Education and Experience
Current
- Senior Research Associate in Phylogenomics (University of Bristol, UK)
My main interest is focused on developing and applying reproducible methods and pipelines to study evolutionary processes, and hence my research is focused on Bayesian timetree inference with molecular and morphological datasets (with both extant and fossil species). As part of the Biological Purpose project I have joined while in Bristol, I will be contributing to processing and analysing genome-scale datasets for deep timetree inference with the aim to unravel the patterns of early evolution 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
- 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 inBACTpipe
. The current open source code is available as part of theBACTpipe
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
- Beginner’s guide on the use of PAML to detect positive selection
Álvarez-Carretero S*, Kapli P*, Yang Z (2023). Mol Biol Evol.
*These authors contributed equally.
» Resources available for this study:
- GitHub repository with data, code, and step-by-step guidelines for reproducing the results of the analyses described in the
CODEML
protocol. - Supplementary material where we discuss (i) analyses and checks you should carry out before running tests of positive selection with CODEML, (ii) gene tree VS species tree, and (iii) the usage of rooted and unrooted trees.
- GitHub repository with data, code, and step-by-step guidelines for reproducing the results of the analyses described in the
- A species-level timeline of mammal evolution integrating phylogenomic data
Álvarez-Carretero S*, Tamuri AU*, et al. (2022) Nature.
*These authors contributed equally.
» Resources available for this study:
- Step-by-step tutorial to reproduce the results of this study.
- Interview I had at the YouTube channel “Evolution soup” with regards to this research. By watching this video, you can learn more about the most precise estimated evolutionary timeline for mammals, each author’s contribution, the outline and main outcome of this research, and a little bit more about my academic career.
- Press release in English.
- Press release in Spanish.
- Bayesian phylogenomic dating
Álvarez-Carretero S and dos Reis M. (2021) In: Ho S (ed.) The Molecular Evolutionary Clock: Theory and Practice (2021).
- Dire wolves were the last of an ancient New World canid lineage
Perri Angela R*, Mitchell Kieren J*, Mouton Alice*, Álvarez-Carretero S*, et al. (2021) Nature.
*These authors contributed equally.
- Phylogenomic resolution of the Cetacean Tree of Life using target sequence capture
McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, dos Reis M, Struebig M, Deaville R, Jepson PD, Jarman S, Polanowski A, Morin PA, Rossiter SJ. (2020) Systematic Biology.
- Identification of functional and druggable sites in Aspergillus fumigatus essential phosphatases by virtual screening
Thornton BP, Johns A, Al-Shidhani R, Álvarez-Carretero S, Storer ISR, Bromley MJ, Tabernero L. (2019) Molecules.
- Bayesian estimation of species divergence times using correlated quantitative characters
Álvarez-Carretero S, Goswami A, Yang Z, dos Reis M. (2019) Systematic Biology.
» Resources available for this study:
- Step-by-step tutorial followed to carry out each computational task of this study.
- The R functions described in this study were implemented in the
mcmc3r
R package, which includes a vignette to reproduce the results obtained with the input data. - Please install
mcmc3r
using the commanddevtools::install_github("dosreislab/mcmc3r", build_vignettes = TRUE)
so you have access to the vignettes included inmcmc3r
too.
- The bile salt glycocholate induces global changes in gene and protein expression and activates virulence in enterotoxigenic Escherichia coli
Joffre E, Nicklasson M, Álvarez-Carretero S, Xiao X, Sun L, Nookaew I, Zhu B, Sjöling Å. (2019) Scientific Reports.
- VSpipe, an integrated resource for virtual screening and hit selection: applications to protein tyrosine phospahatase inhibition
Álvarez-Carretero S, Pavlopoulou N, Adams J, Gilsenan J, and Tabernero L. (2018) Molecules.
» Resources available for this study:
- An evaluation of different partitioning strategies for Bayesian estimation of species divergence times
Konstantinos A, Álvarez-Carretero S, dos Reis M, and Yang Z. (2018) Systematic Biology.
Awards and Scholarships
- USyD-UCL Partnership Collaboration Awards (PCA)
Application to fund the project “Reconstructing the evolutionary timescale of the Tree of Life” together with Prof Simon Ho. Awarded by the University of Sydney in 2022. - Ernst Mayr Award, awarded by the Society of Systematic Biologists.
