Thomas Cantore
@cantore_thomas
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Computational Biologist, Phd Candidate
Joined December 2019
Huge thanks to my amazing co-authors:.Paola Gasperini, Riccardo Bevilacqua, @YariCiani Yari Ciani, @Sanjusinha7 Sanju Sinha, @NCIEytanRuppin Eytan Ruppin & @FrancescaBZNY Francesca Demichelis.
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6/6 PRODE could help prioritize cancer targets more robustly across datasets, screening technologies, & tumor types. 🔗 Read the full paper here:
genomebiology.biomedcentral.com
Gene context-essentiality assessment supports precision oncology opportunities. The variability of gene effects inference from loss-of-function screenings across models and technologies limits...
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5/6 We validated PRODE’s predictions with:.✅ Experimental in vitro viability assays.✅ CRISPR & shRNA datasets.✅ Analysis of clinical datasets (TCGA, patient cohorts).
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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.
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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.
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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.
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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.
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❗️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?👇.
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RT @NCIEytanRuppin: 🚀 Proud to launch ⭐Path2Space⭐ — the first AI to discover spatial biomarkers for cancer treatment!.It predicts spatial….
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RT @FrancescaBZNY: 🥂🙌 A new doctor, Thomas Cantore, Ph.D. @cantore_thomas in the Computational and Functional Oncology DemichelisLab! #PR….
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RT @FedericoVannuc7: Outstanding PhD defence from a huge friend: Thomas Cantore! @cantore_thomas @FrancescaBZNY
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RT @NCIEytanRuppin: Excited to share our recent work published in @MedCellPress, the very first systematic review and analysis on synthetic….
cell.com
Since the seminal work in 1997, much research has been done to apply synthetic lethality in clinical oncology; however, there has been no systematic evaluation of such efforts. Schäffer et al....
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RT @mishabeltran: Noninvasive detection of NEPC by targeted cfDNA methylation @CD_AACR co-led by @FrancescaBZNY and her lab @UniTrento. Con….
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A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization
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RT @FrancescaBZNY: Kudos Riccardo Bevilacqua! II poster prize #ESUR23: vulnerabilities of 9p21 deleted #bladdercancer.@paola_gasperini @….
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RT @Sanjusinha7: I am hiring multiple Computational Biologists for my new lab @sbpdiscovery , San Diego. An alternative to a postdoc, it w….
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RT @Sanjusinha7: With a mixed bag of emotions - nervousness, excitement, fear & determination, I am announcing the start of my lab at @sbpd….
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RT @FedericoVannuc7: Wonderful to be here! #Pezcoller23 @FrancescaBZNY @GMFranceschini @YariCiani @f_orlando_ @GiuliaFracassi_ @FraLo05 @ca….
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