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Preprints

  • Shi Y, Wang M, Shi W, Lee J, Kang H, Jiang H (2018) Accurate and Efficient Estimation of Small P-values with the Cross-Entropy Method: Applications in Genomic Data Analysis
    arXiv preprint. arXiv:1803.03373 [arXiv]

  • Segal B, Elliott M, Braun T, Jiang H (2017) P-splines with an l1 penalty for repeated measures
    arXiv preprint. arXiv:1707.08933 [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]

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

Refereed Publications

2018
  • Liu K, Ye J, Yang Y, Shen L, Jiang H (2018) A Unified Model for Joint Normalization and Differential Gene Expression Detection in RNA-Seq data
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, DOI: 10.1109/TCBB.2018.2790918. [online][arXiv][code]

  • Shi J, Wang X, Lyu L, Jiang, H, Zhu H (2018) Comparison of Protein Expressions between Human Livers and the Hepatic Cell Lines HepG2, Hep3B and Huh7 using SWATH and MRM-HR Proteomics: Focusing on Drug-Metabolizing Enzymes
    Drug Metabolism and Pharmacokinetics, in press. [online]

2017
  • Liu T, Jiang H (2017) Minimizing Sum of Truncated Convex Functions and its Applications
    Journal of Computational and Graphical Statistics, DOI: 10.1080/10618600.2017.1390471. [online][arXiv][code]

  • Shen R, Luo L, Jiang H (2017) Identification of gene pairs through penalized regression subject to constraints
    BMC Bioinformatics, 18:466. [online][code]

  • Segal B, Braun T, Elliott M, Jiang H (2017) Fast Approximation of Small p-values in Permutation Tests by Partitioning the Permutations
    Biometrics, DOI: 10.1111/biom.12731. [online][arXiv][software][code]

  • Jiang H, Zhan T (2017) Unit-Free and Robust Detection of Differential Expression from RNA-Seq Data
    Statistics in Biosciences, 9:178-199. [online][arXiv][code]

  • Zhao L, Wu W, Feng D, Jiang H, Nguyen X (2017) Bayesian Analysis of RNA-Seq Data Using a Family of Negative Binomial Models
    Bayesian Analysis, DOI: 10.1214/17-BA1055. [online][software]

  • Bai L, Zhou B, Yang C, Ji J, McEachern D, Przybranowski S, Jiang H, Hu J, Xu F, Zhao Y, Liu L, Fernandez-Salas E, Xu J, Dou Y, Wen B, Sun D, Meagher JL, Stuckey J, Hayes DF, Li S, Ellis MJ, Wang S (2017) Targeted degradation of BET proteins in triple-negative breast cancer
    Cancer Research, 10.1158/0008-5472.CAN-16-2622. [online]

  • Wang X, Qiao Y, Asangani IA, Ateeq B, Poliakov A, Cieslik M, Pitchiaya S, Chakravarthi BVSK, Cao X, Jing X, Wang CX, Apel IJ, Wang R, Tien JC, Juckette KM, Yan W, Jiang H, Wang S, Varambally S, Chinnaiyan AM (2017) Development of Peptidomimetic Inhibitors of the ERG Gene Fusion Product in Prostate Cancer
    Cancer Cell, 31 (4), 532-548. [online]

  • Shukla S, Evans JR, Malik R, Feng FY, Dhanasekaran SM, Cao X, Chen G, Beer DG, Jiang H, Chinnaiyan AM (2017) Development of RNA-seq based prognostic signature in lung adenocarcinoma
    Journal of the National Cancer Institute, 109 (1): 1-9. [online]

  • Skala SL, Liu T, Udager AM, Weizer AZ, Montgomery JS, Palapattu GS, Siddiqui J, Cao X, Fields K, Abugharib AE, Soliman M, Hafez KS, Miller D, Lee CT, Alva A, Chinnaiyan AM, Morgan TM, Spratt DE, Jiang H, Mehra R (2017) Programmed Death-ligand 1 Expression in Upper Tract Urothelial Carcinoma
    European Urology Focus, 10.1016/j.euf.2016.11.011. [online]

  • Castillo CG, Kauffman CA, Zhai J, Jiang H, Agozino SM, Miceli MH (2017) Testing the performance of a prototype lateral flow device using bronchoalveolar lavage fluid for the diagnosis of invasive pulmonary aspergillosis in high-risk patients
    Mycoses, 10.1111/myc.12694.
    [online]

2016
  • Jiang H, Mu JC, Yang K, Du C, Lu L, Wong WH (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 JM, 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]

  • Scott LJ, Erdos MR, Huyghe JR, Welch RP, Beck AT, Wolford BN, Chines PS, Didion JP, Narisu N, Stringham HM, Taylor DL, Jackson AU, Vadlamudi S, Bonnycastle LL, Kinnunen L, Saramies J, Sundvall J, Albanus RD, Kiseleva A, Hensley J, Crawford GE, Jiang H, Wen X, Watanabe RM, Lakka TA, Mohlke KL, Laakso M, Tuomilehto J, Koistinen HA, Boehnke M, Collins FS, Parker SC (2016) The genetic regulatory signature of type 2 diabetes in human skeletal muscle
    Nature Communications, 7: 11764. [online]

