Education and Experience

Current

  • Research Fellow (University College London, UK) & Honorary Research Fellow (University of Bristol, UK)
    My main interest is focused on developing and applying reproducible methods and pipelines to study evolutionary processes. Over the years, I have specialised on Bayesian timetree inference analyses with both molecular and morphological continuous data (with both extant and fossil species). As part of the project I have joined at UCL, I shall continue my research on timetree inference, although now focusing on MCMC algorithms and the assembly of empirical datasets to study human speciation and diversification (aDNA), the timescale of vertebrate terrestrialisation, and reconstructing the eukaryotic Tree of Life.

    My ultimate goal is to ensure that all the computational tools that I develop as part of the projects I am involved in are well documented, user-friendly, and reproducible.

Past

  • Senior Research Associate in Phylogenomics (University of Bristol, UK)
    As part of the Biological Purpose project I joined while in Bristol, I developed and applied new methods for deep timetree inference with the aim to unravel the patterns of early evolution. We applied of such methods, cross-bracing, to infer the age of the Last Universal Common Ancestor.
  • Postdoctoral researcher (University College London, UK)
    During these two-year position, I finished my project on mammal evolution using the sequential-subtree approach, worked on analyses for detecting positive selection, collaborated with various media and institutions for scientific outreach, and joined various projects focused on phylogenomic clock-dating analyses. During the academic year 2021-22, I was also a teaching fellow at UCL as part of a secondment, period during which I had the opportunity to further develop my teaching skills.
  • PhD in Computational Biology (Queen Mary University of London, UK)
    Once I completed my MSc studies, I wanted to explore other fields in computational biology such as Bayesian statistics and modelling as I was keen on integrating a more mathematical background with my computational skills at that moment. To achieve this, I started my PhD at the dos Reis Lab, 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.
  • 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. My dissertation “BACTpipe: Characterization of bacterial isolates based on whole-genome sequence data” can be accessed on the DIVA portal (free download). Since I finished my MSc research project, the computational research team at the CTMR has been implementing new features in BACTpipe. The current open source code is available as part of the BACTpipe GitHub repository.
  • BSc in Biochemistry and Molecular Biology (University Rovira I Virgili, Spain)
    During these 4 years as an undergraduate, most of my practical sessions involved wet-lab experiments. Nevertheless, it was not until I took the bioinformatics course when I realised how much I enjoyed coding: if I properly told a computer to do “something” with my biological data, I actually got “this something” done (what I could not always say after my wet-lab 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 knew that my academic career had to integrate two fields: biology and informatics.


Publications

  • Bayesian phylogenomic dating
    Álvarez-Carretero S and dos Reis M. (2021) In: Ho S (ed.) The Molecular Evolutionary Clock: Theory and Practice (2021).


Awards and Scholarships


Teaching

Instructor

Teaching Fellow

  • Biochemistry and Molecular Biology [BIOC0001, UCL] (2021/22).
  • Basics for Molecular Biosciences [BIOC0002, UCL] (2021/22).
  • Introduction to Microbiology [BIOC0004, UCL] (2021/22).
  • Biochemistry and Molecular Biology [BIOC0005, UCL] (2021/22).
  • Advanced Investigative projects in molecular biosciences [BIOC0021, UCL] (2021/22).
  • MSci Biochemistry Year 4 [BIOC0024, BIOC0025, BIOC0026; UCL] (2021/22).

Supervision and Research Guidance

  • PhD project (2023-TBC) – Co-supervising Mingzhu Yang with Prof Phil Donoghue | Thesis: TBC.
  • PhD project (2023-TBC) – Co-supervising Sidney Davies with Prof Phil Donoghue | Thesis: TBC.
  • MSc project (2023) – Morena Nava’s research project with Prof Phil Donoghue and Prof Davide Pisani | Dissertation: “A timescale to Sea Spider’s Evolution (Arthropoda: Pycnogonida)”.
  • MSci project (2020/21) – Co-supervising Léa Cavalli’s research project with Prof Ziheng Yang | Dissertation: “A simulation study to explore the time-dependent rates effect in viral evolution”.
  • Additional supervision and/or research guidance: Since 2017, I have been providing guidance to students and members of staff on a request basis about how to run and/or improve their computational analyses, specially troubleshooting and fixing code as well as providing them with help to run phylogenetic software (e.g., raxml-ng, MCMCtree, CODEML, BPP, etc.). Most of this research guidance has led me to develop new protocols that users can easily customise to fit their datasets while, at the same time, they can run various analysis in a reproducible manner.

Teaching Assistant

  • Computational Molecular Evolution course (May 2018, May 2019 & Jul 2022).

