Selected Publications |
Peer-reviewed Publications
Book/Book Chapters
- R. Du, Zhide Fang* (2014). Analysis of metagenomic data. In: Statistical Analysis of Next Generation Sequencing Data, Daniel Nettleton and Somnath Datta (eds), Springer, 335-353. (*Corresponding author)
Big Data Algorithms
- Z. Chen, Zhide Fang, V. Sheng, J. Zhao, W. Fan, A. Edwards, K. Zhang (2021). Adaptive robust local online density estimation for streaming data. International Journal of Machine Learning & Cybernetics, February, 2021, doi: https://doi.org/10.1007/s13042-021-01275-y.
- Z. Chen, Zhide Fang, W. Fan, A. Edwards, K. Zhang (2018). Online Density Estimation over Streaming Data: A Local Adaptive Solution. IEEE International Conference on Big Data, Seattle, USA, Dec. 10-13. Accepted regular paper
- Z. Chen, Zhide Fang, J. Zhao, W. Fan, A. Edwards, K. Zhang (2017). An Effective Framework for Cost-sensitive Sparse Online Learning. SIAM Data Mining 2017, 759 - 767. PubMed PMID: 29861512; PubMed Central PMCID: PMC5978435.
Bioinformatics/Biostatistics
- S. Yang, K. Zhang, Zhide Fang* (2020). Robust RNA-seq data analysis using an integrated method of ROC curve and Kolmogorov–Smirnov test. Communications in Statistics – Simulation and Computation, doi: https://doi.org/10.1080/03610918.2020.1837165. (*Corresponding author)
- H. Lin, X. Wang, …, Zhide Fang, …, J.Y. Park, The Practical Consortium (2021). Alcohol intake and alcohol-SNP interactions associated with prostate cancer aggressiveness. Journal of Clinical Medicine, 10 (3): 553. Doi: https://doi.org/10.3390/jcm10030553.
- M-A.I. Kautzmann, W.C. Gordon, B. Jun, K.V. Do, B.J. Matherne, Zhide Fang, N.G. Bazan (2020). Membrane‐type frizzled‐related protein regulates lipidome and transcription for photoreceptor function. The FASEB Journal, 01/2020, 34(1): 912 – 929. PMID: 31914617, PMCID: PMC6956729. doi: https://doi.org/10.1096/fj.201902359R.
- M. Heath, R. Buckley, Z. Gerber, P. Davis, L. Linneman, Q. Gong, B. Barkemeyer, Zhide Fang, M. Good, D. Fenn, S. Kim (2019). Association of intestinal alkaline phosphatase with necrotizing enterocolitis among premature infants. The Journal of American Medical Association (JAMA) Network Open, 11/2019; 2(11): e1914996. PMID: 31702803, PMCID: PMC6902776. doi:10.1001/jamanetworkopen.2019.14996.
- S. Sinha, H. Brown, J. Tabak, Zhide Fang, M. Couetoux du Tertre, S. McNamara, K. Gambaro, G. Batist, JF. Buell (2019). Multiplexed real-time polymerase chain reaction cell-free DNA assay as a potential method to monitor stage IV colorectal cancer. Surgery, October 2019, 166 (4): 534 - 539. PMID 31378479. DOI: https://doi.org/10.1016/j.surg.2019.06.004.
- H. Lin, C.Y. Callan, Zhide Fang, H.Y. Tung, J.Y. Park (2019). Interactions of PVT1 and CASC11 on Prostate Cancer Risk in African Americans. Cancer Epidemiology, Biomarkers & Prevention, June 1, 2019, 28(6): 1067 – 1075. DOI: 10.1158/1055-9965.EPI-18-1092. PMID: 30914434.
- A.M. DiGiorgio, P.V. Mummaneni, J.L Fisher, A.G. Podet, C.L. Crutcher II, M.S. Virk, Zhide Fang, J.D. Wilson, G.C. Tender, F. Culicchia (2019). Change in policy allowing overlapping surgery decreases length of stay in an academic, safety- net hospital. Operative Neurosurgery, 2019 Mar 28; doi: 10.1093/ons/opz009. PubMed PMID: 30919890.
