The Hu Lab

Health Data Science, Bioinformatics and Statistical Genetics


​​​​​​​​Research Articles (Trainees, Equal Contribution*, Co-corresponding**)


156. Q Liu*, M Reed*, H Zhu*, Y Cheng, J Almeida, G Fruhbeck, R Ribeiro, P Hu

        Epigenome-wide DNA methylation and transcriptome profiling of localized and locally advanced prostate cancer: uncovering new

        molecular markers

        Genomics, In Press

155. MM Islam, N Mohammed, Y Wang, Pingzhao Hu

        Differential Private Deep Learning Models for analyzing breast cancer omics data

        Frontiers in Oncology, 12:879607.

154. Y Su, Q Liu, W Xie, P Hu

        YOLO-LOGO: A transformer-based YOLO segmentation model for breast mass detection and segmentation in digital


        Computer Methods and Programs in Biomedicine,221:106903,

​153. Q Liu, P Hu

         An integrative computational framework for breast cancer radiogenomic biomarker discovery

         Computational and Structural Biotechnology Journal, 20:2484-2494

152. CJ Walsh, J Batt, MS Herridge, S. Mathur, GD Bader, P Hu, P Khatri, and CC. dos Santos

        Comprehensive multi-cohort transcriptional meta-analysis of muscle diseases identifies a signature of disease severity

        Scientific Reports, 12:11260.

151. Z Zhang, W Xu**, P Hu**.

        Tightly integrated multiomics-based deep tensor survival model for time-to-event prediction

         Bioinformatics, 38:3259-3266.

150. J Zammit, DLX Fung, Q Liu, CKS Leung, P Hu

        Semi-Supervised COVID-19 CT Image Segmentation Using Deep Generative Models

         BMC Bioinformatics, 23:343.‑022‑04878‑6

149. A Sanusi, L Yan, AF Hamad, OF Ayilara, V Vasylkiv, MJ Jozani, S Banerji, J Delaney, P Hu, E Wall-Wieler, LM Lix

        Transitions between Versions of the International Classification of Diseases and Chronic Disease Prevalence Estimates from

         Administrative Health Data: A Population-Based Study

         BMC Public Health, 22:701.

148. H Hadipour, C Liu, R Davis, ST Cardona, P Hu

        Deep clustering of small molecules at large-scale via variational autoencoder embedding and K-means

        BMC Bioinformatics, 23:132.

147. CJ Walsh*, CK Escudero*, M Gupta*, P Plant, MJ Herridge, S Mathur, P Hu, J Correa, S Ahmed, A Bigot, CC dos Santos, J Batt 

         MicroRNA regulatory networks associated with abnormal muscle repair in survivors of critical illness

         Journal of Cachexia, Sarcopenia and Muscle, 13:1262-1276.

146. N Abdelfatah, AA Mostafa, CR French, LP Doucette, C Penney, MB Lucas, A Griffin, V Booth, C Rowley, JE Besaw, L Tranebjærg,

        ND Rendtorff,  KA Hodgkinson, LA Little, S Agrawal, L Parnes, T Batten, S Moore,  P Hu, JA Pater, J Houston, D Galutira,

        T Benteau, C MacDonald, D French, DD O’Rielly, SG Stanton, TL Young

        A pathogenic deletion in Forkhead Box L1 (FOXL1) identifies the first otosclerosis (OTSC) Gene

        Human Genetics, 141:965-979.

145. C Liu, AM Hogan, H Sturm, MW Khan, MM Islam, ASMZ Rahman, R Davis, ST Cardona, P Hu

        Deep learning - driven prediction of drug mechanism of action from large-scale chemical-genetic interaction profiles

        Journal of Cheminformatics, 14:12

144. Y Li, Charles N Bernstein, W Xu, P Hu

        Polygenic risk and causal inference of psychiatric comorbidity in inflammatory bowel disease among patients with European ancestry

        Journal of Translational Medicine, 20:43

143. N Feizi, Q Liu, L Murphy, P Hu

        Computational prediction of the pathogenic status of cancer-specific somatic variants

        Frontiers in Genetics. 12:805656 

142. Benjamin Blum, Weiwei Lin, Matthew L. Lawton, Qian Liu, Julian Kwan, Isabella Turcinovic, Ryan Hekman, Pingzhao Hu,

        Andrew Emili

        Multi-omic metabolic enrichment network analysis reveals metabolite-protein physical interaction subnetworks altered in cancer

        Molecular & Cellular Proteomics. 21 (1):100189

141. Q Liu, P Hu

        Interpretable and extendable deep learning for pan-cancer radiogenomics research

        Current Opinion for Chemical Biology. 66:102111

140. CC dos Santos, H Amatullah, CM Vaswani, T Maron-Gutierrez, M Kim, SHJ Mei, K Szaszi, APT Monteiro , AK Varkouhi, R Herreroz,

         JA Lorente, JN Tsoporis, S Gupta, A Ektesabi, N Kavantzas, V Salpeas, JC Marshall, PRM Rocco, P Marsden, DJ Weiss, DJ Stewart,

         P Hu, WC Liles

         Mesenchymal Stromal (stem) Cell Therapy Modulates miR-193b-5p Expression to Attenuate Sepsis-Induced Acute Lung Injury

         European Respiratory Journal. 59(1):2004216

139. Q Liu*,B Cheng*, Y Jin, P Hu

        Bayesian tensor factorization-driven breast cancer subtyping by integrating multi-omics data

        Journal of Biomedical Informatics. 125:103958


138. LJ Oneil, P Hu, Q Liu, M Islam, V Spicer, J Rech, A Hueber, V Anaparti, I Smolik, H EI-Gabalaway, G Schett, JA Wilkins

        Proteomic Approaches to Defining Remission and the Risk of Relapse in Rheumatoid Arthritis

        Frontiers in Immunology. 12:729681

137. MM Islam, Y Wang P Hu
        A maximum flow-based approach to prioritize drugs for drug repurposing of chronic diseases
        Life, 11(11):1115. 

