Researcher Profile

Researcher Profile

Zhenqiu Liu, PhD

Zhenqiu Liu, PhD

Associate Professor, Department of Public Health Sciences
Division of Biostatistics and Bioinformatics
Scientific Program:Next-Generation Therapies
zxl391@psu.edu

Research Interests

  • Neoplasms
  • Genes
  • Gene Expression
  • Prostatic Neoplasms
  • Biomarkers
  • Messenger RNA
  • Metagenomics
  • Phenotype
  • Non-Small Cell Lung Carcinoma
  • Carrier Proteins
  • Lung Neoplasms
  • Neoplastic Stem Cells

Recent Publications

2021

Grimley, PM, Liu, Z, Darcy, KM, Hueman, MT, Wang, H, Sheng, L, Henson, DE & Chen, D 2021, 'A prognostic system for epithelial ovarian carcinomas using machine learning', Acta Obstetricia et Gynecologica Scandinavica, vol. 100, no. 8, pp. 1511-1519. https://doi.org/10.1111/aogs.14137
Liu, C, Billet, S, Choudhury, D, Cheng, R, Haldar, S, Fernandez, A, Biondi, S, Liu, Z, Zhou, H & Bhowmick, NA 2021, 'Bone marrow mesenchymal stem cells interact with head and neck squamous cell carcinoma cells to promote cancer progression and drug resistance', Neoplasia (United States), vol. 23, no. 1, pp. 118-128. https://doi.org/10.1016/j.neo.2020.11.012
Liu, Z 2021, 'Clustering single-cell rna-seq data with regularized gaussian graphical model', Genes, vol. 12, no. 2, 311, pp. 1-12. https://doi.org/10.3390/genes12020311
Hueman, M, Wang, H, Liu, Z, Henson, D, Nguyen, C, Park, D, Sheng, L & Chen, D 2021, 'Expanding TNM for lung cancer through machine learning', Thoracic Cancer, vol. 12, no. 9, pp. 1423-1430. https://doi.org/10.1111/1759-7714.13926

2020

Kawaguchi, ES, Suchard, MA, Liu, Z & Li, G 2020, 'A surrogate ℓ0 sparse Cox's regression with applications to sparse high-dimensional massive sample size time-to-event data', Statistics in Medicine, vol. 39, no. 6, pp. 675-686. https://doi.org/10.1002/sim.8438
Sun, L, Jiang, L, Grant, CN, Wang, HG, Gragnoli, C, Liu, Z & Wu, R 2020, 'Computational identification of gene networks as a biomarker of neuroblastoma risk', Cancers, vol. 12, no. 8, 2086, pp. 1-17. https://doi.org/10.3390/cancers12082086
Liu, Z, Grant, CN, Sun, L, Miller, BA, Spiegelman, VS & Wang, HG 2020, 'Expression patterns of immune genes reveal heterogeneous subtypes of high-risk neuroblastoma', Cancers, vol. 12, no. 7, 1739, pp. 1-16. https://doi.org/10.3390/cancers12071739
Gebru, MT, Atkinson, JM, Young, MM, Zhang, L, Tang, Z, Liu, Z, Lu, P, Dower, CM, Chen, L, Annageldiyev, C, Sharma, A, Kawasawa, YI, Zhao, Z, Miller, BA, Claxton, DF & Wang, HG 2020, 'Glucocorticoids enhance the antileukemic activity of FLT3 inhibitors in FLT3-mutant acute myeloid leukemia', Blood, vol. 136, no. 9, pp. 1067-1079. https://doi.org/10.1182/blood.2019003124
Rice, SJ, Liu, X, Hyland, V, Liu, Z & Belani, CP 2020, 'Mutations in genes connected with the TCF7L2 transcription factor are associated with a poor prognosis in non-small cell lung cancer', Lung Cancer, vol. 141, pp. 97-100. https://doi.org/10.1016/j.lungcan.2020.01.015
Placencio-Hickok, VR, Madhav, A, Kim, S, Duong, F, Angara, B, Liu, Z & Bhowmick, NA 2020, 'Soluble CD105 is prognostic of disease recurrence in prostate cancer patients', Endocrine-Related Cancer, vol. 27, no. 1, pp. 1-9. https://doi.org/10.1530/ERC-19-0370
Liu, Z 2020, 'Visualizing single-cell rna-seq data with semisupervised principal component analysis', International journal of molecular sciences, vol. 21, no. 16, 5797, pp. 1-12. https://doi.org/10.3390/ijms21165797

