Dr Wu's research focuses on developing statistical methods and softwares for high throughput technologies such as DNA microarrays, second generation sequencing and high throughput screening assays. Recent topics of methodological development include methods for differential expression and normalization in RNA sequencing data, cross platform data combination of microarray and NGS, social network models in gene set analysis. Recent collaborative work involves epigenetic variations in cancer samples, transcriptomic responses in toxicity studies, differential expression in diatom using NGS, identifying biomarkers from high throughput screening.
Visit Dr. Wu's personal website for most up-to-date information.
|Huang YT, Zhang Y, Wu Z, Michaud DS. "Genotype-based gene signature of glioma risk." Neuro-Oncology, 2017.|
|Wu Z, Wu H. "Experimental Design and Power Calculation for RNA-seq Experiments." Methods in Molecular Biology, vol. 1418, 2016, pp. 379-90.|
|Mossman JA, Tross JG, Li N, Wu Z, Rand DM. "Mitochondrial-Nuclear Interactions Mediate Sex-Specific Transcriptional Profiles in Drosophila." Genetics, vol. 204, no. 2, 2016, pp. 613-630.|
|Mossman JA, Tross JG, Jourjine NA, Li N, Wu Z, Rand DM. "Mitonuclear Interactions Mediate Transcriptional Responses to Hypoxia in Drosophila." Molecular biology and evolution, vol. 34, no. 2, 2016, pp. 447-466.|
|Wu, H., Wang, C., Wu, Z. "PROPER: comprehensive power evaluation for differential expression using RNA-seq." Bioinformatics, vol. 31, no. 2, 2014, pp. 233-241.|
|Austin, Andrea, Linkletter, Crystal, Wu, Zhijin. "Covariate-defined latent space random effects model." Social Networks, vol. 35, no. 3, 2013, pp. 338-346.|
|Dunn CW, Luo X, Wu Z. "Phylogenetic analysis of gene expression." Integrative and Comparative Biology, vol. 53, no. 5, 2013, pp. 847-56.|
|Wu, H., Wang, C., Wu, Z. "A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data." Biostatistics, vol. 14, no. 2, 2012, pp. 232-243.|
|Campion SN, Catlin N, Houseman EA, Hensley J, Sui Y, Gaido KW, Wu Z, Boekelheide K. "Molecular alterations underlying the enhanced disruption of spermatogenesis by 2,5-hexanedione and carbendazim co-exposure." Reproductive toxicology (Elmsford, N.Y.), vol. 33, no. 3, 2012, pp. 382-9.|
|Hansen KD, Irizarry RA, Wu Z. "Removing technical variability in RNA-seq data using conditional quantile normalization." Biostatistics, vol. 13, no. 2, 2012, pp. 204-16.|
|Delong AK, Wu M, Bennett D, Parkin N, Wu Z, Hogan JW, Kantor R. "Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase." AIDS Research and Human Retroviruses, vol. 28, no. 8, 2012, pp. 894-901.|
|Dyhrman, Sonya T., Jenkins, Bethany D., Rynearson, Tatiana A., Saito, Mak A., Mercier, Melissa L., Alexander, Harriet, Whitney, LeAnn P., Drzewianowski, Andrea, Bulygin, Vladimir V., Bertrand, Erin M., Wu, Zhijin, Benitez-Nelson, Claudia, Heithoff, Abigail. "The Transcriptome and Proteome of the Diatom Thalassiosira pseudonana Reveal a Diverse Phosphorus Stress Response." PLoS ONE, vol. 7, no. 3, 2012, pp. e33768.|
|Li, Xue, Wu, Zhijin, Chakravarthy, Vasu D., Wu, Zhiqiang. "A Low-Complexity Approximation to Lognormal Sum Distributions via Transformed Log Skew Normal Distribution." IEEE Trans. Veh. Technol., vol. 60, no. 8, 2011, pp. 4040-4045.|
|Aryee MJ, Wu Z, Ladd-Acosta C, Herb B, Feinberg AP, Yegnasubramanian S, Irizarry RA. "Accurate genome-scale percentage DNA methylation estimates from microarray data." Biostatistics, vol. 12, no. 2, 2011, pp. 197-210.|
