• Liu, K., Ye, J., Yang, Y., Shen, L., Jiang, H. (2016) A Unified Model for Differential Expression Analysis of RNA-seq Data via L1-Penalized Linear Regression
    arXiv preprint. arXiv:1610.04078 [arXiv]

  • Liu, T., Jiang, H. (2016) Minimizing Sum of Truncated Convex Functions and its Applications
    arXiv preprint. arXiv:1608.00236 [arXiv]

  • Shi, Y., Kang, H., Lee, J., Jiang, H. (2016) Efficiently estimating small p-values in permutation tests using importance sampling and cross-entropy method
    arXiv preprint. arXiv:1608.00053 [arXiv]

  • Segal, B., Braun, T., Elliott, M., Jiang, H. (2016) Fast Approximation of Small p-values in Permutation Tests by Partitioning the Permutation Space
    arXiv preprint. arXiv:1605.03992 [arXiv]

  • Li, J., Jiang, H. (2014) Robust estimation of isoform expression with RNA-Seq data
    arXiv preprint. arXiv:1410.6560 [arXiv]

Peer Reviewed Publications

  • Jiang, H. Zhan, T. (2016) Unit-Free and Robust Detection of Differential Expression from RNA-Seq Data
    Statistics in Biosciences, DOI 10.1007/s12561-016-9182-8. [online][arXiv][code]

  • Jiang, H., Mu, J. C., Yang, K., Du, C., Lu, L., Wong, W. H. (2016) Computational Aspects of Optional Polya Tree
    Journal of Computational and Graphical Statistics, 25 (1): 301-320. [online][arXiv][software]

  • Bai, Y., Ding, L., Baker, S., Bai, J. M., Rath, E., Jiang, F., Wu, J., Jiang, H., Stuart, G. (2016) Dissecting the biological relationship between TCGA miRNAs and mRNAs sequencing data using MMiRNA-Viewer
    BMC Bioinformatics, 17 (Suppl 13): 336. [online]

  • Shukla, S., Evans, J. R., Malik, R., Feng, F. Y., Dhanasekaran, S. M., Cao, X., Chen, G., Beer, D. G., Jiang, H., Chinnaiyan, A. M. (2016) Development of RNA-seq based prognostic signature in lung adenocarcinoma
    Journal of the National Cancer Institute, 109 (1): djw200. [online]

  • Sun, L., Burnett, J., Gasparyan, M., Xu, F., Jiang, H., Lin, C. C., Myers, I., Korkaya, H., Liu, Y., Connarn, J., He, H., Zhang, N., Wicha, M. S., Sun, D. (2016) Novel Cancer Stem Cell Targets during Epithelial to Mesenchymal Transition in PTEN-deficient Trastuzumab-resistant Breast Cancer
    Oncotarget, 10.18632/oncotarget.9839. [online]

  • Scott, L. J., Erdos, M. R., Huyghe, J. R., Welch, R. P., Beck, A. T., Wolford, B. N., Chines, P. S., Didion, J. P., Narisu, N., Stringham, H. M., Taylor, D. L., Jackson, A. U., Vadlamudi, S., Bonnycastle, L. L., Kinnunen, L., Saramies, J., Sundvall, J., Albanus, R. D., Kiseleva, A., Hensley, J., Crawford, G. E., Jiang, H., Wen, X., Watanabe, R. M., Lakka, T. A., Mohlke, K. L., Laakso, M., Tuomilehto, J., Koistinen, H. A., Boehnke, M., Collins, F. S., Parker, S. C. J. (2016) The genetic regulatory signature of type 2 diabetes in human skeletal muscle
    Nature Communications, 11764. [online]

  • Udager, A. M., Liu, T., Skala, S. L., Magers, M. J., McDaniel, A. S., Spratt, D. E., Feng, F. Y., Siddiqui, J., Cao, X., Fields, K. L., Morgan, T. M., Palapattu, G. S., Weizer, A. Z., Chinnaiyan, A. M., Alva, A., Montgomery, J. S., Tomlins, S. A., Jiang, H., Mehra, R. (2016) Frequent PD-L1 expression in primary and metastatic penile squamous cell carcinoma: potential opportunities for immunotherapeutic approaches
    Annals of Oncology, doi: 10.1093/annonc/mdw216. [online]