2019

Kakuta, Y, Kawai, Y, Naito, T, Hirano, A, Umeno, J, Fuyuno, Y, Liu, Z, Li, D, Nakano, T, Izumiyama, Y, Ichikawa, R, Okamoto, D, Nagai, H, Matsumoto, S, Yamamoto, K, Yokoyama, N, Chiba, H, Shimoyama, Y, Onodera, M, Moroi, R, Kuroha, M, Kanazawa, Y, Kimura, T, Shiga, H, Endo, K, Negoro, K, Yasuda, J, Esaki, M, Tokunaga, K, Nakamura, M, Matsumoto, T, McGovern, DPB, Nagasaki, M, Kinouchi, Y, Shimosegawa, T & Masamune, A 2019, 'A Genome-wide Association Study Identifying RAP1A as a Novel Susceptibility Gene for Crohn's Disease in Japanese Individuals', Journal of Crohn's and Colitis, vol. 13, no. 5, pp. 648-658. https://doi.org/10.1093/ecco-jcc/jjy197
Elcheva, I, Sneed, M, Frazee, S, Liu, Z, Zhu, J, Wood, T, Hendrickson, S, Oehler, C, Garcia, B & Spiegelman, VS 2019, 'A novel hiPSC-derived system for hematoendothelial and myeloid blood toxicity screens identifies compounds promoting and inhibiting endothelial-to-hematopoietic transition', Toxicology in Vitro, vol. 61, 104622. https://doi.org/10.1016/j.tiv.2019.104622
Chen, C, Jiang, L, Fu, G, Wang, M, Wang, Y, Shen, B, Liu, Z, Wang, Z, Hou, W, Berceli, SA & Wu, R 2019, 'An omnidirectional visualization model of personalized gene regulatory networks', NPJ systems biology and applications, vol. 5. https://doi.org/10.1038/s41540-019-0116-1
Liu, Z, Yee, PP, Wei, Y, Liu, Z, Imamura, Y & Li, W 2019, 'Differential YAP expression in glioma cells induces cell competition and promotes tumorigenesis', Journal of Cell Science, vol. 132, no. 5, jcs225714. https://doi.org/10.1242/jcs.225714
Ghoshal, A, Rodrigues, LC, Gowda, CP, Elcheva, IA, Liu, Z, Abraham, T & Spiegelman, VS 2019, 'Extracellular vesicle-dependent effect of RNA-binding protein IGF2BP1 on melanoma metastasis', Oncogene, vol. 38, no. 21, pp. 4182-4196. https://doi.org/10.1038/s41388-019-0797-3
Yang, YM, Noureddin, M, Liu, C, Ohashi, K, Kim, SY, Ramnath, D, Powell, EE, Sweet, MJ, Roh, YS, Hsin, IF, Deng, N, Liu, Z, Liang, J, Mena, E, Shouhed, D, Schwabe, RF, Jiang, D, Lu, SC, Noble, PW & Seki, E 2019, 'Hyaluronan synthase 2-mediated hyaluronan production mediates Notch1 activation and liver fibrosis', Science Translational Medicine, vol. 11, no. 496, eaat9284. https://doi.org/10.1126/scitranslmed.aat9284
Geng, Y, Liu, X, Liang, J, Habiel, DM, Kulur, V, Coelho, AL, Deng, N, Xie, T, Wang, Y, Liu, N, Huang, G, Kurkciyan, A, Liu, Z, Tang, J, Hogaboam, CM, Jiang, D & Noble, PW 2019, 'PD-L1 on invasive fibroblasts drives fibrosis in a humanized model of idiopathic pulmonary fibrosis', JCI Insight, vol. 4, no. 6, e125326. https://doi.org/10.1172/jci.insight.125326
Elcheva, IA, Wood, T, Chiarolanzio, K, Chim, B, Wong, M, Singh, V, Gowda, CP, Lu, Q, Hafner, M, Dovat, S, Liu, Z, Muljo, SA & Spiegelman, VS 2020, 'RNA-binding protein IGF2BP1 maintains leukemia stem cell properties by regulating HOXB4, MYB, and ALDH1A1', Leukemia, vol. 34, no. 5, pp. 1354-1363. https://doi.org/10.1038/s41375-019-0656-9
Liu, Z, Elashoff, D & Piantadosi, S 2019, 'Sparse support vector machines with L0 approximation for ultra-high dimensional omics data', Artificial Intelligence in Medicine, vol. 96, pp. 134-141. https://doi.org/10.1016/j.artmed.2019.04.004
Yang, JW, Murray, B, Barbier-Torres, L, Liu, T, Liu, Z, Yang, H, Fan, W, Wang, J, Li, Y, Seki, E, Mato, JM & Lu, SC 2019, 'The mitochondrial chaperone Prohibitin 1 negatively regulates interleukin-8 in human liver cancers', Journal of Biological Chemistry, vol. 294, no. 6, pp. 1984-1996. https://doi.org/10.1074/jbc.RA118.004863

