Research output per year
Research output per year
- 1 - 50 out of 249 results
Search results
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2024
A tick saliva serpin, IxsS17 inhibits host innate immune system proteases and enhances host colonization by Lyme disease agent
Nguyen, T. T., Kim, T. H., Bencosme-Cuevas, E., Berry, J., Gaithuma, A. S. K., Ansari, M. A., Kim, T. K., Tirloni, L., Radulovic, Z., Moresco, J. J., Yates, J. R. & Mulenga, A., Feb 2024, In: PLoS pathogens. 20, 2, e1012032.Research output: Contribution to journal › Article › peer-review
Open Access -
Dynamic molecular architecture and substrate recruitment of cullin3–RING E3 ligase CRL3KBTBD2
Hu, Y., Zhang, Z., Mao, Q., Zhang, X., Hao, A., Xun, Y., Wang, Y., Han, L., Zhan, W., Liu, Q., Yin, Y., Peng, C., Moresco, E. M. Y., Chen, Z., Beutler, B. & Sun, L., Feb 2024, In: Nature Structural and Molecular Biology. 31, 2, p. 336-350 15 p.Research output: Contribution to journal › Article › peer-review
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E3 ubiquitin ligase Herc3 deficiency leads to accumulation of subretinal microglia and retinal neurodegeneration
Zegeye, Y., Aredo, B., Yuksel, S., Kirman, D. C., Kumar, A., Chen, B., Turpin, E., Shresta, S., He, Y. G., Gautron, L., Tang, M., Li, X., DiCesare, S. M., Hulleman, J. D., Xing, C., Ludwig, S., Moresco, E. M. Y., Beutler, B. A. & Ufret-Vincenty, R. L., Dec 2024, In: Scientific reports. 14, 1Research output: Contribution to journal › Article › peer-review
Open Access -
FOXP1 and KLF2 reciprocally regulate checkpoints of stem-like to effector transition in CAR T cells
Zhu, Z., Lou, G., Teng, X. L., Wang, H., Luo, Y., Shi, W., Yihunie, K., Hao, S., DeGolier, K., Liao, C., Huang, H., Zhang, Q., Fry, T., Wang, T., Yao, C. & Wu, T., Jan 2024, In: Nature immunology. 25, 1, p. 117-128 12 p.Research output: Contribution to journal › Article › peer-review
1 Scopus citations -
Genetic determinants of blood pressure and heart rate identified through ENU-induced mutagenesis with automated meiotic mapping
Teixeira, S. K., Pontes, R., Zuleta, L. F. G., Wang, J., Xu, D., Hildebrand, S., Russell, J. L., Zhan, X., Choi, M., Tang, M., Li, X., Ludwig, S., Beutler, B. & Krieger, J. E., Mar 2024, In: Science Advances. 10, 9, eadj9797.Research output: Contribution to journal › Article › peer-review
Open Access -
UBE2J1 is the E2 ubiquitin-conjugating enzyme regulating androgen receptor degradation and antiandrogen resistance
Rodriguez Tirado, C., Wang, C., Li, X., Deng, S., Gonzalez, J., Johnson, N. A., Xu, Y., Metang, L. A., Sundar Rajan, M., Yang, Y., Yin, Y., Hofstad, M., Raj, G. V., Zhang, S., Lemoff, A., He, W., Fan, J., Wang, Y., Wang, T. & Mu, P., Jan 19 2024, In: Oncogene. 43, 4, p. 265-280 16 p.Research output: Contribution to journal › Article › peer-review
Open Access -
2023
A Deep Learning Approach for Histology-Based Nucleus Segmentation and Tumor Microenvironment Characterization
Rong, R., Sheng, H., Jin, K. W., Wu, F., Luo, D., Wen, Z., Tang, C., Yang, D. M., Jia, L., Amgad, M., Cooper, L. A. D., Xie, Y., Zhan, X., Wang, S. & Xiao, G., Aug 2023, In: Modern Pathology. 36, 8, 100196.Research output: Contribution to journal › Article › peer-review
Open Access -
Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2
Cui, H., Diedrich, J. K., Wu, D. C., Lim, J. J., Nottingham, R. M., Moresco, J. J., Yates, J. R., Blencowe, B. J., Lambowitz, A. M. & Schimmel, P., Apr 2023, In: Nature cell biology. 25, 4, p. 592-603 12 p.Research output: Contribution to journal › Article › peer-review
7 Scopus citations -
Ceftolozane/tazobactam heteroresistance in cystic fibrosis-related Pseudomonas aeruginosa infections
