Hello, I'm Benjamin Demaille! 👋

Research Engineer – INSERM (IPNP, U1266)

Welcome to my GitHub profile!
I am a bioinformatics engineer passionate about cellular biology and developing computational solutions for genomic and transcriptomic research.
Here you'll find a collection of my projects, contributions, and collaborations.

🧬 About Me

• 🎓 Graduated from the BioMed Master's program at the University of Montpellier and the GENIOMHE Bioinformatics Master's program at Paris-Saclay University.
• 🧪 Skilled in cellular biology, developmental biology, and cancer research.
• 💻 Proficient in Python, R, genomics, transcriptomics, statistics, and Machine Learning.
• 🧠 Currently Research Engineer (INSERM, IPNP – U1266) since August 2024.

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🔧 Skills & Tools

🧪 Experimental Biology

• Protein Assay
• PCR
• Transfection
• Western Blot
• Cell Culture

💻 Bioinformatics

• Python, R
• DESeq2, EdgeR, Seurat
• Scikit-Learn
• Hadoop, Snakemake
• Git, Galaxy

🌱 Soft Skills

• Patient, thoughtful
• Team player, autonomous
• Thorough, curious

🌍 Languages

• English: Conversational reading and speaking
• French: Native

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🎓 Education

• Master's in BioMed – University of Montpellier
• Master's in Bioinformatics (GENIOMHE) – Paris-Saclay University

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💼 Professional Experience

Research Engineer (Permanent position)

INSERM – Institut de Psychiatrie et Neurosciences de Paris (IPNP, U1266)
📅 Since August 2024

• Bioinformatics support for transcriptomic and single-cell studies in neuroscience and psychiatry
• Data integration, RNA-seq and spatial transcriptomics analyses

Bioinformatics Engineer

Institut Curie, Paris
📅 2022 – 2023 (20 months)

• Computational Biologist in the U932 - Salmon Team
• Utilized Kallisto for bulk RNA-Seq alignment and RNA Velocity on scRNA-Seq
• Conducted bulk RNA-Seq analysis with DESeq2
• Performed scRNA-Seq, 10X Visium, and Vizgen MERFISH analysis with Seurat

Bioinformatics Engineer

IFB-Core and ARTBio Sorbonne University, Paris
📅 2022 (2 months)

• Developed workflows for COVID-19 surveillance

M2 Internship

LISN, Orsay
📅 2019 (6 months)

• Statistics and Genetics: Dimension reduction adapted to paleogenomics
• Simulated demographic scenarios with msprime (Python)
• Tested and improved dimension reduction methods
• Contributed to the R package TemporalDR

M1 Internship

CEA Fontenay-aux-Roses, Paris
📅 2018 (5 months)

• Transcriptomic analyses of murine neural progenitors
• Whole transcriptome analysis with R of Affymetrix data
• Used Ingenuity Pathway Analysis
• scRNA-Seq analysis via Monocle R

M1 Internship

Institut Cochin Inserm U1016, Paris
📅 2017 (2 months)

• Transcriptomic study on the effect of interleukin 7 on chemokine production by vaginal mucosa cells
• Transcriptomic analysis of primate tissues treated with IL-7
• Created R scripts for whole transcriptome analysis of Affymetrix data

M2 Internship

IGH CNRS UMR9002, Montpellier
📅 2015 (6 months)

• IMGT® Project
• Identification of genotype and haplotypes of IG and TR genes from NGS repertoire sequencing analysis
• Created Perl scripts, used UNIX environment

M1 Internship

IGMM CNRS UMR5535, Montpellier
📅 2014 (2 months)

• Nuclear Control of Cell Proliferation
• Studied phosphorylation of histone H3 at serine 57
• Western blot, BCA, Histone purification, R-HPLC, Cell culture (U2OS)

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📚 Publications

Articles

• Switching of RNA splicing regulators in immature neuroblasts: a key step in adult neurogenesis
  Corentin Bernou, Marc-André Mouthon, Mathieu Daynac, Benjamin Demaille, et al.
  eLife 12:RP87083 — 🔗 Link to article

• Inference of population genetic structure from temporal samples of DNA
  Olivier François, Séverine Liégeois, Benjamin Demaille, Flora Jay
  bioRxiv 801324 — 🔗 Link to article

Posters

• Abstract 7642: Activated FAP+ cancer-associated fibroblasts in non-muscle invasive bladder cancer are associated with progression to muscle-invasive disease
  Abdenour Abbas, Shrisha Maskey, Evan Cheng, Ziao Li, Benjamin Demaille, et al.
  Cancer Research, 15 March 2024; 84 (6_Supplement): 7642.

• Abstract 4603: Single-cell and spatial dissection of the effect of combined PD-L1 and TGFb blockade by bintrafusp alfa from the ICING window-of-opportunity trial in resectable locally advanced HNSCC patients
  Caroline Hoffmann, Jan-Timon Werle, Jocelyn Gal, Benjamin Demaille, et al.
  Cancer Research, 84(6_Supplement), 4603-4603.
  🔗 Link to article

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📫 Contact

• 📱 Phone: +33 6 33 12 17 37
• 📧 Email: benjamin.demaille@icloud.com
• 🏛️ Institution: INSERM U1266 – Institut de Psychiatrie et Neurosciences de Paris (IPNP)

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⭐️ From BenjaminDEMAILLE