(Trainees, Equal Contribution*, Co-corresponding**)
170. E Lin*, B Liu*, L Lac*, DLX Fung, CK Leung, P Hu
scGMM-VGAE: A Gaussian mixture model-based variational graph autoencoder algorithm for clustering single-cell RNA-seq data
Machine Learning: Science and Technology. 4 035013
169. Q Liu, S Huang, D Desautels, KJ McManus, L Murphy, P Hu
Development and validation of a prognostic 15-gene signature for stratifying HER2+/ER+ breast cancer
Computational and Structural Biotechnology Journal. 21:2940-2949.
168. D Fung, Q Liu, L Lac, L O'Neil, C Hitchon**, P Hu**
Deep learning-based joint detection in Rheumatoid arthritis hand radiographs
AMIA (American Medical Informatics Association) Jt Summits Transl Sci Proc. 206-215. PMID: 37350925. Seattle, Washington, USA. .
167. I Paul, D Bolzan, A Youssef, KA Gagnon, H Hook, G Karemore, MUJ Oliphant, W Lin, Q Liu, S Phanse, C White, D Padhorny, S Kotelnikov, CS Chen, P Hu, GV Denis, D Kozakov, B Raught, T Siggers, S Wuchty, SK Muthuswamy, A Emili
Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.
Nature Communications, 14:688.
166. Q Liu, S Huang, Z Zhang, T Lakowski, W Xu, P Hu
Multiomics-based tensor decomposition for characterizing breast cancer heterogeneity
Invited chapter for “Machine Learning Methods for Multi-Omics Data Integration” edited by Luis Rueda. Nature Springer -Verlag Press. In Press
165. DLX Fung, X Li, CKS Leung, P Hu
A self-knowledge distillation-driven CNN-LSTM model for predicting disease outcomes using longitudinal microbiome data
Bioinformatics Advances. 3:vbad059, https://doi.org/10.1093/bioadv/vbad059
164. C Liu, Y Sun, R Davis, ST Cardona, P Hu
ABT-MPNN: An atom-bond transformer-based message passing neural network for molecular property prediction
Journal of Cheminformatics,15:29.
163. Q Liu, P Hu
Radiogenomic association of deep MR imaging features with genomic profiles and clinical characteristics in breast cancer
Biomarker Research, 11:9. https://doi.org/10.1186/s40364-023-00455-y
162. S Huang, P Hu**, TM Lakowski**
Bioinformatics driven discovery of small molecule compounds to modulate the FOXM1 and PPARA pathway activities in breast cancer.
The Pharmacogenomics Journal, 23:61-72 (**Co-corresponding author)
161. J Zhang, W Kong, P Hu, D Joniker, M Moore, J Ringash, J Shapiro, J Zalcberg, J Simes, D Tu, CJ O'Callaghan, G Liu**, Wei Xu**
Clustering on longitudinal quality-of-life measurements using growth mixture models for clinically prognosis: Implementation on CCTG/AGITG CO.20 trial
159. Y Sun, M Islam, E Zahedi, M Kuenemann, H Chou, P Hu
Molecular Property Prediction based on Bimodal Supervised Contrastive Learning
2022 IEEE International Conference on Bioinformatics and Biomedicine. Las Vegas, NV, USA, 2022 pp. 394-397. doi: 10.1109/BIBM55620.2022.9995689
158. ASMZ Rahman, C Liu, H Sturm, AM Hogan, R Davis, P Hu, ST Cardona.
A Machine Learning Model trained on a High-Throughput Antibacterial Screen Increases the Hit Rate of Drug Discovery
Plos Computational Biology, 18(10):e1010613.
157. VC de Jesus, BA Mittermuller, P Hu, RJ Schroth, P Chelikani
Genetic variants in taste genes play a role in oral microbial composition and severe early childhood caries
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
155. MM Islam, N Mohammed, Y Wang, P 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,
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
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
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-
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
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. B Blum, W Lin, ML Lawton, Q Liu, J Kwan, I Turcinovic, R Hekman, P Hu, A 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
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
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
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
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
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
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.
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
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
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
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.
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.
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.
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 inflammatory bowel 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-.
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
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.
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.
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.
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.
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.
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 Medicine 17:747-752.
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
Pattern Analysis and Applications 18:535-551.
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.
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
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
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
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
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.
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.
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..
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.
17. P Hu, G Bader, DA Wigle, A Emili
Computational Prediction of cancer gene function
Nature Reviews Cancer 7:23-34.
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
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.
7. P Hu, CMT Greenwood, J Beyene
Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models
BMC Bioinformatics 6:128.