Matteo Di Bernardo

EVOLVEpro is now out in @ScienceMagazine! It was wonderful to work with @idmjky, @jgooten, @omarabudayyeh, and the entire team on this!

We've had so much fun seeing how targeted & steered interventions with Claude improve and accelerate the ways we interpret results in the @iaincheeseman lab! Very thankful to @AnthropicAI's AI for Science program for the support and for highlighting our work!

From an accidental discovery of hidden biology to a new framework to understanding and diagnosing rare disease. Thrilled to share the most recent work from our lab and the amazing Jimmy Ly. wi.mit.edu/news/alternate…

Today @AnthropicAI released PubMed integration for Claude. No hallucinations. Just real science, real data. As a beta tester, this has been a game changer—like having a supercharged research assistant. Here are 6 prompts that will transform how you search the literature. A 🧵

We’re @BlaineyLab sharing a major update to CROPseq-multi, our versatile system for CRISPR screens that is compatible with individual and combinatorial perturbations, diverse SpCas9-based technologies, and multiple high-content, single-cell readouts. biorxiv.org/content/10.110…

🚫 No dyes. No bleaching. 🔬 Just AI + label-free microscopy = vivid virtually stained images New in @NatMachIntell: A deep learning model that enables robust virtual staining across microscopes, cell types & conditions. #CZBiohubSF @mattersOfLight explains:

@AllyNguyen9 @iaincheeseman Thanks @AllyNguyen9 we miss you!

@mat10_d @iaincheeseman Amazing work Matteo and team!! 👏 This is going to be an amazing resource

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 conversions, and lack of standardized frameworks. Together with Roshan Kern, Alexa Mallar, and Andy Nutter-Upham, we developed Brieflow, the first end-to-end computational pipeline for optical pooled screening analysis

You can get started with Brieflow here: github.com/cheeseman-lab/… Documentation: brieflow.readthedocs.io And explore our reanalysis results: screens.wi.mit.edu/aconcagua. We are excited to see what you think and how we can continue improving Brieflow as a community!

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 clusters, novel ribosome biogenesis components that we experimentally validated, refined MYC transcriptional networks, and unexpected connections between mRNA processing and vesicular trafficking. We also developed MozzareLLM (github.com/cheeseman-lab/…) for automated biological interpretation and candidate prioritization

@jgooten @idmjky @Princeton @omenndarlingbio Congrats Kaiyi!! @idmjky

Congratulations @idmjky on a fantastic defense! So excited to see you move on as Assistant Professor @Princeton @omenndarlingbio, can't wait to see what comes out of your lab.

Great to have you @BoWang87!

"AI: Advancing Foundational Biology," a symposium exploring AI's impact on biology research, is happening one week from tomorrow. Register: wi.mit.edu/events/ai-adva…

Check out @WhiteheadInst's symposium – AI: Advancing Foundational Biology – today (Tuesday, April 8), from 2-5:00 p.m., followed by a poster session and reception at 5 p.m. @Schmidt_Center Director Caroline Uhler will be keynoting at 2:15 p.m. Learn more: calendar.mit.edu/event/ai-advan…

New preprint drop! Check out work from Jimmy Ly et al for how protein isoforms generated by alternate translation initiation create dual localization, contribute to mitochondrial function, and are mutated in disease. Tweet-tutorial thread below. biorxiv.org/content/10.110…

Our most recent Nature Cell Biology paper describes an innovative Perturbation-response Score (PS) method to decode heterogeneous responses of cells to perturbations at single-cell level. Particularly helpful for analyzing Perturb-seq data. nature.com/articles/s4155…

(1/8) IMPA is published now in @NatureComms. (a) It can generate phenotypic cell painting/microscopy data images under unseen drug and genetic perturbations. (b) It learns a perturbation map of treatment similarities (small molecules together with genetic) and (c) it corrects batch effects in microscopy data. This was @ale__palmaa’s master’s thesis, which I supervised with @fabian_theis. link to the paper: shorturl.at/USp57

New preprint w/ surprising insights into proteasomes + mitosis. Océane Marescal found strikingly different cellular phenotypes for proteasome knockouts. 19S lid depletion results in ubiquitin-INDEPENDENT degradation of KIF11 motor + monopolar spindles. biorxiv.org/content/10.110…

Excited to share that the Nguyen lab website is live Nguyenlab.org ! Check out what we are working on and if you are at ASCB next week come say hello! We will be presenting a poster Monday at board B277

Now on biorxiv! The JUMP-Cell Painting Consortium’s paper: “Morphological map of under- and over-expression of genes in human cells” This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months biorxiv.org/content/10.110…