  • Kang, Q., Henry, N. L., Paoletti, C., Jiang, H., Vats, O., Chinnaiyan, A. M., Hayes, D. F., Merajver, S. D., Rae, J. M., Tewari, M. (2016) Comparative Analysis of Circulating Tumor DNA Stability in K3EDTA, Streck and CellSave Blood Collection Tubes
    Clinical Biochemistry, doi:10.1016/j.clinbiochem.2016.03.012.  [online]

  • Udager, A. M., DeMarzo, A. M., Shi, Y., Hicks, J. L., Cao, X., Siddiqui, J., Jiang, H., Chinnaiyan, A., Mehra, R. (2016) Concurrent nuclear ERG and MYC protein overexpression defines a subset of locally advanced prostate cancer: Potential opportunities for synergistic targeted therapeutics
    The Prostate, 76 (9) 845-853. [online]

  • Chen, L., Sun, Y., Wang, J., Jiang, H., Muntean, A. G. (2016) Differential regulation of the c-Myc/Lin28 axis discriminates subclasses of rearranged MLL leukemia
    Oncotarget, 7 (18) 25208-25223. [online]

  • Jiang, H., Salzman, J. (2015) A penalized likelihood approach for robust estimation of isoform expression
    Statistics and Its Interface, 8 (4): 437-445. [online][arXiv]

  • Shi, Y., Chinnaiyan, A. M., Jiang, H. (2015) rSeqNP: A non-parametric approach for detecting differential expression and splicing from RNA-Seq data
    Bioinformatics, 31 (13): 2222-2224. [online][software]

  • Burnett, J. P., Korkaya, H., Ouzounova, M. D., Jiang, H., Conley, S. J., Newman, B. W., Sun, L., Connarn, J. N., Chen, C., Zhang, N., Wicha, M. S., Sun, D. (2015) Trastuzumab resistance induces EMT to transform HER2+PTEN- to a triple negative breast cancer that requires unique treatment options
    Scientific Reports, 5:15821.

  • Magers, M. J., Zhan, T., Udager, A. M., Wei, J. T., Tomlins, S. A., Wu, A. J., Kunju, L. P., Lew, M., Feng, F. Y., Hamstra, D. A., Siddiqui, J., Chinnaiyan, A. M., Montgomery, J. S., Weizer, A. Z., Morgan, T. M., Hollenbeck, B. K., Miller, D. C., Palapattu, G. S., Jiang, H., Mehra R. (2015) Clinicopathologic characteristics of anterior prostate cancer (APC), including correlation with previous biopsy pathology
    Medical Oncology, 32 (11): 249.

  • Liu, Y., Baker, S., jiang, H., Stuart, G., Bai, Y. (2015) Correlating Bladder Cancer Risk Genes with Their Targeting MicroRNAs Using MMiRNA-Tar
    Genomics, Proteomics & Bioinformatics, 13 (3): 177-182.

  • McDaniel, A. S., Alva, A., Zhan, T., Xiao, H., Cao, X., Gursky, A., Siddiqui, J., Chinnaiyan, A. M., Jiang, H., Lee, C. T., Mehra, R. (2015) Expression of PDL1 (B7-H1) Before and After Neoadjuvant Chemotherapy in Urothelial Carcinoma
    European Urology Focus, 1 (3): 265-268.

  • Miceli, M. H., Goggins, M. I., Chander, P., Sekaran, A. K., Kizy, A. E., Samuel, L., Jiang, H., Thornton, C. R., Ramesh, M., Alangaden, G. (2015) Performance of lateral flow device and galactomannan for the detection of Aspergillus species in bronchoalveolar fluid of patients at risk for invasive pulmonary aspergillosis
    Mycoses, 58 (6) 368-374.

  • Gilbert, C. D., Bai, Y., Jiang, H. (2015) Microbial Evaluation of Cecure-Treated (Post-Chill) Raw Poultry Carcasses and Cut-up Parts in Four Commercial Broiler Processing Facilities
    International Journal of Poultry Science, 14 (3) 120-126.

