Research Contributions (Trainees, Equal Contribution*)


2017


89. MM Islam, R Ajwad, C Chi, Y Wang, P Hu

      OmicsNet: An integrative deep learning framework for molecular classification of breast cancer

      Submitted to Artificial Intelligence in Medicine

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

      Epigenome-wide DNA Methylation Profiling of Periprostatic Adipose Tissue Reveals Important Roles of Obesity in Men with Prostate

      Cancer    

      Submitted to BMC Medicine


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

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

       European Journal of Human Genetics


86. 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, In Press (* Co-first Author)

85. PC Havugimana*, P Hu*, A Emili

      Protein Complexes: Big Data, Machine Learning and Integrative Proteomics

      Expert Review of Proteomics, In Press (* 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 interactions

       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 population

      Oncotarget 8, 10450-10457.


2016


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 Translocation

      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 weakness
      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 study
      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.



2015


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.



2014
   
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. 

 


2013


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.


2012

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. 



2011

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, October 2010. 

 

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, October 2010. 


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. 

 


2010

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 colitis

     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.


 

2009

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, September 2008. 

 

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, September 2008. 

 

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. 

 


2008
 

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. 


 

2007

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. 

 

 

2006


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. 


 

2005

 

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. 



PUBLICATIONS


The Hu Lab

Bioinformatics and Statistical Genetics