Summary

Computational Biologist with a focus on gene expression and sequencing-based screen analyses. Expert in single-cell transcriptomics, epigenetics, genome annotation, large-scale pooled and arrayed screens. Academic, biomedical, and industry background, including team and project management.

Experience

Senior Computational Biologist in the Next Generation Sequencing and Datapoints Teams, Ginkgo Bioworks, Boston, MA, USA (April 2022 - Present)

  • Building bioinformatics workflows and conducting analyses for single-cell RNA sequencing and arrayed DRUG-seq genetic screens
  • Designed single-cell RNA sequencing assays, trained team members, implemented bioinformatics workflow, and conducted analyses to improve packaging yield and tissue-specificity of AAV vectors
  • Implemented bioinformatics workflows and conducted analyses of high-throughput sequencing-based pooled screens to identify sequences improving the stability and translation of RNA vectors
  • Analyzed high-throughput RNA sequencing time-course experiments to identify bottlenecks in molecule biosynthesis following fungi cell engineering
  • Developed annotation standards and contributed reference-based, transcriptome-based, and de novo genome annotations for a yeast genome rewriting project

Single-Cell Genomics Team Lead in the Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA (May 2018 - March 2022)

  • Led team with a focus on molecular profiling of the tumor micro-environment using single-cell RNA and ATAC sequencing
  • Developed workflows from clinical sample collection to sequencing data analysis
  • Contributed to more than 30 clinical studies and atlases, including large consortia such as the Human Tumor Atlas Network

Research Scientist in the Gimelbrant Lab, Dana-Farber Cancer Institute, Boston, MA, USA (July 2013 - May 2018)

  • Investigated the mechanisms and function of genome-wide monoallelic gene expression
  • Developed a machine-learning tool set and web application to infer monoallelic expression from chromatin marks
  • Conducted sequencing-based shRNA and drug screening to identify factors controlling allelic expression
  • Implemented an inDrop single-cell RNA sequencing platform

Research Fellow in the Bartolomei Lab, University of Pennsylvania School of Medicine, Philadelphia, PA, USA (March 2008 - June 2013)

  • Investigated genetic and epigenetic controls of cell-type specific gene expression
  • Characterized functionally distinct classes of binding sites for the transcriptional regulator protein CTCF
  • Developed a cell model for the high-throughput screening of factors capable of reverting Rett syndrome
  • Awards: Post-doctoral fellowships from the French Foundation for Medical Research and the American Heart Association

PhD Candidate in the Avner Lab, Pasteur Institute, Paris, France (September 2003 - September 2007)

  • Investigated genetic and epigenetic factors controlling X chromosome inactivation
  • Identified genomic elements controlling X chromosome inactivation using targeted deletions in mouse
  • Award: Doctoral fellowship from the French Association for Research against Cancer

Education

PhD in Development Biology from Pierre and Marie Curie University, Paris, France (October 2003 - September 2007)

Master in Molecular, Cell, and Developmental Biology from Pierre and Marie Curie University, Paris, France (September 2002 - July 2003)

Bachelor in Cell Biology from Paul Sabatier University, Paris, France (September 1998 - July 2002)

Technical Skills

Programming: Bash, R, Python, Perl, Awk, SQL, Git, Docker, Snakemake, Nextflow

Computational Biology: Bulk and single-cell transcriptomics and epigenomics data analysis, sequencing-based arrayed and pooled screen analysis, genome annotation

Experimental Biology: Transcriptomics, epigenomics, molecular biology, mouse embryology, cell biology, microscopy

Management: Team hiring and training, lab and project management, data and metadata collection and sharing

Other Experiences

Instructor and Editor with Software Carpentry, online and in Boston, MA, USA (2018 - Present)

Learning Circle Facilitator with Peer 2 Peer University and BosLab, online and in Boston, MA, USA (2018 - 2021)

Course Developer with the University of the People, online (2015)

Teaching Assistant with the University of Pennsylvania School of Science, Philadelphia, PA, USA (2012)

Science Project Mentor with iPraxis, Philadelphia, PA, USA (2008-2010)

Publications

Pubmed

protocols.io