Hi, I am Ale

Alejandra Hernandez Segura

Bioinformatician at National Institute for Public Health and the Environment (RIVM)

I am a bioinformatician and project manager working at the National Institute for Public Health and Environment (RIVM, The Netherlands). My tasks include developing pipelines for data analysis of bacterial genomes, automating and improving processes, ensuring data quality, performing data analysis/visualization and managing the projects of the bioinformatics group. I am also an R-ladies Utrecht organizer, an intense reader, a sports enthusiast (doing sports, not really following them) and a lover of Mexican culture.

Organization
Team Work
Communication
Hard Working
Fast Learner

Skills

Experiences

1
National Institute for Public Health and the Environment (RIVM).

Apr 2020 - Present, Bilthoven, The Netherlands

The RIVM promotes public health and safeguards a healthy and safe environment. It has a central role in infectious disease control, national prevention and population screening programmes and monitoring our population’s health and the state of our environment.

Project manager

Sep 2020 - Present

  • Ensuring quality and delivery of the projects delivered by our group.
  • Organizing and chairing stand-up meetings and other group/team meetings.
  • Communicating results to the management team and to other staff and researchers.
  • Different management tasks such as participating in hiring committees, write budgets and proposals, etc.
Bioinformatician

Apr 2020 - Present

  • Tracking and helping improve quality of the data produced by the sequencing facility.
  • Automating data analysis of bacterial sequencing data by building automated, reproducible and parallelized pipelines.
  • Data analysis and visualizations.
  • Writing SOPs and validation reports.
  • Supervising students/interns.
  • Keeping up with the novel techniques in the genomics/bioinformatics field.
  • Advising other researchers about data analysis and reproducibility.
  • Contributing to local and international genomics public health projects.
Grace Systems.

Nov 2018 - Feb 2020, Utrecht, The Netherlands

Grace Systems is a data analysis tool.

Team Lead Data Science

Sep 2019 - Feb 2020

  • Keeping track of the advancements in the bioinformatics and data science fields.
  • Deciding on the approach to take for different projects.
  • Communicating strategies and results to different stakeholders.
  • Writing detailed but understandable reports.
  • Major contributor in the hiring process of new colleagues.
Data Scientist

Nov 2018 - Feb 2020

  • Analyzing data, building models and visualizing epigenomics data in cancer to search of potential biomarkers.
  • Communicating results to supervisors and clients.
  • Constantly improving algorithms and pipelines.
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Researcher - PhD candidate
European Research Institute for the Biology of Ageing.

Jan 2015 - Feb 2019, Groningen, The Netherlands

ERIBA’s goal is to better understand what causes ageing. It aims to develop novel strategies to prevent or combat age-related disease and to provide evidence-based recommendations for healthy ageing.

Responsibilities:
  • Proposing research questions.
  • Doing experiments and data analysis of transcriptomics data.
  • Data visualization for my and other people’s projects.
  • Presenting results in meetings and conferences.
  • Publishing results in peer-reviewed scientific journals.
  • Teaching and mentoring students.
Invited lecturer
Universidad de las Américas Puebla

Aug 2014 - Jan 2015, Puebla, Mexico

UDLAP’s mission is to form professionals who are critical, creative and innovative, wih a high technical capability and social conscience.

Responsibilities:
  • Teaching three practicalcourses (General Pharmacology, Biorganics and Microbiology and Parasitology).
  • Teaching one theoretical course (Pharmaceutical Biotechnology).
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University Medical Center Groningen (UMCG)

Nov 2013 - Jul 2013, Groningen, The Netherlands

The UMCG is one of the biggest hospitals in The Netherlands and it is dedicated to healthcare, research and education.

Intern Biology of Ageing

Jan 2013 - Jul 2013

  • Developing a method to isolate and sequence single-cells of C. elegans adult worms
Intern Human Genetics

Nov 2013 - Jul 2014

  • Analyzing the transcriptome of activated T-cells in celiac disease.
Assistant in Reception and Analysis of Clinical samples
Laboratorios Unilab

Jun 2012 - Aug 2012, Puebla, Mexico

Diagnostic laboratory.

Responsibilities:
  • Acting as receptionist and giving instructions to patients.
  • Assisting in the diagnostics through biometric blood tests, glucose tests, urine culture, among others.
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Biology teacher
Colegio Woodcock

Jan 2010 - Jul 2012, Puebla, Mexico

Secondary and high-school.

Responsibilities:
  • Teaching basic biology to various groups.
Teacher's Assistant
Center for Talented Youth (Johns Hopkins University)

Jul 2011 - Aug 2011, Puebla, Mexico

CTY is a nonprofit dedicated to identifying and developing the talents of academically advanced pre-college students around the world.

Responsibilities:
  • Helping prepare Anatomy and Physiology lessons to talented students.
  • Organizing and directing some technical sessions with the students.
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Education

University of Groningen
2015-2019
Ph.D in Biology
Publications
University of Groningen
2012-2014
Master in Medical and Pharmaceutical Drug Innovation
Universidad de las Américas Puebla
2006-2011
Bachelor in Clinical Biochemistry
Diverse courses
Taken Courses
  • R
  • Data Science Professional Certificate - EdX
  • Genetics Epidemiology
  • Good Research Practices (GCP, GLP)
  • Neural Stem Cells
  • Single-cell Gene Expression - EMBL
  • Systematic Reviews and Meta-analysis
Extracurricular Activities
  • Organizer R-ladies Utrecht (2020-present).
  • Active member Science Outreach Committee ERIBA institute (2017-2019).
  • Start coach for Refugees in the city of Groningen (2016).
  • International Ambassador for the U. of Groningen (2014-2015).

Projects

Juno pipeline
Juno pipeline
Developer and maintainer Apr 2020 - Present

Pre-processing and de novo assembly of short-read sequencing for bacterial genomes.

Star
Advanced-R bookclub
Advanced-R bookclub
Co-organizer Apr 2020 - Present

Together with other R-ladies chapters in the Netherlands, we organized a bookclub for the book Advanced R by Hadley Wickham.

Star
Coding Club
Founder and organizer March 2021 - Present

At work we started a coding club for bioinformaticians.

Details

Recent Posts

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Applied Bioinformatics and Public Health Microbiology Conference

This poster is the result of (part of) the work of the Juno team consisting in bioinformatics students/staff and microbiologists. We started last April (2020) automating many of the analyses done for diagnostic and surveillance at the RIVM. The poster itself should be self-explanatory and although the project is far from finished, we are happy to show our work. You can download the poster here.

April 19, 2021 Read
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United Nations votes - Data Viz exercise

.center { text-align: center align: center } I am really into data visualization and since in my current position as coördinator I get to do it way less than I would like to, I decided to take part of the #TidyTuesday challenge organized by the #rstats community every now and then. Main things I learned It was my first time making a map in a tidy format.

March 28, 2021 Read
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My experience as curator of @WeAreRLadies

.center { text-align: center align: center } To be honest, I took days preparing for my curator week so I had collected information, made a plan and trying to learn to use twitter 🙈 Still, it did not work very smoothly. Only on my second day I learned (or rather, the very nice ex-curator @PipingHotData taught me) how to upload gifs and how to make threads. Anyway, I survived and I got some nice comments, so hopefully people enjoyed it.

March 14, 2021 Read

Achievements

PhD Grant

Cum laude (Master)

Magna Cum Laude (Bachelor)

Full scholarship (Bachelor)

Patent

Sports prizes