136. Q Liu*, D LX Fung*, L Lac*, P Hu

        A novel matrix profile-guided attention LSTM model for forecasting COVID-19 cases in USA

        Frontiers in Public Health. 9:741030. 

​135. D LX Fung*, Q Liu*, J Zammit, CK Leung, P Hu

        Self-supervised deep learning model for COVID-19 lung CT image segmentation highlighting putative causal relationship among 

        age, underlying disease and COVID-19

        Journal of Translational Medicine. 19:318

134. KL Sharma*, S Jia*, TH Beacon, I Adewumi, C López, P Hu, W Xu, JR Davie

        Mitogen-induced transcriptional programming in human fibroblasts

        Gene. 800:145842

133. Y Xu, J Kong, P Hu

        Computational drug repurposing for Alzheimer's disease using risk genes from GWAS and single-cell RNA sequencing studies

        Frontiers in Pharmacology. 12:617537.

132. S Huang, P Hu**, T Lakowski**.(**Co-corresponding authors).

        Predicting breast cancer drug response using a multiple-layer cell line drug response network model

        BMC Cancers. 21:648. 

­131. V Cruz de Jesus, MW Khan, BA Mittermuller, K Duan, P Hu**, RJ Schroth**, P Chelikani** (** Co-corresponding author.)

        Characterization of supragingival plaque and oral swab microbiomes in children with severe early childhood caries 

        Frontiers in Microbiology. 12:683685.


130.  S Jia P Hu

        ChrNet: A re-trainable chromosome-based 1D convolutional neural network for predicting immune cell types

        Genomics. 113:2023-2031.

129. AF Hamad, V Vasylkiv, L Yan, R Sanusi, O Ayilara, J Delaney, E Wall-Wieler, MJ Jozani, P Hu, S Banerji, LM Lix

        Mapping Three Versions of the International Classification of Diseases to Categories of Chronic Conditions

        International Journal of Population Data Science. 6:1-11.

128.  A Bruinooge*, Q Liu*, Y Tian, W Jiang, Y Li, W Xu, CN Bernstein, P Hu

         Genetic predictors of gene expression associated with psychiatric comorbidity in patients with IBD: a pilot  study

         Genomics. 113: 919-932.

127. AM Ektesabi, K Mori, J Tsoporis, C Vaswani, S Gupta, C Walsh, SHJ Mei, DJ Stewart, WC Liles, J Marshall, P Hu, T Parker,
        CC dos Santos
        Mesenchymal Stem/Stromal Cells Increase Cardiac MIR-187-3P Expression in Polymicrobial Animal Model of Sepsis 
        Shock. 56:133-141.

126. R Ajwad, M Domaratzki, Q Liu, N Feizi, P Hu

        Identification of significantly mutated subnetworks in the breast cancer genome

        Scientific Reports. 11:642.


125. A Tran, CJ Walsh (*), Jane Batt, CC dos Santos (**), P Hu 

        A machine learning-based clinical tool for diagnosing myopathy using multi-cohort microarray expression profiles 

        Journal of Translational Medicine. 18:454.

124. Q Liu, CK Leung, P Hu

        A two-dimensional sparse matrix profile DenseNet for COVID-19 diagnosis using chest CT image

        IEEE Access. 8:213718-213728.

123. Y Jin, S Jia, A Ashraf, P Hu

        Integrative data augmentation with U-net segmentation masks improves detection of lymph node metastases in breast cancer patients

        Cancers. 12:2934.

122. MM Islam, S Huang, R Ajwad, C Chi, Y Wang, P Hu

        An integrative deep learning framework for classifying molecular subtypes of breast cancer

        Computational and Structural Biotechnology Journal. 18:2185-2199.

121. MR Peter, M Bilenky, R Isserlin, GD Bader, SY Shen, D de Carvalho, AR Hansen, P Hu, NE Fleshner, AM Joshua, M Hirst, B Bapat

        Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment

        Epigenomics. 12:1317-1332.

120. S Niraula, N Biswanger, P Hu, P Lambert, K Decker

        Incidence, Characteristics, and Outcomes of Interval Breast Cancers Compared to Screening Detected Breast Cancers:

        A Population-Based Cohort Study

        JAMA Network Open. 3(9):e2018179.

119. Z Sun, S Huang, P Jiang, P Hu

        DTF: Deep tensor factorization for predicting anticancer drug synergy

        Bioinformatics. 36:4483-4489.

118. YW Jin, P Hu

       Tumor-Infiltrating CD8 T Cells Predict Clinical Breast Cancer Outcomes in Young Women

       Cancers. 12:1076

117. N Younes*, L Zhou*, H Amatullah, SHJ Mei, R Herrero, JA Lorente, DJ Stewart, P Marsden,  WCW Liles, P Hu, CC dos Santos

        Mesenchymal Stromal/Stem Cells Modulate Response to Experimental Sepsis-Induced Lung Injury via Regulation of miR-27a-5p in

        Recipient Mice

        Thorax. 75:556-567.

