Selected Research Articles

 * The Best AI conferences (CVPR, NeurIPS, ICLR, AAAI, ICML) is based on this ranking

https://research.com/conference-rankings/computer-science/machine-learning

187.G Zhou*, S Janarthanan*, Y Lu, P Hu

CL-MFAP: A contrastive learning-based multimodal foundation model for molecular property prediction and antibiotic screening

The Thirteenth International Conference on Learning Representations (ICLR 2025). Singapore

186. H Hadipour, YY Li, Y Sun, A Deng, L Lac, R Davis, ST Cardona**, P Hu**

GraphBAN: An Inductive Graph-Based Approach for Enhanced Prediction of Compound-Protein Interactions

Nature Communications. 16:2541.  https://doi.org/10.1038/s41467-025-57536-9 

185. Y Shi, W Xu, P Hu

Out-of-Distribution Learning in Multiomics: Advancements and Challenges

Briefings in Bioinformatics. 

184. C Zhang, Y Sun, P Hu

An Interpretable Deep Geometric Learning Model to Predict the Effects of Mutations on Protein-ligand Interactions Using Large-scale Protein Language Model

Journal of Cheminformatics.  DOI: 10.1186/s13321-025-00979-5  

183. S Janarthanan, G Zhou, YY Li, Z Jing, P Hu

Leveraging transfer learning and multimodal foundation models for antibiotic discovery against data-scarce Escherichia coli strains. 

The Thirteenth International Conference on Learning Representations (ICLR) Workshops. Singapore

182. Q Liu, D Fung, H Liu, P Hu

Knockoff Statistics-Driven Interpretable Deep Learning Models for Uncovering Potential Biomarkers for COVID-19 Severity Prediction

The Thirteenth International Conference on Learning Representations (ICLR) Workshops. Singapore

181. SR Enes, I Dzneladze,TH Hampton,SL Neff, L Asarian, J Barua, T Tertel, B Giebel, 

N Pereyra, DH McKenna, P Hu, E Acton, A Ashare, KD Liu, AD Krasnodembskaya, 

K English, BA Stanton, PRM Rocco, MA Matthay, CC dos Santos, DJ Weiss

Acute respiratory distress vs healthy lung environments differently affect mesenchymal stromal cell extracellular vesicle miRNAs

Cytotherapy. https://doi.org/10.1016/j.jcyt.2025.01.006

180. KJ Bosma, M Lafreniere-Roula, A Jiang, A Heath, Y Ouyang, K Wade, P Hu, KEA Burns, CM Martin, Y Skrobik, S Mulligan, KE Thorpe, L Brochard

Proportional Assist Ventilation for Minimizing the Duration of Mechanical Ventilation (The PROMIZING Study): Update to the statistical analysis plan for a randomized controlled trial. Trials. 25:855.

179. L Chen, ZH Huang, Y Sun, M Domaratzki, Q Liu**, P Hu**

Conditional Probabilistic Diffusion Model Driven Synthetic Radiogenomic Applications in Breast Cancer

Plos Computational Biology, 20(10): e1012490. https://doi.org/10.1371/journal.

pcbi.1012490

178. KE Wade, L Chen, C Deng, G Zhou, P Hu

Investigating Alignment-Free Machine Learning Methods for HIV-1 Subtype Classification

Bioinformatics Advances.  vbae108, https://doi.org/10.1093/bioadv/vbae108 .

177. MW Khan, VC de Jesus, BA Mittermuller, S Sareen, V Lee, RJ Schroth, P Hu**, P Chelikani**. Role of socioeconomic factors and inter-kingdom crosstalk in the dental plaque microbiome in early childhood caries.  

Cell Reports, 43:114635.

176   MW Khan, DLX Fung, RJ Schroth, P Chelikani**, P Hu**

A cross-cohort analysis of dental plaque microbiome in early childhood caries

iScience, 27:110447.  DOI:https://doi.org/10.1016/j.isci.2024.110447 .

175. Y Li*, L Lac*, Q Liu, P Hu

ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multiscale manifold learning

Plos Computational Biology. 20(6): e1012254. https://doi.org/10.1371/journal.pcbi.1012254. 

174. Y Jin, P Hu Q Liu

NNICE: a deep quantile neural network algorithm for expression deconvolution

Scientific Reports, 14:14040. .

173. Y Sun, Y Li, C Leung, P Hu

iNGNN-DTI: prediction of drug - target interaction with interpretable nested graph neural network and pretrained molecule models

Bioinformatics. btae135. doi: 10.1093/bioinformatics/btae135.  

172. Z Huang, L Chen, Y Sun, Q Liu, P Hu

Conditional Generative Adversarial Network Driven Radiomic Prediction of Mutation Status Based on Magnetic Resonance Imaging of Breast Cancer

Journal of Translational Medicine, 22:226.

171. L Lac, C Leung, P Hu

Computational frameworks integrating deep learning and statistical models in mining multimodal omics data

Journal Biomedical Informatics,152:104629. 

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

Cancer Medicine.  12:6117-6128.

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

iScience, 25(12):105489. 

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, 114(5):110474. 

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

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

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. 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

Gene, 800:145842

133. Y Xu, J Kong, P Hu

Computational drug repurposing for Alzheimer's disease using risk genes from GWAS and 

single-cell RNA sequencing studies

Frontiers in Pharmacology, 12:617537.

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

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

network model

BMC Cancers. 21:648. 

­131. V Cruz de Jesus, MW Khan, BA Mittermuller, K Duan, P Hu**, RJ Schroth**, 

P Chelikani** (** Co-corresponding author.)

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

early childhood caries 

Frontiers in Microbiology. 12:683685.

130. S Jia, P Hu

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

immune cell types

Genomics. 113:2023-2031.

129. AF Hamad, V Vasylkiv, L Yan, R Sanusi, O Ayilara, J Delaney, E Wall-Wieler, 

MJ Jozani, P Hu, S Banerji, LM Lix

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

Chronic Conditions

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

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

Genetic predictors of gene expression associated with psychiatric comorbidity in patients 

with IBD: a pilot study

Genomics. 113: 919-932.

127. AM Ektesabi, K Mori, J Tsoporis, C Vaswani, S Gupta, C Walsh, SHJ Mei, 

DJ Stewart, WC Liles, J Marshall, P Hu, T Parker, CC dos Santos

Mesenchymal Stem/Stromal Cells Increase Cardiac MIR-187-3P Expression in 

Polymicrobial Animal Model of Sepsis 

Shock. 56:133-141.

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

Identification of significantly mutated subnetworks in the breast cancer genome

Scientific Reports. 11:642.

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

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

Journal of Translational Medicine. 18:454.
 

124. Q Liu, CK Leung, P Hu

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

IEEE Access. 8:213718-213728.
 

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. 

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

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

Thorax. 75:556-567.
 

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

Deep graph embedding for prioritizing synergistic anticancer drug combinations

Computational and Structural Biotechnology Journal. 18:427-438
 

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

Sex-based diverse plaque microbiota in children with severe caries

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

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

Epigenetics of Sepsis

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

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

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

BMC Medical Genetics, 13 (Suppl 3):10

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

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

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

111. Frenkel S, CN Bernstein, M Sargent, W Jiang, Q Kuang, W Xu, P Hu

Copy number variation-based gene set analysis reveals cytokine signaling pathways associated with psychiatric comorbidity in patients with inflammatory bowel disease

Genomics, 112(1): 683-693.

110. P Brown, P Hu (as a member of the RELISH Consortium), Y Zhou

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Database: The Journal of Biological Databases and Curation. Volume 2019, 2019, baz085.
 

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

Genome 56:619-625.

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.