image Hi everyone!

I am Sandra Álvarez-Carretero, a computational scientist working as a post-doctoral researcher and teaching fellow at Ziheng Yang Lab at University College London.

Even though now I cannot imagine a day working without my laptop, my career started at the wet lab and, little by little, I specialised in computer science:



  • BSc in Biochemistry and Molecular Biology (Universidad Rovira I Virgili, Spain)
    During this 4-year BSc, most of my practical sessions involved wet-lab experiments. Nevertheless, it was not until I took the bioinformatics course part of my BSc that I realised how much I enjoyed coding as I could tell my computer to do “something” with my biological data and I actually got “this something” done (what I could not always say after my wet laboratory practical sessions…). Thanks to the Erasmus+ programme, I could work on a bioinformatics project at the University of Manchester, which was focused on troubleshooting and implementing a pipeline to carry out virtual screenings. From then onwards, I was sure that my next steps in science had to integrate two fields: biology and informatics.
  • MSc in Bioinformatics (Högskolan I Skövde, Sweden)
    After finishing the theoretical courses, I carried out my Master’s dissertation at Karolinska Institutet, where I developed a pipeline to characterise bacterial isolates based on whole-genome sequencing data and other software pipelines to analyse transcriptomic and proteomic data. If you are interested in reading my dissertation, “BACTpipe: Characterization of bacterial isolates based on whole-genome sequence data”, you can download it from here. BACTpipe has now been further implemented by the computational research team at the CTMR. You can find the open source code in this GitHub repository.
  • PhD student (Queen Mary University of London, UK)
    Once I finished my MSc, I decided to explore other fields in computer science such as Bayesian statistics and modelling so I could learn more about how I could merge my computing knowledge with the maths used in these two fields. I carried out my PhD at dos Reis Lab research group, at Queen Mary University of London, where I worked on the application of Bayesian MCMC statistical methods to study species divergences through time with both molecular and morphological quantitative data.
  • Post-doctoral researcher and Teaching fellow (University College London, UK)
    Currently, my main interest is focused on developing and applying new methods to estimate species divergence times with molecular and morphological quantitative datasets. I aim to use these tools in Bayesian dating analyses when combining phylogenomic datasets with large-scale morphological datasets (with both extant and fossil species). My ultimate goal is to ensure that all the pipelines and tools that I develop as part of the projects I am involved in are well documented, so they can be easily used to reproduce any reported results generated with them.


Publications


Outreach, events organisation, and research presentations

Academic course 2017-2018

  • NERC DTP induction at QMUL (Nov 2017)
    Overview of the work carried out at dos Reis lab and about my PhD project. The practical part was focused on understanding the usage of the bioinformatics tools we use followed by a quick guide on a morphometrics analysis (acess here).

  • Phylogroup XI (Dec 2017 - Apr 2018)
    During these four months, I supported the organisation of the Phylogroup XI event. My main tasks were to collect the proposals for the oral presentations, to help decide which talks would be selected for the event, and organise the schedule of the event.

  • VI International Symposium SRUK/CERU (Mar 2018 - May 2018) During almost three months, I maintained and developed the website of the event as well as of the symposium forum for accommodation in Glasgow.

  • Bayesian estimation of species divergence times using quantitative characters (Apr 2018)
    Talk at Phylogroup XI about the preliminary results of my PhD research.

  • Scientific Computing Workshop: A practical introduction to R and Python for researchers (Apr 2018)
    Event sponsored by the SRUK/CERU society that I co-organized with Dr. Diego Alonso.

  • Introduction to R (May 2018 | Computational Molecular Evolution course)
    Two-morning sessions about programming in R that I organized during the Computational Molecular Evolution course in Crete.

  • Back to present: Understanding evolution (Jun 2018)
    Activity that I prepared for the Science Zone as part of the VI International Symposium SRUK/CERU in Glasgow.

