Samuel Miravet-Verde personal page

Research

I am a computational biologist specializing in microbiology and artificial intelligence–driven bioinformatics to investigate the genomic and functional complexity of microbial life using proteogenomic approaches.

During my PhD at the Centre for Genomic Regulation in Serrano Lab, I led research demonstrating that small proteins play roles as crucial as larger proteins in microbial systems, developing multiple tools to study them and addressing other challenges such as assessing gene essentiality. I also served as the main data analyst in several collaborative projects, contributing to diverse microbiological studies.

In 2022, I joined the Sunagawa Lab as a postdoctoral researcher at ETH Zurich, where I led the development of the Ocean Microbiome Database (OMDB) — the largest curated resource of marine microbial genomes. This work laid the foundation for my Human Frontiers Science Program (HFSP) Long-Term Postdoctoral Fellowship, under the project Charting the Origin, Diversity, and Biogeography of Small Proteins in the Global Ocean Microbiome.

Links of interest

Experience

Professional & Academic Experience

• Nov 2023 – Present — HFSP Long-Term Postdoctoral Fellow, Sunagawa Lab, ETH Zurich — Zurich, Switzerland.
  Leading the Ocean Microbiome Database development and research on small ORFs and proteins in marine microbiomes.
• Aug 2022 – Oct 2023 — Postdoctoral Researcher, Sunagawa Lab, ETH Zurich — Zurich, Switzerland.
• Jun 2021 – Jun 2022 — Junior Postdoctoral Researcher, Centre for Genomic Regulation (CRG) — Barcelona, Spain.
• Jan 2017 – May 2017 — Visiting PhD Student, Karr Lab, Icahn Institute for Data Science and Genomic Technology — New York, USA.
• Oct 2016 – May 2021 — PhD in Biomedicine & Computational Biology, Serrano Lab, Centre for Genomic Regulation (CRG) — Barcelona, Spain.
• Sep 2015 – Sep 2016 — Bioinformatics Intern, Serrano Lab, Centre for Genomic Regulation (CRG) — Barcelona, Spain.
• Oct 2013 – Aug 2014 — Bioinformatics Intern, GEM Biosoft — Valencia, Spain.
• May 2013 – Aug 2014 — Bioinformatics Intern, Foundation for the Promotion of Health and Biomedical Research — Valencia, Spain.
• Jun 2011 – May 2013 — Research Intern, Foundation for the Promotion of Health and Biomedical Research — Valencia, Spain.

Other Experience

• Nov 2022 – Present — Teaching Fellow, ETH Zurich — Zurich, Switzerland.
  Planning, preparation, teaching, and evaluation for the block course Microbial Community Genomics (551-1119-00L), covering theoretical, practical, and project development aspects of bioinformatics applied to microbiome research (3 editions).
• Sep 2023 – Present — Editorial Board Member, BMC Bioinformatics.
  Since June 2024 also Early Career Reviewer, Blue Biotechnology.

Education

• Oct 2016 – May 2021 — PhD in Biomedicine and Computational Biology, Universitat Pompeu Fabra — Barcelona, Spain.
  Grade: Excellent cum laude — International mention
• Sep 2014 – Jun 2016 — MSc in Bioinformatics for Health Sciences, Universitat Pompeu Fabra / Universitat de Barcelona — Barcelona, Spain.
  Grade: 9.45 — 125 ECTS
• Sep 2010 – Jun 2014 — BSc in Biochemistry and Biomedical Sciences, Universitat de València — Valencia, Spain.
  Grade: 8.37 — 244.5 ECTS

Publications

First-author papers

• "The natural diversity of E. coli transporter-dependent capsules" — Carine Roese Mores*, Samuel Miravet-Verde*, ..., Shinichi Sunagawa, Timothy G. Keys. bioRxiv (07 Aug 2025). 📄 Link
• "Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map" — Samuel Miravet-Verde, Raul Burgos, ..., Luis Serrano. Molecular Systems Biology (13 Aug 2025). 📄 Link
• "ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs" — Samuel Miravet-Verde, Rocco Mazzolini, ..., Maria Lluch-Senar, Luis Serrano. Nature Communications (12 Feb 2024). 📄 Link
• "FASTQINS and ANUBIS: two bioinformatic tools to explore facts and artifacts in transposon sequencing and essentiality studies" — Samuel Miravet-Verde, Raul Burgos, ..., Maria Lluch-Senar, Luis Serrano. Nucleic Acids Research (21 Sep 2020). 📄 Link
• "Unraveling the hidden universe of small proteins in bacterial genomes" — Samuel Miravet-Verde, Toni Ferrar, ..., Luis Serrano, Maria Lluch-Senar. Molecular Systems Biology (20 Feb 2019). 📄 Link
• "Alternative transcriptional regulation in genome-reduced bacteria" — Samuel Miravet-Verde, Veronica Lloréns-Rico, Luis Serrano. Current Opinion in Microbiology (16 Nov 2017). 📄 Link

