(submitted) Chen, H, et al. “Network for biomarker immunoprofiling for cancer immunotherapy: Cancer Immune Monitoring and Analysis Centers-Cancer Immunologic Data Commons (CIMAC-CIDC)”

(submitted) Sahaf, B, et al. “Multi-Center Immune Profiling Mass Cytometry Assay Harmonization”

(submitted) Akturk, G, et al. “Multiplex Tissue Imaging Harmonization: A Multicenter Experience from CIMAC-CIDC Immuno-Oncology Biomarkers Network”

(submitted) Wu, C, et al. “Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms for the CIMAC-CIDC Network”

Akturk, G., Sweeney, R., Remark, R., Merad, M., & Gnjatic, S. (2020). Multiplexed Immunohistochemical Consecutive Staining on Single Slide (MICSSS): Multiplexed Chromogenic IHC Assay for High-Dimensional Tissue Analysis. Methods in molecular biology (Clifton, N.J.)2055, 497–519. https://doi.org/10.1007/978-1-4939-9773-2_23

Akturk, G., et al.  CIMAC-CIDC tissue imaging harmonization. J Clin Oncol (2020);38:15s (suppl; abstr 3125) https://ascopubs.org/doi/abs/10.1200/JCO.2020.38.15_suppl.3125

Alatrash, G., Qiao, N., Zhang, M., Zope, M., Perakis, A. A., Sukhumalchandra, P., Philips, A. V., Garber, H. R., Kerros, C., St John, L. S., Khouri, M. R., Khong, H., Clise-Dwyer, K., Miller, L. P., Wolpe, S., Overwijk, W. W., Molldrem, J. J., Ma, Q., Shpall, E. J., & Mittendorf, E. A. (2019). Fucosylation Enhances the Efficacy of Adoptively Transferred Antigen-Specific Cytotoxic T Lymphocytes. Clinical cancer research : an official journal of the American Association for Cancer Research25(8), 2610–2620. https://doi.org/10.1158/1078-0432.CCR-18-1527

Bendall, S. C., Davis, K. L., Amir, e., Tadmor, M. D., Simonds, E. F., Chen, T. J., Shenfeld, D. K., Nolan, G. P., & Pe’er, D. (2014). Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell157(3), 714–725. https://doi.org/10.1016/j.cell.2014.04.005

Butterfield, L.H., et al. SITC 2018 Workshop Report: Immuno-Oncology Biomarkers: State of the Art. J Immunotherapy Cancer (2018);138. https://doi.org/10.1186/s40425-018-0453-4

Cader, F. Z., Schackmann, R., Hu, X., Wienand, K., Redd, R., Chapuy, B., Ouyang, J., Paul, N., Gjini, E., Lipschitz, M., Armand, P., Wu, D., Fromm, J. R., Neuberg, D., Liu, X. S., Rodig, S. J., & Shipp, M. A. (2018). Mass cytometry of Hodgkin lymphoma reveals a CD4+ regulatory T-cell-rich and exhausted T-effector microenvironment. Blood132(8), 825–836. https://doi.org/10.1182/blood-2018-04-843714

Clifton, G. T., Hale, D., Vreeland, T. J., Hickerson, A. T., Litton, J. K., Alatrash, G., Murthy, R. K., Qiao, N., Philips, A. V., Lukas, J. J., Holmes, J. P., Peoples, G. E., & Mittendorf, E. A. (2020). Results of a Randomized Phase IIb Trial of Nelipepimut-S + Trastuzumab versus Trastuzumab to Prevent Recurrences in Patients with High-Risk HER2 Low-Expressing Breast Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research26(11), 2515–2523. https://doi.org/10.1158/1078-0432.CCR-19-2741

Del Valle, D. M., Kim-Schulze, S., Huang, H. H., Beckmann, N. D., Nirenberg, S., Wang, B., Lavin, Y., Swartz, T. H., Madduri, D., Stock, A., Marron, T. U., Xie, H., Patel, M., Tuballes, K., Van Oekelen, O., Rahman, A., Kovatch, P., Aberg, J. A., Schadt, E., Jagannath, S., … Gnjatic, S. (2020). An inflammatory cytokine signature predicts COVID-19 severity and survival. Nature medicine26(10), 1636–1643. https://doi.org/10.1038/s41591-020-1051-9