  • Udager AM, Liu T, Skala SL, Magers MJ, McDaniel AS, Spratt DE, Feng FY, Siddiqui J, Cao X, Fields KL, Morgan TM, Palapattu GS, Weizer AZ, Chinnaiyan AM, Alva A, Montgomery JS, Tomlins SA, 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, 27(9):1706-1712. [online]

  • Sun L, Burnett J, Gasparyan M, Xu F, Jiang H, Lin C, Myers I, Korkaya H, Liu Y, Connarn J, He H, Zhang N, Wicha MS, Sun D (2016) Novel Cancer Stem Cell Targets during Epithelial to Mesenchymal Transition in PTEN-deficient Trastuzumab-resistant Breast Cancer
    Oncotarget, 7:51408-51422. [online]

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

  • Kang Q, Henry NL, Paoletti C, Jiang H, Vats O, Chinnaiyan AM, Hayes DF, Merajver SD, Rae JM, Tewari M (2016) Comparative Analysis of Circulating Tumor DNA Stability in K3EDTA, Streck and CellSave Blood Collection Tubes
    Clinical Biochemistry, 49 (18): 1354-1360.  [online]

  • Udager AM, DeMarzo AM, Shi Y, Hicks JL, Cao X, Siddiqui J, Jiang H, Chinnaiyan AM, 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]

2015
  • Shi Y, Chinnaiyan AM, 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]

  • 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]

  • 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.
    [online]

  • Burnett JP, Korkaya H, Ouzounova MD, Jiang H, Conley SJ, Newman BW, Sun L, Connarn JN, Chen C, Zhang N, Wicha MS, 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.
    [online]

  • Magers MJ, Zhan T, Udager AM, Wei JT, Tomlins SA, Wu AJ, Kunju LP, Lew M, Feng FY, Hamstra DA, Siddiqui J, Chinnaiyan AM, Montgomery JS, Weizer AZ, Morgan TM, Hollenbeck BK, Miller DC, Palapattu GS, Jiang H, Mehra R (2015) Clinicopathologic characteristics of anterior prostate cancer (APC), including correlation with previous biopsy pathology
    Medical Oncology, 32 (11): 249.
    [online]

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

  • Miceli MH, Goggins MI, Chander P, Sekaran AK, Kizy AE, Samuel L, Jiang H, Thornton CR, 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.
    [online]

  • Gilbert CD, 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.
    [online]

2014
  • Zhang Z, Shiratsuchi H, Lin J, Chen G, Reddy RM, Azizi E, Fouladdel S, Chang AC, Lin L, Jiang H, Waghray M, Luker G, Simeone DM, Wicha MS, Beer DG, 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.
    [online]

  • Mehra R, Shi Y, Udager AM, Prensner JR, Sahu A, Iyer MK, Siddiqui J, Cao X, Wei J, Jiang H, Feng FY, Chinnaiyan AM (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.
    [online]

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

  • Udager AM, Shi Y, Tomlins SA, Alva A, Cao X, Siddiqui J, Pienta KJ, Jiang H, Chinnaiyan AM, 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.
    [online]

  • Hyman RW, Fukushima M, Jiang H, Fung E, Rand L, Johnson B, Vo KC, Caughey AB, Hilton JF, Davis RW, Giudice LC (2014) Diversity of the Vaginal Microbiome Correlates With Preterm Birth testing
    Reproductive Sciences, 21(1): 32-40.
    [online]

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

  • 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][software]

  • Brady JJ, Li M, Suthram S, Jiang H, Wong WH, Blau HM (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.
    [online]

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

  • Mu JC, Jiang H, Kiani A, Mohiyuddin M, Asadi NB, Wong WH (2012) Fast and Accurate Read Alignment for Resequencing
    Bioinformatics, 28 (18): 2366-2373.
    [online][software]

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

  • Hyman RW, Herndon CN, Jiang H, Palm C, Fukushima M, Bernstein D, Vo KC, Zelenko Z, Davis RW, Giudice LC (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]

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

  • Xu W, Seok J, Mindrinos MN, Schweitzer AC, Jiang H, Wilhelmy J, Clark TA, Kapur K, Xing Y, Faham M, Storey JD, Moldawer LL, Maier RV, Tompkins RG, Wong WH, Davis RW, Xiao W (2011) A Human Transcriptome Array for High Throughput Clinical Studies
    Proceedings of the National Academy of Sciences, 108 (9): 3707-12.
    [online]

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

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

  • Au KF, Jiang H, Lin L, Xing Y, Wong WH (2010) Detection of Splice Junctions from Paired-End RNA-Seq Data by SpliceMap
    Nucleic Acids Research, 38 (14): 4570-4578.
    [online][software]

  • Hyman RW, Jiang H, Fukushima M, Davis RW (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]

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

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

2008
  • Jiang H, Wong WH (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 WH (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 WH (2008) Cross-Hybridization Modeling on Affymetrix Exon Arrays
    Bioinformatics, 24 (24): 2887-2893.
    [online][software]

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

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.
    [online]

  • Jiang H, Ngo CW, Tan HK (2006) Gestalt-Based Feature Similarity Measure in Trademark Database
    Pattern Recognition, 39 (5): 988-1001.
    [preprint]

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

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

Book Chapters

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

Thesis and Dissertation

  • 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.