|Gong J, Campos H, McGarvey S, Wu Z, Goldberg R, Baylin A. "Adipose tissue palmitoleic acid and obesity in humans: does it behave as a lipokine?." The American journal of clinical nutrition, vol. 93, no. 1, 2011, pp. 186-91.|
|Yegnasubramanian S, Wu Z, Haffner MC, Esopi D, Aryee MJ, Badrinath R, He TL, Morgan JD, Carvalho B, Zheng Q, De Marzo AM, Irizarry RA, Nelson WG. "Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences." BMC genomics, vol. 12, 2011, pp. 313.|
|Gong J, Campos H, McGarvey S, Wu Z, Goldberg R, Baylin A. "Genetic variation in stearoyl-CoA desaturase 1 is associated with metabolic syndrome prevalence in Costa Rican adults." Journal of Nutrition, vol. 141, no. 12, 2011, pp. 2211-8.|
|Hansen KD, Wu Z, Irizarry RA, Leek JT. "Sequencing technology does not eliminate biological variability." Nat Biotechnol, vol. 29, no. 7, 2011, pp. 572-3.|
|Ghosh M, Fahey JV, Shen Z, Lahey T, Cu-Uvin S, Wu Z, Mayer K, Wright PF, Kappes JC, Ochsenbauer C, Wira CR. "Anti-HIV Activity in Cervical-Vaginal Secretions from HIV-Positive and -Negative Women Correlate with Innate Antimicrobial Levels and IgG Antibodies." PLoS ONE, vol. 5, no. 6, 2010, pp. e11366.|
|Wu Z, Jenkins BD, Rynearson TA, Dyhrman ST, Saito MA, Mercier M, Whitney LP. "Empirical bayes analysis of sequencing-based transcriptional profiling without replicates." BMC Bioinformatics, vol. 11, 2010, pp. 564.|
|Wu Z, Wu Z. "Exploration, visualization, and preprocessing of high-dimensional data." Methods in Molecular Biology, vol. 620, 2010, pp. 267-84.|
|FAGHIRI, Z., SANTIAGO, R. BONILLA, WU, Z., WIDMER, G. "High-throughput screening in suboptimal growth conditions identifies agonists of Giardia lamblia proliferation." Parasitology, vol. 138, no. 02, 2010, pp. 194-200.|
|Miselis NR, Lau BW, Wu Z, Kane AB. "Kinetics of host cell recruitment during dissemination of diffuse malignant peritoneal mesothelioma." Cancer Microenvironment, vol. 4, no. 1, 2010, pp. 39-50.|
|Wu Z, Aryee MJ. "Subset quantile normalization using negative control features." Journal of Computational Biology, vol. 17, no. 10, 2010, pp. 1385-95.|
|Campion SN, Houseman EA, Sandrof MA, Hensley JB, Sui Y, Gaido KW, Wu Z, Boekelheide K. "Suppression of radiation-induced testicular germ cell apoptosis by 2,5-hexanedione pretreatment. II. Gene array analysis reveals adaptive changes in cell cycle and cell death pathways." Toxicological Sciences, vol. 117, no. 2, 2010, pp. 457-65.|
|Wu, Zhijin, Li, Xue, Husnay, Robert, Chakravarthy, Vasu, Wang, Bin, Wu, Zhiqiang. "A Novel Highly Accurate Log Skew Normal Approximation Method to Lognormal Sum Distributions." 2009 IEEE Wireless Communications and Networking Conference, 2009.|
|Wu Z. "A review of statistical methods for preprocessing oligonucleotide microarrays." Statistical methods in medical research, vol. 18, no. 6, 2009, pp. 533-41.|
|Sui Y, Zhao X, Speed TP, Wu Z. "Background adjustment for DNA microarrays using a database of microarray experiments." Journal of Computational Biology, vol. 16, no. 11, 2009, pp. 1501-15.|
|Ghosh, M., Fahey, J.V., Shen, Z., Cu-Uvin, S., Mayer, K., Wu, Z., Kappes, J., Ochsenbauer-Jambor, C., Wright, P.F., Wira, C.R. "Cervical-vaginal lavages from HIV positive- and HIV negative-women contain immune factors that have intrinsic anti-HIV activity." Journal of Reproductive Immunology, vol. 81, no. 2, 2009, pp. 172-173.|
