Dr. Samuel Miravet-Verde
Dr. Samuel Miravet-Verde
Staff of Professorship for Microbiome Research
Additional information
Research area
Samuel Miravet-Verde is a computational biologist with expertise in microbiology and artificial intelligence-based bioinformatic approaches to understand complex microbiological genomic and functional aspects. Throughout his PhD he led research to show that small proteins are as important as larger proteins in microbial systems, developing multiple tools to study them, as well as other problems such as assessing gene essentiality, and as main data-analyst in several collaborative projects. He joined the Sunagawa lab as a postdoc in 2022 to work in the development of the Ocean Microbiomic Database and projects deriving from this resource. In particular, he is interested in providing better small protein annotations and understanding their functional role in marine microbiomes.
Education & Experience
2022 - current: Postdoc at the Sunagawa lab. in ETH Zurich (Zurich, Switzerland)
2021-2022: Junior Postdoc, Centre for Genomic Regulation (Barcelona, Spain)
2017-2017: Visiting PhD, Karr lab. at Icahn Institute for Data Science and Genomic Technology (New York, United States)
2016-2021: PhD in Biomedicine and Computational Biology, Serrano lab. at Centre for Genomic Regulation (Barcelona, Spain)
2015-2016: Bioinformatics Intern, Serrano lab. at Centre for Genomic Regulation (Barcelona, Spain)
2014-2016: MSc in Bioinformatics for Health Sciences, Universitat Pompeu Fabra (Barcelona, Spain)
2013-2014: Bioinformatics Intern, GEM Biosoft (Valencia, Spain)
2013-2014: Bioinformatics Intern, Foundation for the Promotion of Health and Biomedical Research (Valencia, Spain)
2011-2013: Research Intern, Foundation for the Promotion of Health and Biomedical Research (Valencia, Spain)
2010-2014: BSc in Biochemistry and Biomedical Sciences, Universitat de València (Valencia, Spain)
Publications
Anglada-Girotto, M., Miravet-Verde, S., Serrano, L., & Head, S. A. (2022) robustica: customizable robust independent component analysis. BMC Bioinformatics.
Broto, A., Gaspari, E., Miravet-Verde, S., Dos Santos, V. A. P. M., & Isalan, M. (2022). A genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications. Nature Communications, 13(1), 1910.
Ciampi, L., Mantica, F., López-Blanch, L., Permanyer, J., Rodriguez-Marín, C., Zang, J., Cianferoni, D., Jiménez-Delgado, S., Bonnal, S., Miravet-Verde, S., Ruprecht, V., Neuhauss, S. C. F., Banfi, S., Carrella, S., Serrano, L., Head, S. A., & Irimia, M. (2022). Specialization of the photoreceptor transcriptome by Srrm3-dependent microexons is required for outer segment maintenance and vision. Proceedings of the National Academy of Sciences of the United States of America, 119(29), e2117090119.
Piñero-Lambea, C., Garcia-Ramallo, E., Miravet-Verde, S., Burgos, R., Scarpa, M., Serrano, L., & Lluch-Senar, M. (2022). SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome. Nucleic Acids Research. https://doi.org/10.1093/nar/gkac836
Shaw, D., Miravet-Verde, S., Piñero-Lambea, C., Serrano, L., & Lluch-Senar, M. (2021). LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions. Microbial Biotechnology, 14(6), 2403–2419.
Montero-Blay, A., Piñero-Lambea, C., Miravet-Verde, S., Lluch-Senar, M., & Serrano, L. (2020). Inferring Active Metabolic Pathways from Proteomics and Essentiality Data. Cell Reports, 31(9), 107722.
*** Miravet-Verde, S., Burgos, R., Delgado, J., Lluch-Senar, M., & Serrano, L. (2020). FASTQINS and ANUBIS: two bioinformatic tools to explore facts and artifacts in transposon sequencing and essentiality studies. Nucleic Acids Research, 48(17), e102.
Montero-Blay, A., Miravet-Verde, S., Lluch-Senar, M., Piñero-Lambea, C., & Serrano, L. (2019). SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 26(4), 327–339.
Martín-Pardillos, A., Valls Chiva, Á., Bande Vargas, G., Hurtado Blanco, P., Piñeiro Cid, R., Guijarro, P. J., Hümmer, S., Bejar Serrano, E., Rodriguez-Casanova, A., Diaz-Lagares, Á., Castellvi, J., Miravet-Verde, S., Serrano, L., Lluch-Senar, M., Sebastian, V., Bribian, A., López-Mascaraque, L., López-López, R., & Ramón Y Cajal, S. (2019). The role of clonal communication and heterogeneity in breast cancer. BMC Cancer, 19(1), 666.
*** Miravet-Verde, S., Ferrar, T., Espadas-García, G., Mazzolini, R., Gharrab, A., Sabido, E., Serrano, L., & Lluch-Senar, M. (2019). Unraveling the hidden universe of small proteins in bacterial genomes. Molecular Systems Biology, 15(2), e8290.
*** Miravet-Verde, S., Lloréns-Rico, V., & Serrano, L. (2017). Alternative transcriptional regulation in genome-reduced bacteria. Current Opinion in Microbiology, 39, 89–95.
Gosalbes, M. J., Vallès, Y., Jiménez-Hernández, N., Balle, C., Riva, P., Miravet-Verde, S., de Vries, L. E., Llop, S., Agersø, Y., Sørensen, S. J., Ballester, F., & Francino, M. P. (2016). High frequencies of antibiotic resistance genes in infants’ meconium and early fecal samples. Journal of Developmental Origins of Health and Disease (Vol. 7, 1, pp. 35–44).
Dorado-Morales, P., Iglesias, A., Zafrilla, G., Valero, A., Torres, A., Miravet-Verde, S., de Loma, J., Mañas, M., Ruiz, A., Corman, A., Morales, L.J., Peretó, J., Vilanova, C., Porcar, M. (2014). Engineering bacteria to form a biofilm and induce clumping in Caenorhabditis elegans. ACS Synthetic Biology. 2014, 3, 12, 941–943.