116. P Jiang*, S Huang*, Z Sun, Z Fu, T Lakowski, P Hu.

        Deep graph embedding for prioritizing synergistic anticancer drug combinations

        Computational and Structural Biotechnology Journal. 18:427-438

115. VCruz de Jesus, R Shikder, D Oryniak, K Mann, A Alamri, BA Mittermuller, K Duan, P Hu**, RJ Schroth** and P Chelikani**

       Sex-based diverse plaque microbiota in children with severe caries

       Journal of Dental Research, 99(6):703-712 (**Co-corresponding authors)

114. A Binnie, JLY Tsang, P Hu, G Carrasqueiro, P Castelo-Branco, CC. dos Santos

        Epigenetics of Sepsis

        Critical Care Medicine. 48(5):745-756

113. M Altaf-Ul-Amin, MB Karim, P Hu, N ONO, S Kanaya

        Discovery of inflammatory bowel disease-associated miRNAs using a novel bipartite clustering approach

        BMC Medical Genetics, 13 (Suppl 3):10

112. A Binnie*, CJ Walsh*, P Hu, D Dwivedi, A Fox-Robichaud, PC Liaw, JLY Tsang, J Batt, G Carrasqueiro, S Gupta, JC Marshall,

       P   Castelo-Branco, CC dos Santos

       Epigenetic profiling in severe sepsis (EPSIS): A pilot study of DNA methylation profile in critical illness

       Critical Care Medicine, 48(2):142-150

111. Frenkel S, CN Bernstein, M Sargent, W Jiang, Q Kuang, W Xu, P Hu
        Copy number variation-based gene set analysis reveals cytokine signaling pathways associated with psychiatric comorbidity in
        patients with inflammatory bowel disease

        Genomics, 112(1): 683-693.


110. P Brown, P Hu (as a member of the RELISH Consortium), Y Zhou
        Large expert-curated database for benchmarking document similarity detection in biomedical literature search
        Database: The Journal of Biological Databases and Curation. Volume 2019, 2019, baz085.

109. Q Liu, A Junker, K Murakami, P Hu

        Automated cancer cell counting by ensembling deep features

        Cells, 8:1019

108. V Bhat, VL Wing, P Hu, A Raouf

        Isolation and characterization of a new basal-like luminal progenitor in human breast tissue

        Stem Cell Research & Therapy, 10:269.

107. S Frenkel, CN Bernstein, YW Jin, M Sargent, W Jiang, Q Kuang, J Wei, B Thiruvahindrapuram, SW Scherer, P Hu

        A genome-wide copy number variant data set for inflammatory bowel disease in a Caucasian population

        Data in Brief, 25:104203.

106. S Frenkel, CN Bernstein, M Sargent, Q Kuang, W Jiang, J Wei, B Thiruvahindrapuram, B Spriggs, SW Scherer, P Hu

        Genome-wide analysis identifies rare copy number variations associated with inflammatory bowel disease

        Plos One, 14(6):e0217846.

105 R Shikder, P Thulasiraman, P Irani, P Hu

       An openAM-based tool for finding longest common subsequence in bioinformatics

       BMC Research Notes, 12:220.

104. Q Liu, P Hu

        Association analysis of deep genomic features extracted by denoising autoencoders with breast cancer clinical outcomes

        Cancers, 11:494.

103. S Huang, W Xu, P Hu**, T Lakowski** (**Co-corresponding authors)

        Integrative analysis reveals subtype-specific regulatory determinants in triple negative breast cancer

        Cancers, 11:507.

102. S Jahan, TH Beacon, S He, C Gonzalez, W Xu, GP Delcuve, S Jia, P Hu, JR Davie

        Chromatin organization of transcribed genes in chicken polychromatic erythrocytes.  

        Gene, 699:80-87.

101. R Shikder, P Irani, P Hu
       Genome-wide canonical correlation analysis-based computational methods for mining information from microbiome and gene

       expression data
       In: Rudzicz F. and Meurs M.J. (eds) Advances in Artificial Intelligence. Canadian AI 2019

       Lecture Notes in Artificial Intelligence 11489, Springer, Cham. DOI:10.1007/978-3-030-18305-9_53.

100 Q Liu, A Junker, K Murakami, P Hu
      A novel convolutional regression network for cell counting
      2019 IEEE 7th International Conference on Bioinformatics and Computational Biology. Hangzhou, China

      Won Best Oral Presentation Paper

99. L Grenier, P Hu

      Computational drug repurposing for inflammatory bowel disease using genetic information

      Computational and Structural Biotechnology Journal. 17: 127-135.

98. X Hou, J You, P Hu

     Predicting drug-drug interactions using deep neural network

     Proceedings of the 2019 11th International Conference on Machine Learning and Computing. Pp. 168-172. Zhuhai, China. and ISBN: 978-1-4503-6600-7, ACM New York, NY, USA@2019

     Won Best Presentation Award

97. J You, R McLeod, P Hu

      Predicting drug-target interaction network using deep learning modes

      Computational Biology and Chemistry, 80:90-101.

96. PC Havugimana*, P Hu*, A Emili (* Co-first Author)
      Functional proteomics: systematic characterization of the physical and functional organization of cell systems

      Veenstra TD and Yates JR. Proteomics for Biological Discovery. 2th Edition. Wiley Press, ISBN: 978-1-118-27924-3. pp197-214.

95. J Zhang, X Ye, C Wu, H Fu**, W Xu**, P Hu** (**Co-corresponding authors)

      Modelling gene-environment interaction for the risk of non-Hodgkin lymphoma

      Frontiers in Oncology, 8:657. doi: 10.3389/fonc.2018.00657.



94. MM Islam, K Jeffers, AM Hogan, Q Liu, R Davis, S Cardona, P Hu
       Deep neural network model for predicting gene activity using three-dimensional structures of chemical compounds
       In Joint Statistical Meeting Proceedings, Section on Statistical Learning and data Science. pp. 1126-1135.
       Vancouver: American Statistical Association.

