Dalla Lana School of Public Health

Faculty Member

Pingzhao Hu PhD,Statistical Genetics and Bioinformatics

Research Interests

My research program focuses on developing and applying computational and statistical techniques for integrative analysis of big multimodal health data (omics data, imaging data, administrative and electronic medical records) for precision medicine. My group also collaborates very closely with local, national and international life science scientists and clinicians on different omics projects. Current PhD/MSc students’ thesis projects are in the research areas: radiogenomics, medical imaging, rare disease diagnosis using facial photos and phenotypes, drug discovery, microbiome, single cell RNA sequencing and omics data integration.

• Radiogenomics, medical imaging and electronic medical records
• Genetic epidemiology and statistical genetics
• Tensor-based multidimensional omics data integration
• Machine Learning and big data science

We are looking for excellent candidates (MSc and PhD) to join my team at Western University.  The candidates should have strong backgrounds in computer science,  (bio)statistics, and/or bioinformatics. The positions are fully funded. 

To apply for the positions, please send a CV, transcripts and related reports/publications written in English to Dr. Pingzhao Hu at pingzhao.hu@utoronto.ca or phu49@uwo.ca. More details can be found at https://phulab.org/positions.

My lab also remotely hosts senior undergraduate students in genetics/life science, mathematics, statistics, and computer science from the University of Toronto.

Leadership in Professional Association

2018 August – 2020 June        Chair of Case Studies in Data Analysis Committee,                                                                               Statistical Society of Canada (SSC)

Other affiliation

Tenured Associate Professor, Department of Biochemistry, Western University

Member of Temerty Centre for AI Research and Education in Medicine (T-CAIREM)
Temerty Faculty of Medicine,  University of Toronto

Honors & Awards

• 2021 September, University of Manitoba Graduate Students’ Association Teaching Award. University of Manitoba Graduate Students’ Association (UMGSA), University of Manitoba. The purpose of the award is to recognize faculty members who have made, in the estimate of their graduate students, a significant contribution to their teaching profession. It is awarded to only one faculty member at the University of Manitoba in each year.
• 2021 Jun, Ed Kroeger Mentorship Award. Health Sciences Graduate Student Association (HSGSA), University of Manitoba. It recognizes excellence and distinction in mentorship, teaching, and research. It is awarded to only one faculty member in Rady Faculty of Health Sciences in each year.
• 2020 September, Terry G. Falconer Memorial Rh Institute Foundation Emerging Researcher Award (Interdisciplinary Category). The Winnipeg Rh Institute Foundation and the University of Manitoba. The most prestigious award for junior faculty members at the University of Manitoba, which is awarded to the only one who made Outstanding Contributions to Scholarship and Research in the Interdisciplinary Category at the University of Manitoba in each year.
• 2020 May, MMSF Allen Rouse Basic Science Career Development Research Award. The Manitoba Medical Service Foundation (MMSF). It is awarded to only one or two of the most promising health researchers in basic
• science in Manitoba in every three years.
• 2019 March, Best Oral Presentation Paper Award (Corresponding author) in 2019 IEEE 7th International Conference on Bioinformatics and Computational Biology.
• 2019 February, Best Presentation Paper Award (Corresponding author) in 2019 11^th International Conference on Machine Learning and Computing.
• 2018 May, The Interstellar Initiative Award by New York Academy of Sciences and Japan Agency for Medical Research and Development. The award recognizes “the world’s most promising Early Career Investigators in the fields of cancer, neuroscience, and artificial intelligence”.
• 2015 Jul, New Principal Investigator Award, Careers in Cancer Research Development Program by CIHR Institute of Cancer Research and Canadian Cancer Society Research The award recognizes the research excellence of new investigators in Canada.

Selected Grants

2017 May – 2023 Apr: Visual and Automated Disease Analytics (VADA), NSERC Collaborative Research and Training Experience (CREATE) Program. Co-I.

2020 Jan – 2023 Dec: Prediction and prevention of rheumatoid arthritis in First Nations people, CIHR Team grant: human immunology Initiative: Research Teams. Co-I.

2019 Sep – 2024 Aug:   EpiGen marks for human sepsis,  Canada Institutes of Health Research (CIHR), Project Grant Spring 2019. Co-I.

2018 Aug – 2023 Jul:  Role of taste signaling and host-microbial interactions on caries risk in young children, Canada Institutes of Health Research (CIHR), Project Grant Spring 2018. Co-I.

