Y, Gulzar N, Pan Y, Wu T-J, Yang C, Zhang H, and Mazumder R. BioXpress: An integrated RNA-seq derived gene expression database for pan-cancer analysis. Database (Oxford). 2015 Mar 28. pii: bav019. PMID: 25819073.

Anticipated publication 6. Application of BioCompute Object to a virus detection pipeline: database curation, in silico read generation, evaluation of analysis pipelines (#Naila Gulzar, #Jonathon Keeney et al., 2022) #Co-first authors/equal contribution. Available in bioRxiv

Bioinformatics skills

3

NGS data analysis Bioinformatics tools (e.g., Bioconductor), Seurat, DESeq2, LimmaVoom, edgeR Alignment tools: STAR, HIVE-hexagon, BWA, Bowtie, Gene Cutter SNV profiling tools: HIVE-heptagon

Metagenomics analysis tools: HIVE-CensuScope

Phylogenetic analysis tools: MEGA

De novo assemblers: PRICE, Geneious prime, IDBA-ud, velvet Programming skills R and Linux command line,

working in a Linux HPC cluster environment (e.g., Slurm), pipeline tools (e.g., Snakemake), Talks presented Scientific Advisory Board (SAB) meeting at Duke Human Vaccine Institute 2021 7. Analysis of NGS data for Drug Resistance Mutations and Quality Control analysis of HIV-1 subtype reference sequences from Los Alamos National Laboratory (LANL) HIV-1 sequence database

8. Progress on the manuscript "Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing". And the analysis of HIV-1 samples for GenBank submission

2020

Poster presented Analysis of HIV-1 quasispecies sequences generated by High-throughput Sequences (HTS) using HIVE at GW Research Days

2017

References Prof. Raja Mazumder, Ph.D.

Department of Biochemistry and Molecular Medicine

School of Medicine & Health Sciences

The George Washington University

Ross Hall, Room 540

2300 Eye Street N.W.

Washington, DC 20037

Phone office: 202-***-****

Email: ************@***.***

Jonathon Keeney, Ph.D.

Assistant Research Professor

Managing Director, Executive Steering Committee

for BioCompute

The George Washington University

Ross Hall, 543B

2300 Eye Street N.W.

Washington, D.C. 20052

Office Phone: 202-***-****

Email: ********@***.***

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