Jeremie Kalfon
Doctorat Joint - Mathématiques Appliquées - ENS ULM
Paris, Ile-de-France
Summary
👤
Senior🎓
Top SchoolJeremie Kalfon is a computational biologist and engineer with nine years of experience blending AI, genomics, and full-stack software to accelerate translational research and drug target discovery. Currently pursuing a joint PhD at ENS Ulm and Institut Pasteur, he has held senior roles at the Broad Institute and led the computational biology team at WhiteLab Genomics, building an Atlas of cellular biomarkers aggregating 800+ single-cell datasets. A co-founder of PiPle and active open-source contributor (notably improvements to the CaImAn calcium-imaging toolbox), he moves fluidly between production engineering—Nextflow, Terra, GCP, Python/R—and advanced ML for multi-omic integration and conditional VAEs. Known for translating academic research into startup projects and clinical insights, he also mentors biotech entrepreneurship through Nucleate Paris.
8 years of coding experience
5 years of employment as a software developer
Studen exchange ( one semester ) , Information Technology, Studen exchange ( one semester ) , Information Technology at Tecnológico de MonterreyBaccalauréat, Scientific, Baccalauréat, Scientific at Lycée Janson-de-SaillyPh.D. in Artificial Intelligence, Artificial Intelligence, Ph.D. in Artificial Intelligence, Artificial Intelligence at Pasteur Institute - ENS UlmMaster of science, Computational Intelligence, Master of science, Computational Intelligence at University of KentFrench Diplome d'ingénieur, Biomedical/Medical Engineering, French Diplome d'ingénieur, Biomedical/Medical Engineering at ECE. Ecole d'ingénieurs. Engineering School.Graduate Certificate, Biology, Graduate Certificate, Biology at Harvard University
French, English, Spanish
Stackoverflow
1reputation
0reached
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Github Skills (3)
python10
deconvolution9
jupyter-notebook8
Programming languages (14)
Github contributions (5)
flatironinstitute/CaImAn
May 2017 - Jul 2017
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
Role in this project:
Backend Developer
Backend DeveloperContributions:93 commits, 3 PRs, 64 pushes in 1 month
Contributions summary:Jeremie contributed to the codebase by creating an efficiency calculator and reviewing pipeline implementations, specifically within the context of calcium imaging analysis. The user modified the demo pipeline, incorporating a new package that calculates differences within the caiman software. These changes suggest involvement in expanding functionality and debugging aspects of the calcium imaging analysis toolbox.
extractionpythondeconvolutionimagingcnmf
jkobject/AMLproject
Feb 2020 - Nov 2022
We are working on the AML pedDep project with DFCi & the BroadInsitute, looking at CRCs and their relation to genomic dependencies
Contributions:1 PR, 149 pushes, 1 branch in 2 years 9 months
dependenciesworking-ongenomicsamlbioinformatics
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