2018 Nov – 2020 Oct:   Antibiotic discovery for Burkholderia cepacia complex, Cystic Fibrosis Foundation (CFF), USA, Pilot and Feasibility Awards – Spring Cycle. Co-I.

Selected External Grant Reviews

2021 Feb                             Canada Research Chair (CRC) Tier I Application, Canadian Institute of Health Research

2020 Jul-Aug                       Canadian Institute of Health Research (CIHR) – Project Grant: Spring 2020 Competition –Peer Reviewer and Member on the Genetics Committee.

2020 Mar – 2020 Apr           National Science Center, Poland, Review Panel for the Computer Science and Informatics.

2019 Nov – 2020 Jan            Juvenile Diabetes Research Foundation (JDRF), Review Panel for the Repositioning Drugs to Improve Metabolic Control in Established Type 1 Diabetes Competition, New York, USA

2019 Oct                             Florida Department of Health’s Ed & Ethel Moore Alzheimer’s Disease Research program, Oak Ridge Associated Universities, USA

2019 Jul                              Wellcome Trust / DBT Fellowship (1 Proposal). Note: This is a partnership between the Wellcome Trust (UK) and the Department of Biotechnology (Government of India).

2019 May-Jun                     Operating Grant, Deutsche Forschungsgemeinschaft (German Research Foundation), German.

2019 Dec – 2020 Jan           Individual Discovery Grant, Natural Sciences and Engineering Research Council (NSERC)

2019 Nov –Dec                    Expert Reviewer for John R. Evans Leaders Fund, Canada Foundation for Innovation (CFI)

2019 Aug                            Cancer Early Detection -2018/19 Competition, Alberta Cancer Foundation

2018 Aug-Sep                     Grand Challenges Canada Transition to Scale program, Round 8 and Canadian Institute of Health Research (CIHR)

2018 Aug                            Collaborative Research and Development Grant, Natural Sciences and Engineering Research Council (NSERC)

2018 Apr                             Scholar Program, The Michael Smith Foundation for Health Research (MSFHR)

2017 Oct –                           Canadian Institute of Health Research (CIHR) – 2017 Catalyst Grant: Personalized Health Catalyst Grants

2017 Feb                             Canadian Institute of Health Research (CIHR) – Project Grant Program 2016 Fall Competition

Selected Publications

* indicates co-first author or equal contribution and ** indicates co-corresponding author. Boldface underlined names are the HQP I supervised or co-supervised and boldface name is my name.