93. P Basak, S Chatterjee, V Bhat, A Su, H Jin,V Lee-Wing, Q Liu, P Hu, LC Murphy, A Raouf

      H19 acts as an estrogen receptor modulator that is required for endocrine therapy resistance in ER+ breast cancer cells

      Journal of Cellular Physiology and Biochemistry, 51:1518-1532.

92. L Zhang*, N Feizi*, C Chi, P Hu (* Co-first Author)

      Association analysis of somatic copy number alteration burden with breast cancer survival

      Frontiers in Genetics, 9:421, doi: 10.3389/fgene.2018.00421

91. R Eguchi, MB Karim, P Hu, T Sato, N Ono, S Kanaya, M Altaf-Ul-Amin

      An integrative network-based approach to identify novel disease genes and pathways: A case study in the context of

      inflammatorybowel disease

      BMC Bioinformatics, 19:264

90. Y Chen, C Monteiro, A Matos, J You, A Fraga, C Pereira, V Catalán, A Rodríguez, J Gómez-Ambrosi, G Frühbeck, R Ribeiro**,

      P Hu** (**Co-corresponding authors)

      Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess

      adiposity – a pilot study. 

      Clinical Epigenetics, 10:54.

89.  J You, MM Islam, L Grenier, Q Kuang, R McLeod, P Hu

       Drug-target interaction network predictions for drug repurposing using LASSO-based regularized linear classification model

       In: Bagheri E., Cheung JCK. (eds) Advances in Artificial Intelligence. AI 2018. Lecture Notes in Computer Science, Vol 10832.

       Springer, Cham.

 88. MM Islam, Y Wang, P Hu

       Deep learning models for predicting phenotypic traits and diseases from omic data

       Artificial Intelligence (ISBN 978-953-51-6129-5), Edited by Marco Antonio Aceves-Fernandez. InTechOpen Press.

       DOI: 10.5772/intechopen.75311.

87. MM Islam*, Y Tian*, Y Cheng, Y Wang, P Hu (* Co-first Author)
      A deep neural network based regression model for triglyceride concentrations prediction using epigenome-wide DNA

      methylation profiles
      BMC Proceedings, 12(Suppl 9):21

86. C Chi, LC Murphy, P Hu
      Recurrent copy number alterations in young women with breast cancer
Oncotarget,  9:11541-11558


85. PC Havugimana*, P Hu*, A Emili (* Co-first Author)
      Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic

      analysis of protein interaction networks
      Expert Review of Proteomics 14, 845-855

84.  MM Islam, R Ajwad, C Chi, M Domaratzki, Y Wang, P Hu
       Somatic copy number alteration-based prediction of molecular subtypes of breast cancer using deep learning model
       In Mouhoub M., Langlais P. (eds) Advances in Artificial Intelligence. AI 2017. Lecture Notes in Computer Science, Vol 10233.

       Springer, Cham.

83.  C Yang, L Kari, GL Sturdevant, L Song, M Patton, CE Couch, JM Ilgenfritz, TR Southern, WM Whitmire, M Briones, C Bonner,

       C Grant, P Hu, G McClarty, and HD Caldwell
       Chlamydia trachomatis ChxR is a transcriptional regulator of virulence factors that function in in vivo host pathogen

       Pathogens and Disease.75(3). doi: 10.1093/femspd/ftx035.

82.  H Amatullah, Y Shan, BL Beauchamp, PL Gali, S Gupta, T Maron-Gutierrez, ER Speck, AE Fox-Robichaud, JLY Tsang,

       SHJ Mei, TW Mak, PRM Rocco, JW Semple, H Zhang, P Hu, JC Marshall, DJ Stewart, M Harper, PC Liaw, WC Liles,

       CC dos Santos
       DJ-1/PARK7 impairs bacterial clearance in sepsis
       American Journal of Respiratory and Critical Care Medicine 195, 889-905.

81.  X Ye, K Zhao, C Wu, P Hu, H Fu
      Associations between genetic variations in immunoregulatory genes and risk of non-hodgkin lymphoma in a Chinese

      Oncotarget 8, 10450-10457.


80. MJ Patton, S McCorrister, C Grant, G Westmacott, R Fariss, P Hu, K Zhao, M Blake, B Whitmire,C Yang, HD Caldwell,

      G McClarty
      The Chlamydial Protease-like Activity Factor (CPAF) and T3S Proteins Cooperate in the Inhibition of p65 Nuclear

      mBio 7, e01427-16.

79.CJ Walsh, J Batt, P Hu, CC Dos Santos
      Discovering microRNA-regulatory modules in multi-dimensional cancer genomic data: a survey of computational methods
      Cancer Informatics Suppl2, 25-42.

78. CJ Walsh, J Batt, MS Herridge, S Mathur, G Bader, P Hu, CC Dos Santos
      Transcriptomic analysis reveals abnormal repair and remodeling in survivors of critical illness with sustained muscle

      Scientific Reports 6, 29334.

77.  C Chi, R Ajwad, Q Kuang, P Hu
      A graph-based algorithm for detecting recurrent copy number variants in cancer studies
      Cancer Informatics Suppl.2, 43-50.

76. U Allen, P Hu, SL Pereira, J Robinson, T Paton, J Beyene, N Khodai-Booran, A Dipchand, D Hebert, V Ng, T Nalpathamkalam,

      S Read
      The genetic diversity of Epstein-Barr virus in the setting of transplantation relative to non-transplant settings: a feasibility

      Pediatric Transplantation 20, 124-129.