Monogue, M. L., Sanders, J. M., Pybus, C. A., Kim, J., Zhan, X., Clark, A. E. & Greenberg, D. E., Aug 1 2023, In: JAC-Antimicrobial Resistance. 5, 4, dlad083.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Comparative analysis of dimension reduction methods for cytometry by time-of-flight data
Wang, K., Yang, Y., Wu, F., Song, B., Wang, X. & Wang, T., Dec 2023, In: Nature communications. 14, 1, 1836.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Consequences of depleting TNRC6, AGO, and DROSHA proteins on expression of microRNAs
Johnson, K. C., Johnson, S. T., Liu, J., Chu, Y., Arana, C., Han, Y., Wang, T. & Corey, D. R., Aug 2023, In: RNA. 29, 8, p. 1166-1184 19 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Cytomulate: accurate and efficient simulation of CyTOF data
Yang, Y., Wang, K., Lu, Z., Wang, T. & Wang, X., Dec 2023, In: Genome biology. 24, 1, 262.Research output: Contribution to journal › Article › peer-review
Open Access -
Deep-Learning-Based Hepatic Ploidy Quantification Using H&E Histopathology Images
Wen, Z., Lin, Y. H., Wang, S., Fujiwara, N., Rong, R., Jin, K. W., Yang, D. M., Yao, B., Yang, S., Wang, T., Xie, Y., Hoshida, Y., Zhu, H. & Xiao, G., Apr 2023, In: Genes. 14, 4, 921.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Deep learning of cell spatial organizations identifies clinically relevant insights in tissue images
Wang, S., Rong, R., Zhou, Q., Yang, D. M., Zhang, X., Zhan, X., Bishop, J., Chi, Z., Wilhelm, C. J., Zhang, S., Pickering, C. R., Kris, M. G., Minna, J., Xie, Y. & Xiao, G., Dec 2023, In: Nature communications. 14, 1, 7872.Research output: Contribution to journal › Article › peer-review
Open Access -
Differential Precipitation of Proteins: A Simple Protein Fractionation Strategy to Gain Biological Insights with Proteomics
Pinto, A. F. M., Diedrich, J. K., Moresco, J. J. & Yates, J. R., Sep 6 2023, In: Journal of the American Society for Mass Spectrometry. 34, 9, p. 2025-2033 9 p.Research output: Contribution to journal › Article › peer-review
2 Scopus citations -
Enhanced Pathology Image Quality with Restore–Generative Adversarial Network
Rong, R., Wang, S., Zhang, X., Wen, Z., Cheng, X., Jia, L., Yang, D. M., Xie, Y., Zhan, X. & Xiao, G., Apr 2023, In: American Journal of Pathology. 193, 4, p. 404-416 13 p.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Essential requirement for IER3IP1 in B cell development
Zhong, X., Moresco, J. J., Keller, K., Lazaro, D. R., Ely, C., Moresco, E. M. Y., Beutler, B. & Choi, J., 2023, In: Proceedings of the National Academy of Sciences of the United States of America. 120, 46, e2312810120.Research output: Contribution to journal › Article › peer-review
Open Access -
Essential role of MFSD1-GLMP-GIMAP5 in lymphocyte survival and liver homeostasis
Zhong, X., Moresco, J. J., Diedrich, J. K., Pinto, A. M., SoRelle, J. A., Wang, J., Keller, K., Ludwig, S., Moresco, E. M. Y., Beutler, B. & Choi, J. H., 2023, In: Proceedings of the National Academy of Sciences of the United States of America. 120, 50, e2314429120.Research output: Contribution to journal › Article › peer-review
Open Access -
Forward genetic screening using fundus spot scale identifies an essential role for Lipe in murine retinal homeostasis
Yuksel, S., Aredo, B., Zegeye, Y., Zhao, C. X., Tang, M., Li, X., Hulleman, J. D., Gautron, L., Ludwig, S., Moresco, E. M. Y., Butovich, I. A., Beutler, B. A. & Ufret-Vincenty, R. L., Dec 2023, In: Communications Biology. 6, 1, 533.Research output: Contribution to journal › Article › peer-review
Open Access -
Generation of epitope tag knock-in mice with CRISPR-Cas9 to study the function of endogenous proteins
Zhang, Z., Sep 15 2023, In: STAR Protocols. 4, 3, 102518.Research output: Contribution to journal › Article › peer-review
Open Access -
