Curriculum Vitae
Kevin Rue-Albrecht, Computational Biologist (Dipl. Ing., Ph.D.)
Education
2011 - 2015
PhD - Computational Infection Biology
University College Dublin (Ireland)
- Three rotation projects in computational and molecular biology.
- A thesis in computational infection biology.
For more details, please see the Research Experience section below.
2008 - 2011
Ingénieur diplômé
École Polytechnique Universitaire Polytech Nice-Sophia (France)
Major: Bioinformatics and Modelling for Biology
2006 - 2008
Class Préparatoire aux Grandes Écoles BCPST-Véto
Lycée Jean Rostand, Strasbourg (France)
BCPST: Biology, Chemistry, Physics, Earth Sciences
Research Experience
2020 - present
Computational Biologist & Biomedical Data Science Trainer
Sims Group (University of Oxford)
Contributing to computational biology research and training programs in functional genomics and single-cell sequencing analysis.
2017 - 2020
Postdoctoral Researcher - Computational Biology
Sansom Group (University of Oxford)
Contributed to the study of Inflammatory bowel disease pathogenesis and T-cell development through the development of computational pipelines for bespoke data analysis.
2016 - 2017
Postdoctoral Researcher - Computational Biology
Ratcliffe Group (University of Oxford)
Managed data and computational workflows for high-throughput sequencing projects including targeted DNA resequencing, ChIP-seq, and RNA-seq for renal cancer research.
2015 - 2016
Research associate - Bioinformatics & Biostatistics
Wilkins Group (Imperial College London)
Integrated genetic variation, proteomic and metabolomics data with associated deep phenotype data, in collaboration with the Morrell Group.
2012 - 2015
PhD - Computational Infection Biology
University College Dublin (Ireland)
Thesis: Comparative systems biology analyses of the bovine transcriptional response to species of the Mycobacterium genus.
Apr 2012 -
Jul 2012
PhD Rotation Project (3 of 3) - Molecular biology
O’Gara Group (University College Dublin)
Evaluated the role of a gene candidate underlying Staphylococcus aureus antibiotic resistance by Sanger sequencing and biofilm assay.
Jan 2012 -
Apr 2012
PhD Rotation Project (2 of 3) - Molecular biology
Ferguson Group (University College Dublin)
Expressed and purified a Hepatitis B protein construct for experimental screening of interacting drug fragments.
Sep 2011 -
Jan 2012
PhD Rotation Project (1 of 3) - Molecular biology
Shield Group / Gordon Group (University College Dublin)
Predicted Mycobacterium bovis epitopes in cattle using in silico structure-based modelling.
Jun 2010 -
Sep 2010
Intern - Computational Biology
Shield Group (University College Dublin)
Analysed structural disorder in Saccharomyces cerevisiae interacting proteins.
Project supervisor: Dr. Nora Khaldi
Jul 2009 -
Aug 2009
Intern - Molecular Biology
INSERM, Unité Mixte de Recherche S725, Biologie des Cellules Dendritiques Humaines (Strasbourg, France)
Expressed recombinant MHC class II molecules in HeLa cells.
Project supervisor: Henri de la Salle
Professional Experience
Oct 2022 -
Oct 2023
Software Developer - Consultant
Self-employed (Oxford, UK)
Developed three extension packages in the iSEE framework for the analysis and visualisation of omics data sponsored by Denali Therapeutics Inc.
Apr 2011 -
Jul 2011
Software Developer - Intern
MEDIT S.A. (Palaiseau, France)
Implemented functionality for structurally-constrained multiple alignment of protein sequences for the commercial software MED-SuMo.
Teaching Experience
2021 - present
Bioconductor Education Committee
Co-lead and contributor to the Bioconductor Education Committee, developing educational materials and organising training events for the Bioconductor community.
- Delivered lesson Orchestrating Large-Scale Single-Cell Analysis with Bioconductor (15-16 September 2025 – Barcelona, Spain).
- Developed lesson The Bioconductor project.
2020 - present
Oxford Biomedical Data Science (OBDS) Training Programme
Sims Group (University of Oxford)
Hands-on training delivered to small groups of researchers for the Oxford Biomedical Data Science (OBDS) Training Programme covering:
- Genomics on the Linux command line
- Python programming and data science
- R for data science and genomics
- Introduction to single-cell RNAseq data analysis using R
- Spatial Transcriptomics data analysis using R
- Containers for Reproducible Research
Jun 2020
iSEE: Interactive visualization of SummarizedExperiment objects
SIB Days 2020 (Online)
Co-organised and delivered a 2h30 online workshop (9-10 June 2020).
2019-
2020
R Code Clinic
Big Data Institute (University of Oxford)
Volunteer assisting individuals with any R programming questions as part of the BDI R Code Clinic series.
Jun 2019
Interactive visualisation of SummarizedExperiment objects using iSEE
Bioconductor conference 2019 (New York, USA)
Co-instructed a 2-hour workshop (26 June 2019).
2014
Molecular Genetics and Biotech
University College Dublin (Ireland)
Teaching assistant of BMOL20090 practicals for undergraduate students.
