Resume

PROFESSIONAL SUMMARY

  § 10+ years coding experience (Python, R, MATLAB) in various domains including research and teaching

§ Collaborated with a team of 15+ researchers to analyze single-cell cancer genomics data (Python & R)

§ Analyzed IRB-approved survey data in R of mental health climate among UNC’s student population in collaboration with psychology researchers and occupational therapists

§ Recipient of  2 highly prestigious fellowships and 1 travel grant to support my graduate training

 

EDUCATION

Ph.D., Bioinformatics and Computational Biology, Department of Genetics 2018 – 2023 University of North Carolina at Chapel Hill (UNC) Biological and Biomedical Sciences Program (BBSP)

B.S. Mathematics, B.S. Statistics 2014 – 2018 University of Maryland Baltimore County (UMBC) Magna Cum Laude, Meyerhoff Scholar

DATA SCIENCE EXPERIENCE

Graduate Researcher at UNC 2018 – Present

§ Analyzed cell cycle dynamics in differentiating human embryonic stem cells using Python in the context of image analysis and single-cell genomics

§ Trained graph neural networks in TensorFlow via SLURM to study the effects of experimental perturbations in single-cell RNA sequencing data

§ Collaborated with cancer researchers at UNC to study role of ZBP1 in necroptosis by analyzing single-cell RNA sequencing data with Python and R

§ Presented at 7 professional meetings – including 2 international – and gave 1 invited talk

§ Was awarded $5000 from Burroughs Wellcome Fund to support conference travel

UNDERGRADUATE RESEARCHER UMBC 2016 – 2018

§ Modeled biochemical reaction-diffusion systems using stochastic simulation algorithms in MATLAB

§ Applied this methodology to study cell polarization in a traveling wave model

§ Authored senior thesis

§ Received NSF Graduate Research Fellowship based on a proposal directly related to this work

Technical Writer at Towards Data Science, Medium.com 2021 – Present

§ Published 8 articles on single-cell genomics methods, machine learning, and AI for a data science publication with over 650,000 readers as of February 2023

§ Authored articles that have been featured in the weekly newsletter, editorial columns, and specialized columns, receiving 55,000+ views and 200+ followers

Co-Investigator, Stigma-Free Carolina, UNC 2019, 2020

§ Collaborated with graduate students in psychology and occupational therapy in fellowship program to evaluate the efficacy of a student-run campaign to destigmatize mental health at UNC

§ Co-authored IRB application to survey UNC students and analyze resulting data in R

§ Organized mental health awareness events in response to survey findings Instructor and Co-administrator, How to Learn to Code, UNC 2019, 2022

§ Taught interactive graduate student-led course on programming in R (2019) and Python (2022) for a class of biologists spanning undergraduates and faculty

§ Developed course materials, recruited students, and assigned teachers

Tutor, BCB 720: Introduction to Statistical Modeling, UNC 2020, 2021

§ Tutored first-year students in statistics using RStudio and facilitated weekly sessions to discuss core concepts and set goals for next week’s session

§ Managed logistics, collaborated with instructor and staff to ensure student needs were met and recruit additional students to tutoring sessions

SCIENTIFIC MANUSCRIPTS

(under review) 1. Shahir JA, Stanley N, Purvis JE. Cellograph: A semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks [Internet]. bioRxiv. 2023. p. 2023.02.24.528672. Available from: http://biorxiv.org/content/early/2023/02/27/2023.02.24.528672.abstract

2. Cho M-G, Kumar RJ, Lin C-C, Boyer JA, Shahir JA, Fagan-Solis K, et al. Mre11 liberates cGAS from nucleosome sequestration during tumorigenesis [Internet]. bioRxiv. 2022. p. 2022.12.09.519750. Available from: http://biorxiv.org/content/early/2022/12/10/2022.12.09.519750.abstract

COMPUTATIONAL SKILLS (selected)

Programming Languages: Python | R | MATLAB

Research tools: LaTeX | Linux | SLURM | Cloud Computing | High-Performance Computing | TensorFlow | Keras | PyTorch | OpenCV | PIL | Mathematical Modeling | Statistical Modeling

HONORS AND AWARDS Hector Fellow Academy Best Poster Award 2023 • Awarded for outstanding presentation at the Innovations in Single Cell Omics conference • Presented “Elucidating the role of the cell cycle in stem cell fate using multiplexed imaging”

Burroughs Wellcome Fund Graduate Diversity Enrichment Program 2021 – 2023

§ Nominated by advisor for competitive grant to support training of 10 graduate students from underrepresented backgrounds enrolled at universities in North Carolina

§ Awarded $5000 over 2 years for conference travel and research supplies

National Science Foundation Graduate Research Fellowship Program 2018 – 2023

§ Prestigious national fellowship

§ Awarded >$100,000 in stipend to support graduate training

Caroline H. and Thomas S. Royster Society of Fellows 2018 – 2023

§ Awarded the premier doctoral fellowship program at UNC, providing 5 years § Provides 5 years of support, including a stipend

§ Received $2000 for conference travel

NIH MARC U*STAR Scholarship (now called U-RISE), UMBC 2016 – 2018 § Highly competitive, NIH-funded scholarship program at UMBC to prepare students for graduate school § Provided full tuition and funds for conference travel § Focused on increasing diversity of STEM workforce

Meyerhoff Scholarship, UMBC 2014 – 2018

§ Highly competitive scholarship program at UMBC to prepare students for graduate school, with a focus on increasing diversity in STEM

CONFERENCES/PRESENTATIONS (Selected)

Innovations in Single Cell Omics, Berlin, Germany 2023

Single Cell Genomics 2022, Utrecht, The Netherlands 2022

International Society for Stem Cell Research Annual Meeting, Virtual 2022 Winter Q-Bio, O’ahu, Hawaii (2022), Maui, Hawaii (2018) 2018, 2022

LEADERSHIP EXPERIENCE (Selected) Lead Peer Mentor, First-year Group BBSP, UNC 2021 – 2022

§ Oversaw a team of 7 peer mentors to ensure students receive consistent mentoring and guidance during a year-long course introducing first-year graduate students to graduate school

§ Managed a $1,250 budget for social events in line with UNC’s COVID-19 guidelines Chair, Graduate and Professional Student Government Travel Awards Committee 2022 – 2023

§ Elected by peers as student representative of my PhD program for the GPSG § Served on and later led a committee that dispersed competitive financial awards for conference travel to graduate students, overseeing an $33,000 budget for the school year

§ Delegated tasks in reviewing applications to committee members in a double-blind review process

§ Drafted and presented legislature of the committee’s decision and total funds dispersed for Senate confirmation in monthly meetings