SPH-Data Sciences in Precision

Research output

Research output per year 2015 2019 2020 2021 2022 2023 2024

• 218 Article
• 10 Review article
• 8 Comment/debate
• 2 Conference contribution
• 3 More
  • 2 Letter
  • 1 Chapter

Research output per year

Research output per year

Search results

• 2024

  CD73 contributes to the pathogenesis of fusion-negative rhabdomyosarcoma through the purinergic signaling pathway

  Hernandez, K. C., Shah, A. M., Lopez, V. A., Tagliabracci, V. S., Chen, K., Xu, L., Bassel-Duby, R., Olson, E. N. & Liu, N., 2024, In: Proceedings of the National Academy of Sciences of the United States of America. 121, 4, e2315925121.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Rhabdomyosarcoma 100%
  • Growth 42%
  • Adenosine A2 Receptor Agonists 27%
  • ectoATPase 24%
  • Adenosine Monophosphate 18%

• CRISPR-Cas9 base editing of pathogenic CaMKIIδ improves cardiac function in a humanized mouse model

  Lebek, S., Caravia, X. M., Straub, L. G., Alzhanov, D., Tan, W., Li, H., McAnally, J. R., Chen, K., Xu, L., Scherer, P. E., Liu, N., Bassel-Duby, R. & Olson, E. N., Jan 20 2024, In: Journal of Clinical Investigation. 134, 1, e175164.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Calcium-Calmodulin-Dependent Protein Kinase Type 2 100%
  • Clustered Regularly Interspaced Short Palindromic Repeats 90%
  • Reperfusion Injury 30%
  • Dependovirus 19%
  • Human Genome 16%
  1 Scopus citations

• Deep Learning–Based H-Score Quantification of Immunohistochemistry-Stained Images

  Wen, Z., Luo, D., Wang, S., Rong, R., Evers, B. M., Jia, L., Fang, Y., Daoud, E. V., Yang, S., Gu, Z., Arner, E. N., Lewis, C. M., Solis Soto, L. M., Fujimoto, J., Behrens, C., Wistuba, I. I., Yang, D. M., Brekken, R. A., O'Donnell, K. A., Xie, Y., & 1 othersXiao, G., Feb 2024, In: Modern Pathology. 37, 2, 100398.

  Research output: Contribution to journal › Article › peer-review

  • Immunohistochemistry 100%
  • Staining and Labeling 66%
  • Biomedical Research 41%
  • Hematoxylin 41%
  • Pathologists 40%
  2 Scopus citations

• 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

  • Chimeric Antigen Receptors 100%
  • T-Lymphocytes 45%
  • CD8 Antigens 22%
  • Transcription Factors 18%
  • Gene Regulatory Networks 17%
  1 Scopus citations

• Inflammatory markers for improved recurrent UTI diagnosis in postmenopausal women

  Ebrahimzadeh, T., Basu, U., Lutz, K. C., Gadhvi, J., Komarovsky, J. V., Li, Q., Zimmern, P. E. & De Nisco, N. J., Apr 2024, In: Life Science Alliance. 7, 4, e202302323.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Prostaglandin E2 100%
  • woman 70%
  • cytokines 69%
  • infection 69%
  • urinary tract diseases 69%
  1 Scopus citations

• 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

  • Ubiquitin-Conjugating Enzymes 100%
  • Androgen Antagonists 91%
  • Androgen Receptors 74%
  • Ubiquitination 37%
  • Prostatic Neoplasms 18%
• 2023

  Ablation of CaMKIId oxidation by CRISPR-Cas9 base editing as a therapy for cardiac disease

  Lebek, S., Chemello, F., Caravia, X. M., Tan, W., Li, H., Chen, K., Xu, L., Liu, N., Bassel-Duby, R. & Olson, E. N., Jan 13 2023, In: Science. 379, 6628, p. 179-185 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Gene Editing 100%
  • Clustered Regularly Interspaced Short Palindromic Repeats 93%
  • Heart Diseases 66%
  • Induced Pluripotent Stem Cells 30%
  • Mutation 30%
  35 Scopus citations

• A comparative study of neuroendocrine heterogeneity in small cell lung cancer and neuroblastoma

