Giacomo Bruno Marino
About
Research
Publications
2026
GSFM: A gene set foundation model pre-trained on a massive collection of diverse gene sets
Clarke D, Marino G, Ma’ayan A. GSFM: A gene set foundation model pre-trained on a massive collection of diverse gene sets. Patterns 2026, 101565. DOI: 10.1016/j.patter.2026.101565.Peer-Reviewed Original ResearchThe CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs
Evangelista J, Clarke D, Byrd A, Srinivasan S, Srinivasan S, Maurya M, Jenkins S, Diamant I, Sanchez E, Xie Z, Olaiya S, Kim H, Marino G, Ahmed N, Ramachandran S, Subramaniam S, Ma'ayan A. The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs. Journal Of Molecular Biology 2026, 438: 169631. PMID: 41506317, DOI: 10.1016/j.jmb.2026.169631.Peer-Reviewed Original Research
2025
Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures
Satpathy S, Clark N, Chen Y, Hosseini N, Chang Y, Hsiao Y, Lei J, Petralia F, Chen J, Geffen Y, Heiman D, Paul I, Cho H, Hollenberg M, Marino G, Lin K, Mannan R, White C, Allen J, Avanessian S, Kane M, Wolfe A, Kinarivala M, Liu W, Anand S, Lin M, Haines M, Bergstrom E, Hussey G, Li G, Mani D, Fang H, Jaehnig E, Keshishian H, Miller B, Su K, Hsiao Y, Hsu H, Hsieh M, Hsu K, Monovoukas A, Gohsman S, Thorup J, Deng Y, Akiyama Y, Deng E, Chen E, Krek A, Espinoza R, Ma W, Charytonowicz D, Sebra R, Lin J, Chen Y, Hsu Y, Lin Z, Chen K, Yeh C, Wang Y, Lazar A, Mesri M, An E, Zhang X, Clauser K, Fenyö D, Chinnaiyan A, Zhang B, Ding L, Ruggles K, Newton C, Zhang H, Wang P, Hostetter G, Omenn G, Kumar-Sinha C, Thiagarajan M, Govindan R, Paik P, Parolia A, Li Q, Ma’ayan A, Getz G, Dhanasekaran S, Robles A, Chang G, Yang P, Yu S, Chen H, Nesvizhskii A, Carr S, Mani D, Cieslik M, Chen Y, Gillette M, Program T, Lu C, Chu C, Shen C, Han C, Lin C, Lin C, Chen C, Lin C, Hsu H, Tsai H, Wu J, Lin J, Waniwan J, Liao K, Chen P, Huang P, Huang S, Lin T, Lai W, Chiu W, Chiang X, Chang Y, Chen Y, Chen Y, Wang Y, Lin Y, Chang Y, Huang Y, Lien Y, Zheng Z, Consortium C, Hashimi A, Mohan A, Pandey A, Pilozzi A, Webster A, Paulovich A, Dagar A, Godwin A, Pruetz B, Williams B, Druker B, Rohrer D, Chan D, Petrov D, Chesla D, Davaar D, Duffy E, Wilson G, Zhao G, Kołodziejczak I, Lubinski J, Huang J, Hafron J, Tyner J, Koomen J, Zaalishvili K, Ketchum K, Wiznerowicz M, Domagalski M, Anurag M, Borucki M, Edwards N, Vatanian N, Grady P, Piehowski P, Bogdan P, Li Q, Fonseca R, Madan R, Thangudu R, Crispen R, Matteotti R, Bremner R, Cerda S, Cottingham S, Tsang S, Cai S, Liu T, Bauer T, Maggio W, Jing X, Zhang Y, Shutack Y, Andric Z. Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures. Cancer Cell 2025, 43: 1731-1757.e17. PMID: 40749670, PMCID: PMC12393171, DOI: 10.1016/j.ccell.2025.07.011.Peer-Reviewed Original ResearchL2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine
Marino G, Evangelista J, Clarke D, Ma’ayan A. L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine. Nucleic Acids Research 2025, 53: w338-w350. PMID: 40308216, PMCID: PMC12230732, DOI: 10.1093/nar/gkaf373.Peer-Reviewed Original ResearchPlaybook workflow builder: Interactive construction of bioinformatics workflows
Clarke D, Evangelista J, Xie Z, Marino G, Byrd A, Maurya M, Srinivasan S, Yu K, Petrosyan V, Roth M, Milinkov M, King C, Vora J, Keeney J, Nemarich C, Khan W, Lachmann A, Ahmed N, Agris A, Pan J, Ramachandran S, Fahy E, Esquivel E, Mihajlovic A, Jevtic B, Milinovic V, Kim S, McNeely P, Wang T, Wenger E, Brown M, Sickler A, Zhu Y, Jenkins S, Blood P, Taylor D, Resnick A, Mazumder R, Milosavljevic A, Subramaniam S, Ma’ayan A. Playbook workflow builder: Interactive construction of bioinformatics workflows. PLOS Computational Biology 2025, 21: e1012901. PMID: 40179105, PMCID: PMC11967941, DOI: 10.1371/journal.pcbi.1012901.Peer-Reviewed Original ResearchlncRNAlyzr: Enrichment Analysis for lncRNA Sets
Evangelista J, Ali-Nasser T, Malek L, Xie Z, Marino G, Bester A, Ma’ayan A. lncRNAlyzr: Enrichment Analysis for lncRNA Sets. Journal Of Molecular Biology 2025, 437: 168938. PMID: 40133794, PMCID: PMC12145269, DOI: 10.1016/j.jmb.2025.168938.Peer-Reviewed Original ResearchGeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets
Marino G, Olaiya S, Evangelista J, Clarke D, Ma'ayan A. GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets. GigaScience 2025, 14: giaf025. PMID: 40208796, PMCID: PMC11984350, DOI: 10.1093/gigascience/giaf025.Peer-Reviewed Original Research
2024
sc2DAT: workflow for targeting tumor subpopulations of single cells
Marino G, Byrd A, Ahmed N, Clarke D, Ma’ayan A. sc2DAT: workflow for targeting tumor subpopulations of single cells. Bioinformatics Advances 2024, 5: vbaf237. PMID: 41079221, PMCID: PMC12512136, DOI: 10.1093/bioadv/vbaf237.Peer-Reviewed Original ResearchProtocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays
Marino G, Deng E, Clarke D, Diamant I, Resnick A, Ma W, Wang P, Ma’ayan A. Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays. STAR Protocols 2024, 5: 103457. PMID: 39565691, PMCID: PMC11617449, DOI: 10.1016/j.xpro.2024.103457.Peer-Reviewed Original ResearchRummaGEO: Automatic mining of human and mouse gene sets from GEO
Marino G, Clarke D, Lachmann A, Deng E, Ma’ayan A. RummaGEO: Automatic mining of human and mouse gene sets from GEO. Patterns 2024, 5: 101072. PMID: 39569206, PMCID: PMC11573963, DOI: 10.1016/j.patter.2024.101072.Peer-Reviewed Original Research