- W.J. Lukiw, T.P.A. Kruck, M.E. Percy, A. I. Pogue, P, N. Alexandrov, W. J. Walsh, N. M. Sharfman, V. R. Jaber, Y. Zhao, W. Li, C. Bergeron, F. Culicchia, Zhide Fang, D. R.C. McLachla (2019). Aluminum in neurological disease – a 36 year multicenter study. Journal of Alzheimers Disease & Parkinsonism. 2019, 8(6). doi: 10.4172/2161-0460.1000457. Epub 2018 Nov 29. PubMed PMID: 31179161; PubMed Central PMCID: PMC6550484.
- R. Du, L. An, Zhide Fang* (2018). Performance evaluation of normalization approaches for metagenomic compositional data on differential abundance analysis. In: Frontiers of Biostatistics and Bioinformatics (eds: Y. Zhang and D.G. Chen), Springer, to appear. (*Corresponding author)
- R. Du, Zhide Fang* (2018). Statistical correction for functional metagenomic profiling of a microbial community with short NGS reads. Journal of Applied Statistics, 45(14): 2521 - 2535.(*corresponding author)
- T.F. Ferguson, X. Wang, L. Dyer, S. Straif-Bourgeois, D. Rojas, P. Maloney, Zhide Fang, L. Besch (2018). Increasing CVD and CVD risk among PLWHA in Louisiana 2002-2012. Circulation, 2018, 137(Suppl_1): AP187.
- H. Bazan, Y. Lu, B. Jun, Zhide Fang, T.C. Woods, S. Hong (2017). Circulating inflammation-resolving lipid mediators mediators RvD1 and DHA are decreased in patients with acutely symptomatic carotid disease. Prostaglandins, Leukotrienes and Essential Fatty Acids (PLEFA), 125: 43 – 47. PubMed PMID: 28987721; PubMed Central PMCID: PMC5909403.
- S. Yang, Zhide Fang* (2017). Beta approximation of ratio distribution and its application to next generation sequencing read counts. Journal of Applied Statistics, 44(1): 57 - 70. PubMed PMID: 29456282; PubMed Central PMCID: PMC5812702 (*Corresponding author)
- A. E. Musto, R. F. Rosencrans, C. P. Walker, S. Bhattacharjee, Zhide Fang, C. M. Raulji, W. C. Gordon, N. G. Bazan (2016). Corrigendum: Dysfunctional epileptic neuronal circuits and dysmorphic dendritic spines are mitigated by platelet-activating factor receptor antagonism. Scientific Reports, 6: 32253.
- C.D. Kim, R.E. Reed, M.A. Juncker, Zhide Fang, S.D. Desai (2017). Evidence for the Deregulation of Protein Turnover Pathways in Atm-deficient Mouse Cerebellum: An Organotypic Study. Journal of Neuropathology and Experimental Neurology, 2017 76(7): 578 - 584.
- H. Lin, D. Chen, ..., Zhide Fang, ..., J. Park (2017). SNP Interaction Pattern Identifier (SIPI): An Intensive Search for SNP-SNP Interaction Patterns. Bioinformatics, 33(6): 822 - 833.
- A Musto, R Rosencrans, C Walker, S Bhattacharjee, C Raulji, L Belayev, Zhide Fang, WC Gordon, N Bazan (2016). Dysfunctional epileptic neuronal circuits and dysmorphic dendritic spines are mitigated by platelet-activating factor receptor antagonism. Scientific Reports, 6: 30289.
- S. Yang, D. Mercante, K. Zhang, Zhide Fang* (2016). An Integrated Approach for RNA-seq Data Normalization. Cancer Informatics, 15: 129 - 141. (*Corresponding author)
- W. Zhang, A. Edwards, Zhide Fang, E. Flemington, K. Zhang (2016). Integrative Genomics and Transcriptomics Analysis Reveals Potential Mechanisms for Favorable Prognosis of Patients with HPV-Positive Head and Neck Carcinomas. Scientific Reports, 6: 24927.
- L. Peres, E. Trapido, A. Rung, D. Harrington, E. Oral, Zhide Fang, E. Fontham, E. Peters (2016). The Deepwater Horizon Oil Spill and Physical Health among Adult Women in Southern Louisiana: The Women and Their Children’s Health (WaTCH) Study. Environmental Health Perspectives, 124(8): 1208 - 1213. DOI:10.1289/ehp.1510348.
