Epistasis in cardiac traits.
Stamp, J., Crawford, L. Epistasis in cardiac traits. Nat Cardiovasc Res (2025). https://doi.org/10.1038/s44161-024-00595-w
CV
My resume as PDF.
Summary
I am a researcher with a strong technical and statistical background, and 5+ years of experience in research and industry. My work focuses on machine learning and statistical modeling, using Python, R, and C++. I am the author and maintainer of multiple open-source statistical software packages.
Education
- Ph.D in Computer Science & Computational Biology – Brown University, Providence, RI, USA 2025 (expected)
- Thesis: Statistical and Computational Advances for Detecting Nonlinear Contributions to Complex Traits
- Committee: Dr. Lorin Crawford, Dr. Daniel Weinreich, Dr. Roberta De Vito, Dr. Bogdan Pasaniuc. (* Advisors)
- M.S. in Computational Biology – Brown University, Providence, RI, USA, 2024
- M.S. in Physics – Ludwig Maximilian University, Munich, BY, Germany, 2019
- B.S. in Physics – University of Konstanz, Konstanz, BW, Germany 2016
Technical Skills
- Languages: Python, R, C++, Groovy, Matlab
- Frameworks: PyTorch, TensorFlow, ScikitLearn
- Dev Tools: Git, Github, Bitbucket, OpenShift, Jenkins, Docker, JetBrains IDEs
- Other: Statistics, Research, Genetics, Project Management, HPC, Slurm, OpenMP
Research and Engineering Experience
Doctoral Studies (2021 – present)
Brown University (Providence, RI, USA)
- Identified open scientific questions, mathematical problems and algorithmic challenges in studying human disease.
- Developed statistical models and machine learning algorithms capable to analyze large human data improving power by up to 80% compared to state of the art models.
- Developed open-source softare implementations of the machine learning algorithms that run 10x – 90x faster than comparable state of the art algorithms.
Software Consultant (2019 – 2020)
TNG Technology Consulting GmbH (Munich, BY, Germany)
- Collaboratively developed targets and road maps for the cloud migration and automation of the software build infrastructure of a global insurance company.
- Developed software build & testing automation and cloud deployment infrastructure & automation for testing and production environments.
Research Assistant (2017)
Max Planck Institute for Neurobiology (Munich, BY, Germany)
- Independently reviewed scientific literature to learn algorithms to process 2-dimensional images to reconstruct a 3-dimensional anatomical representation of a mouse brain.
- Developed software for image alignment and 3-dimensional reconstruction of anatomical images.
Research Assistant (2016)
Columbia University (New York, NY, USA)
- Visiting Scholar at the Molecular Electronics laboratory of Dr. Latha Venkataraman
- Bachelor Thesis research: single-molecule junction characterization with MCBJ and STM-BJ
Research Assistant (2014 – 2015)
Stony Brook University (Stony Brook, NY, USA)
- Research assistant at the Cognitive Neuroscience laboratory of Dr. Hoi-Chung Leung
- Topic: spatial working memory maintenance
- Poster presentation at the 2015 URECA Undergraduate Research Symposium: Stamp JD, Lee AS, Manza P, O’Rawe J, Leung HC. (2015). Exploring the neurochemical basis of human spatial working memory maintenance with eye blink activity. 2015 URECA Undergraduate Research Symposium, Stony Brook, NY, April 29. *Authors contributed equally to this work.
Publications
Incorporation of Epstein–Barr viral variation implicates significance of Latent Membrane Protein 1 in survival prediction and prognostic subgrouping in Burkitt lymphoma.
Kim Jr, I. E., Oduor, C., Stamp, J., Luftig, M. A., Moormann, A. M., Crawford, L., & Bailey, J. A. Incorporation of Epstein–Barr viral variation implicates significance of Latent Membrane Protein 1 in survival prediction and prognostic subgrouping in Burkitt lymphoma. International Journal of Cancer.
cphMAPIT: Cox Proportional Hazards Marginal Epistasis Test.
J. Stamp, L. Crawford (2025 expected). cphMAPIT: Cox Proportional Hazards Marginal Epistasis Test. https://github.com/jdstamp/cphMAPIT. (R Package)
Sparse modeling of interactions enables fast detection of genome-wide epistasis in biobank-scale studies.
J. Stamp, S. Pattillo Smith, D. Weinreich, L. Crawford (2025). Sparse modeling of interactions enables fast detection of genome-wide epistasis in biobank-scale studies. biorxiv; doi: 10.1101/2025.01.11.632557
smer: Sparse Marginal Epistasis Test.
J. Stamp, L. Crawford (2025). smer: Sparse Marginal Epistasis Test. https://github.com/lcrawlab/sme. (R Package)
Considerations in the search for epistasis.
Balvert, M., Cooper-Knock, J., Stamp, J. et al. Considerations in the search for epistasis. Genome Biol 25, 296 (2024). https://doi.org/10.1186/s13059-024-03427-z
Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections.
Li, K., Chaguza, C., Stamp, J., Chew, Y. T., Chen, N. F., Ferguson, D., ... & Grubaugh, N. D. (2024). Ge-nome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections. PLOS Computational Biology, 20(9), e1012469.
Discovering non-additive heritability using additive GWAS summary statistics.
Samuel Pattillo Smith, Gregory Darnell, Dana Udwin, Julian Stamp, Arbel Harpak, Sohini Ramachandran, Lorin Crawford (2024) Discovering non-additive heritability using additive GWAS summary statistics eLife 13:e90459
Leveraging the Genetic Correlation between Traits Improves the Detection of Epistasis in Genome-wide Association Studies.
J. Stamp, A. DenAdel, D. Weinreich, L. Crawford (2023). Leveraging the Genetic Correlation between Traits Improves the Detection of Epistasis in Genome-wide Association Studies. G3; doi: 10.1093/g3journal/jkad118
mvMAPIT: Multivariate Genome Wide Marginal Epistasis Test.
J. Stamp, L. Crawford (2023). mvMAPIT: Multivariate Genome Wide Marginal Epistasis Test. https://github.com/lcrawlab/mvMAPIT. (R Package)
Continuous nonenzymatic cross-replication of DNA strands with in situ activated DNA oligonucleotides.
Edeleva, E., Salditt, A., Stamp, J., Schwintek, P., Boekhoven, J., & Braun, D. (2019). Continuous nonenzymatic cross-replication of DNA strands with in situ activated DNA oligonucleotides. Chemical science, 10(22), 5807-5814.
Talks
mvMAPIT: Leveraging the genetic correlation between traits improves the detection of epistasis in genome-wide association studies.
Talk at Auditorium Lumiere, Centre de Congres, Lyon, France
Partitioning the non-additive variation of complex traits.
Talk at Lorentz Center, Leiden University, Leiden, Netherlands
Service and leadership
- 2015: Working for the Fundación Alalay in La Paz, Bolivia
- 2011 - 2012: Volunteering as Educational assistant at École Perceval in Paris, France
Languages
- German (native)
- English (proficient)
- French (fluent)
- Spanish (beginner)