2018

Madhav, A, Andres, A, Duong, F, Mishra, R, Haldar, S, Liu, Z, Angara, B, Gottlieb, R, Zumsteg, ZS & Bhowmick, NA 2018, 'Antagonizing CD105 enhances radiation sensitivity in prostate cancer', Oncogene, vol. 37, no. 32, pp. 4385-4397. https://doi.org/10.1038/s41388-018-0278-0
Dai, L, Chen, K, Sun, Z, Liu, Z & Li, G 2018, 'Broken adaptive ridge regression and its asymptotic properties', Journal of Multivariate Analysis, vol. 168, pp. 334-351. https://doi.org/10.1016/j.jmva.2018.08.007
Kato, M, Placencio-Hickok, VR, Madhav, A, Haldar, S, Tripathi, M, Billet, S, Mishra, R, Smith, B, Rohena-Rivera, K, Agarwal, P, Duong, F, Angara, B, Hickok, D, Liu, Z & Bhowmick, NA 2019, 'Heterogeneous cancer-associated fibroblast population potentiates neuroendocrine differentiation and castrate resistance in a CD105-dependent manner', Oncogene, vol. 38, no. 5, pp. 716-730. https://doi.org/10.1038/s41388-018-0461-3
Liu, T, Yang, H, Fan, W, Tu, J, Li, TWH, Wang, J, Shen, H, Yang, JW, Xiong, T, Steggerda, J, Liu, Z, Noureddin, M, Maldonado, SS, Annamalai, A, Seki, E, Mato, JM & Lu, SC 2018, 'Mechanisms of MAFG Dysregulation in Cholestatic Liver Injury and Development of Liver Cancer', Gastroenterology, vol. 155, no. 2, pp. 557-571.e14. https://doi.org/10.1053/j.gastro.2018.04.032
Liu, Z & Lin, S 2018, Sparse Treatment-Effect Model for Taxon Identification with High-Dimensional Metagenomic Data. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1849, Humana Press Inc., pp. 309-318. https://doi.org/10.1007/978-1-4939-8728-3_19
Mishra, R, Haldar, S, Placencio, V, Madhav, A, Rohena-Rivera, K, Agarwal, P, Duong, F, Angara, B, Tripathi, M, Liu, Z, Gottlieb, RA, Wagner, S, Posadas, EM & Bhowmick, NA 2018, 'Stromal epigenetic alterations drive metabolic and neuroendocrine prostate cancer reprogramming', Journal of Clinical Investigation, vol. 128, no. 10, pp. 4472-4484. https://doi.org/10.1172/JCI99397

