Resume

SUMMARY

Ph.D.-trained biomedical data scientist with expertise in bioinformatics, data pipeline development, and high-dimensional analytics. Experienced in next-generation sequencing analysis (bulk, single-cell, spatial), multi-omic data integration, scalable workflow automation, statistical and AI-driven modeling, and data visualization. Effective collaborator and communicator with a track record of delivering results and developing solutions across teams and stakeholders.

EDUCATION

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

TECHNICAL SKILLS

  • Programming: R, Python, Bash, SQL, Julia, Git, Markdown, LaTeX
  • NGS Analysis: bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics, clustering (graph-based, partition-based, hierarchical), dimensionality reduction (PCA, UMAP, t-SNE), differential expression analysis, linear modeling, 10x Genomics (Chromium, Visium, Cell Ranger, Space Ranger), Seurat
  • Libraries: tidyverse, ggplot2, shiny, quarto, pandas, Numpy, SciPy, scikit-learn, Plotly, Dash
  • HPC/Cloud Computing: Linux, GCP, AWS, HDFS

EXPERIENCE

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

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

  • Streamlined 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 (Jun. 2018 – Jan. 2022)
University of Texas Southwestern Medical Center (Dallas, TX)

  • Led a multi-group collaboration to publish novel single-cell RNA-seq datasets in neurobiology, resulting in a co-first-author paper in Science (145+ citations) and a second-author paper in Nature Communications (30+ citations)
  • Independently analyzed large-scale single-cell RNA-seq data by applying computational pipelines, dataset integration, unsupervised clustering (k-nearest neighbor + Louvain method), and statistical modeling to generate biological insights across research domains
  • Delivered spatial transcriptomics capabilities to research group, encompassing molecular library preparation, data and analytics pipelines, documentation, and training for new users

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 (700+ 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., Spool, J. A., Zhao, C., & Riters, L. V. (2018). Co-localization patterns of neurotensin receptor 1 and tyrosine hydroxylase in brain regions involved in motivation and social behavior in male European starlings. Journal of Chemical Neuroanatomy, 89, 1–10.

  • 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.

  • Merullo, D. P., Cordes, M. A., DeVries, M. S., Stevenson, S. A., & Riters, L. V. (2015). Neurotensin neural mRNA expression correlates with vocal communication and other highly-motivated social behaviors in male European starlings. Physiology and Behavior, 151, 155–161.

  • Merullo, D. P., Cordes, M. A., Stevenson, S. A., & Riters, L. V. (2015). Neurotensin immunolabeling relates to sexually-motivated song and other social behaviors in male European starlings (Sturnus vulgaris). Behavioural Brain Research, 282, 133–143.