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CTSI Directory
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Zhenqiu Liu, Ph.D. [ Edit Your Profile ]

Email Address: zhenqiu.liu@cshs.org
Work Email Address: zhenqiu.liu@cshs.org

Work
Cedar-Sinai Medical Center Director, Biostatistics and Bioinformatics
UCLA Adjunct Associate Professor, Medicine

Education:
Degrees:
Ph.D., University of Tennessee, Knoxville, TN
M.S., University of Tennessee, Knoxville, TN
M.S., Shandong University, P.R. China
Academic Experience:
Bioinformatics Cell, USAMRMC, Frederick, MD, Bioinformatics
Ohio State University, Columbus, OH, Statistical Genetics, Bioinformatics

About

Dr. Liu is the Director of Bioinformatics and Associate Professor at the Division of Hematology/Oncology, Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center. His research interests are in the broad areas of bioinformatics, computational biology, and big data mining. Currently, his research mainly concentrates on (I) Bayesian and machine learning methods for next generation sequencing data, (II) Integrated genomic/metagenomic data mining and visualization, (III) ROC-based methods for disease diagnosis, prognosis, and biomarker identification and evaluation, and (IV) methods for pathway and network construction with multisource genomic and metagenomic data. He has also done extensive collaborative research involving laboratory investigations, biomarker evaluation, omics, and clinical and epidemiological studies. Dr. Liu’s research has been continually supported by multiple federal grants. He has also been participating in the multicenter IBD genetic consortium. His track record in bioinformatics, big data mining, and collaborative research enable him to provide strong support for the UCLA CTSI.

Publications
Huang Chengrui, Haritunians Talin, Okou David T, Cutler David J, Zwick Michael E, Taylor Kent D, Datta Lisa W, Maranville Joseph C, Liu Zhenqiu, Ellis Shannon, Chopra Pankaj, Alexander Jonathan S, Baldassano Robert N, Cross Raymond K, Dassopoulos Themistocles, Dhere Tanvi A, Duerr Richard H, Hanson John S, Hou Jason K, Hussain Sunny Z, Isaacs Kim L, Kachelries Kelly E, Kader Howard, Kappelman Michael D, Katz Jeffrey, Kellermayer Richard, Kirschner Barbara S, Kuemmerle John F, Kumar Archana, Kwon John H, Lazarev Mark, Mannon Peter, Moulton Dedrick E, Osuntokun Bankole O, Patel Ashish, Rioux John D, Rotter Jerome I, Saeed Shehzad, Scherl Ellen J, Silverberg Mark S, Silverman Ann, Targan Stephan R, Valentine John F, Wang Ming-Hsi, Simpson Claire L, Bridges S Louis, Kimberly Robert P, Rich Stephen S, Cho Judy H, Di Rienzo Anna, Kao Linda W H, McGovern Dermot P B, Brant Steven R, Kugathasan Subra, Characterization of Genetic Loci That Affect Susceptibility to Inflammatory Bowel Diseases in African Americans. Gastroenterology. 2015; 149(6): 1575-86.
Han Bingchen, Qu Ying, Jin Yanli, Yu Yi, Deng Nan, Wawrowsky Kolja, Zhang Xiao, Li Na, Bose Shikha, Wang Qiang, Sakkiah Sugunadevi, Abrol Ravinder, Jensen Tor W, Berman Benjamin P, Tanaka Hisashi, Johnson Jeffrey, Gao Bowen, Hao Jijun, Liu Zhenqiu, Buttyan Ralph, Ray Partha S, Hung Mien-Chie, Giuliano Armando E, Cui Xiaojiang, FOXC1 Activates Smoothened-Independent Hedgehog Signaling in Basal-like Breast Cancer. Cell reports. 2015; 13(5): 1046-58.
Liu Zhenqiu, Beach Jessica A, Agadjanian Hasmik, Jia Dongyu, Aspuria Paul-Joseph, Karlan Beth Y, Orsulic Sandra, Suboptimal cytoreduction in ovarian carcinoma is associated with molecular pathways characteristic of increased stromal activation. Gynecologic oncology. 2015; 149(6): .
Liu Zhenqiu, Sun Fengzhu, Braun Jonathan, McGovern Dermot P B, Piantadosi Steven, Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data. Bioinformatics (Oxford, England). 2015; 31(7): 1067-74.
Haldar Subhash, Dru Christopher, Choudhury Diptiman, Mishra Rajeev, Fernandez Ana, Biondi Shea, Liu Zhenqiu, Shimada Kenichi, Arditi Moshe, Bhowmick Neil A, Inflammation and pyroptosis mediate muscle expansion in an interleukin-1β (IL-1β)-dependent manner. The Journal of biological chemistry. 2015; 290(10): 6574-83.