  Cai, L., De Berardinis, R. J., Xie, Y., Minna, J. D. & Xiao, G., Aug 1 2023, In: Molecular Cancer Research. 21, 8, p. 795-807 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Small Cell Lung Carcinoma 100%
  • Neuroblastoma 89%
  • myc Genes 22%
  • Cell Line 21%
  • Drug Resistance 16%

• 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

  • Deep Learning 100%
  • Tumor Microenvironment 75%
  • Histology 57%
  • Pathology 46%
  • Liver Neoplasms 36%
  1 Scopus citations

• A Deep Learning Onion Peeling Approach to Measure Oral Epithelium Layer Number

  Zhang, X., Gleber-Netto, F. O., Wang, S., Jin, K. W., Yang, D. M., Gillenwater, A. M., Myers, J. N., Ferrarotto, R., Pickering, C. R. & Xiao, G., Aug 2023, In: Cancers. 15, 15, 3891.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Onions 100%
  • Deep Learning 99%
  • Epithelium 55%
  • Oral Diagnosis 22%
  • Cell Shape 21%
  3 Scopus citations

• Artificial intelligence in mental healthcare: an overview and future perspectives

  Jin, K. W., Li, Q., Xie, Y. & Xiao, G., Oct 2023, In: British Journal of Radiology. 96, 1150, 20230213.

  Research output: Contribution to journal › Review article › peer-review

  • Artificial Intelligence 100%
  • Delivery of Health Care 45%
  • Psychiatry 37%
  • Health Care Surveys 33%
  • Research Personnel 17%
  2 Scopus citations

• Base editing correction of hypertrophic cardiomyopathy in human cardiomyocytes and humanized mice

  Chai, A. C., Cui, M., Chemello, F., Li, H., Chen, K., Tan, W., Atmanli, A., McAnally, J. R., Zhang, Y., Xu, L., Liu, N., Bassel-Duby, R. & Olson, E. N., Feb 2023, In: Nature medicine. 29, 2, p. 401-411 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Hypertrophic Cardiomyopathy 100%
  • Cardiac Myocytes 81%
  • Adenine 81%
  • Thickening 54%
  • Heart Diseases 35%
  44 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 Access

  • tazobactam drug combination ceftolozane 100%
  • Pseudomonas Infections 72%
  • Cystic Fibrosis 56%
  • Pseudomonas aeruginosa 53%
  • Microbial Sensitivity Tests 13%
  2 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 Access

  • cytometry 100%
  • Cytometry 77%
  • Small Cytoplasmic RNA 66%
  • Dimension 55%
  • sequencing 50%
  5 Scopus citations

• Comprehensive characterization of patient-derived xenograft models of pediatric leukemia

  Rogojina, A., Klesse, L. J., Butler, E., Kim, J., Zhang, H., Xiao, X., Guo, L., Zhou, Q., Hartshorne, T., Garcia, D., Weldon, K., Holland, T., Bandyopadhyay, A., Prado, L. P., Wang, S., Yang, D. M., Langevan, A. M., Zou, Y., Grimes, A. C., Assanasen, C., & 10 othersGidvani-Diaz, V., Zheng, S., Lai, Z., Chen, Y., Xie, Y., Tomlinson, G. E., Skapek, S. X., Kurmasheva, R. T., Houghton, P. J. & Xu, L., Nov 17 2023, In: iScience. 26, 11, 108171.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Heterografts 100%
  • Leukemia 91%
  • Pediatrics 71%
  • Hispanic Americans 23%
  • Methylation 22%

• Comprehensive isotopomer analysis of glutamate and aspartate in small tissue samples

  Cai, F., Bezwada, D., Cai, L., Mahar, R., Wu, Z., Chang, M. C., Pachnis, P., Yang, C., Kelekar, S., Gu, W., Brooks, B., Ko, B., Vu, H. S., Mathews, T. P., Zacharias, L. G., Martin-Sandoval, M., Do, D., Oaxaca, K. C., Jin, E. S., Margulis, V., & 3 othersMalloy, C. R., Merritt, M. E. & DeBerardinis, R. J., Oct 3 2023, In: Cell Metabolism. 35, 10, p. 1830-1843.e5

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Aspartic Acid 100%
  • Mass Spectrometry 86%
  • Glutamic Acid 84%
  • Magnetic Resonance Spectroscopy 64%
  • Isotope Labeling 56%

