Samuel MV
@Samuel_BIO2810
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Computational biologist looking to understand complex genomic and functional aspects of microbes using AI.
Zurich
Joined June 2011
Which tiny pieces of a bacterium’s DNA are truly essential, not just the obvious genes, but also the small control switches that help them run? We explore this and more in our latest publication with @lab_serrano, out now in @MolSystBiol! https://t.co/12f7DJkXnb
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Our new “fitness map” of M. pneumoniae reveals which DNA parts are vital, and how much each contributes to survival. Even within essential genes, some bits can be broken without killing the cell! like a engine running even if it’s in two pieces, as long as both halves are there.
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Essentiality studies usually focus on genes. Here, we checked every single base in the genome; like inspecting a machine, not just the big gears, but every screw and switch. And instead of just “yes/no,” we scored how much the cell falters when each piece is removed.
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This month, we featured Dr Samuel Miravet-Verde @Samuel_BIO2810 from @eth_en on our monthly #Translatomics Newsletter. He specializes in artificial intelligence-based #bioinformatics approaches for understanding complex microbiological and #proteogenomic aspects. #newsletter
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Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map https://t.co/8JnBEd1lEw
#biorxiv_sysbio
biorxiv.org
Essentiality studies have traditionally focused on coding regions, often overlooking other small genetic regulatory elements. To address this, we obtained a high-resolution essentiality map at...
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The mOTUs4 genome database: 2.83Mio systematically reconstructed MAGs and >900K isolate and single cell-assembled genomes, all clustered into 124K species-level clusters. Paper out at @NAR_Open: https://t.co/tviEEeLObk 1/5
academic.oup.com
Abstract. Determining the taxonomic composition (taxonomic profiling) is a fundamental task in studying environmental and host-associated microbial communi
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Congratulations to @marija_dmit, @hjruscheweyh, @Samuel_BIO2810, @aasintsova, @pangenomics, and @ZellerGroup 🎉 5/5
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The GMSC manuscript is now published in @NatureComms (open access) We constructed a small protein catalog from the global microbiome https://t.co/DM7ptf2jvH
nature.com
Nature Communications - Here, the authors built a non-redundant catalogue of nearly 1 billion putative small proteins from the global microbiome as a publicly-available resource, and highlight how...
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Cancer dysregulates thousands of exons; some are drivers and could lead to therapies. But which ones? Similar to VEP models for mutations, we model potential cancer driver exons genome-wide and predict exon fitness in cancer. @NatureComms: https://t.co/6I9zZmTDxh 🧵
nature.com
Nature Communications - While alternative splicing is known to drive oncogenesis and be a source of potential therapeutic targets, identifying such drivers on a genome-wide scale has proven...
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Read the Launch Editorial for Blue Biotechnology by Editor-in-Chief Ning He, introducing the vision for the journal as the journal's first articles are published. https://t.co/lCWQhUNNkh
link.springer.com
Blue Biotechnology is an open access, peer-reviewed journal featuring studies that cover all areas of applied research and biotechnology involving marine ...
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A full thread on the science later, but I'm very happy that, after 5 years of work, the AMPSphere manuscript is out at @CellCellPress Congrats to @celiodiasjunior @mdt_torres @delafuenteupenn @cocodyq @TSBSchm @alvarordr @jhcepas @BorkLab ... https://t.co/LGso0OARj8
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Tuve el placer de hablar de mi carrera, trabajo, bacterias, el mar y la vida en el nuevo proyecto de uno de mis mejores amigos de toda la vida, Fran Arzo. A ver que os parece! https://t.co/jnm2ZqSU0P
#ciencia #microbiomas #proteinas
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And access the full research article here: https://t.co/aFM4aURbif
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You can read a post about the project here: https://t.co/NcX6yBCig1
communities.springernature.com
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This was a collaborative effort from @lab_serrano at @CRGenomica. Special thanks Rocco Mazzolini, Carolina Segura and Alicia Broto for their experimental support, and Luis Serrano and Maria Lluch Senar for supporting and guiding this project!
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Overall, ProTInSeq offers a cost-effective method to explore small proteins via DNA sequencing. It provides quantitative insights into SEPs and proteome characteristics that can guide the discovery of new protein sequences and facilitate further functional studies.
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In perspective, Escherichia coli has ~4,000 proteins in its proteome, while a human's proteome is predicted to contain ~20,000 proteins. If the trends observed in M. pneumoniae extend to these organisms, the number of SEPs awaiting annotation could be in the thousands.
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ProTInSeq identifies 80% of known proteins in M. pneumoniae and uncovers 153 SEPs and 5 larger proteins missed by other experimental methods. Integration with other techniques shows that M. pneumoniae's genome encodes 997 proteins, a 43% increase from previous estimates.
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In our new research, we present ProTInSeq, a method based on random transposon mutagenesis and sequencing to explore a proteome of interest. This is achieved by using transposons carrying mutated markers that are expressed only when inserted in-frame to a protein-coding ORF.
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Nonetheless, small ORF-Encoded Proteins (#SEPs) can play crucial roles in cellular processes, including bacterial competition and communication. However, SEPs are overlooked due to a lack of experimental evidence.
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