Wang Wenhui, Zhou Xianghong, Liu Zhenqiu, Sun Fengzhu, Network tuned multiple rank aggregation and applications to gene ranking. BMC bioinformatics. 2015; 16 Suppl 1(10): S6.
Mannoor Kaiissar, Shen Jun, Liao Jipei, Liu Zhenqiu, Jiang Feng, Small nucleolar RNA signatures of lung tumor-initiating cells. Molecular cancer. 2014; 13(10): 104.
Mazan-Mamczarz Krystyna, Zhao X Frank, Dai Bojie, Steinhardt James J, Peroutka Raymond J, Berk Kimberly L, Landon Ari L, Sadowska Mariola, Zhang Yongqing, Lehrmann Elin, Becker Kevin G, Shaknovich Rita, Liu Zhenqiu, Gartenhaus Ronald B, Down-regulation of eIF4GII by miR-520c-3p represses diffuse large B cell lymphoma development. PLoS genetics. 2014; 10(1): e1004105.
Zhao Jun, Ma Mark Z, Ren Hening, Liu Zhenqiu, Edelman Martin J, Pan Hong, Mao Li, Anti-HDGF targets cancer and cancer stromal stem cells resistant to chemotherapy. Clinical cancer research : an official journal of the American Association for Cancer Research. 2013; 19(13): 3567-76.
Liu Zhenqiu, Chen Dechang, Sheng Li, Liu Amy Y, Class prediction and feature selection with linear optimization for metagenomic count data. PloS one. 2013; 8(3): e53253.
Seekatz Anna M, Panda Aruna, Rasko David A, Toapanta Franklin R, Eloe-Fadrosh Emiley A, Khan Abdul Q, Liu Zhenqiu, Shipley Steven T, Detolla Louis J, Sztein Marcelo B, Fraser Claire M, Differential response of the cynomolgus macaque gut microbiota to Shigella infection. PloS one. 2013; 8(6): e64212.
Zupancic Margaret L, Cantarel Brandi L, Liu Zhenqiu, Drabek Elliott F, Ryan Kathleen A, Cirimotich Shana, Jones Cheron, Knight Rob, Walters William A, Knights Daniel, Mongodin Emmanuel F, Horenstein Richard B, Mitchell Braxton D, Steinle Nanette, Snitker Soren, Shuldiner Alan R, Fraser Claire M, Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome. PloS one. 2012; 7(8): e43052.
Younis Rania H, Cao Wei, Lin Ruxian, Xia Ronghui, Liu Zhenqiu, Edelman Martin J, Mei Yuping, Mao Li, Ren Hening, CDC25A(Q110del): a novel cell division cycle 25A isoform aberrantly expressed in non-small cell lung cancer. PloS one. 2012; 7(10): e46464.
Liu Zhenqiu, Bensmail Halima, Tan Ming, Efficient feature selection and multiclass classification with integrated instance and model based learning. Evolutionary bioinformatics online. 2012; 8(3): 197-205.
Scheibner Kara A, Teaboldt Brianne, Hauer Mary Claire, Chen Xiaochun, Cherukuri Srujana, Guo Yin, Kelley Shannon M, Liu Zhenqiu, Baer Maria R, Heimfeld Shelly, Civin Curt I, MiR-27a functions as a tumor suppressor in acute leukemia by regulating 14-3-3θ. PloS one. 2012; 7(12): e50895.
Hsiao William Wl, Li Kevin L, Liu Zhenqiu, Jones Cheron, Fraser-Liggett Claire M, Fouad Ashraf F, Microbial transformation from normal oral microbiota to acute endodontic infections. BMC genomics. 2012; 13(3): 345.
Liu Zhenqiu, Hsiao William, Cantarel Brandi L, Drábek Elliott Franco, Fraser-Liggett Claire, Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. Bioinformatics (Oxford, England). 2011; 27(23): 3242-9.
Tian Guo-Liang, Tang Man-Lai, Zhenqiu Liu Man-Lai, Ming Tan Man-Lai, Tang Nian-Sheng, Sample size determination for the non-randomised triangular model for sensitive questions in a survey. Statistical methods in medical research. 2011; 20(3): 159-73.
Yu Lei, Todd Nevins W, Xing Lingxiao, Xie Ying, Zhang Howard, Liu Zhenqiu, Fang Hongbin, Zhang Jian, Katz Ruth L, Jiang Feng, Early detection of lung adenocarcinoma in sputum by a panel of microRNA markers. International journal of cancer. Journal international du cancer. 2010; 127(12): 2870-8.
Liao Jipei, Yu Lei, Mei Yuping, Guarnera Maria, Shen Jun, Li Ruiyun, Liu Zhenqiu, Jiang Feng, Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer. Molecular cancer. 2010; 9(12): 198.