Main data analyst

• "SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome" — Carlos Piñero-Lambea, Eva Garcia-Ramallo, Samuel Miravet-Verde, ..., Maria Lluch-Senar, Luis Serrano. Nucleic Acids Research (15 Dec 2022). 📄 Link
• "LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions" — Daniel Shaw, Samuel Miravet-Verde, ..., Maria Lluch-Senar, Luis Serrano. Microbial Biotechnology (16 Nov 2020). 📄 Link
• "Inferring active metabolic pathways from proteomics and essentiality data" — Ariadna Montero-Blay, Samuel Miravet-Verde, ..., Maria Lluch-Senar, Luis Serrano. Cell Reports (02 Jun 2020). 📄 Link
• "SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes" — Ariadna Montero-Blay, Samuel Miravet-Verde, ..., Maria Lluch-Senar, Luis Serrano. DNA Research (01 Aug 2019). 📄 Link

Supervisor

• "Exon inclusion signatures enable accurate estimation of splicing factor activity" — Miquel Anglada-Girotto, Daniel F. Moakley, ..., Samuel Miravet-Verde, ..., Andrea Califano, Luis Serrano. bioRxiv (29 Jul 2025). 📄 Link
• "Using single-cell perturbation screens to decode the regulatory architecture of splicing factor programs" — Miquel Anglada-Girotto, Samuel Miravet-Verde, Luis Serrano. bioRxiv (07 Feb 2025). 📄 Link
• "In silico RNA isoform screening to identify potential cancer driver exons with therapeutic applications" — Miquel Anglada-Girotto, Ludovica Ciampi, ..., Samuel Miravet-Verde, Luis Serrano. Nature Communications (26 Dec 2024). 📄 Link
• "robustica: customizable robust independent component analysis" — Miquel Anglada-Girotto, Samuel Miravet-Verde, ..., Sarah A. Head. BMC Bioinformatics (16 Aug 2022). 📄 Link

Other collaborations

• "Transcriptomic profiles of single-copy marker genes enable predicting bacterial growth states in microbial communities" — Melanie Staeubli, ..., Samuel Miravet-Verde, ..., Shinichi Sunagawa. bioRxiv (26 Aug 2025). 📄 Link
• "Genome-resolved diversity and biosynthetic potential of the coral reef microbiome" — Lucas Paoli, Fabienne Wiederkehr, ..., Samuel Miravet-Verde, ..., Shinichi Sunagawa. bioRxiv (18 Aug 2024). 📄 Link
• "Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota" — Mara D. Maeke, Xiuran Yin, ..., Samuel Miravet-Verde, ..., Christiane Hassenrück. Microbiome (03 Aug 2025). 📄 Link
• "The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities" — Marija Dmitrijeva, Hans-Joachim Ruscheweyh, ..., Samuel Miravet-Verde, ..., Shinichi Sunagawa. Nucleic Acids Research (06 Jan 2025). 📄 Link
• "Engineering Mycoplasma pneumoniae to bypass the association with Guillain-Barré syndrome" — Alicia Broto, Carlos Piñero-Lambea, ..., Samuel Miravet-Verde, ..., Luis Serrano. Microbes and Infection (15 Jul 2024). 📄 Link
• "Specialization of the photoreceptor transcriptome by Srrm3-dependent microexons is required for outer segment maintenance and vision" — Ludovica Ciampi, Federica Mantica, ..., Samuel Miravet-Verde, ..., Manuel Irimia. PNAS (19 Jul 2022). 📄 Link
• "A genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications" — Alicia Broto, Erika Gaspari, Samuel Miravet-Verde, Victor AP Martins dos Santos, Mark Isalan. Nature Communications (07 Apr 2022). 📄 Link
• "The role of clonal communication and heterogeneity in breast cancer" — Ana Martín-Pardillos, Ángeles Valls Chiva, ..., Samuel Miravet-Verde, ..., Santiago Ramón y Cajal. BMC Cancer (10 Jul 2019). 📄 Link
• "High frequencies of antibiotic resistance genes in infants' meconium and early fecal samples" — Maria José Gosalbes, Yvonne Vallès, ..., Samuel Miravet-Verde, ..., Maria Pilar Francino. Journal of Developmental Origins of Health and Disease (06 Feb 2016). 📄 Link
• "Engineering bacteria to form a biofilm and induce clumping in Caenorhabditis elegans" — Pedro Dorado-Morales, Alba Iglesias, ..., Samuel Miravet-Verde, ..., Manuel Porcar. ACS Synthetic Biology (15 Dec 2014). 📄 Link