Best practices for single-cell histone modification analysis
Felix Raimundo, Pacôme Prompsy, Jean-Philippe Vert, Celine Vallot (2023). " Best practices for single-cell histone modification analysis ." Genome Biology.
CV
Education
- PhD in Computational Biology, Mines Paris, 2022
- M.S. in Computer Science, Telecom Paris, 2016
- B.S. in Mathematics and Physics, Janson de Sailly 2012
Work experience
- 2024-present: Postdoctoral Fellow, UMass Chan Medical School
- Part of Pr. Jill Moore’s group.
- 2023-2024: Senior Computational Biologist, ErvImmune
- Topic: Cancer immunotherapies target discovery on Endogenous Retro Viruses (ERV).
- Lead for the computational biology team.
- Moved the legacy academic analysis to reproducible and scalable pipelines.
- Oversaw the team grow from 1 to 4 people.
- 2023-2024: Associate Researcher, Centre de recherche en cancerologie de Lyon
- Topic: Machine learning for immunology.
- 2019-2022: Student Researcher / PhD Candidate, Google Deepmind (previously Google Brain) and Institut Curie
- Topic: Unsupervised deep learning for single-cell epigenomics and transcriptomics data in breast cancer: tumor heterogeneity and resistance to chemotherapy
- Supervisors: Jean-Philippe Vert, PhD and Celine Vallot, PhD
- Summer 2018: Research Intern, Google Brain
- Topic: Speeding up variant calling in DeepVariant
- Supervisor: Cory McLean, PhD
- 2017-2018: PhD Candidate, Ecole Polytechnique
- Dropped out
- Topic: New Algorithms and Optimizations for Population-Scale Deep Genome Analysis
- Worked on adapting DeepVariant for detecting Structural Variations with paired end short read sequencing.
- Supervisors: Yanlei Diao, PhD and Avinash Abhyankar, MD, PhD
- Spring-Summer 2015: Software Engineer Intern, Youtube
- Topic: Leveraging the properties of entities in ontologies to organize YouTube Content.
- Lead to a patent: Methods, systems, and media for presenting content organized by category
- Supervisor: Alexander Pak, PhD
- Fall-Winter 2014: Firmware Engineer Intern, Sigma Designs
- Topic: Implement secure Suspend-to-RAM on a muti-processor chip.
Service
- PC for the MLCSB COSI at ISMB: 2023, 2024
- Reviewer for RECOMB: 2022, 2023, 2024
- Reviewer for ICLR: 2022, 2023
- Co-organizer of Bits in Bio Paris
Publications
Methods, systems, and media for presenting content organized by category
Alexander Pak, Felix Raimundo, Sertan Girgin, Raphael Marinier, Vincent Simonet (2021). " Methods, systems, and media for presenting content organized by category ." US Patent.
Machine learning for single-cell genomics data analysis
Felix Raimundo, Laetitia Meng-Papaxanthos, Celine Vallot, Jean-Philippe Vert (2021). " Machine learning for single-cell genomics data analysis ." Current Opinion in Systems Biology.
Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis
Felix Raimundo, Celine Vallot, Jean-Philippe Vert (2020). " Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis ." Genome Biology.
Missdeepcausal: Causal inference from incomplete data using deep latent variable models
Mayer, Imke and Josse, Julie and Raimundo, Félix and Vert, Jean-Philippe (2020). " MissDeepCausal: Causal Inference from Incomplete Data Using Deep Latent Variable Models ." arXiv.