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.

72 Articles

Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors
Heiser, C. N., Simmons, A. J., Revetta, F., McKinley, E. T., Ramirez-Solano, M. A., Wang, J., Shao, J., Ayers, G. D., Wang, Y., Glass, S. E., Kaur, H., Rolong, A., Chen, B., Vega, P. N., Drewes, J. L., Saleh, N., Vandekar, S., Jones, A. L., Washington, M. K., Roland, J. T., Sears, C. L., Liu, Q., Shrubsole, M. J., Coffey, R. J., Lau, K. S.
10.1101/2023.03.09.530832 — Posted: 2023-03-12
Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data
Wang, Y., Sarfraz, I., Teh, W. K., Sokolov, A., Herb, B. R., Creasy, H. H., Virshup, I., Dries, R., Degatano, K., Mahurkar, A., Schnell, D. J., Madrigal, P., Hilton, J., Gehlenborg, N., Tickle, T., Campbell, J. D.
10.1101/2023.03.06.531314 — Posted: 2023-03-07
SEG: Segmentation Evaluation in absence of Ground truth labels
Sims, Z., Strgar, L., Thirumalaisamy, D., Heussner, R., Thibault, G., Chang, Y. H.
10.1101/2023.02.23.529809 — Posted: 2023-02-24
SlideCNA: Spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data
Zhang, D. K., Segerstolpe, A., Slyper, M., Waldman, J., Murray, E., Cohen, O., Ashenberg, O., Abravanel, D., Jane-Valbuena, J., Mages, S., Lako, A., Helvie, K., Rozenblatt-Rosen, O., Rodig, S., Chen, F., Wagle, N., Regev, A., Klughammer, J.
10.1101/2022.11.25.517982 — Posted: 2022-11-27
Integrated Molecular Characterization of Intraductal Papillary Mucinous Neoplasms: An NCI Cancer Moonshot Precancer Atlas Pilot Project
Semaan, A., Bernard, V., Wong, J., Makino, Y., Swartzlander, D., Rajapakshe, K. I., Lee, J., Officer, A., Schmidt, C. M., Wu, H. H., Scaife, C. L., Affolter, K. E., Nachmanson, D., Firpo, M. A., Yip-Schneider, M., Lowy, A. M., Harismendy, O., Sen, S., Maitra, A. A., Jakubek, Y. A., Guerrero, P. A.
10.1101/2022.10.14.512148 — Posted: 2022-10-18
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

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