Cell reports. Medicine
2026Proteogenomic analysis of pediatric and AYA high-grade glioma reveals age-dependent biology, female-male differences, and kinase targets.
Tignor NL, Koptyra M, Chowdhury S, Petralia F, Gritsenko MA, Ma W, Zhu Y, Marino GB, Song X, Migliozzi S, Whiteaker JR, Rykunov D, Hu Y, Hosseini N, Rokita JL, da Veiga Leprevost F, Rathi KS, Chen L, Wang YT, Weitz KK, Chu RK, Moore RJ, Krek A, Fu W, Wang X, Deng EZ, Tsai CF, Sagendorf T, Petyuk VA, Shi T, Fillmore TL, Zhao R, Monroe ME, Dannappel MV, Daniel P, Zhao L, Ivey RG, Voytovich UJ, Yaron-Barir TM, Huntsman EM, Johnson JL, Abedin N, Li YC, Santi M, Dupal D, Lilly J, Kraya A, Dybas JM, Zhang B, Zhong C, Brown MA, Phul S, Wafula E, Farrel A, Geng Z, Corbett RJ, Naqvi AS, Miller DP, Mason J, Patton TS, McGrory S, Robins S, Heath A, Sullivan C, Coleman N, Morgan A, Garofano L, Reva B, Schadt EE, Smith RD, Mesri M, Robles AI, Cantley LC, Ding L, Rodland KD, Zhang B, Nesvizhskii AI, Iavarone A, Cieslik M, Ippolito JE, Storm PB, Rubin JB, Firestein R, Ma'ayan A, Zhang H, Paulovich AG, Liu T, Resnick A, Rood BR, Wang P
Journal of molecular biology
2026The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs.
Evangelista JE, Clarke DJB, Byrd AI, Srinivasan S, Srinivasan S, Maurya MR, Jenkins SL, Diamant I, Sanchez E, Xie Z, Olaiya S, Kim H, Marino GB, Ahmed N, Ramachandran S, Subramaniam S, Ma'ayan A
GSFM: A gene set foundation model pre-trained on a massive collection of diverse gene sets.
Clarke DJB, Marino GB, Ma'ayan A
Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures.
Satpathy S, Clark NM, Chen YJ, Hosseini N, Chang YH, Hsiao Y, Lei JT, Petralia F, Chen JS, Geffen Y, Heiman DI, Paul I, Cho H, Hollenberg M, Marino GB, Lin KT, Mannan R, White CJ, Allen J, Avanessian SC, Kane MH, Wolfe A, Kinarivala M, Liu W, Anand S, Lin MW, Haines M, Bergstrom EJ, Hussey G, Li GX, Mani DC, Fang H, Jaehnig EJ, Keshishian H, Miller B, Su KY, Hsiao YJ, Hsu HH, Hsieh MS, Hsu KH, Monovoukas A, Gohsman S, Thorup JR, Deng Y, Akiyama Y, Deng E, Sheng-Wen Chen E, Krek A, Espinoza R, Ma W, Charytonowicz D, Sebra R, Lin JH, Chen YS, Hsu YC, Lin ZS, Chen KC, Yeh CW, Wang YT, Lazar AJ, Mesri M, An E, Zhang X, Clauser KR, Fenyö D, Chinnaiyan AM, Zhang B, Ding L, Ruggles K, Newton C, Zhang H, Wang P, Hostetter G, Omenn GS, Kumar-Sinha C, Thiagarajan M, Govindan R, Paik P, Parolia A, Li QK, Ma'ayan A, Getz GA, Dhanasekaran SM, Robles AI, Chang GC, Yang PC, Yu SL, Chen HY, Nesvizhskii AI, Carr SA, Mani DR, Cieslik MP, Chen YJ, Gillette MA, Taiwan Cancer Moonshot Program, Clinical Proteomic Tumor Analysis Consortium
Journal of molecular biology
2025lncRNAlyzr: Enrichment Analysis for lncRNA Sets.
Evangelista JE, Ali-Nasser T, Malek LE, Xie Z, Marino GB, Bester AC, Ma'ayan A
Nucleic acids research
2025L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine.
Marino GB, Evangelista JE, Clarke DJB, Ma'ayan A
PLoS computational biology
2025Playbook workflow builder: Interactive construction of bioinformatics workflows.
