Publications

22 results

22 results

2025

Wanderley CWS, Michaud DE, Shimada K, Nelson A, Fu J, Schnitt SJ, Tolaney SM, Mittendorf EA, Barroso-Sousa R, Waks A, et al. APOE+ Tumor-Associated Macrophages and CD4-DOCK4 T Cells Reveal Distinct Microenvironmental Features in HER2-Low and HER2-0 Hormone Receptor-Positive Breast Cancer. bioRxiv. 2025.
Wanderley CWS, Michaud DE, Shimada K, Nelson A, Fu J, Schnitt SJ, Tolaney SM, Mittendorf EA, Barroso-Sousa R, Waks A, et al. APOE+ Tumor-Associated Macrophages and CD4-DOCK4 T Cells Reveal Distinct Microenvironmental Features in HER2-Low and HER2-0 Hormone Receptor-Positive Breast Cancer. bioRxiv. 2025.

2024

Shimada K, Michaud DE, Cui YX, Zheng K, Goldberg J, Ju Z, Schnitt SJ, Pastorello R, Kania LD, Hoffer J, et al. An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer. bioRxiv. 2024.
Shimada K, Michaud DE, Cui YX, Zheng K, Goldberg J, Ju Z, Schnitt SJ, Pastorello R, Kania LD, Hoffer J, et al. An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer. bioRxiv. 2024.
Guerriero JL, Lin J-R, Pastorello R, Du Z, Chen Y-A, Townsend MG, Shimada K, Hughes ME, Ren S, Tayob N, et al. Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer. NPJ Breast Cancer. 2024;10(1).
Guerriero JL, Lin J-R, Pastorello R, Du Z, Chen Y-A, Townsend MG, Shimada K, Hughes ME, Ren S, Tayob N, et al. Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer. NPJ Breast Cancer. 2024;10(1).

2021

Weng J-H, Koch PD, Luan H, Tu H-C, Shimada K, Ngan I, Ventura R, Jiang R, Mitchison T. Colchicine acts selectively in the liver to induce hepatokines that inhibit myeloid cell activation. Nat Metab. 2021;3(4):513–522. doi:10.1038/s42255-021-00366-y
Weng J-H, Koch PD, Luan H, Tu H-C, Shimada K, Ngan I, Ventura R, Jiang R, Mitchison T. Colchicine acts selectively in the liver to induce hepatokines that inhibit myeloid cell activation. Nat Metab. 2021;3(4):513–522. doi:10.1038/s42255-021-00366-y
Shimada K, Bachman J, Muhlich J, Mitchison T. shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data. Elife. 2021;10. doi:10.7554/eLife.57116
Shimada K, Bachman J, Muhlich J, Mitchison T. shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data. Elife. 2021;10. doi:10.7554/eLife.57116

2020

Stokes M, Small JC, Vasciaveo A, Shimada K, Hirschhorn T, Califano A, Stockwell B. Mesenchymal subtype neuroblastomas are addicted to TGF-βR2/HMGCR-driven protein geranylgeranylation. Sci Rep. 2020;10(1):10748. doi:10.1038/s41598-020-67310-0
Stokes M, Small JC, Vasciaveo A, Shimada K, Hirschhorn T, Califano A, Stockwell B. Mesenchymal subtype neuroblastomas are addicted to TGF-βR2/HMGCR-driven protein geranylgeranylation. Sci Rep. 2020;10(1):10748. doi:10.1038/s41598-020-67310-0

2019

Nakanishi M, Mitchell R, Benoit Y, Orlando L, Reid J, Shimada K, Davidson K, Shapovalova Z, Collins T, Nagy A, et al. Human Pluripotency Is Initiated and Preserved by a Unique Subset of Founder Cells. Cell. 2019;177(4):910–924.e22. doi:10.1016/j.cell.2019.03.013
Nakanishi M, Mitchell R, Benoit Y, Orlando L, Reid J, Shimada K, Davidson K, Shapovalova Z, Collins T, Nagy A, et al. Human Pluripotency Is Initiated and Preserved by a Unique Subset of Founder Cells. Cell. 2019;177(4):910–924.e22. doi:10.1016/j.cell.2019.03.013
Shimada K, Mitchison T. Unsupervised identification of disease states from high-dimensional physiological and histopathological profiles. Mol Syst Biol. 2019;15(2):e8636. doi:10.15252/msb.20188636
Shimada K, Mitchison T. Unsupervised identification of disease states from high-dimensional physiological and histopathological profiles. Mol Syst Biol. 2019;15(2):e8636. doi:10.15252/msb.20188636

2018

Shimada K, Reznik E, Stokes M, Krishnamoorthy L, Bos P, Song Y, Quartararo C, Pagano N, Carpizo D, , et al. Copper-Binding Small Molecule Induces Oxidative Stress and Cell-Cycle Arrest in Glioblastoma-Patient-Derived Cells. Cell Chem Biol. 2018;25(5):585–594.e7. doi:10.1016/j.chembiol.2018.02.010
Shimada K, Reznik E, Stokes M, Krishnamoorthy L, Bos P, Song Y, Quartararo C, Pagano N, Carpizo D, , et al. Copper-Binding Small Molecule Induces Oxidative Stress and Cell-Cycle Arrest in Glioblastoma-Patient-Derived Cells. Cell Chem Biol. 2018;25(5):585–594.e7. doi:10.1016/j.chembiol.2018.02.010

2017

Viswanathan V, Ryan M, Dhruv H, Gill S, Eichhoff O, Seashore-Ludlow B, Kaffenberger S, Eaton J, Shimada K, Aguirre A, et al. Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature. 2017;547(7664):453–457. doi:10.1038/nature23007
Viswanathan V, Ryan M, Dhruv H, Gill S, Eichhoff O, Seashore-Ludlow B, Kaffenberger S, Eaton J, Shimada K, Aguirre A, et al. Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature. 2017;547(7664):453–457. doi:10.1038/nature23007

2016

Shimada K, Skouta R, Kaplan A, Yang WS, Hayano M, Dixon S, Brown L, Valenzuela C, Wolpaw A, Stockwell B. Global survey of cell death mechanisms reveals metabolic regulation of ferroptosis. Nat Chem Biol. 2016;12(7):497–503. doi:10.1038/nchembio.2079
Shimada K, Skouta R, Kaplan A, Yang WS, Hayano M, Dixon S, Brown L, Valenzuela C, Wolpaw A, Stockwell B. Global survey of cell death mechanisms reveals metabolic regulation of ferroptosis. Nat Chem Biol. 2016;12(7):497–503. doi:10.1038/nchembio.2079
Shimada K, Stockwell B. tRNA synthase suppression activates de novo cysteine synthesis to compensate for cystine and glutathione deprivation during ferroptosis. Mol Cell Oncol. 2016;3(2):e1091059. doi:10.1080/23723556.2015.1091059
Shimada K, Stockwell B. tRNA synthase suppression activates de novo cysteine synthesis to compensate for cystine and glutathione deprivation during ferroptosis. Mol Cell Oncol. 2016;3(2):e1091059. doi:10.1080/23723556.2015.1091059