Dobry, A. S., Zogg, C. K., Hodi, F. S., Smith, T. R., Ott, P. A., & Iorgulescu, J. B. (2018). Management of metastatic melanoma: improved survival in a national cohort following the approvals of checkpoint blockade immunotherapies and targeted therapies. Cancer immunology, immunotherapy : CII67(12), 1833–1844. https://doi.org/10.1007/s00262-018-2241-x

Fu, J., Li, K., Zhang, W., Wan, C., Zhang, J., Jiang, P., & Liu, X. S. (2020). Large-scale public data reuse to model immunotherapy response and resistance. Genome medicine12(1), 21. https://doi.org/10.1186/s13073-020-0721-z

Gentles, A. J., Hui, A. B., Feng, W., Azizi, A., Nair, R. V., Bouchard, G., Knowles, D. A., Yu, A., Jeong, Y., Bejnood, A., Forgó, E., Varma, S., Xu, Y., Kuong, A., Nair, V. S., West, R., van de Rijn, M., Hoang, C. D., Diehn, M., & Plevritis, S. K. (2020). A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk. Genome biology21(1), 107. https://doi.org/10.1186/s13059-020-02019-x

Glass, D. R., Tsai, A. G., Oliveria, J. P., Hartmann, F. J., Kimmey, S. C., Calderon, A. A., Borges, L., Glass, M. C., Wagar, L. E., Davis, M. M., & Bendall, S. C. (2020). An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity. Immunity53(1), 217–232.e5. https://doi.org/10.1016/j.immuni.2020.06.013

Good, Z., Borges, L., Vivanco Gonzalez, N., Sahaf, B., Samusik, N., Tibshirani, R., Nolan, G. P., & Bendall, S. C. (2019). Proliferation tracing with single-cell mass cytometry optimizes generation of stem cell memory-like T cells. Nature biotechnology37(3), 259–266. https://doi.org/10.1038/s41587-019-0033-2

Gruber, C. N., Patel, R. S., Trachtman, R., Lepow, L., Amanat, F., Krammer, F., Wilson, K. M., Onel, K., Geanon, D., Tuballes, K., Patel, M., Mouskas, K., O’Donnell, T., Merritt, E., Simons, N. W., Barcessat, V., Del Valle, D. M., Udondem, S., Kang, G., Gangadharan, S., … Bogunovic, D. (2020). Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C). Cell183(4), 982–995.e14. https://doi.org/10.1016/j.cell.2020.09.034

Gruber, C., Patel, R., Trachman, R., Lepow, L., Amanat, F., Krammer, F., Wilson, K. M., Onel, K., Geanon, D., Tuballes, K., Patel, M., Mouskas, K., Simons, N., Barcessat, V., Valle, D. D., Udondem, S., Kang, G., Gangadharan, S., Ofori-Amanfo, G., Rahman, A., … Bogunovic, D. (2020). Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C). medRxiv : the preprint server for health sciences, 2020.07.04.20142752. https://doi.org/10.1101/2020.07.04.20142752

Hartmann, F. J., Babdor, J., Gherardini, P. F., Amir, E. D., Jones, K., Sahaf, B., Marquez, D. M., Krutzik, P., O’Donnell, E., Sigal, N., Maecker, H. T., Meyer, E., Spitzer, M. H., & Bendall, S. C. (2019). Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy. Cell reports28(3), 819–831.e4. https://doi.org/10.1016/j.celrep.2019.06.049

Hartmann, F. J., & Bendall, S. C. (2020). Immune monitoring using mass cytometry and related high-dimensional imaging approaches. Nature reviews. Rheumatology16(2), 87–99. https://doi.org/10.1038/s41584-019-0338-z

Hartmann, F. J., Mrdjen, D., McCaffrey, E., Glass, D. R., Greenwald, N. F., Bharadwaj, A., Khair, Z., Verberk, S., Baranski, A., Baskar, R., Graf, W., Van Valen, D., Van den Bossche, J., Angelo, M., & Bendall, S. C. (2020). Single-cell metabolic profiling of human cytotoxic T cells. Nature biotechnology, 10.1038/s41587-020-0651-8. Advance online publication. https://doi.org/10.1038/s41587-020-0651-8

