Research Articles (Trainees, Equal Contribution*, Co-corresponding**)
2022
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
mammograms
Computer Methods and Programs in Biomedicine,221:106903, https://doi.org/10.1016/j.cmpb.2022.106903
153. Q Liu, P Hu
An integrative computational framework for breast cancer radiogenomic biomarker discovery
Computational and Structural Biotechnology Journal, 20:2484-2494
https://www.sciencedirect.com/science/article/pii/S2001037022001878
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. https://doi.org/10.1186/s12859‑022‑04878‑6
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
2021
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.
2020
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. https://ieeexplore.ieee.org/document/9268138
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.
2019
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.
https://doi.org/10.1145/3318299.3318323 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.
2018
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. doi.org/10.1186/s13148-018-0490-.
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
2017
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
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 (* 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.
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
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.
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
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.
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.