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Preprints

Jiang, H., Salzman, J. (2013) A penalized likelihood approach for robust estimation of isoform expression
arXiv preprint. arXiv:1310.0379 [online]

Jiang, H., Mu, J. C., Yang, K., Du, C., Lu, L., Wong, W. H. (2013) Computational Aspects of Optional Polya Tree
arXiv preprint. arXiv:1309.5489 [online]

Methodological Journal Papers

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

Lu, L., Jiang, H., Wong, W. H. (2013) Multivariate density estimation by Bayesian Sequential Partitioning
Journal of the American Statistical Association, DOI:10.1080/01621459.2013.813389. [online]

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

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. [online]

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

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

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

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. [online][software]

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

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. [online]

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

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. [online][software]

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

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

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

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

Collaborative Journal Papers

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, doi:10.1038/ncb2835. [online]

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. (2013) Diversity of the Vaginal Microbiome Correlates With Preterm Birth testing
Reproductive Sciences, doi: 10.1177/1933719113488838. [online]

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. [online]

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. [online]

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. [online]

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. [online]

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. [online][software]

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. [online]

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

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. [online]

Technical Reports

Salzman, J., Jiang, H., Wong, W. H. (2010) Statistical Modeling of RNA-Seq Data
Technical Report in Biostatistics, Stanford University. [online]

Dissertations

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.