2017

Yoon, SM, Haritunians, T, Chhina, S, Liu, Z, Yang, S, Landers, C, Li, D, Ye, BD, Shih, D, Vasiliauskas, EA, Ippoliti, A, Rabizadeh, S, Targan, SR, Melmed, GY & McGovern, DPB 2017, 'Colonic Phenotypes Are Associated with Poorer Response to Anti-TNF Therapies in Patients with IBD', Inflammatory bowel diseases, vol. 23, no. 8, pp. 1382-1393. https://doi.org/10.1097/MIB.0000000000001150
Lew, D, Yoon, SM, Yan, X, Robbins, L, Haritunians, T, Liu, Z, Li, D & McGovern, DPB 2017, 'Genetic associations with adverse events from anti-tumor necrosis factor therapy in inflammatory bowel disease patients', World journal of gastroenterology, vol. 23, no. 40, pp. 7265-7273. https://doi.org/10.3748/wjg.v23.i40.7265
Brant, SR, Okou, DT, Simpson, CL, Cutler, DJ, Haritunians, T, Bradfield, JP, Chopra, P, Prince, J, Begum, F, Kumar, A, Huang, C, Venkateswaran, S, Datta, LW, Wei, Z, Thomas, K, Herrinton, LJ, Klapproth, JMA, Quiros, AJ, Seminerio, J, Liu, Z, Alexander, JS, Baldassano, RN, Dudley-Brown, S, Cross, RK, Dassopoulos, T, Denson, LA, Dhere, TA, Dryden, GW, Hanson, JS, Hou, JK, Hussain, SZ, Hyams, JS, Isaacs, KL, Kader, H, Kappelman, MD, Katz, J, Kellermayer, R, Kirschner, BS, Kuemmerle, JF, Kwon, JH, Lazarev, M, Li, E, Mack, D, Mannon, P, Moulton, DE, Newberry, RD, Osuntokun, BO, Patel, AS, Saeed, SA, Targan, SR, Valentine, JF, Wang, MH, Zonca, M, Rioux, JD, Duerr, RH, Silverberg, MS, Cho, JH, Hakonarson, H, Zwick, ME, McGovern, DPB & Kugathasan, S 2017, 'Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease', Gastroenterology, vol. 152, no. 1, pp. 206-217.e2. https://doi.org/10.1053/j.gastro.2016.09.032
Kulkarni, M, Leszczynska, A, Wei, G, Winkler, MA, Tang, J, Funari, VA, Deng, N, Liu, Z, Punj, V, Deng, SX, Ljubimov, AV & Saghizadeh, M 2017, 'Genome-wide analysis suggests a differential microRNA signature associated with normal and diabetic human corneal limbus', Scientific reports, vol. 7, no. 1, 3448. https://doi.org/10.1038/s41598-017-03449-7
Lugea, A, Waldron, RT, Mareninova, OA, Shalbueva, N, Deng, N, Su, HY, Thomas, DD, Jones, EK, Messenger, SW, Yang, J, Hu, C, Gukovsky, I, Liu, Z, Groblewski, GE, Gukovskaya, AS, Gorelick, FS & Pandol, SJ 2017, 'Human Pancreatic Acinar Cells: Proteomic Characterization, Physiologic Responses, and Organellar Disorders in ex Vivo Pancreatitis', American Journal of Pathology, vol. 187, no. 12, pp. 2726-2743. https://doi.org/10.1016/j.ajpath.2017.08.017
Liu, TC, Naito, T, Liu, Z, VanDussen, KL, Haritunians, T, Li, D, Endo, K, Kawai, Y, Nagasaki, M, Kinouchi, Y, McGovern, DP, Shimosegawa, T, Kakuta, Y & Stappenbeck, TS 2017, 'LRRK2 but not ATG16L1 is associated with Paneth cell defect in Japanese Crohn's disease patients', JCI Insight, vol. 2, no. 6, pp. e91917. https://doi.org/10.1172/jci.insight.91917
Xie, T, Liang, J, Geng, Y, Liu, N, Kurkciyan, A, Kulur, V, Leng, D, Deng, N, Liu, Z, Song, J, Chen, P, Noble, PW & Jiang, D 2017, 'MicroRNA-29c prevents pulmonary fibrosis by regulating epithelial cell renewal and apoptosis', American journal of respiratory cell and molecular biology, vol. 57, no. 6, pp. 721-732. https://doi.org/10.1165/rcmb.2017-0133OC
Liu, Z, Sun, F & McGovern, DP 2017, 'Sparse generalized linear model with L 0 approximation for feature selection and prediction with big omics data', BioData Mining, vol. 10, no. 1, 39. https://doi.org/10.1186/s13040-017-0159-z

Clinical Trials Search


Children (age < 18 years)
Adults (age >= 18 years)