  • Comparison of relaxed-clock models using the Bayesian model selection implemented in MCMCtree (Evolution 2018 meeting, poster) (Aug 2018 | Evolution 2018 meeting, poster)
    Poster presentation at the joint Evolution 2018 meeting showing how to use the mcmc3r R package to estimate the marginal likelihood using the likelihood collected during MCMC chains ran in MCMCtree and compute Bayes factors for model selection. You can find the poster here.

Academic course 2018/2019

  • NERC DTP induction at QMUL (Nov 2018)
    Overview of the work carried out at dos Reis lab and a hands-on tutorial on how to generate a molecular alignment, estimate a molecular tree, and process morphometrics data.

  • Bayesian estimation of species divergence times using correlated quantitative characters (Nov 2018 | YSF18 meeting, talk)
    Talk at the YSF2018 1-day symposium on the paper already submitted about the main method I had been working on my PhD.

  • VII International Symposium SRUK/CERU (Nov 2018 - Jun 2019) I was part of the organising committee of the symposium. My main task during these months was to develop and maintain the website to keep up with the latest updates regarding the event.

  • II Scientific Computing Workshop: A practical introduction to R and Python for researchers (Mar 2019)
    Event sponsored by the SRUK/CERU society that I co-organized with Dr. Diego Alonso.

  • Introduction to R (May 2019 | Computational Molecular Evolution course)
    One-morning session about programming in R that I organized during the Computational Molecular Evolution course in Hinxton.

  • Back to present: Understanding evolution (Jun 2018)
    Activity that I prepared for the Science Zone as part of the VII International Symposium SRUK/CERU in Liverpool.

  • Bayesian estimation of species divergence times using correlated quantitative characters (June 2019 | Evolution 2019 meeting, awards talk)
    Talk at the Evolution 2019 meeting, with which I was granted the Ernst Mayr award.

Academic course 2019/2020

  • NERC DTP induction at QMUL (Nov 2019)
    Overview of the work carried out at dos Reis lab and a hands-on tutorial on how to generate a molecular alignment, estimate a molecular tree, and process morphometrics data.

  • Estimating the divergence of dire wolves from their common ancestor with living canids using a Bayesian dating approach (Nov 2019 | YSF19 meeting, poster)
    Poster presentation at the YSF2019 1-day symposium on the submitted manuscript about the evolution of canids with a special focus on the dispersal and speciation of dire wolves.

  • SRUK Research Computing Workshop - R, Bash and Python (Feb & Jun 2020, two sessions)
    Events sponsored by the SRUK/CERU society that I co-organized with Dr. Diego Alonso.

Academic course 2020/2021

  • NERC DTP induction at QMUL (Nov 2020)
    Overview of the work carried out at dos Reis lab and a hands-on tutorial on how to generate a molecular alignment, estimate a molecular tree, and process morphometrics data.

  • Bayesian estimation of species divergence times using GMM data (Nov 2020)
    Talk at the CLOE Joint Group Meeting organised by UCL.

  • Estimating the divergence of dire wolves from their common ancestor with living canids using a Bayesian dating approach (Jun 2021 | Evolution 2021 online conference, talk)
    Talk at the Virtual Evolution 2021 conference.

  • A Bayesian approach to estimate species divergence times using geometric morphometrics data (Jun 2021)
    Talk as part of the seminars organised by the Palaebiology Research group at University of Bristol.

Academic course 2021/2022

  • NERC DTP induction at QMUL (Nov 2021)
    Overview of the work carried out at dos Reis lab and a hands-on tutorial on how to generate a molecular alignment, estimate a molecular tree, and process morphometrics data.

  • Breaking down the steps in Bayesian phylogenomic dating (Nov 2021)
    Talk as part of the seminars organised by Instituto de Ciencias Matmáticas at CSIC.

  • Phylogenomics course (Dec 2021)
    Workshop organised by Physalia where I taught the practical sessions of Bayesian inference analyses. See resources here.

  • CLOE Winter Quarterly Symposium (Dec 2021)
    Part of the organising committee of the CLOE anniversary symposium.

