Curriculum Vitae

Elena Bernabeu, MSc, PhD

Employment

Bioinformatician - Research Services

Genomics England
London, UK (Hybrid) - June 2023 to Present

Research bioinformatician within the bioconsulting team.

Post-doctoral Research Fellow

Institute of Genetics and Cancer, The University of Edinburgh
Edinburgh, UK - October 2021 to June 2023

Researching ageing and Alzheimer’s disease making use of multi-omics data from Generation Scotland, within Dr. Riccardo Marioni’s group. Collaboration with Dr. Catalina Vallejos and Dr. Matthew Robinson. Work funded by Alzheimer’s Society.

Education

PhD in Genetics and Genomics

The Roslin Institute, The University of Edinburgh
Edinburgh, UK - September 2017 to August 2021

Thesis title: Unraveling the effect of sex on human genetic architecture

Supervised by Professor Albert Tenesa and Dr. James Prendergast. Funded by The Roslin Foundation’s Steve Bishop Scholarship. Worked with large population cohort UK Biobank to find sex differences in genetic programming across human phenotypes using quantitative genetics and bioinformatics pipelines.

MSc in Bioinformatics

The University of Edinburgh
Edinburgh, UK - September 2016 to August 2017

Master’s thesis title: Linking the genome to the immunome: a search for markers of response to immunotherapy

Graduated with Distinction. Courses included programming and systems management, systems biology, statistics and data analysis, next generation sequencing technologies, and bioinformatics algorithms. Master’s thesis supervised by Dr. Nizar Batada. Managed clinical and RNA-seq data from multiple studies in The Cancer Genome Atlas.

BSc in Biotechnology

Universitat Politècnica de València
Valencia, Spain - September 2012 to July 2016

Bachelor’s thesis title: Integration of multi-omics data to describe link between developmental exposure to pesticides and impaired neurodevelopment

Part of the High-Academic Performance group. Graduated with a 9.1/10 grade average. Highly interdisciplinary degree. Numerous Summer internships. Bachelor’s thesis supervised by Dr. Sonia Tarazona and Dr. Ana Conesa. Managed metabolomics, proteomics, transcriptomics, and behavioral data originating from the EU-funded DENAMIC project.

Teaching

Intermediate/Advanced Epidemiology

MSc Epidemiology, University of Edinburgh (2022/2023)

Helped develop and imparted lesson on prediction modelling, as well as accompanying exercises.

Introduction to Genetic and Molecular Epidemiology

MSc Epidemiology, University of Edinburgh (2022/2023)

Helped impart lesson introducing basic epidemiology and multi-omics concepts at the post-graduate level.

Introduction to Genomics

Biomedical AI PhD Programme, University of Edinburgh (2022/2023)

Lesson part of induction week for Biomedical AI PhD students. Helped develop and imparted lesson on basics of genomics, including basic molecular biology, association modeling approaches/GWAS, linkage disequilibrium, and polygenic risk scores.

Predicting Age from a DNA Sample: Consultancy Style Dissertation Summer project

MSc Statistics and Data Science, University of Edinburgh (2021/2022)

Helped develop and imparted a Consultancy Style Dissertation Summer project titled “Predicting Age from a DNA sample” for the MSc in Statistics and Data Science at the University of Edinburgh, supervising over 30 students.

Demonstrated, marked, and tutored for a number of master’s level courses at the University of Edinburgh (over 200 hours), including:

Bioinformatics Programming and Systems Management

MSc Bioinformatics (2019-2020)

Comparative and Evolutionary Genomics

MSc Bioinformatics (2019-2020)

Statistics and Data Analysis

MSc Bioinformatics, MSc in Quantitative Genetics and Genomic Analysis (2019)

Student supervision

• Kris Holt (Co-supervised rotation project for Wellcome Trust Translational Neuroscience PhD programme, Spring 2022)
• Krystal Laing (Co-supervised rotation project for Wellcome Trust Translational Neuroscience PhD programme, Spring 2022)
• Hannah Smith (Co-supervised rotation project for Wellcome Trust Translational Neuroscience PhD programme, Spring 2022)

Other Experience

Freelance Graphic Designer

February 2020 to Present

Post-graduate Student Representative

April 2018 to August 2021

• The Roslin Institute’s Genetics and Genomics division
• Easter Bush Campus Post-graduate Studies Committee
• Improving Culture Facilitation Committee

Under-grad Research Intern

July 2014 to August 2015

• Summer 2015: Dr. Ana Conesa’s Functional Genomics Lab, Valencia, Spain.
• Summer 2014: Dr. Jordi Perez-Tur’s Molecular Genetics Lab, Valencia, Spain.