Genetic determinants underlying the progressive phenotype of β-lactam/β-lactamase inhibitor resistance in Escherichia coli
Shropshire, W. C., Amiji, H., Bremer, J., Selvaraj Anand, S., Strope, B., Sahasrabhojane, P., Gohel, M., Aitken, S., Spitznogle, S., Zhan, X., Kim, J., Greenberg, D. E. & Shelburne, S. A., Dec 12 2023, In: Microbiology Spectrum. 11, 6, p. e0222123Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Image-based quantification of histological features as a function of spatial location using the Tissue Positioning System
Rong, R., Wei, Y., Li, L., Wang, T., Zhu, H., Xiao, G. & Wang, Y., Aug 2023, In: EBioMedicine. 94, 104698.Research output: Contribution to journal › Article › peer-review
Open Access -
Immune checkpoint blockade induces gut microbiota translocation that augments extraintestinal antitumor immunity
Choi, Y., Lichterman, J. N., Coughlin, L. A., Poulides, N., Li, W., Del Valle, P., Palmer, S. N., Gan, S., Kim, J., Zhan, X., Gao, Y., Evers, B. M., Hooper, L. V., Pasare, C. & Koh, A. Y., Mar 2023, In: Science Immunology. 8, 81, eabo2003.Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
IsoAnalytics: A single-cell proteomics web server
Palmer, S. N., Koh, A. Y. & Zhan, X., 2023, In: Bioinformatics Advances. 3, 1, vbad077.Research output: Contribution to journal › Article › peer-review
Open Access -
Loss of SYNCRIP unleashes APOBEC-driven mutagenesis, tumor heterogeneity, and AR-targeted therapy resistance in prostate cancer
Li, X., Wang, Y., Deng, S., Zhu, G., Wang, C., Johnson, N. A., Zhang, Z., Tirado, C. R., Xu, Y., Metang, L. A., Gonzalez, J., Mukherji, A., Ye, J., Yang, Y., Peng, W., Tang, Y., Hofstad, M., Xie, Z., Yoon, H., Chen, L., & 11 others, Aug 14 2023, In: Cancer Cell. 41, 8, p. 1427-1449.e12Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Osteosarcoma Explorer: A Data Commons With Clinical, Genomic, Protein, and Tissue Imaging Data for Osteosarcoma Research
Yang, D. M., Zhou, Q., Furman-Cline, L., Cheng, X., Luo, D., Lai, H., Li, Y., Jin, K. W., Yao, B., Leavey, P. J., Rakheja, D., Lo, T., Hall, D., Barkauskas, D. A., Shulman, D. S., Janeway, K., Khanna, C., Gorlick, R., Menzies, C., Zhan, X., & 6 others, Sep 1 2023, In: JCO Clinical Cancer Informatics. 7, p. e2300104Research output: Contribution to journal › Article › peer-review
Open Access -
OVOL2: an epithelial lineage determiner with emerging roles in energy homeostasis
Jiang, Y. & Zhang, Z., Oct 2023, In: Trends in Cell Biology. 33, 10, p. 824-833 10 p.Research output: Contribution to journal › Review article › peer-review
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OVOL2 sustains postnatal thymic epithelial cell identity
Zhong, X., Peddada, N., Wang, J., Moresco, J. J., Zhan, X., Shelton, J. M., SoRelle, J. A., Keller, K., Lazaro, D. R., Moresco, E. M. Y., Choi, J. H. & Beutler, B., Dec 2023, In: Nature communications. 14, 1, 7786.Research output: Contribution to journal › Article › peer-review
Open Access -
Phase 2 Trial of Stereotactic Ablative Radiotherapy for Patients with Primary Renal Cancer
Hannan, R., McLaughlin, M. F., Pop, L. M., Pedrosa, I., Kapur, P., Garant, A., Ahn, C., Christie, A., Zhu, J., Wang, T., Robles, L., Durakoglugil, D., Woldu, S., Margulis, V., Gahan, J., Brugarolas, J., Timmerman, R. & Cadeddu, J., Sep 2023, In: European urology. 84, 3, p. 275-286 12 p.Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
Publisher Correction: Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2 (Nature Cell Biology, (2023), 25, 4, (592-603), 10.1038/s41556-023-01118-8)
Cui, H., Diedrich, J. K., Wu, D. C., Lim, J. J., Nottingham, R. M., Moresco, J. J., Yates, J. R., Blencowe, B. J., Lambowitz, A. M. & Schimmel, P., Jul 2023, In: Nature cell biology. 25, 7, p. 1073 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Radiation-Induced Innate Neutrophil Response in Tumor Is Mediated by the CXCLs/CXCR2 Axis