1. Q Liu*, M Reed*, H Zhu*, Y Cheng, J Almeida, G Fruhbeck, R Ribeiro, P Hu (2022).
   Epigenome-wide DNA methylation and transcriptome profiling of localized and locally advanced prostate cancer: uncovering new molecular markers
   Genomics, In Press.
2. MM Islam, N Mohammed, Y Wang, P Hu (2022). Differential Private Deep Learning Models for analyzing breast cancer omics data. Frontiers in Oncology. 12:879607.
3. Y Su, Q Liu, W Xie, P Hu (2022). 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.
4. Q Liu, P Hu (2022). An integrative computational framework for breast cancer radiogenomic biomarker discovery. Computational and Structural Biotechnology Journal, 20:2484-2494.
5. Z Zhang, W Xu**, P Hu** (2022). Tightly integrated multiomics-based deep tensor survival model for time-to-event prediction. Bioinformatics,38:3259-3266.
6. J Zammit, DLX Fung, Q Liu, CKS Leung, P Hu (2022). Semi-Supervised COVID-19 CT Image Segmentation Using Deep Generative Models. BMC Bioinformatics, 23:343.
7. H Hadipour*, C Liu*, R Davis, ST Cardona, P Hu (2022). Deep clustering of small molecules at large-scale via variational autoencoder embedding and K-means. BMC Bioinformatics, 23:132.
8. C Liu, AM Hogan, H Sturm, MW Khan, MM Islam, ASMZ Rahman, R Davis, ST Cardona, P Hu (2022). Deep learning – driven prediction of drug mechanism of action from large-scale chemical-genetic interaction profiles. Journal of Cheminformatics, 14:12.
9. Y Li, Charles N Bernstein, W Xu, P Hu (2022). Polygenic risk and causal inference of psychiatric comorbidity in inflammatory bowel disease among patients with European ancestry. Journal of Translational Medicine, 20:43.
10. N Feizi, Q Liu, L Murphy, P Hu (2022). Computational prediction of the pathogenic status of cancer-specific somatic variants. Frontiers in Genetics. 12:805656.
11. Q Liu, P Hu (2022). Interpretable and extendable deep learning for pan-cancer radiogenomics research. Current Opinion for Chemical Biology. 66:102111.
12. Q Liu*,B Cheng*, Y Jin, P Hu (2022). Bayesian tensor factorization-driven breast cancer subtyping by integrating multi-omics data. Journal of Biomedical Informatics. 125:103958.
13. Q Liu*, D LX Fung*, L Lac*, P Hu (2021). A novel matrix profile-guided attention LSTM model for forecasting COVID-19 cases in USA. Frontiers in Public Health. 9:741030.
14. D LX Fung*, Q Liu*, J Zammit, CK Leung, P Hu (2021). 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
15. Y Xu, J Kong, P Hu (2021). Computational drug repurposing for Alzheimer’s disease using risk genes from GWAS and single-cell RNA sequencing studies. Frontiers in Pharmacology, 12:617537.
16. S Huang, P Hu**, T Lakowski**. (2021). Predicting breast cancer drug response using a multiple-layer cell line drug response network model. BMC Cancer. 21:648. [SRA] **Co-corresponding authors.
17. Cruz de Jesus, MW Khan, BA Mittermuller, K Duan, P Hu**, RJ Schroth**, P Chelikani** (2021) Characterization of supragingival plaque and oral swab microbiomes in children with severe early childhood caries. Frontiers in Microbiology, 12:683685 [SRA] ** Co-corresponding author.
18. Jia, P Hu (2021). ChrNet: A re-trainable chromosome-based 1D convolutional neural network for predicting immune cell types. Genomics. 113:2023-2031.
19. A Bruinooge*, Q Liu*, Y Tian, W Jiang, Y Li, W Xu, CN Bernstein, P Hu (2021). Genetic predictors of gene expression associated with psychiatric comorbidity in patients with inflammatory bowel disease – a pilot study. Genomics. 113: 919-932.
20. Ajwad, M Domaratzki, Q Liu, N Feizi, P Hu (2021). Identification of significantly mutated subnetworks in the breast cancer genome. Scientific Reports. 11:642.
21. ​A Tran, CJ Walsh (*), Jane Batt, CC dos Santos (**), P Hu  (2020). A machine learning-based clinical tool for diagnosing myopathy using multi-cohort microarray expression profiles. Journal of Translational Medicine. 18:454.
22. Q Liu, CK Leung, P Hu (2020). A two-dimensional sparse matrix profile DenseNet for COVID-19 diagnosis using chest CT image. IEEE Access. 8:213718-213728.
23. Y Jin, S Jia, A Ashraf, P Hu (2020). Integrative data augmentation with U-net segmentation masks improves detection of lymph node metastases in breast cancer patients. Cancers. 12:2934.
24. MM Islam, S Huang, R Ajwad, C Chi, Y Wang, P Hu (2020). An integrative deep learning framework for classifying molecular subtypes of breast cancer. Computational and Structural Biotechnology Journal. 18:2185-2199.
25. Z Sun, S Huang, P Jiang, P Hu. (2020). DTF: Deep tensor factorization for predicting anticancer drug synergy. Bioinformatics. 36:4483-4489.
26. YW Jin, P Hu (2020). Tumor-Infiltrating CD8 T Cells Predict Clinical Breast Cancer Outcomes in Young Women. Cancers. 12:1076.
27. P Jiang*, S Huang*, Z Sun, Z Fu, T Lakowski, P Hu. (2020) Deep graph embedding for prioritizing synergistic anticancer drug combinations. Computational and Structural Biotechnology Journal. 18:427-438.