Hartmann, F. J., Simonds, E. F., & Bendall, S. C. (2018). A Universal Live Cell Barcoding-Platform for Multiplexed Human Single Cell Analysis. Scientific reports8(1), 10770. https://doi.org/10.1038/s41598-018-28791-2

Hartmann, F. J., Simonds, E. F., Vivanco, N., Bruce, T., Borges, L., Nolan, G. P., Spitzer, M. H., & Bendall, S. C. (2019). Scalable Conjugation and Characterization of Immunoglobulins with Stable Mass Isotope Reporters for Single-Cell Mass Cytometry Analysis. Methods in molecular biology (Clifton, N.J.)1989, 55–81. https://doi.org/10.1007/978-1-4939-9454-0_5

Hu, X., Zhang, J., Wang, J., Fu, J., Li, T., Zheng, X., Wang, B., Gu, S., Jiang, P., Fan, J., Ying, X., Zhang, J., Carroll, M. C., Wucherpfennig, K. W., Hacohen, N., Zhang, F., Zhang, P., Liu, J. S., Li, B., & Liu, X. S. (2019). Landscape of B cell immunity and related immune evasion in human cancers. Nature genetics51(3), 560–567. https://doi.org/10.1038/s41588-018-0339-x

Jiang, P., Gu, S., Pan, D., Fu, J., Sahu, A., Hu, X., Li, Z., Traugh, N., Bu, X., Li, B., Liu, J., Freeman, G. J., Brown, M. A., Wucherpfennig, K. W., & Liu, X. S. (2018). Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. Nature medicine24(10), 1550–1558. https://doi.org/10.1038/s41591-018-0136-1

Jiang, P., Sellers, W. R., & Liu, X. S. (2018). Big Data Approaches for Modeling Response and Resistance to Cancer Drugs. Annual review of biomedical data science1, 1–27. https://doi.org/10.1146/annurev-biodatasci-080917-013350

Keren, L., Bosse, M., Marquez, D., Angoshtari, R., Jain, S., Varma, S., Yang, S. R., Kurian, A., Van Valen, D., West, R., Bendall, S. C., & Angelo, M. (2018). A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging. Cell174(6), 1373–1387.e19. https://doi.org/10.1016/j.cell.2018.08.039

Keren, L., Bosse, M., Thompson, S., Risom, T., Vijayaragavan, K., McCaffrey, E., Marquez, D., Angoshtari, R., Greenwald, N. F., Fienberg, H., Wang, J., Kambham, N., Kirkwood, D., Nolan, G., Montine, T. J., Galli, S. J., West, R., Bendall, S. C., & Angelo, M. (2019). MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure. Science advances5(10), eaax5851. https://doi.org/10.1126/sciadv.aax5851

Kimmey, S. C., Borges, L., Baskar, R., & Bendall, S. C. (2019). Parallel analysis of tri-molecular biosynthesis with cell identity and function in single cells. Nature communications10(1), 1185. https://doi.org/10.1038/s41467-019-09128-7

Lee, B. H., Kelly, G., Bradford, S., Davila, M., Guo, X. V., Amir, E. D., Thrash, E. M., Solga, M. D., Lannigan, J., Sellers, B., Candia, J., Tsang, J., Montgomery, R. R., Tamaki, S. J., Sigdel, T. K., Sarwal, M. M., Lanier, L. L., Tian, Y., Kim, C., Hinz, D., … Rahman, A. H. (2019). A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer. Cytometry. Part A : the journal of the International Society for Analytical Cytology95(9), 1019–1030. https://doi.org/10.1002/cyto.a.23866

Leiter, A., Gnjatic, S., Fowkes, M., Kim-Schulze, S., Laface, I., Galsky, M. D., & Gallagher, E. J. (2020). A COMMON PITUITARY AUTOANTIBODY IN TWO PATIENTS WITH IMMUNE CHECKPOINT INHIBITOR-MEDIATED HYPOPHYSITIS: ZCCHC8. AACE clinical case reports6(4), e151–e160. https://doi.org/10.4158/ACCR-2019-0585