|Paruthiyil, Sreenivasan, Cvoro, Aleksandra, Zhao, Xiaoyue, Wu, Zhijin, Sui, Yunxia, Staub, Richard E., Baggett, Scott, Herber, Candice B., Griffin, Chandi, Tagliaferri, Mary, Harris, Heather A., Cohen, Isaac, Bjeldanes, Leonard F., Speed, Terence P., Schaufele, Fred, Leitman, Dale C. "Drug and Cell Type-Specific Regulation of Genes with Different Classes of Estrogen Receptor β-Selective Agonists." PLoS ONE, vol. 4, no. 7, 2009, pp. e6271.|
|Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP. "The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores." Nature Genetics, vol. 41, no. 2, 2009, pp. 178-86.|
|Yegnasubramanian, S., Haffner, M. C., Zhang, Y., Gurel, B., Cornish, T. C., Wu, Z., Irizarry, R. A., Morgan, J., Hicks, J., DeWeese, T. L., Isaacs, W. B., Bova, G. S., De Marzo, A. M., Nelson, W. G. "DNA Hypomethylation Arises Later in Prostate Cancer Progression than CpG Island Hypermethylation and Contributes to Metastatic Tumor Heterogeneity." Cancer Research, vol. 68, no. 21, 2008, pp. 8954-8967.|
|BONILLASANTIAGO, R, WU, Z, ZHANG, L, WIDMER, G. "Identification of growth inhibiting compounds in a Giardia lamblia high-throughput screen." Molecular and Biochemical Parasitology, vol. 162, no. 2, 2008, pp. 149-154.|
|Wu Z, Liu D, Sui Y. "Quantitative assessment of hit detection and confirmation in single and duplicate high-throughput screenings." Journal of biomolecular screening, vol. 13, no. 2, 2008, pp. 159-67.|
|Miselis, N. R., Wu, Z. J., Van Rooijen, N., Kane, A. B. "Targeting tumor-associated macrophages in an orthotopic murine model of diffuse malignant mesothelioma." Molecular Cancer Therapeutics, vol. 7, no. 4, 2008, pp. 788-799.|
|Miselis NR, Wu ZJ, Van Rooijen N, Kane AB. "Targeting tumor-associated macrophages in an orthotopic murine model of diffuse malignant mesothelioma." Molecular Cancer Therapeutics, vol. 7, no. 4, 2008, pp. 788-99.|
|Wu, Zhijin, Irizarry, Rafael A. "A statistical framework for the analysis of microarray probe-level data." Ann. Appl. Stat., vol. 1, no. 2, 2007, pp. 333-357.|
|Sui Y, Wu Z. "Alternative statistical parameter for high-throughput screening assay quality assessment." Journal of biomolecular screening, vol. 12, no. 2, 2007, pp. 229-34.|
|Irizarry, R. A., Wu, Z., Jaffee, H. A. "Comparison of Affymetrix GeneChip expression measures." Bioinformatics, vol. 22, no. 7, 2006, pp. 789-794.|
|Wu, Zhijin, Irizarry, Rafael A. "Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays." Journal of Computational Biology, vol. 12, no. 6, 2005, pp. 882-893.|
|Cope, L. M., Irizarry, R. A., Jaffee, H. A., Wu, Z., Speed, T. P. "A benchmark for Affymetrix GeneChip expression measures." Bioinformatics, vol. 20, no. 3, 2004, pp. 323-331.|
|Wu, Zhijin, Irizarry, Rafael A, Gentleman, Robert, Martinez-Murillo, Francisco, Spencer, Forrest. "A Model-Based Background Adjustment for Oligonucleotide Expression Arrays." Journal of the American Statistical Association, vol. 99, no. 468, 2004, pp. 909-917.|
|Wu, Zhijin, Irizarry, Rafael A. "Preprocessing of oligonucleotide array data." Nat Biotechnol, vol. 22, no. 6, 2004, pp. 656-658.|
|Wu, Zhijin, Irizarry, Rafael A. "Stochastic models inspired by hybridization theory for short oligonucleotide arrays." Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04, 2004.|
Zhijin (Jean) Wu's research interest is in statistical methodology for data from biological experiments, especially those generated from high-throughput biotechnologies.
