Huge thanks to my amazing co-authors: Paola Gasperini, Riccardo Bevilacqua, @YariCiani Yari Ciani, @Sanjusinha7 Sanju Sinha, @NCIEytanRuppin Eytan Ruppin & @FrancescaBZNY Francesca Demichelis.

6/6 PRODE could help prioritize cancer targets more robustly across datasets, screening technologies, & tumor types. 🔗 Read the full paper here:

5/6 We validated PRODE’s predictions with: ✅ Experimental in vitro viability assays ✅ CRISPR & shRNA datasets ✅ Analysis of clinical datasets (TCGA, patient cohorts)

4/6 PRODE outperforms standard gene effect-based approaches: ✅ Recovers essential genes lost in shRNA screens ✅ Improves the prioritization of context essentiality, such as Synthetic Lethality ✅ Pinpoints novel cancer vulnerabilities

3/6 Enter PRODE! We integrate gene effects with protein-protein interactions (PPIs) to compute: ✅ NIE (Neighborhood-Informed Essentiality) ✅ NICE (Neighborhood-Informed Context Essentiality) This boosts precision in finding missed essential & context essential genes.

2/6 Traditional methods rely on gene effect scores from loss-of-function (LoF) screens (shRNA, CRISPR-KO). But these scores vary across cell lines and technologies, making it hard to identify robust hits.

1/6 Why does gene essentiality matter? Essential genes are crucial for cell survival, while context-essential genes are only essential in certain condition—making them prime cancer therapeutic targets.

❗️Excited to share my PhD work in Genome Biology: PRODE recovers essential and context-essential genes through neighborhood-informed scores. What is PRODE, and how does it help?👇

🚀 Proud to launch ⭐Path2Space⭐ — the first AI to discover spatial biomarkers for cancer treatment! It predicts spatial gene expression from histopathology, enabling large-scale tumor microenvironment profiling. https://t.co/kYFfWEYqyi 🧵1/11

🥂🙌 A new doctor, Thomas Cantore, Ph.D. @cantore_thomas in the Computational and Functional Oncology DemichelisLab! #PRODE @CIBIO_UniTrento @paola_gasperini @YariCiani @MariannKruithof @NCIEytanRuppin

Outstanding PhD defence from a huge friend: Thomas Cantore! @cantore_thomas @FrancescaBZNY

Excited to share our recent work published in @MedCellPress, the very first systematic review and analysis on synthetic lethality in oncology, led by Alejandro Schäffer, @ChungYoungmin, @AKammula and @joo_sang_lee. Buckle up! 🚀

Noninvasive detection of NEPC by targeted cfDNA methylation @CD_AACR co-led by @FrancescaBZNY and her lab @UniTrento. Congrats to first author @GMFranceschini and thank you to many amazing collaborators @PCF_Science @DanaFarber_GU #NEMO https://t.co/rToG0QfXB1

A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization

Kudos Riccardo Bevilacqua!⁦ II poster prize #ESUR23: vulnerabilities of 9p21 deleted #bladdercancer ⁦@paola_gasperini ⁦@cantore_thomas⁩ @CIBIO_UniTrento With ⁦@FaltasLab⁩ @MariannKruithof ⁩⁦@ERC_Research⁩ #SternbergFoundation

I am hiring multiple Computational Biologists for my new lab @sbpdiscovery , San Diego. An alternative to a postdoc, it will pay higher (70-90K$; Be the change you want to see in the world) & is tailored to develop skills to industry transition. https://t.co/HxsGeevb9S My lab

With a mixed bag of emotions - nervousness, excitement, fear & determination, I am announcing the start of my lab at @sbpdiscovery, San Diego. Our focus will be to develop new preventative therapies for cancer using machine learning.

Wonderful to be here! #Pezcoller23 @FrancescaBZNY @GMFranceschini @YariCiani @f_orlando_ @GiuliaFracassi_ @FraLo05 @cantore_thomas