Funding and Awards

Fellowships

• November 2021 to Present: Associate Fellow of the Higher Education Academy

Awards

• Best Poster: European Society of Human Genetics Conference (2020)
• Best Presentation: Advances in Computational Biology Conference (2019)
• Best Poster: Roslin Institute Research Student Day (2019)
• Runner-up Best Poster: Roslin Institute Research Student Day (2018)
• Best Student Presentation: XIII Symposium on Bioinformatics (2016)
• Baccalaureate Extraordinary Prize (2012)

Scholarships

• 2017-2021 - The Roslin Foundation’s Steve Bishop PhD Scholarship
• 2016-2017 - La Caixa International Post-graduate Scholarship

Travel and Training Funding

• Birrell-Gray Traveling Scholarship (2019) - £500
• Genetics Society Travel Grant (2019) - £750
• Genetics Society Training Grant (2018) - £550

Other Funding

• Engage @ Roslin Small Grants Fund (2020) - £500

Invited Talks

UK Conference of Bioinformatics and Computational Biology

Earlham Institute, Norwich, United Kingdom (Online) - 2022

INIA Genetics Seminars

Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain (Online) - 2022

ISCB Academy Webinars

International Society of Computational Biology (Online) - 2022

Social Genomics at the University of Wisconsin

University of Wisconsin-Madison, Madison, Wisconsin, USA (Online) - 2021

Bioinfo4Women and BSC Seminars

Barcelona Supercomputing Center, Barcelona, Spain (Online) - 2021

Computational Genetics Discussion Group

The Roslin Institute, Edinburgh, UK (Online) - 2021

Edinburgh Alliance for Complex Trait Genetics

Royal College of Physicians of Edinburgh, Edinburgh, UK - 2019

Conference Contributions

Organizing committees

• Gordon Research Seminar in Quantitative Genetics and Genomics (2023) - Co-chairing, Ventura, California, USA

Posters

• European Society of Human Genetics (2020), Online
• Century in Genetics (2019), Edinburgh, UK
• Gordon Research Conference in Quantitative Genetics and Genomics (2019), Lucca, Italy

Oral Presentations

• European Conference on Computational Biology (2021), Online
• European Society of Human Genetics (2020), Online - Poster Pitch
• Advances in Computational Biology (2019), Barcelona, Spain
• Century in Genetics (2019), Edinburgh, UK - Poster Pitch
• XIII Symposium on Bioinformatics (2016), Valencia, Spain

Publications

Google scholar here.
ORCID here.

Selected publications:

Reply to: Genotype by sex interactions in ankylosing spondylitis

Elena Bernabeu, Konrad Rawlik, Oriol Canela-Xandri, Andrea Talenti, James Prendergast, and Albert Tenesa
Nature Genetics (2023), doi: 10.1038/s41588-022-01251-4

Refining epigenetic prediction of chronological and biological age

Elena Bernabeu, Daniel L McCartney, Danni A Gadd, Robert F Hillary, Ake T Lu, Lee Murphy, Nicola Wrobel, Archie Campbell, Sarah E Harris, David Liewald, Caroline Hayward, Cathie Sudlow, Simon R Cox, Kathryn L Evans, Steve Horvath, Andrew M McIntosh, Matthew R Robinson, Catalina Vallejos, and Riccardo E Marioni
Genome Medicine (2022), doi: 10.1101/2022.09.08.507115

Sex differences in genetic architecture in the UK Biobank

Elena Bernabeu, Oriol Canela-Xandri, Konrad Rawlik, Andrea Talenti, James Prendergast and Albert Tenesa
Nature Genetics (2021), doi: 10.1038/s41588-021-00912-0

A multiomic study to unravel the effects of developmental exposure to endosulfan in rats: molecular explanation for sex-dependent effects

Sonia Tarazona, Elena Bernabeu, Héctor Carmona, Belén Gómez-Giménez, Javier García-Planells, Pim E. G. Leonards, Stephan Jung, Ana Conesa, Vicente Felipo, and Marta Llansola
ACS Chemical Neuroscience (2019). doi: 10.1021/acschemneuro.9b00304

Relevant Training

Ed-DaSH Workflows with Nextflow

The University of Edinburgh, Edinburgh, UK (2022)
2 full day course on Nextflow workflows, using The Carpentries platform.

Edinburgh Teaching Award (EdTA) Cohort

The University of Edinburgh, Edinburgh, UK (2021)
Mentored route to obtain Higher Education Academy accreditation.

Engage @ Roslin Cohort

The Roslin Institute, Edinburgh, UK (2020)
Series of courses to develop a public engagement activity.

Advanced Python for Biologists

Edinburgh Genomics, Edinburgh, UK (2018)
Course by Dr. Martin Jones.

The Search for Selection

The Roslin Institute, Edinburgh, UK (2018)
Course by Professor Bruce Walsh.

Nature Masterclass

The University of Edinburgh, Edinburgh, UK (2018)
Course by the Nature Publishing Group.

Skills

Dry lab

• Python, R, Bash, Unix, HPC systems.
• Statistics, data analysis, and quantitative genetics.
• Bioinformatics and NGS methods and pipelines; familiarity with genomics and transcriptomics data sets.
• Handling of large population cohort data, including health records.

Wet lab

• Basic wet-lab protocols: PCR, immunoassays, electrophoresis, bacterial culture, etc.

Other skills

• Extensive knowledge of Adobe Creative Suite and Microsoft Office Suite.
• Strong presentation and writing skills.

Public Engagement

Dog Meets Dog - A Population Genetics Game

The Roslin Institute, Edinburgh, UK (2020-2021)
Population genetics game activity designed for classroom use by high school students. Created in collaboration with Dr. Enrique Sánchez-Molano with the help of the Roslin Institute’s Public Engagement team. Supported by Engage @ Roslin Small Grants Fund.

The Roslin Institute Infographics

The Roslin Institute, Edinburgh, UK (2020)
Created a set of infographics to communicate main research lines at the Roslin Institute on social media.

Languages

• English
• Spanish
• Catalan