Li, S., Sun, J., Allesøe, R., Datta, K., Bao, Y., Oliveira, G., Forman, J., Jin, R., Olsen, L. R., Keskin, D. B., Shukla, S. A., Wu, C. J., & Livak, K. J. (2019). RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis. Nature protocols14(8), 2571–2594. https://doi.org/10.1038/s41596-019-0195-x

Miao, D., Margolis, C. A., Gao, W., Voss, M. H., Li, W., Martini, D. J., Norton, C., Bossé, D., Wankowicz, S. M., Cullen, D., Horak, C., Wind-Rotolo, M., Tracy, A., Giannakis, M., Hodi, F. S., Drake, C. G., Ball, M. W., Allaf, M. E., Snyder, A., Hellmann, M. D., … Van Allen, E. M. (2018). Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science (New York, N.Y.)359(6377), 801–806. https://doi.org/10.1126/science.aan5951

Moen, E., Bannon, D., Kudo, T., Graf, W., Covert, M., & Van Valen, D. (2019). Deep learning for cellular image analysis. Nature methods16(12), 1233–1246. https://doi.org/10.1038/s41592-019-0403-1

Pan, D., Kobayashi, A., Jiang, P., Ferrari de Andrade, L., Tay, R. E., Luoma, A. M., Tsoucas, D., Qiu, X., Lim, K., Rao, P., Long, H. W., Yuan, G. C., Doench, J., Brown, M., Liu, X. S., & Wucherpfennig, K. W. (2018). A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science (New York, N.Y.)359(6377), 770–775. https://doi.org/10.1126/science.aao1710

Rahman, A., et al. CIMAC-CIDC CyTOF harmonization. J Clin Oncol (2020);38:15s (suppl; abstr e15242) https://ascopubs.org/doi/abs/10.1200/JCO.2020.38.15_suppl.e15242

Sahaf, B., Rahman, A., Maecker, H. T., & Bendall, S. C. (2020). High-Parameter Immune Profiling with CyTOF. Methods in molecular biology (Clifton, N.J.)2055, 351–368. https://doi.org/10.1007/978-1-4939-9773-2_16

Salmon, H., Remark, R., Gnjatic, S., & Merad, M. (2019). Host tissue determinants of tumour immunity. Nature reviews. Cancer19(4), 215–227. https://doi.org/10.1038/s41568-019-0125-9

Sarkizova, S., Klaeger, S., Le, P. M., Li, L. W., Oliveira, G., Keshishian, H., Hartigan, C. R., Zhang, W., Braun, D. A., Ligon, K. L., Bachireddy, P., Zervantonakis, I. K., Rosenbluth, J. M., Ouspenskaia, T., Law, T., Justesen, S., Stevens, J., Lane, W. J., Eisenhaure, T., Lan Zhang, G., … Keskin, D. B. (2020). A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nature biotechnology38(2), 199–209. https://doi.org/10.1038/s41587-019-0322-9

Tsai, A. G., Glass, D. R., Juntilla, M., Hartmann, F. J., Oak, J. S., Fernandez-Pol, S., Ohgami, R. S., & Bendall, S. C. (2020). Multiplexed single-cell morphometry for hematopathology diagnostics. Nature medicine26(3), 408–417. https://doi.org/10.1038/s41591-020-0783-x

Zhang, J., Hu, X., Wang, J., Sahu, A. D., Cohen, D., Song, L., Ouyang, Z., Fan, J., Wang, B., Fu, J., Gu, S., Sade-Feldman, M., Hacohen, N., Li, W., Ying, X., Li, B., & Liu, X. S. (2019). Immune receptor repertoires in pediatric and adult acute myeloid leukemia. Genome medicine11(1), 73. https://doi.org/10.1186/s13073-019-0681-3

Zhou, J., Li, J., Guleria, I., Chen, T., Giobbie-Hurder, A., Stevens, J., Gupta, M., Wu, X., Brennick, R. C., Manos, M. P., & Hodi, F. S. (2019). Immunity to X-linked inhibitor of apoptosis protein (XIAP) in malignant melanoma and check-point blockade. Cancer immunology, immunotherapy : CII68(8), 1331–1340. https://doi.org/10.1007/s00262-019-02370-4