Marino GB, Deng EZ, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma'ayan A. 2024. Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays STAR Protocols. 10.1016/j.xpro.2024.103457
Marino GB, Clarke DJB, Lachmann A, Deng EZ, Ma'ayan A. 2024. RummaGEO: Automatic mining of human and mouse gene sets from GEO Patterns. 10.1016/j.patter.2024.101072
Deng EZ, Marino GB, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma'ayan A. 2024. Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics Cell Reports Methods. 10.1016/j.crmeth.2024.100839
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. 2024. Pan-cancer proteogenomics characterization of tumor immunity Cell. 10.1016/j.cell.2024.01.027
Marino GB, Ngai M, Clarke DJB, Fleishman RH, Deng EZ, Xie Z, Ahmed N, Ma'ayan A. 2023. GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. Nucleic acids research. 10.1093/nar/gkad399
Marino GB, Wojciechowicz ML, Clarke DJB, Kuleshov MV, Xie Z, Jeon M, Lachmann A, Ma'ayan A. 2023. lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. Database : the journal of biological databases and curation. 10.1093/database/baad009
Marino GB, Ahmed N, Xie Z, Jagodnik KM, Han J, Clarke DJB, Lachmann A, Keller MP, Attie AD, Ma’ayan A et al.. 2023. D2H2: diabetes data and hypothesis hub Bioinformatics Advances. 10.1093/bioadv/vbad178
Clarke DJB, Marino GB, Deng EZ, Xie Z, Evangelista JE, Ma’ayan A. 2024. Rummagene: massive mining of gene sets from supporting materials of biomedical research publications Communications Biology. 10.1038/s42003-024-06177-7
Evangelista JE, Clarke DJB, Xie Z, Marino GB, Utti V, Jenkins S, Ahooyi TM, Bologa CG, Yang JJ, Binder JL et al.. 2023. Toxicology knowledge graph for structural birth defects. Communications medicine. 10.1038/s43856-023-00329-2
Evangelista JE, Xie Z, Marino GB, Nguyen N, Clarke DJB, Ma'ayan A. 2023. Enrichr-KG: bridging enrichment analysis across multiple libraries. Nucleic acids research. 10.1093/nar/gkad393
Deng EZ, Fleishman RH, Xie Z, Marino GB, Clarke DJB, Ma'ayan A. 2023. Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells. Aging cell. 10.1111/acel.13809
Raufer S, C I, Zosuls A, Marino G, N Blanke, IJ Bigio, O'Malley JT, BJ Burgess, JB Nadol, Guinan J et al.. 2020. Anatomy of the Human Osseous Spiral Lamina and Cochlear Partition Bridge: Relevance for Cochlear Partition Motion. Journal of the Association for Research in Otolaryngology : JARO. 10.1007/s10162-020-00748-1
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. 2024. Regulatory elements in SEM1-DLX5-DLX6 (7q21.3) locus contribute to genetic control of coronal nonsyndromic craniosynostosis and bone density-related traits Genetics in Medicine Open. 10.1016/j.gimo.2024.101851