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
  • Messenger RNA
  • Metagenomics
  • Phenotype
  • Non-Small Cell Lung Carcinoma
  • Carrier Proteins
  • Neoplastic Stem Cells
  • Population
  • MicroRNAs

Recent Publications

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
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

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

2016

Jia, D, Liu, Z, Deng, N, Tan, TZ, Huang, RYJ, Taylor-Harding, B, Cheon, DJ, Lawrenson, K, Wiedemeyer, WR, Walts, AE, Karlan, BY & Orsulic, S 2016, 'A COL11A1-correlated pan-cancer gene signature of activated fibroblasts for the prioritization of therapeutic targets', Cancer Letters, vol. 382, no. 2, pp. 203-214. https://doi.org/10.1016/j.canlet.2016.09.001
Liu, Z & Li, G 2016, 'Efficient Regularized Regression with L0 Penalty for Variable Selection and Network Construction', Computational and Mathematical Methods in Medicine, vol. 2016, 3456153. https://doi.org/10.1155/2016/3456153
Yu-Rice, Y, Jin, Y, Han, B, Qu, Y, Johnson, J, Watanabe, T, Cheng, L, Deng, N, Tanaka, H, Gao, B, Liu, Z, Sun, Z, Bose, S, Giuliano, AE & Cui, X 2016, 'FOXC1 is involved in ERα silencing by counteracting GATA3 binding and is implicated in endocrine resistance', Oncogene, vol. 35, no. 41, pp. 5400-5411. https://doi.org/10.1038/onc.2016.78
Sheyn, D, Ben-David, S, Shapiro, G, de Mel, S, Bez, M, Ornelas, L, Sahabian, A, Sareen, D, Da, X, Pelled, G, Tawackoli, W, Liu, Z, Gazit, D & Gazit, Z 2016, 'Human induced pluripotent stem cells differentiate into functional mesenchymal stem cells and repair bone defects', Stem Cells Translational Medicine, vol. 5, no. 11, pp. 1447-1460. https://doi.org/10.5966/sctm.2015-0311
Kind, T, Cho, E, Park, TD, Deng, N, Liu, Z, Lee, T, Fiehn, O & Kim, J 2016, 'Interstitial Cystitis-Associated Urinary Metabolites Identified by Mass-Spectrometry Based Metabolomics Analysis', Scientific reports, vol. 6, 39227. https://doi.org/10.1038/srep39227
Guo, W, Liu, Z & Ma, S 2016, 'Nonparametric Regularized Regression for Phenotype-Associated Taxa Selection and Network Construction with Metagenomic Count Data', Journal of Computational Biology, vol. 23, no. 11, pp. 877-890. https://doi.org/10.1089/cmb.2016.0023
Kaur, M, Panikkath, D, Yan, X, Liu, Z, Berel, D, Li, D, Vasiliauskas, EA, Ippoliti, A, Dubinsky, M, Shih, DQ, Melmed, GY, Haritunians, T, Fleshner, P, Targan, SR & McGovern, DPB 2016, 'Perianal Crohn's disease is associated with distal colonic disease, stricturing disease behavior, IBD-associated serologies and genetic variation in the JAK-STAT pathway', Inflammatory bowel diseases, vol. 22, no. 4, pp. 862-869. https://doi.org/10.1097/MIB.0000000000000705
Liu, Z, Lin, S, Deng, N, McGovern, DPB & Piantadosi, S 2016, 'Sparse Inverse Covariance Estimation with L0 Penalty for Network Construction with Omics Data', Journal of Computational Biology, vol. 23, no. 3, pp. 192-202. https://doi.org/10.1089/cmb.2015.0102
Liu, Z, Beach, JA, Agadjanian, H, Jia, D, Aspuria, PJ, Karlan, BY & Orsulic, S 2016, 'Suboptimal Cytoreduction in Ovarian Carcinoma Is Associated with Molecular Pathways Characteristic of Increased Stromal Activation', Obstetrical and Gynecological Survey, vol. 71, no. 5, pp. 285-286. https://doi.org/10.1097/OGX.0000000000000320

Clinical Trials Search


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