Demonstrator

  • Statistics for Bioinformaticians [BIO782P, QMUL] (2019/20).
  • IT stats for Molecular and Cellular Biology [BIO190, QMUL] (2019/20).
  • Practical laboratories and Seminars [SEF033, QMUL] (2018/19).
  • Stats & R [BIO309, QMUL] (2017/18 – 2019/20).
  • Free style laboratories [BIO193 & BIO199, QMUL] (2016/17).
  • Thinking workshops [BIO193 & BIO199, QMUL] (2016/17 – 2017/18).
  • Dry lab tutorials [BIO193 & BIO199, QMUL] (2016/17).
  • Biochemistry laboratories [BIO199, QMUL] (2016/17).


Invited Talks and Science Communication (outreach)

  • Bayesian methods to infer evolutionary timelines when deep divergences are present and large genomic datasets used (Jul 2024) – Invited talk at the Genome Science conference that took place the University of Bristol.
  • Bayesian phylogenomic dating: a journey on reproducible timetree inference (Jun 2024) – Invited talk at the “11th International Biennial Conference” organised by the Systematics Association at the University of Reading.
  • XXIII International Congress of Genetics (Jul 2023) – Invited talk at the “Molecular Evolution” symposium at the Evolutionary Genetics session.
  • Native Schools workshop (Nov 2022) – Scientific activity sponsored by Native Scientist aimed at promoting science and language among school pupils.
  • Silwood Ecology and Evolution Seminar, Imperial College London (Jun 2022) – Invited talk (virtual).
  • “Data, tools and applications: Creating a pipeline from Omics to AI” meeting, Alan Turing Institute (May 2022) – Invited talk.
  • Brunel Bioinformatics Workshop 2022 (May 2022) – Invited talk at the “Statistical Modelling” session of the workshop.
  • Interview at “En Fase Experimental” radio podcast (May 2022) – Interview about the day-to-day of a computational biologist and my research in evolutionary biology (virtual). You can listen to this podcast episode on the SRUK/CERU website
  • Seminar on Phylogenomics analyses with MCMCtree, University of Oklahoma (Apr 2022) – Invited talk (virtual).
  • Interview by the students at IE Cañada Blanch for the International Day of Women and Girls in Science (Feb 2022) – Interview about my research and how it feels to pursue a career as a woman in STEM. You can see the videos with my answers to the students’ questions on YouTube. This event was a collaboration between IE Cañada Blanch and the Office for Cultural and Scientific Affairs (Embassy of Spain in London).
  • Interview at “Evolution Soup” YouTube channel (Jan 2022) – Interview about my research on mammals’ evolution and my academic career available to watch on YouTube (virtual).
  • Seminar at the Instituto de Ciencias Matemáticas, Consejo Superior de Investigaciones Científicas (Nov 2021) – Invited talk (virtual).
  • Seminar at the Palaebiology Research group, University of Bristol (Jun 2021) – Invited talk (virtual).
  • Graduate Phylogenomics seminar, Michigan State University (Feb 2021) – Invited talk (virtual).
  • CLOE Joint Group Meeting, University College London (Nov 2020) – Invited talk (virtual).
  • Back to present: Understanding evolution (Jun 2018 & Jun 2019) – Scientific activity for children presented during the V and VI SRUK/CERU International Symposia.


Events Organisation and Participation


Research Presentations

  • Using a Bayesian cross-bracing approach to infer the age of the Last Universal Common Ancestor (Jul 2024) – In-person talk at the “Computational Biology II” session that was part of the Evolution meeting in Montréal.
  • Inferring species level timelines with phylogenomic data: A Bayesian sequential subtree approach (Jun and Aug 2022) – Virtual talk at the online session of the Evolution meeting and in-person talk at the ESEB conference.
  • Estimating the divergence of dire wolves from their common ancestor with living canids using a Bayesian dating approach (Jun 2021) – Talk at the online Evolution meeting.
  • Estimating the divergence of dire wolves from their common ancestor with living canids using a Bayesian dating approach (Nov 2019) – Poster presentation at the Young Systematists’ Forum meeting.
  • Bayesian estimation of species divergence times using correlated quantitative characters (Jun 2019) – Talk at the Evolution meeting awarded with the Ernst Mayr Award.
  • Bayesian estimation of species divergence times using correlated quantitative characters (Nov 2018) – Talk at the Young Systematists’ Forum meeting.
  • Comparison of relaxed-clock models using the Bayesian model selection implemented in MCMCtree (Aug 2018) – Poster presentation at the Evolution meeting, available at the dos Reis Lab website.
  • Bayesian estimation of species divergence times using quantitative characters (Apr 2018) – Talk at Phylogroup XI meeting.


Society Memberships


Peer-review

Manuscripts reviewed 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, Bioinformatics Advances, Nature, Palaeontology, Genome Biology and Evolution, Molecular Biology and Evolution.


Additional Information

Native speaker of Spanish, fluent in English and Catalan, basic level in Greek and Modern Standard Arabic. Mysore Ashtanga practitioner. Piano player and amateur composer.


Last update: 2024/08/21.