Resume

SUMMARY

Biomedical data scientist experienced in building products and solutions for drug discovery. Collaborates across teams and disciplines to deliver scalable, AI-enabled workflows that streamline drug development. Projects include LLMs for scientific knowledge applications, automated data pipelines for genomic data integration, ML techniques to identify structure in high-dimensional bioinformatics data, and user-focused data visualization and communication to guide decisions.

EDUCATION

  • Ph.D., Integrative Biology: University of Wisconsin-Madison (2018)
  • B.S., Biopsychology (cum laude): Tufts University (2013)

TECHNICAL SKILLS

  • AI/ML: LLMs, knowledge extraction, automated data interpretation, AI-driven evaluation and prioritization, unsupervised clustering, dimensionality reduction (PCA, UMAP, t-SNE)
  • Programming: Python, R, Bash, SQL, Git, Markdown
  • Libraries: pandas, NumPy, SciPy, scikit-learn, Plotly, Dash, tidyverse, ggplot2, Shiny, Quarto
  • HPC & Cloud: Linux, GCP, AWS, HDFS
  • Bioinformatics: single-cell RNA sequencing, spatial transcriptomics, linear modeling, differential gene expression analysis, 10x Genomics (Chromium, Visium, Cell Ranger, Space Ranger), Seurat

EXPERIENCE

Associate Consultant, Biomedical Data Science (Jul. 2025 – Present)
ZS Associates (Boston, MA)

Senior Scientist, Bioinformatics (Jan. 2022 – Oct. 2024)
Parexel International (Remote)

  • Improved latency of data delivery by 10x for a major pharmaceutical client by developing novel data ingestion pipelines in R, Python, and Bash to drive biomarker discovery
  • Collaborated across bioinformatics and data engineering teams to deliver 1000s of genomic datasets (GWAS & eQTL) scaling to terabytes in size, integrating data and metadata from UK Biobank, 1000 Genomes Project, FinnGen, Open Targets, GWAS Catalog, and more
  • Automated high-throughput quality control workflows to enable 24-hour client turnaround

Postdoctoral Researcher, Neuroscience (Jun. 2018 – Jan. 2022)
University of Texas Southwestern Medical Center (Dallas, TX)

  • Led a multi-group collaboration to publish large-scale single-cell RNA sequencing datasets in neuroscience, producing a co-first-author paper in Science (145+ citations), a second-author paper in Nature Communications (30+ citations), and a nationally-competitive NIH Postdoctoral Fellowship (F32)
  • Independently analyzed single-cell RNA sequencing data by applying computational pipelines, dataset integration, unsupervised clustering, and statistical modeling for 20,000 genes in 200,000+ cells across multiple brain regions, species, and cell types
  • Delivered spatial transcriptomics capabilities to research group, encompassing molecular library preparation, data and analytics pipelines, documentation, and training for new users

Graduate Researcher, Integrative Biology (Sep. 2013 – May 2018)
University of Wisconsin-Madison (Madison, WI)

  • Produced 5 first-author publications, 5 conference poster presentations, and a nationally-competitive NSF Graduate Research Fellowship
  • Applied multiple linear regression techniques to analyze gene expression, protein labeling, and behavioral data from molecular biology experiments in neuroscience (quantitative PCR, in situ hybridization, immunohistochemistry, and confocal microscopy)

INDEPENDENT PROJECTS

Project ESPAÑOL (https://github.com/dmerullo/project-espanol)

  • Generated a dataset of 10,000+ Spanish-language poems (>2.5 million words) using high-throughput web scraping (rvest)
  • Developed an unsupervised clustering (k-means) pipeline in Python to classify poems into 4 difficultly levels based on verb usage
  • Built an interactive Plotly Dash web application for text exploration and visualization

SELECTED PUBLICATIONS (12 total; 750+ citations total)

  • Colquitt, B. M.*, Merullo, D. P.*, Konopka, G., Roberts, T. F., & Brainard, M. S. (2021). Cellular transcriptomics reveals evolutionary identities of songbird vocal circuits. Science, 371(6530), eabd9704. *co-first author

  • Xiao, L., Merullo, D. P., Koch, T. M. I., Cao, M., Co, M., Kulkarni, A., Konopka, G., & Roberts, T. F. (2021). Expression of FoxP2 in the basal ganglia regulates vocal motor sequences in the adult songbird. Nature Communications, 12(1), 2617.

  • Kulkarni, A., Anderson, A. G., Merullo, D. P., & Konopka, G. (2019). Beyond bulk: A review of single cell transcriptomics methodologies and applications. Current Opinion in Biotechnology, 58, 129–136.

  • Merullo, D. P., Asogwa, C. N., Sanchez-Valpuesta, M., Hayase, S., Pattnaik, B. R., Wada, K., & Riters, L. V. (2018). Neurotensin and neurotensin receptor 1 mRNA expression in song-control regions changes during development in male zebra finches. Developmental Neurobiology, 78(7), 671–686.

  • Merullo, D. P., Angyal, C. S., Stevenson, S. A., & Riters, L. V. (2016). Song in an affiliative context relates to the neural expression of dopamine- and neurotensin-related genes in male European starlings. Brain, Behavior and Evolution, 88, 81–92