  • Mehra, R., Shi, Y., Udager, A. M., Prensner, J. R., Sahu, A., Iyer, M. K., Siddiqui, J., Cao, X., Wei, J., Jiang, H., Feng, F. Y., Chinnaiyan, A. M. (2014) A Novel RNA In Situ Hybridization Assay for the Long Noncoding RNA SChLAP1 Predicts Poor Clinical Outcome After Radical Prostatectomy in Clinically Localized Prostate Cancer
    Neoplasia, 16 (12) 1121-1127.

  • Zhang, Z., Shiratsuchi, H., Lin, J., Chen, G., Reddy, R. M., Azizi, E., Fouladdel, S., Chang, A. C., Lin, L., Jiang, H., Waghray, M., Luker, G., Simeone, D. M., Wicha, M. S., Beer, D. G., Ramnath, N., Nagrath, S. (2014) Expansion of CTCs from early stage lung cancer patients using a microfluidic co-culture model
    Oncotarget, 5 (23): 12383-97.

  • Wei, I. H., Shi, Y., Jiang, H., Kumar-Sinha, C., Chinnaiyan, A. M. (2014) RNA-Seq Accurately Identifies Cancer Biomarker Signatures to Distinguish Tissue of Origin
    Neoplasia, 16 (11) 918-927.

  • Udager, A. M., Shi, Y., Tomlins, S. A., Alva, A., Siddiqui, J., Cao, X., Pienta, K. J., Jiang, H., Chinnaiyan, A., Mehra, R. (2014) Frequent discordance between ERG gene rearrangement and ERG protein expression in a rapid autopsy cohort of patients with lethal, metastatic, castration-resistant prostate cancer
    The Prostate, 74 (12): 1199-1208.

  • Hyman, R. W., Fukushima, M., Jiang, H., Fung, E., Rand, L., Johnson, B., Vo, K. C., Caughey, A. B., Hilton, J. F., Davis, R. W., Giudice, L. C. (2014) Diversity of the Vaginal Microbiome Correlates With Preterm Birth testing
    Reproductive Sciences, 21(1): 32-40.

  • Shi, Y., Jiang, H. (2013) rSeqDiff: Detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test
    PLoS One, 8 (11): e79448.

  • Lu, L., Jiang, H., Wong, W. H. (2013) Multivariate density estimation by Bayesian Sequential Partitioning
    Journal of the American Statistical Association, Theory and Methods, 108 (504): 1402-1410.

  • Brady, J. J., Li, M., Suthram, S., Jiang, H., Wong, W. H., Blau, H. M. (2013) Early role for IL-6 signalling during generation of induced pluripotent stem cells revealed by heterokaryon RNA-Seq
    Nature Cell Biology, 15(10):1244-52.

  • Jiang, H.*, Salzman, J.* (2012) Statistical properties of an early stopping rule for resampling-based multiple testing
    Biometrika, 99 (4): 973-980.

  • Mu, J. C., Jiang, H., Kiani, A., Mohiyuddin, M., Asadi, N. B., Wong, W. H. (2012) Fast and Accurate Read Alignment for Resequencing
    Bioinformatics, 28 (18): 2366-2373.

  • Seok, J., Xu, W., Jiang, H., Davis, R. W., Xiao, W. (2012) Knowledge-Based Reconstruction of mRNA Transcripts with Short Sequencing Reads for Transcriptome Research
    PLoS One, 7 (2): e31440.

  • Hyman, R. W., Herndon, C. N., Jiang, H., Palm, C., Fukushima, M., Bernstein, D., Vo, K. C., Zelenko, Z., Davis, R. W., Giudice, L.C. (2012) The dynamics of the vaginal microbiome during infertility therapy with in vitro fertilization-embryo transfer
    Journal of Assisted Reproduction and Genetics, 29 (2): 105-15.

  • Salzman, J.*, Jiang, H.*, Wong, W. H. (2011) Statistical Modeling of RNA-Seq Data
    Statistical Science, 26 (1): 62-83.
    [online][arXiv][technical report][software]

  • Xu, W., Seok, J., Mindrinos, M. N., Schweitzer, A. C., Jiang, H., Wilhelmy, J., Clark, T. A., Kapur, K., Xing, Y., Faham, M., Storey, J. D., Moldawer, L. L., Maier, R. V., Tompkins, R. G., Wong, W. H., Davis, R. W., Xiao, W. (2011) A Human Transcriptome Array for High Throughput Clinical Studies
    Proceedings of the National Academy of Sciences, 108 (9): 3707-12.