2014
Agricultural Microbiology
University College Dublin (Ireland)
Teaching assistant of MICR20010 practicals for undergraduate students.
Talks
2021
Bioconductor Conference
Airmeet (Online)
Oral presentations:
- Introduction to workshops - Informal welcome: Opening talk for the conference
- velociraptor: A Bioconductor toolkit for single-cell RNA velocity
- Bioconductor 20th anniversary: Set up an automated repository converting community contributions into an HTML slide deck
Jun 2019
Bioconductor Conference
New York, USA
Oral presentations:
- Talk: Interactive and reproducible visualization of
SummarizedExperimentobjects - Workshop: Interactive visualization of
SummarizedExperimentobjects withiSEE - Special Interest Group: Extending gene set and signature representations
2018
Genome Informatics
Cambridge, UK
Poster: Promiscuous expression of lincRNAs in medullary thymic epithelial cells
2017
NGS-SIG - Single-cell RNA-seq
Oxford, UK
Oral presentation: Variability of human dendritic cells responses to differentially invasive Salmonella strains at single-cell level
2017
Bioconductor Conference
Boston, USA
Oral presentations:
GOexpress: Visualise and summarise gene expression data using Gene OntologyTVTB: The VCF Tool Box: an effort to summarise and visualise variants
2015
Quantitative Genomics
London, UK
Poster: GOexpress: A R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data
2015
BOSC - ISMB/ECCB Conference
Dublin, Ireland
Oral presentation and poster:
2014
Society for General Microbiology (SGM)
Dublin, Ireland
Poster: Microarray analysis of the bovine macrophage response to Mycobacterium bovis, M. bovis Bacille Calmette-Guérin (BCG) and M. avium subspecies paratuberculosis
2014
Virtual Institute of Bioinformatics & Evolution (VIBE)
Carlow, Ireland
Oral presentation: The quest for meaningful visualisation of genome-wide expression data
2014
EMBO Conference: Microbiology after the genomics revolution - Genomes 2014
Paris, France
Poster: Transcriptome analysis reveals differential innate immune response to members of the Mycobacterium tuberculosis complex
2014
The Acid Fast Club, Summer Meeting
Berlin, Germany
Oral presentation: Transcriptome analysis reveals differential innate immune response of bovine macrophages to strains of the Mycobacterium tuberculosis complex
2014
UCD Conway Festival of Research & Innovation
Dublin, Ireland
Poster: Transcriptome analysis reveals differential innate immune response to members of the Mycobacterium tuberculosis complex
2014
Wellcome Trust Final Year PhD Students’ Meeting
London, UK
Poster: Transcriptome analysis reveals differential innate immune response to members of the Mycobacterium tuberculosis complex
2013
Association of Veterinary Teachers and Research Workers (AVTRW)
Hillsborough, Ireland
Oral presentation: Systems Biology of Host-Pathogen Interactions and Bovine Tuberculosis - Differential transcriptional response of bovine monocyte-derived macrophages following different mycobacterial infections
2013
Animal Health Ireland Workshop & Conference
Rochestown Park Hotel, Cork
Poster: Microarray analysis of the bovine macrophage response to Mycobacterium bovis, M. bovis Bacille Calmette-Guérin (BCG) and M. avium subspecies paratuberculosis
2013
Virtual Institute of Bioinformatics and Evolution (VIBE)
Galway, Ireland
Oral presentation: Systems Biology of Host-Pathogen Interactions and Bovine Tuberculosis - Differential transcriptional response of bovine monocyte-derived macrophages following different mycobacterial infections
2013
Computational Biology & Innovation Symposium
Dublin, Ireland
Poster: Microarray analysis of the bovine macrophage response to Mycobacterium bovis, M. bovis Bacille Calmette-Guérin (BCG) and M. avium subspecies paratuberculosis
2013
Dublin Academy of Pathogenomics & Infection Biology (DAPI)
Dublin, Ireland
Poster: Microarray analysis of the bovine macrophage response to Mycobacterium bovis, M. bovis Bacille Calmette-Guérin (BCG) and M. avium subspecies paratuberculosis
Certifications
Jul 2017 -
Sep 2017
Machine Learning
Coursera (Online)
Supervised and unsupervised learning, best practices, and key algorithms.
Oct 2015 -
Nov 2015
Python for Genomic Data Science
Coursera (Johns Hopkins University)
Introduction to Python programming for genomic data analysis using Jupyter notebooks.
Oct 2015 -
Nov 2015
Command Line Tools for Genomic Data Science
Coursera (Johns Hopkins University)
Managing and analyzing large-scale genomic datasets using Unix command-line tools and workflows.
Oct 2015 -
Nov 2015
Bioconductor for Genomic Data Science
Coursera (Johns Hopkins University)
Using the Bioconductor project in R to perform analysis of genomic data.
Oct 2015 -
Nov 2015
Statistics for Genomic Data Science
Coursera (Johns Hopkins University)
Statistical methods for genomic data analysis including experimental design and inference.
Aug 2013 -
Dec 2013
Network Analysis in Systems Biology
Coursera (Online)
Data integration and statistical methods for systems biology including clustering, enrichment analysis, and network construction.