Unraveling transcriptional flow from single cell transcriptomic data...

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Louis Faure

PhD candidate

Medical University of Vienna

About me

My PhD aims to to expand our views on the evolution of neural crest properties. More precisely by unravelling the cell fate decisions of neural crests cells during mouse development and by exploring the heterogeneity of glial cells during development and adulthood in mouse.

My current work is mainly based on the usage of bioinformatic tools such as single-cell transcriptomics data analysis, clustering, pseudotime ordering, combined with biological experiments for validation.

Interests

  • Computational Biology
  • Developmental Biology
  • Evolution
  • Exo-biology

Education

  • PhD candidate in Neuroscience, 2018

    Medical University of Vienna

  • Diploma Institute for Technology Innovation, 2017

    PSL University, Paris

  • Msc in Interdisciplinary Approaches in Life Science, 2016

    Center for Research and Interdisciplinarity, Paris

  • BSc in Life Science, 2013

    Center for Research and Interdisciplinarity, Paris

Skills

python

Python

R

R

Tux

Linux

server

Server managment

gpu3

GPU data analysis

Fiji

ImageJ

insitu

FISH techniques

Cloning

Cloning

ableton

Music production

Software

*

a python package for the study of particle dynamics from 2D tracks

a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.

A python implementation of SimplePPT algorithm, with GPU acceleration.

PhD Publications

Surface flow for colonial integration in reef-building corals

Current Biology, (2022)

Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin

Nature Genetics, (2021)

Prototypical pacemaker neurons interact with the resident microbiota

Proceedings of the National Academy of Sciences, (2020)

Single cell RNA sequencing identifies early diversity of sensory neurons forming via bi-potential intermediates

Nature Communications, (2020)

Master Publications

Two different cell-cycle processes determine the timing of cell division in Escherichia coli

eLife, (2021)

Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph

Entropy, (2020)

Experience

 
 
 
 
 

Lecturer

EMBL-EBI: NEUcrest Big Data course

April 2021 – April 2021 Online
Presentation about methods related to trajectory inference analysis.
 
 
 
 
 

Intern

INSERM U900 Bioinformatics and computational biology of cancer unit

January 2018 – June 2018 Curie Institute, Paris
Gene Regulation Network inference using pseudotime ordering of scRNAseq data.
 
 
 
 
 

Intern

Institute for Theoretical Biology

April 2017 – July 2017 Humboldt University, Berlin
Mathematical modeling of microbial metabolism & cyanobacterial phototrophic growth. Kinetic modeling and flux balance analysis.
 
 
 
 
 

Intern

Inserm u1001 Research Lab

January 2017 – April 2017 Descartes University, Paris
Heterogeneity of the spontaneous DNA replication errors in single isogenic E.coli cells.
 
 
 
 
 

Intern

Laboratory of Biochemistery

September 2016 – December 2016 ESPCI, Paris
Abzymes Project: Quantitative selection and evolution at by high throughput screening of antibodies libraries for DNAse reaction, using microfluidics.
 
 
 
 
 

Teaching Assistant

Labsprint at Petnica Science Center

August 2016 – August 2016 Petnica, Serbia
Worked as a teaching assistant for 2nd year students from Undergraduate program “Frontiers in Life Science”. Helping the lecturer for the setup of the courses, preparing lab supplies, Giving advices to the students for their projects.
 
 
 
 
 

Intern

Microbial Morphogenesis and Growth Lab

January 2016 – July 2016 Pasteur Institute, Paris
Single-cell study, tracking of the starting of chromosomal segregation over several generations in E. coli, using fluorescence microscopy and quantitative image analysis.
 
 
 
 
 

Intern

Laboratory of Molecular and Cellular Biology of Eukaryotes

January 2015 – June 2015 Curie Institute, Paris
Study of regulations of mitochondrial fusion/fission mechanisms in S. cerevisiae. Gene tagging/deletion; Glycerol growth analysis; Microscopy with GFP-tagged strains; Cell transformation.

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