Clarke DJB, Evangelista JE, Xie Z, Marino GB, Byrd AI, Maurya MR, Srinivasan S, Yu K, Petrosyan V, Roth ME, Milinkov M, King CH, Vora JK, 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 MA, Sickler A, Zhu Y, Jenkins SL, Blood PD, Taylor DM, Resnick AC, Mazumder R, Milosavljevic A, Subramaniam S, Ma'ayan A
GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.
Marino GB, Olaiya S, Evangelista JE, Clarke DJB, Ma'ayan A
Bioinformatics advances
2025sc2DAT: workflow for targeting tumor subpopulations of single cells.
Marino GB, Byrd AI, Ahmed N, Clarke DJB, Ma'ayan A
Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays.
Marino GB, Deng EZ, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma'ayan A
Patterns (New York, N.Y.)
2024RummaGEO: Automatic mining of human and mouse gene sets from GEO.
Marino GB, Clarke DJB, Lachmann A, Deng EZ, Ma'ayan A
Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics.
Deng EZ, Marino GB, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma'ayan A
Communications biology
2024Rummagene: massive mining of gene sets from supporting materials of biomedical research publications.
Clarke DJB, Marino GB, Deng EZ, Xie Z, Evangelista JE, Ma’ayan A
Pan-cancer proteogenomics characterization of tumor immunity.
Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MG, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma'ayan A, Lazar AJ, Ceccarelli M, Wang P
Genetics in medicine open
2024Regulatory elements in SEM1-DLX5-DLX6 (7q21.3) locus contribute to genetic control of coronal nonsyndromic craniosynostosis and bone density-related traits
Nicoletti P, Zafer S, Matok L, Irron I, Patrick M, Haklai R, Evangelista JE, Marino GB, Ma'ayan A, Sewda A, Holmes G, Britton SR, Lee WJ, Wu M, Ru Y, Arnaud E, Botto L, Brody LC, Byren JC, Caggana M, Carmichael SL, Cilliers D, Conway K, Crawford K, Cuellar A, Di Rocco F, Engel M, Fearon J, Feldkamp ML, Finnell R, Fisher S, Freudlsperger C, Garcia-Fructuoso G, Hagge R, Heuzé Y, Harshbarger RJ, Hobbs C, Howley M, Jenkins MM, Johnson D, Justice CM, Kane A, Kay D, Gosain AK, Langlois P, Legal-Mallet L, Lin AE, Mills JL, Morton JEV, Noons P, Olshan A, Persing J, Phipps JM, Redett R, Reefhuis J, Rizk E, Samson TD, Shaw GM, Sicko R, Smith N, Staffenberg D, Stoler J, Sweeney E, Taub PJ, Timberlake AT, Topczewska J, Wall SA, Wilson AF, Wilson LC, Boyadjiev SA, Wilkie AOM, Richtsmeier JT, Jabs EW, Romitti PA, Karasik D, Birnbaum RY, Peter I
Communications medicine
2023Toxicology knowledge graph for structural birth defects.
Evangelista JE, Clarke DJB, Xie Z, Marino GB, Utti V, Jenkins S, Ahooyi TM, Bologa CG, Yang JJ, Binder JL et al.
Nucleic acids research
2023GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery.
Marino GB, Ngai M, Clarke DJB, Fleishman RH, Deng EZ, Xie Z, Ahmed N, Ma'ayan A
Nucleic acids research
2023Enrichr-KG: bridging enrichment analysis across multiple libraries.
Evangelista JE, Xie Z, Marino GB, Nguyen N, Clarke DJB, Ma'ayan A
Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells.
Deng EZ, Fleishman RH, Xie Z, Marino GB, Clarke DJB, Ma'ayan A
Database : the journal of biological databases and curation
2023lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs.
Marino GB, Wojciechowicz ML, Clarke DJB, Kuleshov MV, Xie Z, Jeon M, Lachmann A, Ma'ayan A
Bioinformatics advances
2023D2H2: diabetes data and hypothesis hub.
Marino GB, Ahmed N, Xie Z, Jagodnik KM, Han J, Clarke DJB, Lachmann A, Keller MP, Attie AD, Ma’ayan A et al.
Journal of the Association for Research in Otolaryngology : JARO
2020Anatomy of the Human Osseous Spiral Lamina and Cochlear Partition Bridge: Relevance for Cochlear Partition Motion.
Raufer S, C I, Zosuls A, Marino G, N Blanke, IJ Bigio, O'Malley JT, BJ Burgess, JB Nadol, Guinan J et al.