• 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 Access

  • Argonaute Proteins 100%
  • MicroRNAs 54%
  • Trinucleotide Repeats 6%
  • Proteins 5%
  • Immunoprecipitation 4%
  2 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

  • simulation 100%
  • RNA-Seq 89%
  • learning 69%
  • evaluation 65%
  • methodology 61%

• 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 Access

  • Deep Learning 100%
  • Ploidies 87%
  • Hematoxylin 72%
  • Eosine Yellowish-(YS) 72%
  • Liver 37%
  1 Scopus citations

• Deep learning-based pathology image analysis predicts cancer progression risk in patients with oral leukoplakia

  Zhang, X., Gleber-Netto, F. O., Wang, S., Martins-Chaves, R. R., Gomez, R. S., Vigneswaran, N., Sarkar, A., William, W. N., Papadimitrakopoulou, V., Williams, M., Bell, D., Palsgrove, D., Bishop, J., Heymach, J. V., Gillenwater, A. M., Myers, J. N., Ferrarotto, R., Lippman, S. M., Pickering, C. R. & Xiao, G., Mar 2023, In: Cancer Medicine. 12, 6, p. 7508-7518 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Oral Leukoplakia 100%
  • Deep Learning 93%
  • Mouth Neoplasms 46%
  • Pathology 43%
  • Mouth Mucosa 23%
  4 Scopus citations

• Deep learning in digital pathology for personalized treatment plans of cancer patients

  Wen, Z., Wang, S., Yang, D. M., Xie, Y., Chen, M., Bishop, J. & Xiao, G., Mar 2023, In: Seminars in Diagnostic Pathology. 40, 2, p. 109-119 11 p.

  Research output: Contribution to journal › Review article › peer-review

  • Deep Learning 100%
  • Pathology 46%
  • Artificial Intelligence 27%
  • Biomarkers 27%
  • Neoplasms 23%
  6 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

  • Tyrosine Kinase Inhibitor 100%
  • Deep Learning 98%
  • learning 77%
  • Biological Marker 64%
  • Disorder 61%

• Dissecting embryonic and extraembryonic lineage crosstalk with stem cell co-culture

  Wei, Y., Zhang, E., Yu, L., Ci, B., Sakurai, M., Guo, L., Zhang, X., Lin, S., Takii, S., Liu, L., Liu, J., Schmitz, D. A., Su, T., Zhang, J., Shen, Q., Ding, Y., Zhan, L., Sun, H. X., Zheng, C., Xu, L., & 4 othersOkamura, D., Ji, W., Tan, T. & Wu, J., Dec 21 2023, In: Cell. 186, 26, p. 5859-5875.e24

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Growth Inhibition 100%
  • Embryonic Stem Cells 89%
  • Coculture Techniques 83%
  • Cell Culture Techniques 63%
  • Stem Cells 61%
  4 Scopus citations

• Dissecting molecular, pathological, and clinical features associated with tumor neural/neuroendocrine heterogeneity

  Cai, L., DeBerardinis, R. J., Xiao, G., Minna, J. D. & Xie, Y., Jun 16 2023, In: iScience. 26, 6, 106983.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Neuroendocrine Tumors 100%
  • Neoplasms 28%
  • Datasets 15%

• Ectopic PLAG1 induces muscular dystrophy in the mouse

  Aguayo, J. S., Shelton, J. M., Tan, W., Rakheja, D., Cai, C., Shalaby, A., Lee, J., Iannaccone, S. T., Xu, L., Chen, K., Burns, D. K. & Zheng, Y., Jul 12 2023, In: Biochemical and Biophysical Research Communications. 665, p. 159-168 10 p.

