The Hu Lab

Bioinformatics and Statistical Genetics

Research Contributions (Trainees, Equal Contribution*)


98. X Hou, J You, P Hu

     Predicting drug-drug interactions using deep neural network

     Accepted by 11th International Conference on Machine Learning and Computing. Zhuhai, China.

97. J You, R McLeod, P Hu

      Predicting drug-target interaction network using deep learning modes

      Accepted by APBC2019: The Seventeenth Asia Pacific Bioinformatics Conference. Wuhan, China.

 96.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. Vancouver: American Statistical Association.

95. PC Havugimana*, P Hu*, A Emili
      Functional proteomics: systematic characterization of the physical and functional organization of cell systems

      Yates J and Veenstra T. Proteomics for Biological Discovery. 2th Edition. Accepted/In press (* Co-first Author)

94. 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, In Press

93. L Zhang*, N Feizi*, C Chi, P Hu

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

      Frontiers in Genetics. doi: 10.3389/fgene.2018.00421.

92. 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

91. 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*

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

      adiposity – a pilot study. 

      Clinical Epigenetics, 10:54.

90.  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.

 89. 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.

88. MB Karim, N ONO, R Eguchi, K Shigehiko, P Hu, MA Amin

      Identification of IBD-associated miRNAs by bi-clustering

      Proceedings of International Conference on Computational Mathematics, Physics and Its Applications ( ICCMPA). In Press

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

      methylation profiles
      BMC Proceedings, 12(Suppl 9):21(* Co-first Author)

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
      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 (* Co-first Author)

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
      Gene expression analysis of “young adult type” breast cancer: a retrospective analysis
      Oncotarget 6:13688-13702  (* Co-first author)

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.