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Mount Sinai Center for Bioinformatics

Organization profile

Organization profile

The Mount Sinai Center for Bioinformatics develops analytic methods to help experimental biologists to study the increasingly diverse and complex data that are collected from human cells, tissues, and patients. Our Center builds on many of the strengths of the Icahn School of Medicine at Mount Sinai. The Medical School has strong departments in basic science research and clinical care, and we aim to strengthen between these departments.

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Collaborations and top research areas from the last five years

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  • A tool based on objective data to identify patients at elevated risk of hospital-onset Staphylococcus aureus bacteremia: a nested case–control study

    Silvera, R., Jeon, M., Ma’Ayan, A., Aberg, J., Camins, B. & Factor, S. H., 7 Apr 2026, In: Antimicrobial Stewardship and Healthcare Epidemiology. 6, 1, e94.

    Research output: Contribution to journal › Article › peer-review

    Open Access

  • GSFM: A gene set foundation model pre-trained on a massive collection of diverse gene sets

    Clarke, D. J. B., Marino, G. B. & Ma’ayan, A., 2026, (Accepted/In press) In: Patterns. 101565.

    Research output: Contribution to journal › Article › peer-review

    Open Access

  • Molecular signatures and signaling interactions of the hair follicle stem cell niche

    Ghuwalewala, S., Cao, J., Rezza, A., Rangl, M., Kwiatkowski, A., Brown, A., Grisanti, L., Heitman, N., Schober, M., Wang, Z., Ma’ayan, A., Almet, A. A., Plikus, M. V. & Rendl, M., 2026, (Accepted/In press) In: Journal of Investigative Dermatology.

    Research output: Contribution to journal › Article › peer-review

    Open Access

  • The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs

    Evangelista, J. E., Clarke, D. J. B., Byrd, A. I., Srinivasan, S., Srinivasan, S., Maurya, M. R., Jenkins, S. L., Diamant, I., Sanchez, E., Xie, Z., Olaiya, S., Kim, H., Marino, G. B., Ahmed, N., Ramachandran, S., Subramaniam, S. & Ma'ayan, A., 2026, (Accepted/In press) In: Journal of Molecular Biology. 169631.

    Research output: Contribution to journal › Article › peer-review

    Open Access

  • Transcriptional response to combination antiretroviral therapy predicts side effects and novel targets

    Lachmann, A., Amadori, L., Nicoletti, P., Crane, H. M., Giannarelli, C., Ma’ayan, A. & Peter, I., 2026, In: Frontiers in Pharmacology. 16, 1743543.

    Research output: Contribution to journal › Article › peer-review

    Open Access

  • Creating an Interactive Web Interface for Networks Stored in Knowledge Graph Databases

    Evangelista, J. E., Lutsky, A. D., Byrd, A. I., Clarke, D. J. B., Prabhakaran, A., Jenkins, S. L. & Ma'ayan, A., Sep 2025, In: Current Protocols. 5, 9, e70200.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    1 Scopus citations

  • GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets

    Marino, G. B., Olaiya, S., Evangelista, J. E., Clarke, D. J. B. & Ma’ayan, A., 2025, In: GigaScience. 14

    Research output: Contribution to journal › Article › peer-review

    Open Access
    2 Scopus citations

  • Genomic Ascertainment of CHEK2 -Related Cancer Predisposition

    Geisinger-Regeneron DiscovEHR Collaboration and Penn Medicine Biobank, 2025, (Accepted/In press) In: JAMA network open. e2549730.

    Research output: Contribution to journal › Article › peer-review

    Open Access

  • Harmonizome 3.0: Integrated knowledge about genes and proteins from diverse multi-omics resources

    Diamant, I., Clarke, D. J. B., Evangelista, J. E., Lingam, N. & Ma'Ayan, A., 6 Jan 2025, In: Nucleic Acids Research. 53, D1, p. D1016-D1028