  Research output: Contribution to journal › Article › peer-review

  • Muscular Dystrophies 100%
  • Mutation 71%
  • Skeletal Muscle 55%
  • Dystrophin 52%
  • Lethal 50%
  1 Scopus citations

• Elimination of CaMKIIδ Autophosphorylation by CRISPR-Cas9 Base Editing Improves Survival and Cardiac Function in Heart Failure in Mice

  Lebek, S., Caravia, X. M., Chemello, F., Tan, W., McAnally, J. R., Chen, K., Xu, L., Liu, N., Bassel-Duby, R. & Olson, E. N., Nov 7 2023, In: Circulation. 148, 19, p. 1490-1504 15 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Calcium-Calmodulin-Dependent Protein Kinase Type 2 100%
  • Clustered Regularly Interspaced Short Palindromic Repeats 90%
  • Heart Failure 57%
  • Constriction 27%
  • Cardiac Myocytes 19%
  3 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 Access

  • Deep Learning 100%
  • Pathology 46%
  • Staining and Labeling 23%
  • Pathologists 17%
  • Color 15%
  2 Scopus citations

• Evaluation of a large-scale aptamer proteomics platform among patients with kidney failure on dialysis

  Ren, Y., Ruan, P., Segal, M., Dobre, M., Schelling, J. R., Banerjee, U., Shafi, T., Ganz, P. & Dubin, R. F., Dec 2023, In: PloS one. 18, 12 December, e0293945.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Proteomics 100%
  • Renal Insufficiency 95%
  • Dialysis 92%
  • Proteins 40%
  • Individual Biological Variation 27%

• Features of tumor-microenvironment images predict targeted therapy survival benefit in patients with EGFR-mutant lung cancer

  Wang, S., Rong, R., Yang, D. M., Fujimoto, J., Bishop, J. A., Yan, S., Cai, L., Behrens, C., Berry, L. D., Wilhelm, C., Aisner, D., Sholl, L., Johnson, B. E., Kwiatkowski, D. J., Wistuba, I. I., Bunn, P. A., Minna, J., Xiao, G., Kris, M. G. & Xie, Y., Jan 17 2023, In: Journal of Clinical Investigation. 133, 2, e160330.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Tumor Microenvironment 100%
  • ErbB Receptors 91%
  • Lung Neoplasms 76%
  • Protein-Tyrosine Kinases 68%
  • Survival 53%
  5 Scopus citations

• 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. e0222123

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Lactams 100%
  • lactams 98%
  • phenotype 76%
  • inhibitor 65%
  • anti-infective agents 54%
  1 Scopus citations

• Genetic or therapeutic neutralization of ALK1 reduces LDL transcytosis and atherosclerosis in mice

  Lee, S., Schleer, H., Park, H., Jang, E., Boyer, M., Tao, B., Gamez-Mendez, A., Singh, A., Folta-Stogniew, E., Zhang, X., Qin, L., Xiao, X., Xu, L., Zhang, J., Hu, X., Pashos, E., Tellides, G., Shaul, P. W., Lee, W. L., Fernandez-Hernando, C., & 2 othersEichmann, A. & Sessa, W. C., May 2023, In: Nature Cardiovascular Research. 2, 5, p. 438-448 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Transcytosis 100%
  • LDL Lipoproteins 76%
  • Neutralization 75%
  • Atherosclerosis 60%
  • Activin Receptors 56%
  4 Scopus citations

• Genomic profiling of subcutaneous patient-derived xenografts reveals immune constraints on tumor evolution in childhood solid cancer

  He, F., Bandyopadhyay, A. M., Klesse, L. J., Rogojina, A., Chun, S. H., Butler, E., Hartshorne, T., Holland, T., Garcia, D., Weldon, K., Prado, L. N. P., Langevin, A. M., Grimes, A. C., Sugalski, A., Shah, S., Assanasen, C., Lai, Z., Zou, Y., Kurmashev, D., Xu, L., & 8 othersXie, Y., Chen, Y., Wang, X., Tomlinson, G. E., Skapek, S. X., Houghton, P. J., Kurmasheva, R. T. & Zheng, S., Dec 2023, In: Nature communications. 14, 1, 7600.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • tumors 100%
  • cancer 97%
  • Heterogeneity 96%
  • Antitumor 96%
  • Heterografts 94%

• Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm

  Bhattacharyya, S., Kollipara, R. K., Orquera-Tornakian, G., Goetsch, S., Zhang, M., Perry, C., Li, B., Shelton, J. M., Bhakta, M., Duan, J., Xie, Y., Xiao, G., Evers, B. M., Hon, G. C., Kittler, R. & Munshi, N. V., Feb 1 2023, In: Journal of Clinical Investigation. 133, 3, e153635.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genetic Enhancer Elements 100%
  • Chromatin 69%
  • Transcription Factors 59%
  • Transposases 55%
  • Biomass 48%
  2 Scopus citations

