Sr. Scientist in Computational Biology

Curriculum Vitae

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Email: domenick@dbraccia.com
Website: dbraccia.com
Address: 1151 Canterbury Dr., Lansdale, PA 19446

Computational Biologist with over 6 years of experience across academic and industry settings working with high-throughput genomic, transcriptomic, and proteomic sequencing data. Broad expertise across biology, statistics, software engineering, pipeline development, and machine learning.

Work Experience

Sr. Scientist, Computational Biology
Cabaletta Bio, Philadelphia, PA
August 2023 – Present
Bioinformatics Consultant
C M Cherry Consulting, Philadelphia, PA
May 2023 – Present
Data Scientist – Bioinformatics
Scipher Medicine, Waltham, MA
July 2022 – February 2023
  • Designed bioinformatic workflows to process, analyze, and assess the quality of high-throughput transcriptomics data.
  • Built cloud computing infrastructure to aid high-throughput hypothesis testing and biomarker discovery.
  • Designed and trained classification models predicting pathology of early Rheumatoid Arthritis (RA) patients from whole-blood RNA-seq gene expression data.
  • Performed feature selection of proteomics characteristics correlated with early RA clinical endpoints.
Graduate Research Assistant
University of Maryland, College Park, MD | Dr. Brantley Hall Lab
August 2017 – July 2022
  • Collected, integrated, mined, and analyzed large multi-omic datasets to characterize the progression of inflammatory bowel disease (IBD) and researched microbiome therapy options for neonatal jaundice and colorectal cancer.
  • Utilized DNA and RNA sequence data for hypothesis generation and experimental design.
  • Oversaw team Git repository for collaborative software development validating wearable medical devices.
  • Performed statistical power analysis for a successful $250,000 grant application using repeated-measures ANOVA.

Education

PhD, Computational Biology & Genomics
University of Maryland, College Park
July 2022
BS, Physics (Minor in Mathematics)
Pennsylvania State University, University Park
August 2016

Technical Skills

Programming:
R Python Bash SQL
Pipelines & Workflow:
Nextflow Snakemake Git/GitHub
Cloud & OS:
AWS SLURM HPC Linux MacOS
Visualization:
Adobe Illustrator ggplot2 matplotlib

Publications

  1. Case study of resecabtagene autoleucel in a subject with diffuse cutaneous Systemic Sclerosis treated in the RESET-SScTM phase I/II trial.
    Molecular Therapy. 2025.
  2. Mechanistic basis of the acute safety profile of rese-cel, an autologous CD19-CAR T, in patients with autoimmune disease treated in four ongoing phase 1/2 clinical trials.
    Blood. 2025.
  3. Orchestrating Microbiome Analysis with Bioconductor.
    bioRxiv. 2025.
  4. Hall B, Levy S, Default-Tompson K, Minabou G, Weiss A, Braccia DJ, Jenkins C, Yang Y, Arp G, Abeysinghe S, Jermain M. Discovery of the gut microbial enzyme responsible for bilirubin reduction to urobilinogen. bioRxiv Preprint. 2023.
  5. Braccia DJ, Ndjite GM, Weiss A, Levy S, Abeysinghe S, Jiang X, Pop M, Hall B. Gut Microbiome–Wide Search for Bacterial Azoreductases Reveals Potentially Uncharacterized Azoreductases Encoded in the Human Gut Microbiome. Drug Metabolism and Disposition. 2023.
  6. Braccia DJ, Jiang X, Pop M, Hall AB. The capacity to produce hydrogen sulfide (H2S) via cysteine degradation is ubiquitous in the human gut microbiome. Frontiers in Microbiology. 2021.
  7. Olson ND, Kumar MS, Li S, Braccia DJ, Hao S, Timp W, Salit ML, Stine OC, Bravo HC. A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures. Microbiome. 2020.
  8. Wagner J, Kancherla J, Braccia DJ, Matsumara J, Felix V, Crabtree J, Mahurkar A, Bravo HC. Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz. F1000Research. 2020.
  9. Paulson JN, Olson ND, Braccia DJ, Wagner J, Talukder H, Pop M, Bravo HC, Paulson MJ. Package ‘metagenomeSeq’. Bioconductor. 2013.

Research Grants

Employing smart underwear to measure gut microbial hydrogen sulfide production
NIH R21 (1R21DK132310) | 2022 – 2024
Role: Significant Contributor (Statistical Analysis Plan)
Developing a Smart Underwear device to help living well with IBS
Maryland Innovation Initiative (MII) | 2021 – 2022
Role: Significant Contributor (Statistical Analysis Plan)

Honors & Awards

Front cover art of Drug Metabolism and Disposition (Vol 51. Issue 1) 2023
National Science Foundation Research Traineeship (COMBINE) 2018 – 2021
UMD Dean's Fellowship ($5,000) 2020
COMBINE Travel Grant ($1,500) 2018
UMD Dean's Fellowship ($5,000) 2018
UMD Dean's Fellowship ($5,000) 2017
Penn State Summer Research Experience Internship ($5,000) 2015

Teaching Experience

BSCI 441 – Mammalian Physiology Lab (TA)
University of Maryland, College Park
2019 – 2020
  • Oversaw rat surgical operations including cannulation, IV administration, and nerve stimulation.
  • Developed at-home teaching materials, virtual labs, and lectures in response to the COVID-19 pandemic.
BSCI 330 – Cell Biology and Physiology Lab (Senior TA)
University of Maryland, College Park
2017 – 2019
  • Guided 200 students in cell biology procedures such as SDS-PAGE, protein quantification, and in vivo psychoactive drug administration.
  • Coached junior TAs in lab protocols, safety standards, and pedagogical strategies.
PHYS 220 – Electricity and Magnetism Lab (TA)
Pennsylvania State University, University Park
2016
  • Led 50 students in lab techniques and delivered mini-lectures explaining the core principles of electromagnetism.

Online Coursework & Certifications

Codecademy Certifications
  • Analyze Data with Python — Completed April 2023
  • Full Stack Engineer Career Path — In Progress
  • Software Engineering for Data Scientists — In Progress

Presentations & Posters

  • American Society of Microbiology Annual Meeting, Washington D.C. (2022)
  • Keystone Symposium: Harnessing the Microbiome for Disease Prevention and Therapy (2021)
  • Bioconductor Europe Conference (2020)