We are developing methods for genomics in general, with a current focus on single cell gene expression (single cell RNAseq), and gene set/network analysis.
Statistical Methods for Single‐Cell RNA‐Seq
CAREER: Statistical and Computational Methods for RNA-seq data
Nuclear-mitochondrial fitness interactions in Drosophila
Li, N., McCall, M. N., & Wu, Z. (2016). Establishing Informative Prior for Gene Expression Variance from Public Databases. Statistics in Biosciences,
Wu H, Chi Wang and Wu Z (2015) PROPER: comprehensive power evaluation for differential expression using RNA‐seq. Bioinformatics 31 (2): 233‐241
Wu H, Wang C and WU Z. A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data. Biostatistics 14(2) 232-243
Hansen KD, Irizarry RA and Wu Z (2012). Removing technical variability in RNA‐seq data using conditional quantile normalization. Biostatistics,13(2):204‐216
Wu Z, Jenkins BD, Rynears TA and others (2010). Empirical Bayes Analysis of Sequencing-based Transcriptional Profiling without Replicates. BMC Bioinformatics. 11:564.
Hansen KD, Wu Z, Irizarry RA and Leek JT (2011). Sequencing technology does not eliminate biological variability. Nature Biotechnology 29:572
Wu Z and Aryee M. Subset Quantile Normalization using Negative Control Features (2010) Journal of Computational Biology, 17(10).
Aryee, M, Wu Z, Ladd-Acosta C, Herb B, Feinberg Ap, Yegnasubramanian S And Irizarry R. Accurate genome-scale percentage DNA methylation estimates from microarray data (2010). Biostatistics [PMID: 20858772]
Wu, Z and Irizarry, RA (2005) A Statistical Framework for the Analysis of Microarray Probe-Level Data
Wu, Z and Irizarry, RA, Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays . Proceedings of RECOMB 2004 To appear in JCB.
Wu, Z , Irizarry, RA, Gentleman, R, Martinez Murillo, F, Spencer, F (2004) A Model Based Background Adjustement for Oligonucleotide Expression Arrays . JASA. Vol.99, No. 468, December 2004 pp.909-917.
Irizarry, RA, Ooi, SL, Wu, Z , and Boeke, Jef (2003) Use of Mixture Models in a Microarray-Based Screening Procedure for Detecting Differentially Represented Yeast Mutants. Statistical Applications in Genetics and Molecular Biology. Vol. 2, Issue 1.
Cope, LM, Irizarry , RA, Jaffee, H, Wu , Z, Speed, TP (2003) A Benchmark for Affymetrix GeneChip Expression Measures. Bioinformatics 20: 323-331.
|2005||PhD||The Johns Hopkins University|
2005 Margaret Merrell Award for outstanding research
2011 CAREER Award, National Science Foundation
|Jamieson, Amanda||Associate Professor of Molecular Microbiology and Immunology, Pathobiology Graduate Program Co-Director|
|Neretti, Nicola||Associate Professor of Molecular Biology, Cell Biolgy, and Biochemistry|
|Padbury, James||William and Mary Oh - William and Elsa Zopfi Professor of Pediatrics for Perinatal Research|
|Rand, David||Stephen T. Olney Professor of Natural History, Professor of Biology, Chair of Ecology and Evolutionary Biology|
|Sanes, Jerome||Professor of Neuroscience, Director of MRI Facility|
American Statistical Association
|PHP 0100 - First year seminar: Statistics is everywhere|
|PHP 2520 - Statistical Inference I|
|PHP 2620 - Statistical Methods in Bioinformatics, I|
|PHP 2690A - Advanced Topics in Biostatistics|
|PHP 2950 - Doctoral Seminar in Public Health|