Liu Zhenqiu, Magder Laurence S, Hyslop Terry, Mao Li, Survival associated pathway identification with group Lp penalized global AUC maximization. Algorithms for molecular biology : AMB. 2010; 5(12): 30.
Liu Zhenqiu, Chen Dechang, Tan Ming, Jiang Feng, Gartenhaus Ronald B, Kernel based methods for accelerated failure time model with ultra-high dimensional data. BMC bioinformatics. 2010; 11(3): 606.
Zhou Hua, Mazan-Mamczarz Krystyna, Martindale Jennifer L, Barker Andrew, Liu Zhenqiu, Gorospe Myriam, Leedman Peter J, Gartenhaus Ronald B, Hamburger Anne W, Zhang Yuexing, Post-transcriptional regulation of androgen receptor mRNA by an ErbB3 binding protein 1 in prostate cancer. Nucleic acids research. 2010; 38(11): 3619-31.
Sun Ying, Wang Lin, Jiang Minghu, Huang Juxiang, Liu Zhenqiu, Wolfl Stefan, Secreted phosphoprotein 1 upstream invasive network construction and analysis of lung adenocarcinoma compared with human normal adjacent tissues by integrative biocomputation. Cell biochemistry and biophysics. 2010; 56(2-3): 59-71.
Li Ting, Su Yun, Mei Yuping, Leng Qixin, Leng Bingjie, Liu Zhenqiu, Stass Sanford A, Jiang Feng, ALDH1A1 is a marker for malignant prostate stem cells and predictor of prostate cancer patients' outcome. Laboratory investigation; a journal of technical methods and pathology. 2010; 90(2): 234-44.
Su Yun, Qiu Qi, Zhang Xingqiao, Jiang Zhengran, Leng Qixin, Liu Zhenqiu, Stass Sanford A, Jiang Feng, Aldehyde dehydrogenase 1 A1-positive cell population is enriched in tumor-initiating cells and associated with progression of bladder cancer. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2010; 19(2): 327-37.
Xie Ying, Todd Nevins W, Liu Zhenqiu, Zhan Min, Fang Hongbin, Peng Hong, Alattar Mohammed, Deepak Janaki, Stass Sanford A, Jiang Feng, Altered miRNA expression in sputum for diagnosis of non-small cell lung cancer. Lung cancer (Amsterdam, Netherlands). 2010; 67(2): 170-6.
Liu Zhenqiu, Chen Dechang, Tian Guoliang, Tang Man-Lai, Tan Ming, Sheng Li, Efficient support vector machine method for survival prediction with SEER data. Advances in experimental medicine and biology. 2010; 680(2): 11-8.
Zhang Yuexing, Ali Tehmina Z, Zhou Hua, D'Souza David R, Lu Yan, Jaffe Jonathan, Liu Zhenqiu, Passaniti Antonino, Hamburger Anne W, ErbB3 binding protein 1 represses metastasis-promoting gene anterior gradient protein 2 in prostate cancer. Cancer research. 2010; 70(1): 240-8.
Liu Zhenqiu, Lin Shili, Tan Ming T, Sparse support vector machines with Lp penalty for biomarker identification. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM. 2010; 7(1): 100-7.
Liu Zhenqiu, Gartenhaus Ronald B, Chen Xue-Wen, Howell Charles D, Tan Ming, Survival prediction and gene identification with penalized global AUC maximization. Journal of computational biology : a journal of computational molecular cell biology. 2009; 16(12): 1661-70.
Jiang Feng, Todd Nevins W, Qiu Qi, Liu Zhenqiu, Katz Ruth L, Stass Sanford A, Combined genetic analysis of sputum and computed tomography for noninvasive diagnosis of non-small-cell lung cancer. Lung cancer (Amsterdam, Netherlands). 2009; 66(1): 58-63.
Jiang Feng, Qiu Qi, Khanna Abha, Todd Nevins W, Deepak Janaki, Xing Lingxiao, Wang Huijun, Liu Zhenqiu, Su Yun, Stass Sanford A, Katz Ruth L, Aldehyde dehydrogenase 1 is a tumor stem cell-associated marker in lung cancer. Molecular cancer research : MCR. 2009; 7(3): 330-8.
Liu Zhenqiu, Chen Dechang, Chen Xuewen, Jia Haomiao, Computational data mining in cancer bioinformatics and cancer epidemiology. Journal of biomedicine & biotechnology. 2009; 2009(4): 582697.
Liu Zhenqiu, Jiang Feng, Gene identification and survival prediction with Lp Cox regression and novel similarity measure. International journal of data mining and bioinformatics. 2009; 3(4): 398-408.
Liu Zhenqiu, Tan Ming, Jiang Feng, Regularized F-measure maximization for feature selection and classification. Journal of biomedicine & biotechnology. 2009; 2009(4): 617946.
