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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  • 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

  • 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
    1 Scopus citations

  • 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
    44 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

  • 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

    2 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

  • Playbook workflow builder: Interactive construction of bioinformatics workflows

    Clarke, D. J. B., Evangelista, J. E., Xie, Z., Marino, G. B., Byrd, A. I., Maurya, M. R., Srinivasan, S., Yu, K., Petrosyan, V., Roth, M. E., Milinkov, M., King, C. H., Vora, J. K., Keeney, J., Nemarich, C., Khan, W., Lachmann, A., Ahmed, N., Agris, A. & Pan, J. & 21 others, Ramachandran, S., Fahy, E., Esquivel, E., Mihajlovic, A., Jevtic, B., Milinovic, V., Kim, S., McNeely, P., Wang, T., Wenger, E., Brown, M. A., Sickler, A., Zhu, Y., Jenkins, S. L., Blood, P. D., Taylor, D. M., Resnick, A. C., Mazumder, R., Milosavljevic, A., Subramaniam, S. & Ma’ayan, A., Apr 2025, In: PLoS Computational Biology. 21, 4 April, e1012901.

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

    1 Scopus citations

  • Causal inference can lead us to modifiable mechanisms and informative archetypes in sepsis

    Baillie, J. K., Angus, D., Burnham, K., Calandra, T., Calfee, C., Gutteridge, A., Hacohen, N., Khatri, P., Langley, R., Ma’ayan, A., Marshall, J., Maslove, D., Prescott, H. C., Rowan, K., Scicluna, B. P., Seymour, C., Shankar-Hari, M., Shapiro, N., Joost Wiersinga, W. & Singer, M. & 1 others, Randolph, A. G., Dec 2024, In: Intensive Care Medicine. 50, 12, p. 2031-2042 12 p.

    Research output: Contribution to journal › Review article › peer-review

    Open Access
    6 Scopus citations

  • Comprehensive proteogenomic characterization of rare kidney tumors

    Chinnaiyan, A. M., Cieslik, M., Dhanasekaran, S. M., Zhang, H., Nesvizhskii, A. I. & Clinical Proteomic Tumor Analysis Consortium, 21 May 2024, In: Cell Reports Medicine. 5, 5, 101547.

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

    Open Access
    25 Scopus citations

  • Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics

    Deng, E. Z., Marino, G. B., Clarke, D. J. B., Diamant, I., Resnick, A. C., Ma, W., Wang, P. & Ma'ayan, A., 19 Aug 2024, In: Cell Reports Methods. 4, 8, 100839.

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

    Open Access
    6 Scopus citations

  • Pan-cancer proteogenomics characterization of tumor immunity

    Clinical Proteomic Tumor Analysis Consortium, 29 Feb 2024, In: Cell. 187, 5, p. 1255-1277.e27

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

    53 Scopus citations

  • Programming a Ferroptosis-to-Apoptosis Transition Landscape Revealed Ferroptosis Biomarkers and Repressors for Cancer Therapy

    Vinik, Y., Maimon, A., Dubey, V., Raj, H., Abramovitch, I., Malitsky, S., Itkin, M., Ma'ayan, A., Westermann, F., Gottlieb, E., Ruppin, E. & Lev, S., 8 May 2024, In: Advanced Science. 11, 17, 2307263.

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

    Open Access
    30 Scopus citations
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