- National awards after University degree completion during the 2014-15 academic course, awarded by Ministerio de Educación, Cultura y Deporte.
(Original award name: Premios Nacionales de Fin de Carrera de Educación Universitaria para el curso académico 2014-2015) - Student excellence award for the BSc in Biochemistry and Molecular Biology, awarded by University Rovira I Virgili.
(Original award name: Premi Extraordinari de Final d’Estudis del grau de Bioquímica I Biologia Molecular) - Scholarship for research funding during the academic course 2014-15, awarded by Ministerio de Educación, Cultura y Deporte in 2014.
(Original award name: Becas de Colaboración 2014-15)
Teaching
Instructor
- Phylogenomics and Population Genomics Advanced Course [University of Barcelona] (Jun 2023. Resources for the “Molecular dating” session I taught are available on my GitHub account).
- ITAPHY - Phylogenetics workshop [University of Trento] (Jul 2023. Resources for the genome-scale dating session I taught are now merged with those I later used in the PPG course in July 2023).
- Computational Molecular Evolution course (May 2023).
- Evolutionary Analysis Using PAML workshop [USyD-UCL PCA] (Jan 2023).
- Bayesian statistics [MSc CMEE, Imperial College] (2021/22 & 2022/23).
- Phylogenomics course [Physalia course] (Dec 2021 & Dec 2023 (upcoming). Resources for the practical sessions I taught are available on my GitHub account).
- Molecular Evolution [BIOL0033, UCL] (2020/21 – 2021/22).
- Research Computing Workshop – R, Bash, and Python (Feb & Jun 2020, workshop sponsored by SRUK/CERU, co-organised with Dr Diego Alonso. Material and content available on GitHub for the R and Bash workshop and for the Phyton workshop).
- A practical introduction to R and Python for researchers (Apr 2018 & Mar 2019, workshop sponsored by SRUK/CERU, co-organised with Dr Diego Alonso. Material and content available on GitHub).
- Morphometrics and the Procrustes alignment (2017-2021, workshop I organised to engage the NERC-DTP students with the research carried out at the dos Reis lab during their induction at QMUL. The material is available on my website as a post).
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
- 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)
- 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
- XXIII International Congress of Genetics (Nov 2022 – Jul 2023) – Co-convenor at the “Molecular Evolution” symposium at the Evolutionary Genetics session.
- X SRUK/CERU International Symposium (Nov 2022 – Jul 2023) – Member of the organising committee (website development and management).
- CLOE Winter Quarterly Symposium (Oct – Dec 2021) – Member of the organising committee of the CLOE anniversary symposium. You can find more information about this event and the invited speakers at the CLOE website
- IX SRUK/CERU International Symposium (Nov 2021 – Jun 2022) – Member of the organising committee (website development and management).
- SSB Awards Committee (Jun 2021) – Member of the judging panel for the talks presented at the SSB Excellence Symposium.
- VIII SRUK/CERU International Symposium (virtual) (Nov 2020 – Jun 2021) – Member of the organising committee (website development and management).
- VII SRUK/CERU International Symposium (Nov 2018 – Jun 2019) – Member of the organising committee (website development and management).
- VI SRUK/CERU International Symposium (Mar – May 2018) – Member of the organising committee (website development and management).
- Phylogroup XI (Dec 2017 – Apr 2018) – Co-organiser of the meeting.
Research Presentations
- 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
- ESEB (May 2022 – Present) – Regular member of the European Society of Evolutionary Biology.
- SSE (Feb 2019 – Present) – Regular member of the Society for the Study of Evolution.
- SSB (Jan 2018 – Present) – Regular member of the Society of Systematic Biologists.
- SRUK/CERU (Nov 2017 - Present) – Regular member of the Society of Spanish Researchers in the United Kingdom (SRUK/CERU). Involvement in the Society:
- Active roles:
- Since 2017: Member of the SRUK/CERU London working group.
- Since 2018: Member of the SRUK/CERU Press Department.
- Since 2019: Co-editor-in-chief of the SRUK/CERU blog since 2019.
- Since 2021: Director of the Press department.
- Since 2021: Website manager.
- Past roles:
- 2019-2021: secretary of the SRUK/CERU London constituency.
- Active roles:
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.
Grants reviewed for the 2019, 2021, and 2022 Graduate Student Research Awards (SSB).
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: 2023/08/10.