Ying Hu, Ph.D.

Staff Scientist

Biography

Dr. Ying Hu is a staff scientist and an integrated member of CBIIT’s Computational Genomics and Bioinformatics Group, who supports the research of NCI’s Center for Cancer Research, Division of Cancer Epidemiology and Genetics, and other NCI initiatives. Dr. Hu joined NCI in 1998 after his postdoctoral work at Fox Chase Cancer Center of Philadelphia. He developed popular OmicCircos and OmicPath tools, which have been downloaded over 10,000 times through Bioconductor and used in NIH bioinformatics training courses. He also developed several algorithms in the omics-data analysis, such as the graphical based k-means that has been employed in the single cell transcriptome analysis. Dr. Hu was recognized as the best performer in the Heritage Provider Network Dialogue for Reverse Engineering Assessments and Methods (HPN-DREAM) breast cancer network inference challenge. He manages the algorithms and data analysis pipeline on biostatistics, systems biology, and machine learning in studies on clinical outcomes, omics, and high-throughput functional genomics data. Dr. Hu received his doctorate in population genetics from the Sichuan University of China.

Projects

  • APOLLO

Publications

  • Liang X, Hu Y, Yan C, Xu K. i2d: an R package for simulating data from images and the implications in biomedical research. Bioinformatics. 2021 Aug 25;37(16):2497-2498. doi: 10.1093/bioinformatics/btaa991. PMID: 33244599
  • Heinrich B, Gertz EM, Schäffer AA, Craig A, Ruf B, Subramanyam V, McVey JC, Diggs LP, Heinrich S, Rosato U, Ma C, Yan C, Hu Y, Zhao Y, Shen TW, Kapoor V, Telford W, Kleiner DE, Stovroff MK, Dhani HS, Kang J, Fishbein T, Wang XW, Ruppin E, Kroemer A, Greten TF, Korangy F. The tumour microenvironment shapes innate lymphoid cells in patients with hepatocellular carcinoma. Gut. 2021 Aug 2:gutjnl-2021-325288. doi: 10.1136/gutjnl-2021-325288. Online ahead of print. PMID: 34340996
  • Ying Hu1, Mohini Ranganathan2,3, Chang Shu 2,3, Xiaoyu Liang 2,3, Suhas Ganesh2,3, Awo Osafo-Addo2,3, Chunhua Yan1, Xinyu Zhang 2,3, Bradley E. Aouizerat4,5, John H. Krystal2,3, Deepak C. D’Souza2,3 & Ke Xu2,3* Single-cell Transcriptome Mapping Identifies Common and Cell-type Specific Genes Affected by Acute Delta9-tetrahydrocannabinol in Humans. Sci Rep. 2020 Feb 26;10(1):3450. doi: 10.1038/s41598-020-59827-1. PMID: 32103029
  • Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R; DREAM Module Identification Challenge Consortium, Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D. Assessment of network module identification across complex diseases. Nat Methods. 2019 Sep;16(9):843-852. doi: 10.1038/s41592-019-0509-5. Epub 2019 Aug 30.
  • Deasy SK, Uehara R, Vodnala SK, Yang HH, Dass RA, Hu Y, Lee MP, Crouch RJ, Hunter KW. Aicardi-Goutières syndrome gene Rnaseh2c is a metastasis susceptibility gene in breast cancer. PLoS Genet. 2019 May 24;15(5):e1008020. doi: 10.1371/journal.pgen.1008020. eCollection 2019 May.
  • Bhaskaran N1, Liu Z2, Saravanamuthu SS3, Yan C2, Hu Y2, Dong L3, Zelenka P3, Zheng L4, Bletsos V1, Harris R1, Harrington B1, Weinberg A1, Thiele CJ2, Ye F1, Pandiyan P1. Identification of Casz1 as a Regulatory Protein Controlling T Helper Cell Differentiation, Inflammation, and Immunity. Front Immunol. 2018 Feb 7;9:184. doi: 10.3389/fimmu.2018.00184. eCollection 2018.
  • Jean M. Winter, Natasha L. Curry, Derek M. Gildea, Kendra A. Williams, Minnkyong Lee, Ying Hu and Nigel P. S. Crawford. Modifier locus mapping of a transgenic F2 mouse population identifies CCDC115 as a novel aggressive prostate cancer modifier gene in humans. BMC Genomics 2018 19:450 https://doi.org/10.1186/s12864-018-4827-2
  • Yang Y, Kohler ME, Chien CD, Sauter CT, Jacoby E, Yan C, Hu Y, Wanhainen K, Qin H, Fry TJ. TCR engagement negatively affects CD8 but not CD4 CAR T cell expansion and leukemic clearance. Sci Transl Med. 2017 Nov 22;9(417). pii: eaag1209. doi: 10.1126/scitranslmed.aag1209. PMID:29167392
  • Gadd S, Huff V, Walz AL, Ooms AHAG, Armstrong AE, Gerhard DS, Smith MA, Auvil JMG, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Hermida LC, Davidsen T, Gesuwan P, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Dome JS, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Ross N, Gastier-Foster JM, Arold ST, Perlman EJ. A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor. Nat Genet. 2017 Oct;49(10):1487-1494. doi: 10.1038/ng.3940. Epub 2017 Aug 21. PMID:28825729
  • Veschi V, Liu Z, Voss TC, Ozbun L, Gryder B, Yan C, Hu Y, Ma A, Jin J, Mazur SJ, Lam N, Souza BK, Giannini G, Hager GL, Arrowsmith CH, Khan J, Appella E, Thiele CJ. Epigenetic siRNA and Chemical Screens Identify SETD8 Inhibition as a Therapeutic Strategy for p53 Activation in High-Risk Neuroblastoma. Cancer Cell. 2017 Jan 9;31(1):50-63. doi: 10.1016/j.ccell.2016.12.002.