75.  FS Siddiqi, S Majumder, K Thai, M Abdalla, P Hu, SL Advani, KE White, BB Bowskill, G Guarna, CC dos Santos, KA Connelly,

        A Advani
       The histone methyltransferase EZH2 protects against podocyte oxidative stress and renal injury in diabetes
       Journal of the American Society of Nephrology 27, 2021-2034.

74.  XQ Liu, J Fazio, P Hu, AD Paterson
      Identity-by-descent mapping for diastolic blood pressure in unrelated Mexican Americans
      BMC Proceedings 10(Supp 7): 263-267.


73.  PF Simon, S McCorrister, P Hu, P Chong, A Silaghi, G Westmacott, KM Coombs, D  Kobasa
       Strains of highly pathogenic H5N1 and novel H7N9 influenza induces a more profound proteomic host response compared

       to those of seasonal and pandemic H1N1 influenza A viruses
       Journal of Proteome Research 14, 4511-4523.

72.  KL Wright, JR Adams, J Liu, AJ Loch, RG Wong, C Jo, LA Beck, DR Santhanam, L Weiss, X Mei, TF Lane, S Koralov, SJ Done,
       JR Woodgett, E Zacksenhaus, P Hu, SE Egan
       Ras signaling is a key determinant of metastatic dissemination and poor survival of luminal breast cancer patients
       Cancer Research 75, 4960-4972.

71.  CJ Walsh, P Hu, J Batt, CC Dos Santos
      Microarray meta-analysis and cross-platform normalization: integrative genomics for robust biomarker discovery
      Microarrays 4:389-406.

70.  R Johnson*, P Hu*, C Fan, C Anders (* Co-first Author)
      Gene expression analysis of “young adult type” breast cancer: a retrospective analysis
      Oncotarget 6:13688-13702 

69. D Merico, N Sharfe, P Hu‎, J Herbrick, C Roifman
      RelB deficiency causes combined immunodeficiency
      LymphoSign Journal 2:147-155.

68. N Kanwar, P Hu, P Bedard, M Clemons, D McCready, SJ Done
      Identification of genomic signatures in circulating tumor cells from breast cancer
      International Journal of Cancer 137:332-344.

67. M Uddin, B Thiruvahindrapuram, S Walker, Z Wang, P Hu, S Lamoureux, J Wei, JR MacDonald, G Pellecchia, C Lu, AC Lionel,
      MJ Gazzellone, JR McLaughlin, C Brown, IL Andrulis, JR Knight, J Herbrick, RF Wintle, P Ray, DJ Stavropoulos, CR Marshall,

      SW Scherer
      A high-resolution copy number variation resource for clinical and population genetics
      Genetics in Medicine17:747-752.

66. KWK Lee, R Richmond, P Hu, L French, J Shin, C Bourdon, E Reischl, M Waldenberger, S Zeilinger, T Gaunt, W McArdle,

     S Ring, G Woodward, L Bouchard, D Gaudet, G Davey-Smith, C Relton, T Paus, Z Pausova
     Prenatal exposure to maternal cigarette smoking and DNA methylation: epigenome-wide association in a discovery sample
     of adolescents and replication in an independent cohort at birth through 17 years of age

     Environmental Health Perspectives 123:193-199.

65. H Jiang, Z Pan, P Hu
     Discriminative learning of generative models: large margin multinomial mixture models for document classification
     Patter Analysis and Applications18:535-551.

64. J Li, S Rohailla, N Gelber, J Rutka, N Sabah, RA Gladstone, C Wei, P Hu, RK Kharbanda, AN Redington
     MicroRNA - 144 is a circulating effector of remote ischemic preconditioning
     Basic Res Cardiol. 109:423-436.

63. M Uddin, K Tammimies, G Pellecchia, B Alipanahi, P Hu, Z Wang, D Pinto, L Lau, T Nalpathamkalam, CR. Marshall,

     BJ Blencowe, BJ Frey, D Merico, R Yuen, SW Scherer
     Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder
     Nature Genetics 46: 742-747.

62. P Hu, AD Paterson
     Dynamic pathway analysis of genes associated with blood pressure using whole genome sequence data
     BMC Proceedings 8(Suppl 1): S106. Special issue of Genetic Analysis Workshop (GAW18), Stevenson, WA, USA, October 2012. 

61. W Xu, S Cohen-Woods, Q Chen, A Noor, J Knight, G Hosang, SV Parikh, V de Luca, F Tozzi, P Muglia, J Forte, A McQuillin,

     P Hu, HMD Gurling, JL Kennedy, P McGuffin, A Farmer, J Strauss, JB Vincent
     Genome-wide association study of bipolar disorder in Canadian and UK populations corroborates disease loci including

     SYNE1 and CSMD1
     BMC Medical Genetics 15:2. 


60. MMG Seno*, FG Gwadry*, P Hu, SW Scherer
     Neuregulin 1-alpha regulates phosphorylation, acetylation and alternative splicing in lymphoblastoid cells
     Genome 56:619-625.

59. P Hu, AM Muise, X Xiang, JH Brumell, MS Silverberg, W Xu
     Association between a multi-locus genetic risk score and inflammatory bowel disease
     Bioinformatics and Biology Insights 7:143-152. 

58. JD Mills, T Nalpathamkalam, HIL Jacobs, C Janitz, D Merico, P Hu, M Janitz
     RNA-Seq analysis of parietal cortex in Alzheimer’s disease reveals alternatively spliced isoforms related to lipid metabolism
     Neuroscience Letters 536:90-95. 

57. P Moffatt, M Ben-Amor, FH Glorieux, P Roschger, K Klaushofer, JA Schwartzentruber, AD Paterson, P Hu, C Marshall, FORGE
     Canada Consortium, S Fahiminiya, J Majewski, CL Beaulieu, KM Boycott, F Rauch
     Metaphyseal dysplasia with maxillary hypoplasia and brachydactyly is caused by a duplication in RUNX2
     American Journal of Human Genetics 92:252-258.


