Matteo Di Bernardo
@mat10_d
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PhD student @MITCSBPhD with @iaincheeseman, previously @FulbrightPrgrm Nigeria, @columbiacancer
Cambridge, MA
Joined November 2013
EVOLVEpro is now out in @ScienceMagazine! It was wonderful to work with @idmjky, @jgooten, @omarabudayyeh, and the entire team on this!.
Thrilled to share that EVOLVEpro is now published @ScienceMagazine Since our preprint, we now demonstrate low-N eningeering of both antibody and enzymes. We hope this model will broadly useful to the protein engineering field.
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RT @russelltwalton: We’re @BlaineyLab sharing a major update to CROPseq-multi, our versatile system for CRISPR screens that is compatible w….
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RT @czbiohub: 🚫 No dyes. No bleaching. 🔬 Just AI + label-free microscopy = vivid virtually stained images. New in @NatMachIntell: A deep le….
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You can get started with Brieflow here: Documentation: And explore our reanalysis results: We are excited to see what you think and how we can continue improving Brieflow as a community!.
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We validated Brieflow by reanalyzing the massive "Vesuvius" dataset: 5,072 genes across 70+ million cells with multiple phenotypic markers. Our improved pipeline uncovered functional relationships completely missed in the original study, including coherent mitochondrial gene
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Brieflow provides a unified framework from raw microscopy images to biological insights through a modular pipeline that handles image preprocessing, barcode identification, cellular feature extraction, data integration, aggregation, and clustering. We've paired this with an
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Optical pooled screening is revolutionizing functional genomics by linking genetic perturbations to complex cellular phenotypes at unprecedented scale. But analyzing these massive datasets has been a major bottleneck - researchers face fragmented tools, multiple format
Optical Pooled Screening has transformed large-scale cell biology, but lacks robust end-to-end computational strategies to process these Tb-sized datasets. New from Di Bernardo et al (@mat10_d):. Brieflow. A game changer for OPS + new biological insights.
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Great to have you @BoWang87!.
Excited to be giving a keynote at the workshop ‘AI: Advancing Foundational Biology’ hosted by @WhiteheadInst at @MIT today! I’ll be speaking about building foundation models for biomedical data, including scGPT and MedSAM. Don’t miss it!
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RT @WhiteheadInst: "AI: Advancing Foundational Biology," a symposium exploring AI's impact on biology research, is happening one week from….
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RT @Schmidt_Center: Check out @WhiteheadInst's symposium – AI: Advancing Foundational Biology – today (Tuesday, April 8), from 2-5:00 p.m.,….
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RT @iaincheeseman: New preprint drop! Check out work from Jimmy Ly et al for how protein isoforms generated by alternate translation initia….
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RT @davidliwei: Our most recent Nature Cell Biology paper describes an innovative Perturbation-response Score (PS) method to decode heterog….
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RT @mo_lotfollahi: (1/8) IMPA is published now in @NatureComms. (a) It can generate phenotypic cell painting/microscopy data images under u….
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RT @iaincheeseman: New preprint w/ surprising insights into proteasomes + mitosis. Océane Marescal found strikingly different cellular phen….
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RT @AllyNguyen9: Excited to share that the Nguyen lab website is live ! . Check out what we are working on and if y….
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RT @DrAnneCarpenter: Now on biorxiv! The JUMP-Cell Painting Consortium’s paper:. “Morphological map of under- and over-expression of genes….
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RT @EricTopol: They're coming fast and furious!.Also today @ScienceMagazine add EVOLVEpro, a protein large language model combined with a r….
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@ScienceMagazine @idmjky @jgooten @omarabudayyeh To optimize EVOLVEpro on other deep mutational scanning datasets, or efficiently improve the activity of your protein of interest, you can take a look at our codebase here:
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