  • Interview at Evolution Soup (Jan 2022)
    Interview I had at Evolution soup with regards to my research contribution to the study on the most precise evolutionary timeline for mammals. You will learn a little bit more about my academic career, the outline of this research study and how each author contributed to this project, how we can apply Bayesian stats to evolutionary biology studies, and what it feels like working as a computational biologist/bioinformatician in academic research.
    You can watch the interview here.

  • International Day of Women and Girls in Science (Jan/Feb 2022)
    Interview with the students at IE Cañada Blanch, where I talked about my career as a computational biologist and answered the students’ questions about how I feel as a woman pursuing a career in science. You can see the videos with my answers to the students’ questions here.
    This was a collaboration between IE Cañada Blanch and the Office for Cultural and Scientific Affairs (Embassy of Spain in London).


Teaching

Academic course 2016 - 2017

  • Demonstrator (TA): Biochemistry laboratories
    Module BIO199, Undergraduate level (year 1), Queen Mary University of London.

  • Demonstrator (TA): Dry lab tutorials
    Modules BIO193 and BIO199, Undergraduate level (year 1), Queen Mary University of London.

  • Demonstrator (TA): Thinking workshops
    Modules BIO193 and BIO199, Undergraduate level (year 1), Queen Mary University of London.

  • Demonstrator (TA): Free style laboratories
    Modules BIO193 and BIO199, Undergraduate level (year 1), Queen Mary University of London.

Academic course 2017 - 2018

  • Demonstrator (TA): Stats & R
    Module BIO309, Undergraduate level (year 3), Queen Mary University of London.

  • Demonstrator (TA): Thinking workshops
    Modules BIO193 and BIO199, Undergraduate level (year 1), Queen Mary University of London.

  • Teaching Assistant (TA): Computational Molecular Evolution course
    Providing support to the participants which ranged from software installation and usage to the theoretical background of using these bioinformatics tools to study molecular evolution.

Academic course 2018 - 2019

  • Demonstrator (TA): Stats & R
    Module BIO309, Undergraduate level (year 3), Queen Mary University of London.

  • Demonstrator (TA): Practical laboratories and Seminars
    Modules SEF033, Foundation level, Queen Mary University of London.

  • Teaching Assistant (TA): Computational Molecular Evolution course
    Providing support to the participants which ranged from software installation and usage to the theoretical background of using these bioinformatics tools to study molecular evolution.

Academic course 2019 - 2020

  • Demonstrator (TA): Stats & R
    Module BIO309, Undergraduate level (year 3), Queen Mary University of London.

  • Demonstrator (TA): IT stats for Molecular and Cellular Biology practicals
    Module BIO190, Undergraduate level (year 1), Queen Mary University of London.

  • Demonstrator (TA): Statistics for Bioinformaticians
    Module BIO782P, Graduate level (MSc programme in Bioinformatics), Queen Mary University of London.

Academic course 2020 - 2021

  • Instructor: Molecular Evolution
    Module BIOL0033, MSci programme (year 4), University College of London.

Academic course 2021 - 2022

  • Teaching fellow: Biochemistry and Molecular Biology
    Module BIOC0001, BSc programme (year 1), University College of London.

  • Teaching fellow: Introdution to Microbiology
    Module BIOC0004, BSc programme (year 1), University College of London.

  • Instructor: Molecular Evolution
    Module BIOL0033, MSci programme (year 4), University College of London.

  • Instructor: Bayesian statistics
    Masters in Computational Methods in Ecology and Evolution, Imperial College London.


Awards and scholarships


Society Memberships


Peer-review

Reviewer for Systematic Biology, Bioinformatics, Methods in Ecology and Evolution, Evolution, Cambridge Elements STM3, Nature Ecology and Evolution, Paleobiology, Proceedings of the Royal Society B, Nature Communications, Communications Biology, and Bioinformatics Advances.


Last update: 2022/02/22.