56. P Hu*, X Wang*, JJ Haitsma, S Furmli, H Masoom, M Liu, AS Slutsky, J Beyene, CM Greenwood, CC dos Santos
     Microarray meta-analysis identifies acute lung injury biomarkers in donor lungs that predict development of primary graft

     failure in recipients
     Plos One 7:e45506. 

55. P Hu
     Machine learning approaches for network-based prediction of disease outcomes and protein functions
     Doctoral Dissertation, Collected by ACM Digital Library, ISBN: 978-0-494-90125-0). York University, Canada ©2012 

54. P Hu, S Bull, H Jiang
     Gene network modular-based classification of microarray samples
     BMC Bioinformatics13 (Suppl 10): S17. 

53. CC dos Santos, S Murthy, P Hu, Y Shan, JJ Haitsma1, SHJ Mei, DJ Stewart, WC Liles
     Network analysis of transcriptional responses induced by mesenchymal stem cells treatment of experimental sepsis
     American Journal of Pathology 181:1681-1692

52. W Wang, W Hu, F Hou, P Hu, Z Wei
     SNVerGUI: A desktop tool for variant analysis of next-generation sequencing data
     Journal of Medical Genetics 12:753-755. 

51. PC Havugimana*, GT  Hart*, T Nepusz*, H Yang*, AL Turinsky, Z Li, PI Wang,, DR Boutz, V Fong , S Phanse, M Babu,

      SA Craig, P Hu, C Wan, J Vlasblom, V Dar, A Bezginov, GW Clark, GC Wu, SJ Wodak, ERM Tillier, A Paccanaro, EM Marcotte,

      A Emili
     A census of human soluble protein complexes
     Cell 150:1068-1081. 

50. R Ribeiro, C Monteiro, V Catalán, P Hu, V Cunha, A Rodriguez, J Gómez-Ambrosi, A Fraga, P Príncipe, C Lobato, F Lobo,

     A Morais, V Silva, J  Sanches-Magalhães, J Oliveira, F Pina, C Lopes, R Medeiros, G Frühbeck
     Obesity and prostate cancer: gene expression signature of human periprostatic adipose tissue
     BMC Medicine 10:108. 

49. D Picard, S Millar, CE Hawkins, E Bouffet, HA Rogers, TSY Chan, SK Kim, YS Ra, J Fangusaro, A Korshunov, H Toledano,
     H Nakamura, JT Hayden, J Chan, L Lafay-Cousin, P Hu, X Fan, KM Muraszko, SL Pomeroy, CC Lau, HK Ng, C Jones, TV
     Meter, SC Clifford, C Eberhart,  A Gajjar, SM Pfister, RG Grundy, A Huang
     Markers of survival and metastatic potential in childhood CNS primitive neuro-ectodermal brain tumors: an integrative
     genomic analysis

     Lancet Oncology 13:838-848.

48. L Smeding, HL Poi,  P Hu, Y Shan, JJ Haitsma, E Horvath, S Furmli, H Masoom, JW Kuiper, AS Slutsky, TG Parker, FB Plötz,
     CC dos Santos
     Salutary effect of Resveratrol on sepsis-induced myocardial depression
     Critical Care Medicine 40:1896-1907. 

47. AM Muise, W Xu, CH Guo, T Walters, VM Wolters, R Fattouh, GY Lam, P Hu, R Murchie, M Sherlock, JC Gana, NEOPICS,

     RK Russell, M Glogauer, RH Duerr, J Cho, CW Lees, J Satsangi, DC Wilson, AD Paterson, AM Griffiths, MS Silverberg,

     JH Brumell
     NADPH oxidase complex and IBD candidate gene studies: identification of a rare variant in NCF2 that results in reduced

     binding to  RAC2
     Gut 61:1028-1035. 


46. P Hu, W Xu, L Chen, X Xing, AD Paterson
     Pathway-based joint effects analysis of rare genetic variants using Genetic Analysis Workshop 17 exon sequence data
     BMC Proceedings 5(Suppl 9):S45. Special issue of Genetic Analysis Workshop (GAW17), Boston, Massachusetts, USA

45. Z Wei, W Wang, P Hu, GJ Lyon, H Hakonarson
     SNVer: a statistical tool for variant calling in analysis of pooling or individual next-generation sequencing data
     Nucleic Acids Research 39:e132. 

44. EJ Parra, JE Below, S Krithika, A Valladares, JL Barta, NJ Cox, CL Hanis, N Wacher, J Garcia-Mena, P Hu, MD Shriver,

     The DIAGRAM Consortium, J Kumate, PM McKeigue,J Escobedo, M Cruz
     Genome-wide association study of type 2 diabetes in a sample from Mexico city and a meta-analysis of a Mexican-American
     sample from Starr county, Texas

     Diabetologia 54:2038-2046. 

43. RF Wintle, AC Lionel, P Hu, SD Ginsberg, D Pinto, B Thiruvahindrapduram, J Wei, CR Marshall, J Pickett, E Cook, SW Scherer
     A genotype resource for postmortem brain samples from the Autism Tissue Program
     Autism Research 4:89 – 97. 

42. MMG Seno, P Hu, FG Gwadry, D Pinto, CR Marshall, G Cassallo, SW Scherer
     Gene and miRNA expression profiles in autism spectrum disorders
     Brain Research 1380:85-97. 