  • Jiang, H., Wang, F., Dyer, N. P., Wong, W. H. (2010) CisGenome Browser: A Flexible Tool For Genomic Data Visualization
    Bioinformatics, 26 (14).

  • Li, J., Jiang, H., Wong, W. H. (2010) Modeling Non-Uniformity in Short-Read Rates in RNA-Seq Data
    Genome Biology, 11: R50.

  • Au, K. F., Jiang, H., Lin, L., Xing, Y., Wong, W. H. (2010) Detection of Splice Junctions from Paired-End RNA-Seq Data by SpliceMap
    Nucleic Acids Research, 38 (14): 4570-4578.

  • Hyman, R. W., Jiang, H., Fukushima, M., Davis, R. W. (2010) A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry
    BMC Research Notes, 3: 257.

  • Jiang, H., Wong, W. H. (2009) Statistical Inferences for Isoform Expression in RNA-Seq
    Bioinformatics, 25 (8): 1026–1032.

  • Hiller, D.*, Jiang, H.*, Xu, W., Wong, W. H. (2009) Identifiability of Isoform Deconvolution from Junction Arrays and RNA-Seq
    Bioinformatics, 25 (23): 3056-3059.

  • Jiang, H., Wong, W. H. (2008) SeqMap: Mapping Massive Amount of Oligonucleotides to the Genome
    Bioinformatics, 24 (20).

  • Ji, H., Jiang, H., Ma, W., Johnson, D., Myers, R., Wong, W. H. (2008) An Integrated Software System for Analyzing ChIP-chip and ChIP-seq Data
    Nature Biotechnology, 26: 1293-1300.

  • Jiang, H., Liu, Y., Su, Z. (2008) Optimizing Chemotherapy Scheduling by Iteratively Solving a Recurrence Equation
    Algorithmic Operations Research, 3 (2).

  • Jiang, H., Liu, Y., Su, Z. (2008) An Optimization Algorithm for Designing Phase I Cancer Clinical Trials
    Contemporary Clinical Trials, 29 (2): 102-108.

  • Kapur, K., Jiang, H., Xing, Y., Wong, W. H. (2008) Cross-Hybridization Modeling on Affymetrix Exon Arrays
    Bioinformatics, 24 (24): 2887-2893.

  • Xing, Y., Stoilov, P., Kapur, K., Han, A., Jiang, H., Shen, S., Black, D. L., Wong, W. H. (2008) MADS: a New and Improved Method for Analysis of Differential Alternative Splicing by Exon-tiling Microarrays
    RNA, 14 (8): 1470-1479.

2007 and earlier
  • Liu, Y., Jiang, H., Su, Z. (2007) Modified Value Iteration for Chemotherapy Scheduling Optimization
    Proceedings of the IEEE International Conference on Industrial Engineering and Engineering Management, 842-846.

  • Jiang, H., Ngo, C. W., Tan, H. K. (2006) Gestalt-Based Feature Similarity Measure in Trademark Database
    Pattern Recognition, 39 (5): 988-1001.

  • Jiang, H., Ngo, C. W. (2004) Graph Based Image Matching
    Proceedings of the 17th International Conference on Pattern Recognition, 3: 658-661.

  • Jiang, H., Ngo, C. W. (2003) Image Mining Using Inexact Maximal Common Subgraph of Multiple ARGs
    International Conference on Visual Information Systems.

Book Chapters

  • Ji, H., Jiang, H., Ma, W., Wong, W. H. (2011) Using CisGenome to Analyze ChIP-chip and ChIP-seq Data.
    Current Protocols in Bioinformatics, Chapter 2: Unit2.13. Wiley.


  • Jiang, H. (2009) Computational and Statistical Approaches in RNA Sequencing Analysis
    Ph.D. Dissertation. [preprint]

  • Jiang, H. (2004) Image Mining and Pattern Discovery Based on Graph Model
    Master's Degree Thesis.