Publications

Publications between 2020 - 2023

1

Hsu LL, Culhane AC. Correspondence analysis for dimension reduction, batch integration, and visualization of single-cell RNA-seq data. Scientific Reports 2023;13:1197. https://doi.org/10.1038/s41598-022-26434-1.

2

Wang Y, Buck A, Grimaud M, Culhane AC, Kodangattil S, Razimbaud C, et al. Anti-CAIX BBζ CAR4/8 t cells exhibit superior efficacy in a ccRCC mouse model. Molecular Therapy Oncolytics 2022;24:385–99. https://doi.org/10.1016/j.omto.2021.12.019.

3

Mirzayi C, Renson A, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, et al. Reporting guidelines for human microbiome research: The STORMS checklist. Nature Medicine 2021;27:1885–92. https://doi.org/10.1038/s41591-021-01552-x.

4

Cao K-AL, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, et al. Author correction: Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biology 2021;22:246. https://doi.org/10.1186/s13059-021-02468-y.

5

Cao K-AL, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, et al. Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biology 2021;22:220. https://doi.org/10.1186/s13059-021-02433-9.

6

Roel E, Pistillo A, Recalde M, Sena AG, Fern’andez-Bertol’ın S, Arag’on M, et al. Characteristics and outcomes of over 300,000 patients with COVID-19 and history of cancer in the united states and spain. Cancer Epidemiology, Biomarkers & Prevention : A Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology 2021;30:1884–94. https://doi.org/10.1158/1055-9965.EPI-21-0266.

7

Sheffer M, Lowry E, Beelen N, Borah M, Amara SN-A, Mader CC, et al. Genome-scale screens identify factors regulating tumor cell responses to natural killer cells. Nature Genetics 2021;53:1196–206. https://doi.org/10.1038/s41588-021-00889-w.

8

Dhimolea E, Matos Simoes R de, Kansara D, Al’Khafaji A, Bouyssou J, Weng X, et al. An embryonic diapause-like adaptation with suppressed myc activity enables tumor treatment persistence. Cancer Cell 2021;39:240–256.e11. https://doi.org/10.1016/j.ccell.2020.12.002.

9

Shirasaki R, Matthews GM, Gandolfi S, Matos Simoes R de, Buckley DL, Vora JR, et al. Functional genomics identify distinct and overlapping genes mediating resistance to different classes of heterobifunctional degraders of oncoproteins. Cell Reports 2021;34:108532. https://doi.org/10.1016/j.celrep.2020.108532.

10

Burn E, You SC, Sena AG, Kostka K, Abedtash H, Abrahão MTF, et al. Deep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study. Nature Communications 2020;11:5009. https://doi.org/10.1038/s41467-020-18849-z.

11

Lane JCE, Weaver J, Kostka K, Duarte-Salles T, Abrahao MTF, Alghoul H, et al. Risk of hydroxychloroquine alone and in combination with azithromycin in the treatment of rheumatoid arthritis: A multinational, retrospective study. The Lancet Rheumatology 2020;2:e698–711. https://doi.org/10.1016/S2665-9913(20)30276-9.

12

Dhimolea E, Matos Simoes R de, Kansara D, Weng X, Sharma S, Awate P, et al. Pleiotropic mechanisms drive endocrine resistance in the three-dimensional bone microenvironment. Cancer Research 2021;81:371–83. https://doi.org/10.1158/0008-5472.CAN-20-0571.

13

Hsu LL, Culhane AC. Impact of data preprocessing on integrative matrix factorization of single cell data. Frontiers in Oncology 2020;10:973. https://doi.org/10.3389/fonc.2020.00973.

14

Burn E, You SC, Sena A, Kostka K, Abedtash H, Abrahao MTF, et al. Deep phenotyping of 34,128 patients hospitalised with COVID-19 and a comparison with 81,596 influenza patients in america, europe and asia: An international network study. medRxiv : The Preprint Server for Health Sciences 2020. https://doi.org/10.1101/2020.04.22.20074336.

15

Schwede M, Waldron L, Mok SC, Wei W, Basunia A, Merritt MA, et al. The impact of stroma admixture on molecular subtypes and prognostic gene signatures in serous ovarian cancer. Cancer Epidemiology, Biomarkers & Prevention : A Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology 2020;29:509–19. https://doi.org/10.1158/1055-9965.EPI-18-1359.

16

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Yang T-HO, et al. The immune landscape of cancer. Immunity 2019;51:411–2. https://doi.org/10.1016/j.immuni.2019.08.004.

17

Meng C, Basunia A, Peters B, Gholami AM, Kuster B, Culhane AC. MOGSA: Integrative single sample gene-set analysis of multiple omics data. Molecular & Cellular Proteomics : MCP 2019;18:S153–68. https://doi.org/10.1074/mcp.TIR118.001251.

18

Li AG, Murphy EC, Culhane AC, Powell E, Wang H, Bronson RT, et al. BRCA1-IRIS promotes human tumor progression through PTEN blockade and HIF-1α activation. Proceedings of the National Academy of Sciences of the United States of America 2018;115:E9600–9. https://doi.org/10.1073/pnas.1807112115.

19

Stein-O’Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, et al. Enter the matrix: Factorization uncovers knowledge from omics. Trends in Genetics : TIG 2018;34:790–805. https://doi.org/10.1016/j.tig.2018.07.003.

20

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Yang T-HO, et al. The immune landscape of cancer. Immunity 2018;48:812–830.e14. https://doi.org/10.1016/j.immuni.2018.03.023.