41. L Chen, P Hu, J Sykes, M Pintilie, G Liu, W Xu
     A pathway-based association analysis model using common and rare variants
     BMC Proceedings 5(Suppl 9):S85. Special issue of Genetic Analysis Workshop (GAW17), Boston, Massachusetts, USA

40. P Hu, H Jiang
     Classification of high-throughput data using correlation-shared gene clusters
     Proceedings of the 2011 International Conference on Bioinformatics & Computational Biology (BIOCOMP 2011),

     ISBN 1-60132-170-8, pp.58-62. CSREA Press. Edited by HR Arabnia and QN Tran. Las Vegas, USA.

39. P Hu, S Bull, H Jiang
     Gene network models-based linear discriminant analysis of microarray expression data
     Proceedings of 7th International Symposium on Bioinformatics Research and Applications (ISBRA’11), LNBI 6674, pp. 286 - 296.
     Springer-Verlag Berlin Heidelberg. Edited by J. Chen, J. Wang and A. Zelikovsky. Changsha, China. 


38. B Kabakchiev, D Turner, J Hyams, D Mack, N Leleiko, W Crandall, J Markowitz, A Otley, W Xu, P Hu, A Griffiths,

      MS Silverberg
      Gene expression changes associated with resistance to intravenous corticosteroid therapy in children with severe ulcerative

      Plos One 5:e13085.   

37. SD Molyneux*, MD Grappa*, AG Beristain, TD McKee, DH Wai, J Paderova, M Kashyap, P Hu, T Maiuri, SP Narala,

      V Stambolic, J Squire, J Penninger, O Sanchez, TJ Triche, GA Wood, LS Kirschner, R Khokha
      PRKAR1A is an Osteosarcoma tumor suppressor and defines a molecular subclass in mice
     Journal of Clinical Investigation 120:3310-3325.

36. MMG Seno, C Trollet, T Athanasopoulos, IR Graham, P Hu, G Dickson
     Transcriptomic analysis of dystrophin RNAi knockdown reveals a central role for dystrophin in muscle differentiation and
     contractile apparatus organization

     BMC Genomics 11:345. 

35. P Hu, H Jiang, A Emili
     Predicting protein functions by relaxation labeling protein interaction network
     BMC Bioinformatics 11(Suppl):S64.   

34. P Hu, H Jiang, A Emili
     Incorporating correlations among gene ontology terms into predicting protein functions
     Invited chapter for Ontology learning and knowledge discovery using the web: challenges and recent advances. pp. 154 – 173. Edited
     by W Wong, W Liu and M Bennamoun. IGI Global Press.


33. E Parkhomenko, D Tritchler, M Lemire, P Hu, J Beyene
     Using a higher criticism statistic to detect modest effects in a genome-wide study of rheumatoid arthritis
     BMC Proceedings 3(Suppl7):S40. Special issue of Genetic Analysis Workshop (GAW16), St. Louis, Missouri, USA

32. J Beyene, P Hu, JS Hamid, E Parkhomenko, AD Paterson, D Tritchler
     Pathway-based analysis of measures of explained variation in a genome-wide case-control association study of

     rheumatoid arthritis
     BMC Proceedings 3(Suppl7):S128. Special issue of Genetic Analysis Workshop (GAW16), St. Louis, Missouri, USA

31. P Hu, CMT Greenwood, J Beyene
     Using the ratio of means as the effect size measure in combining results of microarray experiments
     BMC System Biology 3:106. 

30. P Hu*, SC Janga*, M Babu*, JJ Diaz-Mejia*, G Butland*, W Yang, O Pogoutse, X Guo, S Phanse, P Wong, S Chandran,

     C Christopoulos, A Nazarians-Armavil, NK Nasseri, G Musso, M Ali, N Nazemof, V Eroukova, A Golshni, A Paccanaro,

     JF Greenblatt, G Moreno-Hagelseib, A Emili
     Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins
     PLoS Biology 7:e96. 

29. U Allen, M Barton-Forbes*, J Beyene*, P Hu*, N Khodai-Booran, D Héber, A Diphchand, V Ng, M Soloman, D Grant, A Fecteau,

     B Ngan,  S Read, M Zielenska, S Weitzman
     Gene expression using microarrays in transplant recipients at risk of EBV lymphoproliferation after organ transplantation:
     preliminary proof of concept

     Pediatric Transplantation 13:990-998.  

28. A Hossain, J Beyene, A Willan, P Hu
     A flexible approximate likelihood ratio test for detecting differential expression in microarray data
     Computational Statistics and Data Analysis 53:3685-3695. 

27. JS Hamid, P Hu, NM Roslin, V Ling, CMT Greenwood, J Beyene
     Data integration in genetics and genomics: methods and challenges
     Human Genomics and Proteomics: Article ID 869093. 

26. IH Sung, TH Kim, SY Bang, TJ Kim, B Lee, L Peddle, P Rahman, CMT Greenwood, P Hu, RD Inman
     IL -23R polymorphisms in patients with ankylosing spondylitis in Korea
     The Journal of Rheumatology 36:1003-1005.

25. P Hu*, Z Wei*, Z Wang, AD Paterson, J Beyene, SW Scherer
     Scoring of ChIP-Seq experiments by modeling large-scale correlated tests
     Proceedings of Critical Assessment of Massive Data Analysis (CAMDA), pp. 25 - 32. Chicago, USA. 

24. P Hu, H Jiang, A Emili
     A topology-sharing based method for protein function prediction via analysis of protein functional association networks
     Proceedings of 2009 IEEE International Conference on Bioinformatics and Biomedicine (BIBM’ 09) Workshops, ISBN:

     978-1-4244-5121-0. pp. 243 - 248. Washington D.C., USA. 