- T. Henegan, B. Stefanska, Zhide Fang, A. Navard, J. Ye, N. Lenard, P. Devarshi (2015). Sodium butyrate epigenetically modulates high fat diet-induced skeletal muscle mitochondrial adaptation, obesity and insulin resistance through nucleosome positioning. British Journal of Pharmacology, 172(11): 2782–2798.
- R. Du, D. Mercante, L. An, Zhide Fang* (2014). A statistical approach to correcting cross-annotations in a metagenomic functional profile generated by short reads. Journal of Biometrics & Biostatistics, 5:208. (*Corresponding author)
- L. Fu, Z. Shi, G. Luo, W.Tu, X. Wang, ZhideFang, X. Li (2014). Multiple microRNAs regulate human FOXP2 gene expression by targeting sequences in its 3′ untranslated region. Molecular Brain, 2014, 7: 71.
- S. Yang, X. Cui, Zhide Fang* (2014). BCRgt: A Bayesian Cluster Regression-based Genotyping algorithm for the samples with Copy Number Alterations. BMC Bioinformatics, 2014, 15: 74. (*Corresponding author). Highly accessed.
- Z. Elmageed, Y. Yang, R. Thomas, K. Moparty, M. Ranjan, D. Mondal, K. Moroz, Zhide Fang, B. Rezk, S. Sikka1, O. Sartor, A. Abdel-Mageed (2014). Neoplastic Reprogramming of Patient-Derived Adipose Stem Cells by Prostate Cancer Cell-Associated Exosomes. Stem Cells, 32(4): 983-997.
- W. Zhang, A. Edwards, Zhide Fang, P. Deininger, K. Zhang (2013). Inferring the expression variability of human transposable element-derived exons by linear model analysis of deep RNA sequencing data. BMC Genomics, 14: 584.
- R. Du, D. Mercante, Zhide Fang* (2013). An Artificial Functional Family Filter in Homolog Searching in Next-generation Sequencing Metagenomics. PLoS ONE, 8(3): e58669. (*Corresponding author)
- Z. Shi, G. Luo, L. Fu, Zhide Fang, X. Wang, X. Li (2013). miR-9 and miR-140-5p Target FoxP2 and Are Regulated by the Social Context of Song Behavior in Zebra Finches. Journal of Neuroscience, 33(42): 16510 - 16521.
- Z. Elmageed, K. Moroz, S. Srivastav, Zhide Fang, B. Crawford, K. Moparty, R. Thomas and A. Abdel-Mageed (2013). High Circulating Estrogens and Selective Expression of ERß in Prostate Tumors of Americans: Implications for Racial Disparity of Prostate Cancer. Carcinogenesis, 34(9): 2017 - 2023.
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Zhide Fang
, R. Du, A. Edwards, E. Flemington, K. Zhang (2013). The sequence structures of human microRNA molecules and their implications. PLoS ONE, 8(1): e54215.
- S. Yang, S. Pounds, K. Zhang, Zhide Fang* (2013). PAIR: Paired Allelic log-Intensity-Ratio based normalization method for SNP-CGH arrays. Bioinformatics, 29(3): 299 - 307. (*Corresponding author)
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Zhide Fang
, J. Martin, Z. Wang (2012). Statistical methods for identifying differentially expressed genes in RNA-Seq experiments. Cell & Bioscience, 2: 26. Highly accessed.
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Zhide Fang
, R. Du, X. Cui (2012). Uniform Approximation Is More Appropriate for Wilcoxon Rank-Sum Test in Gene Set Analysis. PLoS ONE, 7(2): e31505.
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Zhide Fang, X. Cui (2011). Design and Validation Issues in RNA-seq Experiments. Briefings in Bioinformatics, 12(3): 280 - 287.
- L. Gao*, Zhide Fang*, K. Zhang, D. Zhi, X. Cui (2011). Length Bias Correction for RNA-seq Data in Gene Set Analyses. Bioinformatics,27(5): 662 - 669. (*Co-first author)
- J. Martin, V. Bruno, Zhide Fang, X. Meng, M. Blow, T. Zhang, G. Sherlock, M. Snyder, Z. Wang (2010). Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics, 11: 663.
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Zhide Fang
, X. Li, L. Xu (2010). A Multivariate Method for Normalization in Affymetrix Oligonucleotide Microarray Experiments. Journal of Data Science, 8(4): 505 - 519.
