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.

73 Articles

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
Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data
Hong, R., Koga, Y., Bandyadka, S., Leshchyk, A., Wang, Z., Alabdullatif, S., Wang, Y., Akavoor, V., Cao, X., Sarfraz, I., Jansen, F., Johnson, W. E., Yajima, M., Campbell, J. D.
10.1101/2020.11.16.385328 — Posted: 2021-02-14
Multicellular immune hubs and their organization in MMRd and MMRp colorectal cancer
Pelka, K., Hofree, M., Chen, J., Sarkizova, S., Pirl, J. D., Jorgji, V., Bejnood, A., Dionne, D., Ge, W. H., Xu, K. H., Chao, S. X., Zollinger, D. R., Lieb, D. J., Reeves, J. W., Fuhrman, C. A., Hoang, M. L., Delorey, T., Nguyen, L. T., Waldman, J., Klapholz, M., Wakiro, I., Cohen, O., Smillie, C. S., Cuoco, M. S., Wu, J., Su, M.-j., Yeung, J., Vijaykumar, B., Magnuson, A. M., Asinovski, N., Moll, T., Goder-Reiser, M. N., Applebaum, A. S., Brais, L. K., DelloStritto, L. K., Denning, S. L., Phillips, S. T., Hill, E. K., Meehan, J. K., Frederick, D. T., Sharova, T., Kanodia, A., Todres, E. Z., J
10.1101/2021.01.30.426796 — Posted: 2021-02-02
GLUER: integrative analysis of single-cell omics and imaging data by deep neural network
Peng, T., Chen, G., Tan, K.
10.1101/2021.01.25.427845 — Posted: 2021-01-26
Spatial drivers and pre-cancer populations collaborate with the microenvironment in untreated and chemo-resistant pancreatic cancer
Cui Zhou, D., Jayasinghe, R. G., Herndon, J. M., Storrs, E., Mo, C.-K., Wu, Y., Fulton, R. S., Wyczalkowski, M. A., Fronick, C. C., Fulton, L. A., Thammavong, L., Sato, K., Zhu, H., Sun, H., Wang, L.-B., Li, Y., Zuo, C., McMichael, J. F., Davies, S. R., Appelbaum, E. L., Robbins, K. J., Chasnoff, S. E., Yang, X., Liu, R., Reeb, A. N., Wendl, M. C., Oh, C., Serasanambati, M., Lal, P., Varghese, R., Mashl, J. R., Ponce, J., Terekhanova, N. V., Naser Al Deen, N., Yao, L., Wang, F., Chen, L., Schnaubelt, M., Puram, S. V., Kim, A. H., Song, S.-K., Shoghi, K. I., Ju, T., Hawkins, W. G., Chen, K., Ch
10.1101/2021.01.13.426413 — Posted: 2021-01-14

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