23. P Hu, W Le, S Lim, B Xing, CMT Greenwood, J Beyene
     Serum Diagnosis of Chronic Fatigue Syndrome Using Array-based Proteomics
     Methods of Microarray Data Analysis VI, (CAMDA’06), edited by McConnell, P, Lim, S., and A.J. Cuticchia. Scotts Valley,
     California:  Create Space Publishing. 

22. S Lim, W Le, P Hu, B Xing, CMT Greenwood, J Beyene
     Integration of clinical, SNP, and microarray gene expression measurements in prediction of chronic fatigue syndrome
     Methods of Microarray Data Analysis VI, (CAMDA’06), edited by McConnell, P, Lim, S., and A.J.
     Cuticchia. Scotts Valley, California:  Create Space Publishing. 

21. TJ Kim, TH Kim, HJ Lee, L Peddle, P Rahman, P Hu, CMT Greenwood, RD Inman
     Interleukin -1 polymorphisms in patients with ankylosing spondylitis in Korea
     The Journal of Rheumatology 35:1603-1608.

20. CC dos Santos, D Okutani, P Hu, B Han, E Crimi, X He, S Keshavjee, CMT Greenwood, AS Slutsky, H Zhang, M Liu
     Differential gene profiling in acute lung injury identifies injury specific gene expression
     Critical Care Medicine 36:855-865. 

19. P Hu, C Chung, H Jiang, A Emili
     Chapter 13: Bioinformatics application: predicting protein subcellular localization by applying machine learning
     A Concept based Introduction to Bioinformatics, edited by VS Mathura et al. Springer-Verlag Press. 


18. P Hu*, H Lan*, W Xu, J Beyene, CMT Greenwood
     Identifying cis-and trans-acting SNPs controlling lymphocyte gene expression in humans
     BMC Proceedings 1 (Suppl 1):S7. Special issue of Genetic Analysis Workshop (GAW15), St. Petersburg Beach, FL,

     USA, November 2006. 

17. P Hu, G Bader, DA Wigle, A Emili
     Computational Prediction of cancer gene function
     Nature Reviews Cancer 7:23-34. 

16. J Beyene, P Hu, E Parkhomenko, D Tritchler
     Impact of normalization and filtering on linkage analysis of gene expression data
     BMC Proceedings 1 (Suppl 1):S150. Special issue of Genetic Analysis Workshop (GAW15), St. Petersburg Beach, FL,

     USA, November 2006. 

15. J Rangrej, J Beyene, P Hu, AD Paterson
     Sex and age effects on genome-wide linkage analysis of gene expression in transformed lymphoblasts
     BMC Proceedings 1 (Suppl 1):S92. Special issue of Genetic Analysis Workshop (GAW15), St. Petersburg Beach, FL,

     USA, November 2006. 

14. W Xu, H Lan, P Hu, SB Bull, CMT Greenwood
     Linkage analysis on chromosome 1 for Rheumatoid arthritis NARAC data: gene-gene and gene-environment interactions
     BMC Proceedings 1 (Suppl 1):S78. Special issue of Genetic Analysis Workshop (GAW15), St. Petersburg Beach, FL,

     USA, November 2006. 

13. P Hu, CMT Greenwood, CE M’lan, J Beyene
     Chromosomal clustering of periodically expressed genes in plasmodium falciparum
     Methods of Microarray Data Analysis V, (CAMDA’04), edited by P McConell, SM Lin and P Hurban. Springer-Verlag Press. 


12. T Kislinger*, B Cox*, A Kannan*, C Chung, P Hu, A Ignatchenko, MS Scott, A Gramolini, Q Morris, T Hughes, J Rossant,

     B Frey, A Emili
     Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling
     Cell 125:173-186. 

11. P Hu, CMT Greenwood, J Beyene
      Integrative analysis of gene expression data including an assessment of pathway enrichment for predicting prostate cancer
      Cancer Informatics 2:289-300. 

10. P Hu, J Beyene, CMT Greenwood
      Testing for differential gene expression in oligonucleotide microarray experiments using weights
      BMC Genomics 7:33. 

9. P Hu, CMT Greenwood, J Beyene
    Statistical methods for meta-analysis of microarray data: a comparative study
    Information Systems Frontiers 8:9-20.   

8. P Hu, CMT Greenwood, J Beyene
    Integrating Affymetrix microarray data sets using probe-level test statistic for predicting prostate cancer
    Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB’06),
    pp. 63-70. Toronto, Canada. 


7. P Hu, CMT Greenwood, J Beyene
   Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models
   BMC Bioinformatics 6:128. 

Before 2005

6. P Hu, CMT Greenwood, J Beyene
   Quality-adjusted modeling of inter-study variation in gene expression profiles
   Proceedings of the 3rd Canadian Working Conference on Computational Biology (CCCB’04), IBM Cascon
   Conference. IBM TR-74-203-8, 2004. 

5. P Hu, MI Heywood
   Predicting Intrusions with Local Linear Models
   Proceedings of IEEE International Joint Conference on Neural Networks, pp. 1780 - 1785. Portland, Oregon, 2003.

4. P Hu, J Pooler
   An empirical test of the competing destinations model
   Journal of Geographical Systems 4:301-323, 2002. 

3. P Hu, J Hou, Z Li
    A software system for statistical analysis of multivariate spatial information
    Remote sensing information 2:2-5 (In Chinese), 1998. 

2. Y Wei, G Sun, P Hu, J Li, J Jin
    The chaotic characteristics of annual precipitation series in JiuJiang
    JiangXi Science 3:141-145 (In Chinese), 1998. 

1. J Hou, Z Yin, W Li, Y Xiang, J Huang, P Hu
    Applied Geostatistics

    Beijing Geological Press. Beijing, China (In Chinese), 1998.