28. VCruz de Jesus, R Shikder, D Oryniak, K Mann, A Alamri, BA Mittermuller, K Duan, P Hu**, RJ Schroth** and P Chelikani** (2020).Sex-based diverse plaque microbiota in children with severe caries. Journal of Dental Research. 99(6):703-712.
29. S Frenkel, CN Bernstein, M Sargent, W Jiang, Q Kuang, W Xu, P Hu (2020). 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.
30. Q Liu, A Junker, K Murakami, P Hu (2019). Automated counting of cancer cell by ensembling deep features. Cells, 8:1019.
31. S Frenkel, CN Bernstein, M Sargent, Q Kuang, W Jiang, J Wei, B Thiruvahindrapuram, B Spriggs, SW Scherer, P Hu (2019). Genome-wide analysis identifies rare copy number variations associated with inflammatory bowel disease. Plos One. 14(6):e0217846.
32. R Shikder, P Thulasiraman, P Irani, P Hu (2019). A openAM-based tool for finding longest common subsequence in bioinformatics. BMC Research Notes, 12:220.
33. Q Liu, P Hu (2019). Association analysis of deep genomic features extracted by denoising autoencoders with breast cancer clinical outcomes. Cancers, 11:494; doi:10.3390/cancers11040494.
34. J You, R McLeod, P Hu (2019). Predicting drug-target interaction network using deep learning model. Computational Biology and Chemistry, 80:90-101.
35. L Grenier, P Hu (2019). Computational drug repurposing for inflammatory bowel disease using genetic information. Computational and Structural Biotechnology Journal, 17: 127-135.
36. J Zhang, X Ye, C Wu, H Fu**, W Xu**, P Hu** (2019). Modelling gene-environment interaction for the risk of non-Hodgkin lymphoma. Frontiers in Oncology, 8:657. **Co-corresponding authors.
37. L Zhang*, N Feizi*, C Chi, P Hu (2018). Association analysis of somatic copy number alteration burden with breast cancer survival. Frontiers in Genetics, 9:421. *Co-first author.
38. 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** (2018). Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity – a pilot study. Clinical Epigenetics, 10:54. **Co-corresponding authors.
39. C Chi, LC Murphy, P Hu (2018). Recurrent copy number alterations in young women with breast cancer. Oncotarget, 9:11541-11558.
40. PC Havugimana*, P Hu*, A Emili (2017). Protein complexes: big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks. Expert Review of Proteomics, 14:845-855. *Co-first author.
41. MM Islam*, Y Tian*, Y Chen, Y Wang, P Hu. A deep learning regression model for phenotype prediction based on GAW20 genome-wide DNA methylation data. Genetic Analysis Workshop (GAW) 20. San Diego, CA, USA, March 2017. BMC Proceedings, 12(Suppl 9):21. *Co-first author.
42. C Chi, R Ajwad, Q Kuang, P Hu (2016). A graph-based algorithm for detecting recurrent copy number variants in cancer studies. Cancer Informatics, Suppl2: 43-50.
43. P Hu, AD Paterson (2014). 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.
44. P Hu*, X Wang*, JJ Haitsma, S Furmli, H Masoom, M Liu, AS Slutsky, J Beyene, CM Greenwood, CC dos Santos (2012). Microarray meta-analysis identifies acute lung injury biomarkers in donor lungs that predict development of primary graft failure in recipients. Plos One 7:e45506.
45. P Hu, S Bull, H Jiang (2012). Gene network modular-based classification of microarray samples. BMC Bioinformatics13 (Suppl 10): S17.
46. W Wang, W Hu, F Hou, P Hu, Z Wei (2012). SNVerGUI: A desktop tool for variant analysis of next-generation sequencing data. Journal of Medical Genetics 12:753-755.
47. 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 (2012). A census of human soluble protein complexes. Cell 150:1068-1081.
48. Z Wei, W Wang, P Hu, GJ Lyon, H Hakonarson (2011). SNVer: a statistical tool for variant calling in analysis of pooling or individual next-generation sequencing data. Nucleic Acids Research 39:e132.
49. P Hu, H Jiang, A Emili (2010). Predicting protein functions by relaxation labeling protein interaction network. BMC Bioinformatics 11(Suppl):S64.
50. P Hu, CMT Greenwood, J Beyene (2009). Using the ratio of means as the effect size measure in combining results of microarray experiments. BMC System Biology 3:106.
51. 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 (2009). Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biology 7:e96.
52. P Hu, G Bader, DA Wigle, A Emili (2007). Computational Prediction of cancer gene function. Nature Reviews Cancer 7:23-34.
53. 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 (2006). Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125:173-186.
54. P Hu, J Beyene, CMT Greenwood (2006). Testing for differential gene expression in oligonucleotide microarray experiments using weights. BMC Genomics 7:33.
55. P Hu, CMT Greenwood, J Beyene (2005). Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models. BMC Bioinformatics 6:128.