Ricard Argelaguet

Ricard Argelaguet

Computational Biologist

Altos Labs

Biography

I am a computational biologist motivated by the applications of machine learning and artifical intelligence to the field of biology.

I did my PhD in the groups of John Marioni (EMBL-EBI, now at Genentech) and Oliver Stegle (EMBL & DKFZ), followed by a short postdoctoral stay in the group of Wolf Reik at the Babraham Institute. I developed methods for single-cell and multi-omics data integration, the most popular one being MOFA. I also worked on generating data resources in the context of embryonic development. Some examples are the single-cell multi-modal atlases of mouse gastrulation and early organogenesis.

Currently, I am working as a Senior Scientist at Altos Labs in the AI/ML team led by Thore Graepel, where I work on modelling gene perturbation screenings to characterise the regulatory networks that underlie cellular rejuvenation programming.

I am a strong advocate of open and reproducible science. If you are interested in my work please check my GitHub page, which includes code to reproduce many of the results from our publications.

Interests
  • Data analysis
  • Machine Learning
  • Computational Biology
  • Multi-omics data integration
  • Single-cell omics
Education
  • PhD in Statistical Genomics, 2020

    EMBL-EBI & University of Cambridge

  • MSc in Bioinformatics, 2016

    Copenhagen University (Copenhagen, Denmark)

  • BSc in Human Biology, 2014

    Universitat Pompeu Fabra (Barcelona, Catalonia, Spain)

Career

Altos Labs
Senior Scientist
I work as a computational biologist in the AI/ML group led by Thore Graepel. I develop and analyse gene perturbation screenings with the aim of characterising the gene regulatory networks that underlie cellular rejuvenation programming
Babraham institute
Postdoctoral scientist
I worked in the group of Wolf Reik on the generation of single-cell multi-modal data resources in the context of embryonic development, including an atlas of mouse early organogenesis and a comprehensive resource of DNA methylation mutants. I also developed computational methods for the prediction of transcription factor binding sites and inference of gene regulatory networks from multi-omics data.
European Bioinformatics Institute (EMBL-EBI)
PhD in Statistical genomics
PhD thesis performed under the supervision of John Marioni and Oliver Stegle.
Thesis title: Statistical methods for the integrative analysis of single-cell multi-omics data.
Financially supported by the international EMBL PhD programme.
University of Copenhagen
MSc in Bioinformatics
MSc thesis performed under the supervision of Anders Krogh, Florian Buettner, and Oliver Stegle.
Thesis title: Bayesian Factor Analysis models for data integration.
Financially supported by La Caixa International Graduate Studies Scholarship.
Universitat Pompeu Fabra
BSc in Human Biology
BSc thesis performed under the supervision of Andreas Meyerhans and Kashif Sadiq.
Thesis title: Kinetic characterization of the mature HIV-1 protease by constructing Markov models from Molecular Dynamics Simulations

Publications

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(2022). 8C-like cells capture the human zygotic genome activation program in vitro.. Cell stem cell.

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(2022). Decoding gene regulation in the mouse embryo using single-cell multi-omics. bioRxiv.

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(2022). Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO. Nature Methods.

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(2022). Inter-gastruloid heterogeneity revealed by single cell transcriptomics time course: implications for organoid based perturbation studies. bioRxiv.

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(2022). Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis.. Genome biology.

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