• Hepatic sialic acid synthesis modulates glucose homeostasis in both liver and skeletal muscle

  Peng, J., Yu, L., Huang, L., Paschoal, V. A., Chu, H., de Souza, C. O., Varre, J. V., Oh, D. Y., Kohler, J. J., Xiao, X., Xu, L., Holland, W. L., Shaul, P. W. & Mineo, C., Dec 2023, In: Molecular Metabolism. 78, 101812.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • N-Acetylneuraminic Acid 100%
  • Skeletal Muscle 68%
  • Homeostasis 63%
  • Glucose 54%
  • Liver 44%
  1 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

  • Strain 100%
  • Deep Learning 28%
  • Gene Expression 24%
  • Nephrons 23%
  • Intestinal Mucosa 21%

• 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 Access

  • Gastrointestinal Microbiome 100%
  • Immunity 82%
  • Lymph Nodes 57%
  • Bacteria 41%
  • Dendritic Cells 36%
  15 Scopus citations

• Integrated genomic analysis reveals aberrations in WNT signaling in germ cell tumors of childhood and adolescence

  Xu, L., Pierce, J. L., Sanchez, A., Chen, K. S., Shukla, A. A., Fustino, N. J., Stuart, S. H., Bagrodia, A., Xiao, X., Guo, L., Krailo, M. D., Shaikh, F., Billmire, D. F., Pashankar, F., Bestrashniy, J., Oosterhuis, J. W., Gillis, A. J. M., Xie, Y., Teot, L., Mora, J., & 6 othersPoynter, J. N., Rakheja, D., Looijenga, L. H. J., Draper, B. W., Frazier, A. L. & Amatruda, J. F., Dec 2023, In: Nature communications. 14, 1, 2636.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Germ Cell and Embryonal Neoplasms 100%
  • tumors 80%
  • aberration 75%
  • Mutation 71%
  • Molecule 29%
  3 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

  • Proteomics 100%
  • Data visualization 85%
  • Data Visualization 73%
  • Servers 54%
  • Bioinformatics 40%

• Itaconate-producing neutrophils regulate local and systemic inflammation following trauma

  Crossley, J. L., Ostashevskaya-Gohstand, S., Comazzetto, S., Hook, J. S., Guo, L., Vishlaghi, N., Juan, C., Xu, L., Horswill, A. R., Hoxhaj, G., Moreland, J. G., Tower, R. J. & Levi, B., Oct 2023, In: JCI Insight. 8, 20, e169208.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • itaconic acid 100%
  • Neutrophils 43%
  • Inflammation 33%
  • Wounds and Injuries 27%
  • Metabolomics 24%
  4 Scopus citations

• Loss of p53 and mutational heterogeneity drives immune resistance in an autochthonous mouse lung cancer model with high tumor mutational burden

  Zhu, M., Kim, J., Deng, Q., Ricciuti, B., Alessi, J. V., Eglenen-Polat, B., Bender, M. E., Huang, H. C., Kowash, R. R., Cuevas, I. C., Bennett, Z. T., Gao, J., Minna, J. D., Castrillon, D. H., Awad, M. M., Xu, L. & Akbay, E. A., Oct 9 2023, In: Cancer Cell. 41, 10, p. 1731-1748.e8

  Research output: Contribution to journal › Article › peer-review

  • Tumor Burden 100%
  • Lung Neoplasms 83%
  • Immunotherapy 46%
  • Neoplasms 33%
  • DNA-Directed DNA Polymerase 29%
  3 Scopus citations

• 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 othersLiu, X., Chen, S., Zhu, H., Strand, D., Liang, H., Raj, G., He, H. H., Mendell, J. T., Li, B., Wang, T. & Mu, P., Aug 14 2023, In: Cancer Cell. 41, 8, p. 1427-1449.e12

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Androgen Receptors 100%
  • Mutagenesis 91%
  • Prostatic Neoplasms 73%
  • Neoplasms 29%
  • Cytosine Deaminase 28%
  6 Scopus citations

• Macrophage-to-endothelial cell crosstalk by the cholesterol metabolite 27HC promotes atherosclerosis in male mice

