Channel: NCI Human Tumor Atlas Network

bioRxiv posts many COVID19-related papers. A reminder: they have not been formally peer-reviewed and should not guide health-related behavior or be reported in the press as conclusive.

47 Articles

Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer

Lin, J.-R., Wang, S., Coy, S., Chen, Y.-A., Yapp, C., Tyler, M. A., Nariya, M., Heiser, C. N., Lau, K., Santagata, S., Sorger, P. K.

10.1101/2021.03.31.437984 — Posted: 2022-09-28

SnFFPE-Seq: towards scalable single nucleus RNA-Seq of formalin-fixed paraffin-embedded (FFPE) tissue

Chung, H., Melnikov, A., McCabe, C., Drokhlyansky, E., Van Wittenberghe, N., Magee, E. M., Waldman, J., Spira, A., Chen, F., Mazzilli, S., Rozenblatt-Rosen, O., Regev, A.

10.1101/2022.08.25.505257 — Posted: 2022-08-25

DCIS genomic signatures define biology and clinical outcome: Human Tumor Atlas Network (HTAN) analysis of TBCRC 038 and RAHBT cohorts

Strand, S. H., Rivero-Gutierrez, B., Houlahan, K. E., Seoane, J. A., King, L. M., Risom, T., Simpson, L. A., Vennam, S., Khan, A., Cisneros, L., Hardman, T., Harmon, B., Couch, F., Gallagher, K., Kilgore, M., Wei, S., DeMichele, A., King, T., McAuliffe, P. F., Nangia, J., Lee, J., Tseng, J., Storniolo, A. M., Thompson, A. M., Gupta, G. P., Burns, R., Veis, D. J., DeSchryver, K., Zhu, C., Matusiak, M., Wang, J., Zhu, S. X., Tappenden, J., Ding, D. Y., Zhang, D., Luo, J., Jiang, S., Varma, S., Anderson, L., Straub, C., Srivastava, S., Curtis, C., Tibshirani, R., Angelo, R. M., Hall, A., Owzar, K

10.1101/2021.06.16.448585 — Posted: 2022-06-23

Stitching and registering highly multiplexed whole slide images of tissues and tumors using ASHLAR

Muhlich, J. L., Chen, Y.-A., Yapp, C., Russell, D. P. W., Santagata, S., Sorger, P. K.

10.1101/2021.04.20.440625 — Posted: 2022-04-25

UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues

Yapp, C., Novikov, E., Jang, W.-D., Vallius, T., Chen, Y.-A., Cicconet, M., Maliga, Z., Jacobson, C. A., Wei, D., Santagata, S., Pfister, H., Sorger, P. K.

10.1101/2021.04.02.438285 — Posted: 2022-02-25

The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution

Nirmal, A. J., Maliga, Z., Vallius, T., Quattrochi, B., Chen, A. A., Jacobson, C. A., Pelletier, R. J., Yapp, C., Arias-Camison, R., Chen, Y.-A., Lian, C. G., Murphy, G. F., Santagata, S., Sorger, P. K.

10.1101/2021.05.23.445310 — Posted: 2022-02-14

An Omic and Multidimensional Spatial Atlas from Serial Biopsies of an Evolving Metastatic Breast Cancer

Johnson, B. E., Creason, A. L., Stommel, J. M., Keck, J. M., Parmar, S., Betts, C. B., Blucher, A., Boniface, C., Bucher, E., Burlingame, E. A., Camp, T., Chin, K., Eng, J., Estabrook, J., Feiler, H. S., Hu, Z., Kolodzie, A., Kong, B. L., Labrie, M., Lee, J., Leyshock, P., Mitri, S., Patterson, J., Riesterer, J. L., Sivagnanam, S., Somers, J., Sudar, D., Thibault, G., Zheng, C., Nan, X., Heiser, L. M., Spellman, P. T., Thomas, G. V., Demir, E., Chang, Y. H., Coussens, L. M., Guimaraes, A. R., Corless, C., Goecks, J., Bergan, R., Mitri, Z., Mills, G. B., Gray, J. W.

10.1101/2020.12.03.408500 — Posted: 2021-07-16

The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ

Nachmanson, D., Officer, A., Mori, H., Gordon, J., Evans, M. F., Steward, J., Yao, H., O'Keefe, T., Hasteh, F., Stein, G. S., Jepsen, K., Weaver, D. L., Hirst, G., Sprague, B. L., Esserman, L. J., Borowsky, A. D., Stein, J. L., Harismendy, O.

10.1101/2021.05.11.443641 — Posted: 2021-06-07

Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Becker, W. R., Nevins, S. A., Chen, D. C., Chiu, R., Horning, A., Laquindanum, R., Mills, M., Chaib, H., Ladabaum, U., Longacre, T., Shen, J., Esplin, E. D., Kundaje, A., Ford, J. M., Curtis, C., Snyder, M. P., Greenleaf, W. J.

10.1101/2021.03.24.436532 — Posted: 2021-03-25

MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging

Schapiro, D., Sokolov, A., Yapp, C., Muhlich, J. L., Hess, J., Lin, J.-R., Chen, Y.-A., Nariya, M. K., Baker, G. J., Ruokonen, J., Maliga, Z., Jacobson, C. A., Farhi, S. L., Abbondanza, D., McKinley, E. T., Betts, C., Regev, A., Coffey, R. J., Coussens, L. M., Santagata, S., Sorger, P. K.

10.1101/2021.03.15.435473 — Posted: 2021-03-16

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