Denis Bebek
Research Engineer at Stanford University School of Medicine
San Francisco, California, United States
Summary
👤
Senior🎓
Top SchoolDenis Bebek is a research engineer with 11 years of experience at the intersection of computational biology and single-cell epigenomics, currently leading a team at Stanford School of Medicine to map immune cell chromatin landscapes. He developed the tSpace algorithm and analytic pipelines that order complex cellular trajectories, applying them to millions of cells and 40 histone marks to reveal oscillatory chromatin conformations linked to immune function. His work has driven novel systems-level integrations of EpiTOF, ChIP-seq, and single-cell transcriptomics, resulting in corresponding authorships and early scientific independence. A proactive mentor and educator, he combines deep wet-lab training in proteomics and genetics with advanced machine learning and statistical tooling to translate high-dimensional data into biologically actionable insights.
11 years of coding experience
6 years of employment as a software developer
Doctor of Philosophy (Ph.D.), Genetics, Cancer Genetics, Proteomics, Doctor of Philosophy (Ph.D.), Genetics, Cancer Genetics, Proteomics at Faculty of Biological and Environmental Sciences, University of HelsinkiHigh school, upper secondary education, High school, upper secondary education at Grammar school Mate Balote - PorecM.Sc., Biotechnology, Molecular Biotechnology, with honors, M.Sc., Biotechnology, Molecular Biotechnology, with honors at Faculty of Food Technology and Biotechnology, University of Zagreb
English, Croatian, Serbian, German
Github Skills (9)
exploratory10
exploratory-data-analysis9
data-analysis8
python8
single-cell-analysis3
pytorch1
machine-learning1
inference1
deep-learning1
Programming languages (1)
Github contributions (5)
hylasD/tSpace
May 2018 - Jun 2020
Contributions:52 commits, 40 pushes, 6 comments in 2 years 1 month
hylasD/MATLAB_version_tSpace
Jun 2018 - Mar 2019
Contributions:24 pushes in 9 months
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