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An hour of #bioinformatics can save a week in the lab. ALSO An hour in the lab can save a week of #bioinformatics.

Thrilled to have attended the EMBO workshop "Plasmids as vehicles of AMR spread" 🧬🔬. Truly inspiring discussions. Thanks to all the brilliant minds who shared their insights and to those who made it happen! AliceLedda, PhD 💙 Zamin Iqbal ICTP #Plasmids #EMBO

New blog post: rrwick.github.io/2023/10/24/ont… I revisit the question of ONT-only accuracy for bacterial genomes, and things have improved a lot since I last looked at this about six months ago!

New blog post: rrwick.github.io/2023/11/06/acc… I took the ONT data from my last post, subsampled to various depths and assembled with Flye. Reveals what ONT-only accuracy looks like with a 'normal' read depth and Flye assembly (as opposed to extra-deep reads and Trycycler assembly).

Excited to present CONGAS+, out now in PLOS Comp Biol CONGAS+ integrates #single_cell #RNA and #ATAC data (either from independent or multimodal assays) to cluster cells into #cancer clones with similar copy number profiles, offering a new way to map genotypes with phenotypes

Happy to have joined the #ESCMIDGlobal 2024 conference in Barcelona. Bacterial genomics and transcriptomics, fun and science all in one place :)

Our last research letter "Single-Cell RNA Sequencing Shows that Circulating #Monocytes, Enriched in #Interferon-Signalling, Are Associated with #Nontuberculous #Mycobacteria Pulmonary Disease in #CysticFibrosis" (1/7) ATS Blue Journal atsjournals.org/doi/abs/10.116…

One in four people are living with the deadliest infectious disease. Tuberculosis has outlasted civilizations. Find out why it's still here as we go deeper into its history and biology with the help of 🐢🐢🐢John Green🐢🐢🐢 : kgs.link/Tuberculosis

A wonderful conference in one of my favourite cities. It's been a pleasure to share our results for the detection of #pathogen transcripts with #SpatialTranscriptomics. Thanks to the European Society of Mycobacteriology for the great time

That's a wrap up! #ESM24

La fortuna di questo governo è che esiste Sinner, altrimenti da domani nei bar si comincerebbe a parlare di politica. [Barabba]

Our group's attempt to implement Spatial Transcriptomics for Host-Pathogen interaction

I finally got around to testing HERRO (github.com/lbcb-sci/herro), the new Oxford Nanopore read correction algorithm which takes simplex ONT reads to PacBio-HiFi-level accuracy. I was impressed! Findings are on my blog in a two-part post: rrwick.github.io/2024/07/26/her… rrwick.github.io/2024/07/31/her…

Happy to share our work on the use of Nanopore-based targeted sequencing for Mycobacterium tuberculosis on JClinMicro EIC #Mycobacteriumtuberculosis #Nanopore journals.asm.org/doi/10.1128/jc…

Single-Cell RNA Sequencing Shows that Circulating Monocytes Enriched in IFN Signaling Are Associated with Nontuberculous Mycobacteria Pulmonary Disease in Cystic Fibrosis Nicola Lorè Stefano de Pretis Ospedale San Raffaele American Thoracic Society (ATS) 🔓 Open Access 🔗 tinyurl.com/y88xbvfc

Extremely happy to share our new work on bacterial probes for Spatial Transcriptomics. A huge group effort with Francesca Nicola Stefano de Pretis Nicola Lorè :) nature.com/articles/s4200…

Di Marco et al. demonstrated that customized bacterial probes can be successfully used to identify host-pathogen interactions in formalin-fixed-paraffin-embedded (FFPE) tissues by probe-based spatial transcriptomics technology ➡️ nature.com/articles/s4200… #singlecell #spatialomics

It's out⚡️⚡️! #Dual spatial gene expression approach to dissect #host-#bacteria interaction in respiratory infections. Communications Biology (1/4) rdcu.be/dWuBQ nature.com/articles/s4200…

An inspiring experience at the EMBO workshop for #Spatialtranscriptomics! Great topics, food and music. Thanks to my bacterial-team for the fun too! 🦠 Nicola Lorè Stefano de Pretis Francesca Nicola #spatial #Bioinformatics #ntm

Postdoc opportunity (18 mos) Join our team to develop pipelines for single-cell seq data in an Fondazione AIRC per la ricerca sul cancro funded project! Looking for bioinformaticians and data scientists passionate about cutting-edge research (and fun too!) Apply by Dec 3rd: unimib.it/ateneo/gare-e-… please RT!