    Research output: Contribution to journal › Article › peer-review

    Open Access
    83 Scopus citations

  • Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures

    Satpathy, S., Clark, N. M., Chen, Y. J., Hosseini, N., Chang, Y. H., Hsiao, Y., Lei, J. T., Petralia, F., Chen, J. S., Geffen, Y., Heiman, D. I., Paul, I., Cho, H., Hollenberg, M., Marino, G. B., Lin, K. T., Mannan, R., White, C. J., Allen, J. & Avanessian, S. C. & 158 others, Kane, M. H., Wolfe, A., Kinarivala, M., Liu, W., Anand, S., Lin, M. W., Haines, M., Bergstrom, E. J., Hussey, G., Li, G. X., Mani, D. C., Fang, H., Jaehnig, E. J., Keshishian, H., Miller, B., Su, K. Y., Hsiao, Y. J., Hsu, H. H., Hsieh, M. S., Hsu, K. H., Monovoukas, A., Gohsman, S., Thorup, J. R., Deng, Y., Akiyama, Y., Deng, E., Sheng-Wen Chen, E., Krek, A., Espinoza, R., Ma, W., Charytonowicz, D., Sebra, R., Lin, J. H., Chen, Y. S., Hsu, Y. C., Lin, Z. S., Chen, K. C., Yeh, C. W., Wang, Y. T., Lazar, A. J., Mesri, M., An, E., Zhang, X., Clauser, K. R., Fenyö, D., Chinnaiyan, A. M., Zhang, B., Ding, L., Ruggles, K., Newton, C., Zhang, H., Wang, P., Hostetter, G., Omenn, G. S., Kumar-Sinha, C., Thiagarajan, M., Govindan, R., Paik, P., Parolia, A., Li, Q. K., Ma'ayan, A., Getz, G. A., Dhanasekaran, S. M., Robles, A. I., Chang, G. C., Yang, P. C., Yu, S. L., Chen, H. Y., Nesvizhskii, A. I., Carr, S. A., Mani, D. R., Cieslik, M. P., Chen, Y. J., Gillette, M. A., Lu, C. W., Chu, C. H., Shen, C. Y., Han, C. L., Lin, C. C., Lin, C. Y., Chen, C. W., Lin, C. H., Hsu, H. E., Tsai, H. J., Wu, J. J., Lin, J. W., Waniwan, J., Liao, K. H., Chen, P. H., Huang, P. R., Huang, S. M., Lin, T. C., Lai, W. C., Chiu, W. T., Chiang, X. H., Chang, Y. L., Chen, Y. M., Chen, Y. L., Wang, Y. W., Lin, Y. W., Chang, Y. C., Huang, Y. T., Lien, Y., Zheng, Z. R., Hashimi, A. S., Mohan, A., Pandey, A., Pilozzi, A., Webster, A., Paulovich, A. G., Dagar, A., Godwin, A. K., Pruetz, B., Williams, B. O., Druker, B. J., Rohrer, D. C., Chan, D. W., Petrov, D., Chesla, D., Davaar, D., Duffy, E., Wilson, G. D., Zhao, G., Kołodziejczak, I., Lubinski, J., Huang, J., Hafron, J., Tyner, J. W., Koomen, J., Zaalishvili, K., Ketchum, K. A., Wiznerowicz, M., Domagalski, M. J., Anurag, M., Borucki, M., Edwards, N. J., Vatanian, N., Grady, P., Piehowski, P. D., Bogdan, P., Li, Q., Fonseca, R., Madan, R., Thangudu, R. R., Crispen, R., Matteotti, R., Bremner, R., Cerda, S., Cottingham, S. L., Tsang, S., Cai, S., Liu, T., Bauer, T., Maggio, W. W., Jing, X., Zhang, Y., Shutack, Y. & Andric, Z., 8 Sep 2025, In: Cancer Cell. 43, 9, p. 1731-1757.e17

    Research output: Contribution to journal › Article › peer-review

    Open Access
    1 Scopus citations

  • L2S2: Chemical perturbation and CRISPR KO LINCS L1000 signature search engine

    Marino, G. B., Evangelista, J. E., Clarke, D. J. B. & Ma'Ayan, A., 7 Jul 2025, In: Nucleic Acids Research. 53, W1, p. W338-W350

    Research output: Contribution to journal › Article › peer-review

    Open Access
    6 Scopus citations

  • lncRNAlyzr: Enrichment Analysis for lncRNA Sets

    Evangelista, J. E., Ali-Nasser, T., Malek, L. E., Xie, Z., Marino, G. B., Bester, A. C. & Ma'ayan, A., 1 Aug 2025, In: Journal of Molecular Biology. 437, 15, 168938.

    Research output: Contribution to journal › Article › peer-review

    4 Scopus citations
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