  Yu, L., Xu, L., Chu, H., Peng, J., Sacharidou, A., Hsieh, H. H., Weinstock, A., Khan, S., Ma, L., Durán, J. G. B., McDonald, J., Nelson, E. R., Park, S., McDonnell, D. P., Moore, K. J., Huang, L. J. S., Fisher, E. A., Mineo, C., Huang, L. & Shaul, P. W., Dec 2023, In: Nature communications. 14, 1, 4101.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • estrogens 100%
  • 27-hydroxycholesterol 99%
  • arteriosclerosis 85%
  • macrophages 85%
  • metabolites 78%

• Methyltransferase Inhibition Enables Tgfβ Driven Induction of CDKN2A and B in Cancer Cells

  Liu, Y. T., Romero, C., Xiao, X., Guo, L., Zhou, X., Applebaum, M. A., Xu, L. & Skapek, S. X., 2023, In: Molecular and cellular biology. 43, 3, p. 115-129 15 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Methyltransferases 100%
  • Rhabdomyosarcoma 63%
  • Neoplasms 28%
  • Clustered Regularly Interspaced Short Palindromic Repeats 20%
  • Neuroblastoma 17%

• Mitochondrial-Encoded Complex I Impairment Induces a Targetable Dependency on Aerobic Fermentation in Hürthle Cell Carcinoma of the Thyroid

  Frank, A. R., Li, V., Shelton, S. D., Kim, J., Stott, G. M., Neckers, L. M., Xie, Y., Williams, N. S., Mishra, P. & McFadden, D. G., Aug 1 2023, In: Cancer discovery. 13, 8, p. 1884-1903 20 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Fermentation 100%
  • Thyroid Neoplasms 95%
  • Respiration 46%
  • Neoplasms 30%
  • Electron Transport Complex I 25%
  3 Scopus citations

• Net39 protects muscle nuclei from mechanical stress during the pathogenesis of Emery-Dreifuss muscular dystrophy

  Zhang, Y., Ramirez-Martinez, A., Chen, K., McAnally, J. R., Cai, C., Durbacz, M. Z., Chemello, F., Wang, Z., Xu, L., Bassel-Duby, R., Liu, N. & Olson, E. N., Jul 3 2023, In: Journal of Clinical Investigation. 133, 13, e163333.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Emery-Dreifuss Muscular Dystrophy 100%
  • Mechanical Stress 75%
  • Nuclear Envelope 42%
  • Muscles 37%
  • DNA Damage 32%
  1 Scopus citations

• Neutrophil metabolomics in severe COVID-19 reveal GAPDH as a suppressor of neutrophil extracellular trap formation

  Li, Y., Hook, J. S., Ding, Q., Xiao, X., Chung, S. S., Mettlen, M., Xu, L., Moreland, J. G. & Agathocleous, M., Dec 2023, In: Nature communications. 14, 1, 2610.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • neutrophils 100%
  • suppressors 93%
  • Extracellular Traps 92%
  • Metabolomics 72%
  • Neutrophils 51%
  5 Scopus citations

• Novel start codons introduce novel coding sequences in the human genomes

  Zhang, H. & Xie, Y., Dec 2023, In: Scientific reports. 13, 1, 8141.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Initiator Codon 100%
  • Human Genome 85%
  • Pan troglodytes 20%
  • Genomics 16%
  • Phenotype 9%

• Opposing gene regulatory programs governing myofiber development and maturation revealed at single nucleus resolution

  Dos Santos, M., Shah, A. M., Zhang, Y., Bezprozvannaya, S., Chen, K., Xu, L., Lin, W., McAnally, J. R., Bassel-Duby, R., Liu, N. & Olson, E. N., Dec 2023, In: Nature communications. 14, 1, 4333.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • genes 100%
  • Regulator Genes 88%
  • Muscle Development 66%
  • skeletal muscle 66%
  • Atlases 61%
  3 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 othersXiao, G., Skapek, S. X., Xu, L., Klesse, L. J., Crompton, B. D. & Xie, Y., Sep 1 2023, In: JCO Clinical Cancer Informatics. 7, p. e2300104

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Osteosarcoma 100%
  • Proteins 35%
  • Information Storage and Retrieval 23%
  • Databases 15%
  • Data Science 12%

• 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

  • Lymphopenia 100%
  • Demethylation 60%
  • maintenance 53%
  • Epithelial Cells 36%
  • disrupting 36%