Zhang, F., Mulvaney, O., Salcedo, E., Manna, S., Zhu, J. Z., Wang, T., Ahn, C., Pop, L. M. & Hannan, R., Dec 2023, In: Cancers. 15, 23, 5686.Research output: Contribution to journal › Article › peer-review
Open Access -
T-Cell Receptor Repertoire Sequencing in the Era of Cancer Immunotherapy
Frank, M. L., Lu, K., Erdogan, C., Han, Y., Hu, J., Wang, T., Heymach, J. V., Zhang, J. & Reuben, A., Mar 15 2023, In: Clinical Cancer Research. 29, 6, p. 994-1008 15 p.Research output: Contribution to journal › Review article › peer-review
Open Access6 Scopus citations -
The dual lipid desaturase/hydroxylase DEGS2 controls phytoceramide levels necessary to counter intestinal inflammation
Song, R., Fond, A., Li, X., Tang, M., Zhan, X., Gordillo, R., Moresco, E. M. Y., Beutler, B. & Turer, E. E., Sep 2023, In: DMM Disease Models and Mechanisms. 16, 9, dmm050043.Research output: Contribution to journal › Article › peer-review
Open Access -
Trans-Golgi protein TVP23B regulates host-microbe interactions via Paneth cell homeostasis and Goblet cell glycosylation
Song, R., McAlpine, W., Fond, A. M., Nair-Gill, E., Choi, J. H., Nyström, E. E. L., Arike, L., Field, S., Li, X., SoRelle, J. A., Moresco, J. J., Moresco, E. M. Y., Yates, J. R., Azadi, P., Ni, J., Birchenough, G. M. H., Beutler, B. & Turer, E. E., Dec 2023, In: Nature communications. 14, 1, 3652.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Unsupervised domain adaptation for nuclei segmentation: Adapting from hematoxylin & eosin stained slides to immunohistochemistry stained slides using a curriculum approach
Wang, S., Rong, R., Gu, Z., Fujimoto, J., Zhan, X., Xie, Y. & Xiao, G., Nov 2023, In: Computer Methods and Programs in Biomedicine. 241, 107768.Research output: Contribution to journal › Article › peer-review
3 Scopus citations -
2022
Analysis of KIR gene variants in The Cancer Genome Atlas and UK Biobank using KIRCLE
Gao, G. F., Liu, D., Zhan, X. & Li, B., Dec 2022, In: BMC Biology. 20, 1, 191.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Arid1a loss potentiates pancreatic β-cell regeneration through activation of EGF signaling
Celen, C., Chuang, J. C., Shen, S., Li, L., Maggiore, G., Jia, Y., Luo, X., Moore, A., Wang, Y., Otto, J. E., Collings, C. K., Wang, Z., Sun, X., Nassour, I., Park, J., Ghaben, A., Wang, T., Wang, S. C., Scherer, P. E., Kadoch, C., & 1 others, Nov 1 2022, In: Cell Reports. 41, 5, 111581.Research output: Contribution to journal › Article › peer-review
Open Access -
A Survey of Statistical Methods for Microbiome Data Analysis
Lutz, K. C., Jiang, S., Neugent, M. L., De Nisco, N. J., Zhan, X. & Li, Q., Jun 14 2022, In: Frontiers in Applied Mathematics and Statistics. 8, 884810.Research output: Contribution to journal › Review article › peer-review
Open Access5 Scopus citations -
Author Correction: Transforming activity of an oncoprotein-encoding circular RNA from human papillomavirus (Nature Communications, (2019), 10, 1, (2300), 10.1038/s41467-019-10246-5)
Zhao, J., Lee, E. E., Kim, J., Yang, R., Chamseddin, B., Ni, C., Gusho, E., Xie, Y., Chiang, C. M., Buszczak, M., Zhan, X., Laimins, L. & Wang, R. C., Dec 2022, In: Nature communications. 13, 1, 2889.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Ectopic JAK–STAT activation enables the transition to a stem-like and multilineage state conferring AR-targeted therapy resistance (Nature Cancer, (2022), 3, 9, (1071-1087), 10.1038/s43018-022-00431-9)
