Timo Saratto
Bioinformatician & web software developer 🇫🇮
- Reposted by Timo SarattoOur new paper on Insertion Sequences (IS) in #Klebsiella - Lineages have vastly different IS loads and profiles - An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution. www.microbiologyresearch.org/content/jour...
- Reposted by Timo Saratto🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup. libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix github.com/ebiggers/lib...
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I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated! - 🧬🖥️ I’m building an open-source framework for easily compiling #bioinformatics pipeline results into pdf/html/xlsx reports. It will have built-in parsers for popular CLI tools Now looking for a few bioinformaticians for a brief usability feedback interview 👩💻 DM me or respond here if interested 👋
- Reposted by Timo SarattoMe getting back to sending nagging emails on January 6th when people return to work from the Christmas break
- Reposted by Timo SarattoNew preprint to close out the year! Led by Alana Papula and together with Daniel Fisher, we used single-cell genomes to infer the evolution of Prochlorococcus—one of the most abundant and genetically diverse bacteria on Earth. Check it out here: doi.org/10.64898/202...
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- Reposted by Timo SarattoWhy so many co-circulating #Klebsiella pneumoniae clones? By studying >7000 isolates, @bananabenana.bsky.social @kelwyres.bsky.social &co identify structured, clone-specific #metabolic specialisation across the population that enables reciprocal cross-feeding @plosbiology.org 🧪 plos.io/4qdC2B2
- Reposted by Timo SarattoSharing a Shiny app I've been working on at @leviwaldron1.bsky.social 's lab: BugSigDBEnrich. The app lets you compare a list of bacteria with published microbial signatures curated in bugsigdb.org. shiny.sph.cuny.edu/BugSigDBEnri... #rstats #microbiome #microbiomeresearch
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- Reposted by Timo SarattoWe’re excited to share our latest study that reshapes our understanding of Mycobacterium tuberculosis (Mtb) lipid composition, with major implications for drug discovery, immunity, and vaccine development. www.nature.com/articles/s41... A thread.
- Reposted by Timo SarattoHey folks, am looking for examples of circularised/full plasmid sequences from "unusual " bacterial species, sequenced since 2020 (as independent validation for a plasmid identification tool that was trained on refseq2020+plsdb). Any tips? #microsky
- Reposted by Timo Saratto💾 mlst 2.25.0 has been released! Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases. #bioinformatiocs #microbiology #genomics github.com/tseemann/mls...
- Reposted by Timo SarattoAntibiotic-resistant typhoid infections are a growing global health problem, made worse now by emerging carbapenem resistance. tinyurl.com/4uy7f6y3 by Thirumoorthy et al.
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- Reposted by Timo SarattoOur recent paper in npj Antimicrobials and Resistance is a great example of scientific serendipity: after staring at thousands of bacterial growth curves over many studies, we started wondering whether the curve shapes themselves carry mechanistic information 1/9 🦠🧪 www.nature.com/articles/s44...
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- Reposted by Timo SarattoI really love this model which brings real mechanistic insight to the barcode data which I had previously found interesting but mysterious! elifesciences.org/reviewed-pre...
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- Reposted by Timo Saratto#microsky #phagesky The 3rd (? Lost track!) manuscript on a CRISPR/anti-CRISPR -based transposon tool to study gene essentiality in #phages www.biorxiv.org/content/10.6...
- Reposted by Timo SarattoWe would be very happy to host a #bioinformatics #postdoc within this call! If you have expertise in #gutmicrobiota, #metagenomics, #machinelearning and/or #multiomics approaches, please get in touch to discuss potential 🧬& 🖥️ projects. Please share! @MicroSky www.scilifelab.se/data-driven/...