Liu Zhenqiu, Gartenhaus Ronald B, Tan Ming, Jiang Feng, Jiao Xiaoli, Gene and pathway identification with Lp penalized Bayesian logistic regression. BMC bioinformatics. 2008; 9(4): 412.
Zhang Yuexing, Linn Douglas, Liu Zhenqiu, Melamed Jonathan, Tavora Fabio, Young Charles Y, Burger Angelika M, Hamburger Anne W, EBP1, an ErbB3-binding protein, is decreased in prostate cancer and implicated in hormone resistance. Molecular cancer therapeutics. 2008; 7(10): 3176-86.
Liu Zhenqiu, Chen Dechang, Tian Jianjun Paul, Classification of proteomic data with multiclass Logistic Partial Least Squares algorithm. International journal of bioinformatics research and applications. 2008; 4(1): 1-10.
Liu Zhenqiu, Guo Zhongmin, Tan Ming, Constructing tumor progression pathways and biomarker discovery with fuzzy kernel kmeans and DNA methylation data. Cancer informatics. 2008; 6(4): 1-7.
Qiu Qi, Todd Nevins W, Li Ruiyun, Peng Hong, Liu Zhenqiu, Yfantis Harris G, Katz Ruth L, Stass Sanford A, Jiang Feng, Magnetic enrichment of bronchial epithelial cells from sputum for lung cancer diagnosis. Cancer. 2008; 114(4): 275-83.
Zhang Yuexing, Lu Yan, Zhou Hua, Lee Myounghee, Liu Zhenqiu, Hassel Bret A, Hamburger Anne W, Alterations in cell growth and signaling in ErbB3 binding protein-1 (Ebp1) deficient mice. BMC cell biology. 2008; 9(4): 69.
Wang Lizhong, Lin Shili, Rammohan Kottil W, Liu Zhenqiu, Liu Jin-qing, Liu Run-hua, Guinther Nikki, Lima Judy, Zhou Qunmin, Wang Tony, Zheng Xincheng, Birmingham Dan J, Rovin Brad H, Hebert Lee A, Wu Yeeling, Lynn D Joanne, Cooke Glenn, Yu C Yung, Zheng Pan, Liu Yang, A dinucleotide deletion in CD24 confers protection against autoimmune diseases. PLoS genetics. 2007; 3(4): e49.
Liu Zhenqiu, Jiang Feng, Tian Guoliang, Wang Suna, Sato Fumiaki, Meltzer Stephen J, Tan Ming, Sparse logistic regression with Lp penalty for biomarker identification. Statistical applications in genetics and molecular biology. 2007; 6(2): Article6.
Chen Xue-Wen, Gerlach Byron, Chen Dechang, Liu Zhenqiu, Structural Risk Minimisation based gene expression profiling analysis. International journal of bioinformatics research and applications. 2007; 3(2): 153-69.
Liu Zhenqiu, Lin Shili, Tan Ming, Genome-wide tagging SNPs with entropy-based Monte Carlo method. Journal of computational biology : a journal of computational molecular cell biology. 2006; 13(9): 1606-14.
Yu Chenggang, Liu Zhenqiu, McKenna Thomas, Reisner Andrew T, Reifman Jaques, A method for automatic identification of reliable heart rates calculated from ECG and PPG waveforms. Journal of the American Medical Informatics Association : JAMIA. 2006; 13(3): 309-20.
Li Ruiyun, Liu Zhenqiu, Fan Tao, Jiang Feng, A novel multiple FISH array for the detection of genetic aberrations in cancer. Laboratory investigation; a journal of technical methods and pathology. 2006; 86(6): 619-27.
Liu Zhenqiu, Lin Shili, Multilocus LD measure and tagging SNP selection with generalized mutual information. Genetic epidemiology. 2005; 29(4): 353-64.
Lin Shili, Ding Jie, Dong Crystal, Liu Zhenqiu, Ma Zhenxu J, Wan Shuyan, Xu Yan, Comparisons of methods for linkage analysis and haplotype reconstruction using extended pedigree data. BMC genetics. 2005; 6 Suppl 1(3): S76.
Liu Zhenqiu, Chen Dechang, Bensmail Halima, Gene expression data classification with Kernel principal component analysis. Journal of biomedicine & biotechnology. 2005; 2005(2): 155-9.
Chen Dechang, Liu Zhenqiu, Ma Xiaobin, Hua Dong, Selecting genes by test statistics. Journal of biomedicine & biotechnology. 2005; 2005(2): 132-8.
Liu Zhenqiu, Chen Dechang, Bensmail Halima, Xu Ying, Clustering gene expression data with kernel principal components. Journal of bioinformatics and computational biology. 2005; 3(2): 303-16.
Liu Zhenqiu, Chen Dechang, Xu Ying, Liu Jian, Logistic support vector machines and their application to gene expression data. International journal of bioinformatics research and applications. 2005; 1(2): 169-82.