Deng, S., Wang, C., Wang, Y., Xu, Y., Li, X., Johnson, N. A., Mukherji, A., Lo, U. G., Xu, L., Gonzalez, J., Metang, L. A., Ye, J., Tirado, C. R., Rodarte, K., Zhou, Y., Xie, Z., Arana, C., Annamalai, V., Liu, X., Vander Griend, D. J., & 6 others, Oct 2022, In: Nature Cancer. 3, 10, p. 1271 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access2 Scopus citations -
BepiTBR: T-B reciprocity enhances B cell epitope prediction
Zhu, J., Gouru, A., Wu, F., Berzofsky, J. A., Xie, Y. & Wang, T., Feb 18 2022, In: iScience. 25, 2, 103764.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Clinically undetected polyclonal heteroresistance among Pseudomonas aeruginosa isolated from cystic fibrosis respiratory specimens
Maxwell, D. N., Kim, J., Pybus, C. A., White, L., Medford, R., Filkins, L. M., Monogue, M. L., Rae, M. M., Desai, D., Clark, A. E., Zhan, X. & Greenberg, D. E., Dec 1 2022, In: Journal of Antimicrobial Chemotherapy. 77, 12, p. 3321-3330 10 p.Research output: Contribution to journal › Article › peer-review
2 Scopus citations -
Ectopic JAK–STAT activation enables the transition to a stem-like and multilineage state conferring AR-targeted therapy resistance
Deng, S., Wang, C., Wang, Y., Xu, Y., Li, X., Johnson, N. A., Mukherji, A., Lo, U. G., Xu, L., Gonzalez, J., Metang, L. A., Ye, J., Tirado, C. R., Rodarte, K., Zhou, Y., Xie, Z., Arana, C., Annamalai, V., Liu, X., Vander Griend, D. J., & 6 others, Sep 2022, In: Nature Cancer. 3, 9, p. 1071-1087 17 p.Research output: Contribution to journal › Article › peer-review
Open Access35 Scopus citations -
Identification and characterization of proteins that form the inner core Ixodes scapularis tick attachment cement layer
Mulenga, A., Radulovic, Z., Porter, L., Britten, T. H., Kim, T. K., Tirloni, L., Gaithuma, A. K., Adeniyi-Ipadeola, G. O., Dietrich, J. K., Moresco, J. J. & Yates, J. R., Dec 2022, In: Scientific reports. 12, 1, 21300.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Interpreting the B-cell receptor repertoire with single-cell gene expression using Benisse
Zhang, Z., Chang, W. Y., Wang, K., Yang, Y., Wang, X., Yao, C., Wu, T., Wang, L. & Wang, T., Jun 2022, In: Nature Machine Intelligence. 4, 6, p. 596-604 9 p.Research output: Contribution to journal › Article › peer-review
Open Access6 Scopus citations -
IκBNS expression in B cells is dispensable for IgG responses to T cell-dependent antigens
Khoenkhoen, S., Ádori, M., Solís-Sayago, D., Soulier, J., Russell, J., Beutler, B., Pedersen, G. K. & Karlsson Hedestam, G. B., Oct 21 2022, In: Frontiers in immunology. 13, 1000755.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Loss of immunity-related GTPase GM4951 leads to nonalcoholic fatty liver disease without obesity
Zhang, Z., Xun, Y., Rong, S., Yan, L., SoRelle, J. A., Li, X., Tang, M., Keller, K., Ludwig, S., Moresco, E. M. Y. & Beutler, B., Dec 2022, In: Nature communications. 13, 1, 4136.Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations -
MB-SupCon: Microbiome-based Predictive Models via Supervised Contrastive Learning
Yang, S., Wang, S., Wang, Y., Rong, R., Kim, J., Li, B., Koh, A. Y., Xiao, G., Li, Q., Liu, D. J. & Zhan, X., Aug 15 2022, In: Journal of Molecular Biology. 434, 15, 167693.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Modulation of autoimmune diabetes by N-ethyl-N-nitrosoureainduced mutations in non-obese diabetic mice
Chatenoud, L., Marquet, C., Valette, F., Scott, L., Quan, J., Bu, C. H., Hildebrand, S., Moresco, E. M. Y., Bach, J. F. & Beutler, B., Jun 2022, In: DMM Disease Models and Mechanisms. 15, 6, dmm049484.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Multiple instance neural networks based on sparse attention for cancer detection using T-cell receptor sequences
Kim, Y., Wang, T., Xiong, D., Wang, X. & Park, S., Dec 2022, In: BMC Bioinformatics. 23, 1, 469.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations