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Kevin Rue-Albrecht
Computational Biologist (Dipl. Ing., Ph.D.)
I am a computational biologist at the University of Oxford.
My research interests in computational biology include software engineering best practices, DevOps, single-cell genomics, and interactive data visualization. I particularly enjoy using and contributing R packages as part of the Bioconductor project. A list of software packages that I maintain or contributed to is available on the “Software” page of my website.
My academic research primarily explores the host immune response to infectious diseases, inflammation, and self-antigens.
Education
University College Dublin
Ph.D. in Computational Infection Biology
Dublin, Ireland
2015
Thesis: Comparative systems biology analyses of the bovine transcriptional response to species of the Mycobacterium genus.
- Bioconductor package for Gene Ontology (GO) analysis of gene expression data (
GOexpress).
École Polytechnique Universitaire Polytech Nice-Sophia
Ingénieur diplômé, MSc
Sophia Antipolis
2011
- Pharmacology
- Biotechnology
- Toxicology
- Environmental Safety
- Bioinformatics
Major: Bioinformatics and Modelling for Biology
CPGE BCPST Véto - Lycée Jean Rostand
Class Préparatoire aux Grandes Écoles
Strasbourg, France
2008
- Biology
- Chemistry
- Physics
- Earth Sciences
- Mathematics
- Programming
Research Experience
Computational Biologist - Biomedical Data Science trainer
Sims Group, MRC WIMM Centre for Computational Biology, University of Oxford
Oxford, UK
2020-present
- Development and delivery of training materials to cohorts of trainees as part of the Oxford Biomedical Data Science Training Programme.
- Development of novel bioinformatics tools and pipelines following software engineering best practices.
- Contribution to scientific reports and publications.
Postdoctoral Researcher - Computational Biologist
Sansom Group, Kennedy Institute of Rheumatology, University of Oxford
Oxford, UK
2017-2020
- Molecular pathogenesis of inflammatory bowel disease, in collaboration with the Powrie Group.
- Role of thymic epithelial cells in T-cell development, in collaboration with the Holländer Group and Ponting Group.
- Contribution to software pipelines for single-cell genomics data analysis ( sansomlab/tenx).
- Bioconductor package for interactive exploration of
SummarizedExperimentobjects (iSEE). - R package for the analysis of ChIP-seq data ( kevinrue/deeperTools).
Postdoctoral Researcher - Computational Biologist
Ratcliffe group, Target Discovery Institute, University of Oxford
Oxford, UK
2016 - 2017
- Management and quality control of genomics data for analyses of DNA targeted resequencing, ChIP-seq, RNA-seq in the context of oxygen sensing and renal cancer.
- Prototype of MeteorJS application to manage sequencing data ( kevinrue/Seqbook).
Research associate - Bioinformatics & Biostatistics
Prof. Martin Wilkins’s Group, Imperial Centre for Translational and Experimental Medicine, Imperial College London
London, UK
2015 - 2016
- Integration of genetic variation, proteomic and metabolomics data and associated deep phenotype data, in collaboration with the Morrell Group.
- Bioconductor package for the analysis of genetic variants (
TVTB).
Ph.D. student - Computational Infection Biology, rotation 3
Prof. James O’Gara’s Group, UCD Science Centre North
Dublin, Ireland
Apr. 2012 - Jul. 2012
- Evaluation of a gene candidate underlying Staphylococcus aureus antibiotic resistance by Sanger sequencing and biofilm assay
Ph.D. student - Computational Infection Biology, rotation 2
Dr Neil Ferguson’s Group, UCD Conway Institute
Dublin, Ireland
Jan. 2012 - Apr. 2012
- Expression and purication of a Hepatitis B protein construct for experimental screening of interacting drug fragments.
Ph.D. student - Computational Infection Biology, rotation 1
Shields Lab, UCD Complex and Adaptive Systems Laboratory (CASL)
Dublin, Ireland
Sep. 2011 - Jan. 2012
- In silico structure-based prediction of Mycobacterium bovis epitopes in cattle (supervisor: Dr. Anthony Chubb).
Research Assistant - Computational Biology, intern
Shields Lab, University College Dublin
Dublin, Ireland
Jun. 2010 - Sep. 2010
- Computational analysis of structural disorder in Saccharomyces cerevisiae interacting proteins.
Research Assistant, intern
INSERM, Unité Mixte de Recherche S725, Biologie des Cellules Dendritiques Humaines
Strasbourg, France
Jul. 2009 - Aug. 2009
- Recombinant protein expression of MHC class II molecules in HeLa cells.
Professional Experience
Software developer, intern
Palaiseau, France
Apr. 2011 - Jul. 2011
- Implementation of structurally-constrained multiple alignment of protein sequences for the commercial software MED-SuMo.
Teaching Experience
Bioconductor teaching committee
Google Meet (online)
2021 - present
Development of online lessons in The Carpentries lesson incubator. Lead developer of the lesson The Bioconductor project.
Oxford Biomedical Data Science training programme
Microsoft Teams (online)
2020 - present
Full-time trainer for a course of four to seven weeks run three times a year. Lessons cover Unix, Python and R for data science and biomedical research.
Intuitive interactive data exploration with iSEE
Swiss Institute of Bioinformatics
Zoom (online)
2020
Co-organizer of a 2h30 workshop at the SIB Days 2020.
R Code Clinic
Big Data Institute, University of Oxford
Oxford, UK
2019 - present
Volunteer to sit with individuals and assist them with any R problems they need help with. Website: https://bdicodeclub.netlify.com/.
Interactive visualisation of SummarizedExperiment objects using iSEE
New York, USA
2019
Co-instructor of a 2-hour workshop at the Bioconductor conference 2019.
Molecular Genetics and Biotech
Dublin, Ireland
2014
Teaching assistant of BMOL20090 at University College Dublin.
Agricultural Microbiology
Dublin, Ireland
2014
Teaching assistant of MICR20010 at University College Dublin.
Funding and Awards
Bioconductor 2019 conference
Conference fee waiver and travel grant for BioC 2019.
New York, USA
2019
- Instructor of a 2-hour workshop at the Bioconductor conference 2019.
- Co-organiser of the Special Interest Group (SIG) Extending gene set and signature representations.
ISMB/ECCB conference
Conference fee waiver
Dublin, Ireland
2015
23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 14th European Conference on Computational Biology (ECCB). Special Interest Group (SIG) Bioinformatics Open Source Conference (BOSC).
5th Annual PhD Symposium in Computational Biology & Innovation
Best oral presentation
Dublin, Ireland
2014
Wellcome Trust Four-year PhD Programme
Computational Infection Biology
Dublin, Ireland
2011
Title: Transcriptome analysis of the bovine macrophage response to Mycobacterium tuberculosis complex strains.
Organiser and Chair
Bioconductor conference 2021
Airmeet (online)
2021
Co-organiser and point of contact for the coordination and testing of live workshops.
European Bioconductor conference 2020
Airmeet (online)
2020
Co-organiser, session chair, and support for the coordination and testing of live workshops.
Special Interest Group
New York, USA
2019
Genomics Forum
Kennedy Institute of Rheumatology, University of Oxford
Oxford, UK
2018-2020
Coordinator of a weekly meeting to present and discuss ongoing projects in the institute.
Bioinformatics Seminar
Dublin, Ireland
2013 - 2014
Co-organiser of a weekly meeting to present and discuss ongoing projects in the university.
Computational Biology and Innovation PhD Symposium
Dublin, Ireland
2012
Co-organiser in charge of sponsorships and the abstract book.
Training and Courses
Bioconductor for Genomic Data Science
Coursera, Johns Hopkins University
N/A
2015
This course is part of the Genomic Data Science Specialization.
Command Line Tools for Genomic Data Science
Coursera, Johns Hopkins University
N/A
2015
This course is part of the Genomic Data Science Specialization.
Python for Genomic Data Science
Coursera, Johns Hopkins University
N/A
2015
This course is part of the Genomic Data Science Specialization.
Statistics for Genomic Data Science
Coursera, Johns Hopkins University
N/A
2015
This course is part of the Genomic Data Science Specialization.
Sequence Data Analysis Training
Wageningen Institute of Animal Sciences
Wageningen, Netherlands
2013
Introductory Statistics using R for Computational Biologists
Dublin, Ireland
2012
Professional memberships
Bioconductor Community Advisory Board
http://www.bioconductor.org/about/community-advisory-board/
N/A
2021 - present
Peer review
Selected Publications and Posters
Orchestrating single-cell analysis with Bioconductor.
Nat Methods.
N/A
2019
Amezquita, R. A., A. T. L. Lun, E. Becht, V. J. Carey, L. N. Carpp, L. Geistlinger, F. Marini, K. Rue-Albrecht, D. Risso, C. Soneson, L. Waldron, H. Pages, M. L. Smith, W. Huber, M. Morgan, R. Gottardo and S. C. Hicks
The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages
Immunity.
N/A
2019
Schulthess, J., S. Pandey, M. Capitani, K. C. Rue-Albrecht, I. Arnold, F. Franchini, A. Chomka, N. E. Ilott, D. G. W. Johnston, E. Pires, J. McCullagh, S. N. Sansom, C. V. Arancibia-Carcamo, H. H. Uhlig and F. Powrie
iSEE: Interactive SummarizedExperiment Explorer.
F1000Res.
N/A
2018
Rue-Albrecht, K., F. Marini, C. Soneson and A. T. L. Lun
Conference presentations
Bioconductor
Oral presentations.
Airmeet (online)
2021
- Introduction to workshops - Informal welcome: Opening talk for the conference.
- Talk:
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.
Bioconductor
Oral presentations.
New York, USA
2019
- Talk: Interactive and reproducible visualization of
SummarizedExperimentobjects. - Workshop: Interactive visualization of
SummarizedExperimentobjects withiSEE. - Special Interest Group: Extending gene set and signature representations.
Genome Informatics
Poster.
Cambridge, UK
2018
Title: Promiscuous expression of lincRNAs in medullary thymic epithelial cells
NGS-SIG - Single-cell RNA-seq
Oral presentation.
Oxford, UK
2017
Title: Variability of human dendritic cells responses to differentially invasive Salmonella strains at single-cell level.
Bioconductor
Oral presentations.
Boston, USA
2017
GOexpress: Visualise and summarise gene expression data using Gene OntologyTVTB: The VCF Tool Box: an effort to summarise and visualise variants
Quantitative Genomics
Poster.
London, UK
2015
Title: GOexpress: A R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data.
BOSC - ISMB/ECCB conference
Oral presentation and poster.
Dublin, Ireland
2015
Society for General Microbiology (SGM)
Poster.
Dublin, Ireland
2014
Title: Microarray analysis of the bovine macrophage response to Mycobacterium bovis, M. bovis Bacille Calmette-Guérin (BCG) and M. avium subspecies paratuberculosis.
Virtual Institute of Bioinformatics & Evolution (VIBE)
Oral presentation.
Carlow, Ireland
2014
Title: The quest for meaningful visualisation of genome-wide expression data.
EMBO conference: Microbiology after the genomics revolution - Genomes 2014
Poster.
Paris, France
2014
Title: Transcriptome analysis reveals differential innate immune response to members of the Mycobacterium tuberculosis complex.
The Acid Fast Club, Summer Meeting
Oral presentation.
Berlin, Germany
2014
Title: Transcriptome analysis reveals differential innate immune response of bovine macrophages to strains of the Mycobacterium tuberculosis complex.
UCD Conway Festival of Research & Innovation
Poster.
Dublin, Ireland.
2014
Title: Transcriptome analysis reveals differential innate immune response to members of the Mycobacterium tuberculosis complex.
Wellcome Trust Final Year PhD Students’ Meeting
Poster.
London, UK
2014
Title: Transcriptome analysis reveals differential innate immune response to members of the Mycobacterium tuberculosis complex.
Association of Veterinary Teachers and Research Workers (AVTRW)
Oral presentation.
Hillsborough, Ireland
2013
Title: Systems Biology of Host-Pathogen Interactions and Bovine Tuberculosis - Differential transcriptional response of bovine monocyte-derived macrophages following different mycobacterial infections
Animal Health Ireland Workshop & Conference
Poster.
Rochestown Park Hotel, Cork
2013
Title: Microarray analysis of the bovine macrophage response to Mycobacterium bovis, M. bovis Bacille Calmette-Guérin (BCG) and M. avium subspecies paratuberculosis.
Virtual Institute of Bioinformatics and Evolution (VIBE)
Oral presentation.
Galway, Ireland
2013
Title: Systems Biology of Host-Pathogen Interactions and Bovine Tuberculosis - Differential transcriptional response of bovine monocyte-derived macrophages following different mycobacterial infections.
Computational Biology & Innovation Symposium
Poster.
Dublin, Ireland
2013
Title: Microarray analysis of the bovine macrophage response to Mycobacterium bovis, M. bovis Bacille Calmette-Guérin (BCG) and M. avium subspecies paratuberculosis.
Dublin Academy of Pathogenomics & Infection Biology (DAPI)
Poster.
Dublin, Ireland
2013
Title: Microarray analysis of the bovine macrophage response to Mycobacterium bovis, M. bovis Bacille Calmette-Guérin (BCG) and M. avium subspecies paratuberculosis.
Language
French
Native.
N/A
N/A
English
Fluent. TOEIC score 970.
N/A
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Italian
Working knowledge.
N/A
N/A
Spanish
Limited. Used to be fluent though .
N/A
N/A
German
Limited. Haven’t practiced in a long time.
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