- Reposted by Timo Saratto🌊 🐟🦭🐋🐧 I have a PhD position available (4 years, start Mid-2026) at NRM Stockholm to work on the macrogenomics of sea warming. Apply here: recruit.visma.com/spa/public/a... #PhD #MarineGenomics #ClimateChange #EvolutionaryBiology #PopGen #Bioinformatics #conservationgenomics
- Reposted by Timo SarattoThe 2025 #BacDive 🦠 release is now online. 🎉🥳 The database now contains information on more than 100,000 strains 🧫. For this update, new data provided by @leibniz-dsmz.bsky.social and information on type strains of newly described species from the #LPSN database were added.
- Reposted by Timo Saratto#AMR #Klebsiella cause >100,000 neonatal deaths globally each year. Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW doi.org/10.1101/2025...
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- Reposted by Timo SarattoAI folks now having to realise what GWAS folks did about studying bacterial genome datasets. Great work by great researchers
- #MachineLearning methods are used to predict #AntimicrobialResistance #AMR from genomic data. @lbarquist.bsky.social &co show that sampling biases driven by population structure severely undermine the accuracy of AMR prediction models even with large datasets @plosbiology.org 🧪 plos.io/4iZ0zXQ
- Reposted by Timo Saratto(1/7) Really pleased to have this published in @natcomms.nature.com We looked at all public genomes encoding blaIMP (carbapenem #AMR ) 🦠🧫🧬💊. We show 5 IMP variants achieved global endemicity while 2 are regionally endemic. www.nature.com/articles/s41... #MicroSky #microbiology #IDSky #EpiSky 🧪
- Reposted by Timo SarattoWe are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬 Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions) (1/7)
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- Reposted by Timo SarattoWow this is a seriously serious supplementary figure from @cellpress.bsky.social today. Panels A through UU. I get that Cell likes to minimize the number of supplementary figures. But is this really what is happening here? www.cell.com/cell/fulltex...
- Reposted by Timo SarattoI am still actively looking for postdoc positions — please lmk if you (or your friends and colleagues) need a hardworking postdoc with field, lab, and bioinformatic skills! I am broadly interested in evolution in the ocean, conservation and population genetics, and rapid evolution.
- Reposted by Timo SarattoNature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/
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- Reposted by Timo SarattoWe're excited to share our lab's first lead paper! We developed OriGen, a language model trained to generate plasmid origins of replication. 🔄🦠 The model generates sequences that are significantly different from wild type origins and, remarkably, they allow for replication in vivo. Read it here ⬇️
- Reposted by Timo SarattoA very nice Preview of our work in @cp-cellhostmicrobe.bsky.social this morning from Chrishan Fernando & Nicole D. Marino! www.cell.com/cell-host-mi...
- Reposted by Timo SarattoOur new Microbial Primer describes the mechanistic action and therapeutic potential of R-pyocins produced by P. aeruginosa. www.microbiologyresearch.org/content/jour...
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- Reposted by Timo SarattoVery happy to see this remarkable work published. Led by @tommclean.bsky.social and @ainsley-beaton.bsky.social. We show how Streptomyces bacteria sense & respond to misfolded secreted proteins. A great collaboration with @barriewilks.bsky.social #microsky 1/2 journals.asm.org/doi/epub/10....
- Reposted by Timo SarattoBacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed. In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts. www.biorxiv.org/content/10.6...
- Reposted by Timo Saratto💾 Shovill 1.4.1 has been released! The best way to de novo assemble microbial genomes from Illumina FASTQ. Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking. #bioinformatiocs #genomics #microbiology github.com/tseemann/sho...
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- Reposted by Timo SarattoThe scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource
- Reposted by Timo SarattoFecal filtrate is less effective than donor stool (FMT) for the treatment of C. difficile recurrence. Now shown in a multicentre trial, out today in @lancetgastrohep.bsky.social . Congratulations to Dina Kao @ualberta.bsky.social & team! Gift link: authors.elsevier.com/c/1lphg8nByr...
- Reposted by Timo SarattoIs the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...
- Reposted by Timo SarattoLong read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...
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