- C. Conrad, J. Zhu, C. Conrad, D. Schoenfeld, Zhide Fang, M. Ingelsson, S. Stamm, G. Church, B. Hyman (2007). Single Molecule Exon Profiling of Tau Gene Expression in Alzheimer's Disease, Journal of Neurochemistry, 103(3): 1228 - 1236.
Statistical Theory
- Y. Zhai, Zhide Fang* (2018). Locally Optimal Designs for Some Binary Dose-Response Models. Canadian Journal of Statistics, 46(2): 336 - 354. (*corresponding author)
- Y. Zhai, Zhide Fang* (2017). Locally Optimal Designs for Some Dose Response Models with Continuous Endpoints. Communications in Statistics – Theory and Methods, 47(16): 3803 - 3819. (*Corresponding author)
- J. Maronge, Y. Zhai, D. Wiens, Zhide Fang* (2017). Optimal Designs for Spline Wavelet Regression Models. Journal of Statistical Planning and Inference, 184: 94 - 104. PubMed PMID: 29033492; PubMed Central PMCID: PMC5638501 (*Corresponding author)
- S. Zhang, Zhide Fang, G. Liu (2013). Characterization of admissible linear estimators in multivariate linear model with respect to inequality constraints under matrix loss function. Communications in Statistics - Theory and Methods, 42(15): 2837 - 2850.
- Q. Yu, B. Li, Zhide Fang, L. Peng (2012). Model Guided Adaptive Design and Analysis in Computer Experiment. Statistical Analysis and Data Mining, 5(5): 399 - 409.
- S Zhang, Zhide Fang, H Qin, L Han (2011). Characterization of admissible linear estimators in the growth curve model with respect to inequality constraints. Journal of Korean Statistical Association, 40(2): 173 – 179.
- Q. Yu, B. Li, Zhide Fang, L. Peng (2010). An Adaptive Sampling Scheme Guided by BART – With an Application to Predict Processor Performance. Canadian Journal of Statistics, 38(1): 136 - 152.
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Zhide Fang
(2006), Some Robust Designs for Polynomial Regression Models, Canadian Journal of Statistics, 34(4): 623 - 638.
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Zhide Fang
, D. Wiens, Z. Wu (2006), Locally D-Optimal Designs for Multi-Stage Models and Heteroscedastic Polynomial Regression Models., Journal of Statistical Planning and Inference, 136(11): 4059 - 4070.
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Zhide Fang, D. Wiens (2004). Bayesian minimally supported D-optimal designs for an exponential regression models., Communication in Statistics-Theory and Methods, 33(5): 1187 - 1204.
- M.J. Zuo, Zhide Fang, J. Huang, X. Xu (2003). Performance Evaluation of Decreasing Multi-State Consecutive k-out-of-n: G Systems,, International Journal of Reliability, Quality and Safety Engineering, special issue on Multi-state Systems Reliability, 10(3): 345 - 358.
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Zhide Fang
(2003). Extrapolation Designs with Constraints, Canadian Journal of Statistics, 31(4): 457 - 468.
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Zhide Fang
, D. Wiens (2003), Robust Regression Designs for Approximate Polynomial Model, Journal of Statistical Planning and Inference, 117(4): 305 - 321.
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Zhide Fang
(2003), D-Optimal Designs for Weighted Polynomial Regression., Statistics & Probability Letter, 63(2): 205 - 213.
- J. Huang, M.J. Zuo, Zhide Fang(2003). Multi-State Consecutive k-out-of n Systems,, IIE Transactions on Quality and Reliability Engineering, 35: 527 - 534.
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Zhide Fang
(2002). D-Optimal Designs for Polynomial Regression Through Origin, Statistics & Probability Letter, 57(4): 343 - 351.
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Zhide Fang
(2000). Robust extrapolation designs for biased polynomial models., Journal of Statistical Planning and Inference, 87: 135 - 147.
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Zhide Fang
, D. Wiens (2000). Integer-valued, minimax robust designs for estimation and extrapolation in heteroscedastic, approximately linear models, Journal of American Statistical Association,95(451): 807 - 818.
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Zhide Fang
, D. Wiens (1999). Robust extrapolation designs and weights for biased regression models with heteroscedastic errors. Canadian Journal of Statistics, 27(4): 751 - 770.
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