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

Jiang, H. (2014) Unit-free and robust detection of differential expression from RNA-Seq data
arXiv preprint. arXiv:1405.4538

Methodological Journal Papers

Jiang, H., Mu, J. C., Yang, K., Du, C., Lu, L., Wong, W. H. (2015) Computational Aspects of Optional Polya Tree
Journal of Computational and Graphical Statistics, in press. DOI: 10.1080/10618600.2014.1002927.

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

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]

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.

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.

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]

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.

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.

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

Collaborative Journal Papers

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, doi:10.1016/j.euf.2015.03.004.

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, in press

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.

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.

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.

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.

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.

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.

Refereed Conference Publications

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. (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.

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