The Hu Lab

Bioinformatics and Statistical Genetics
























Our group develops novel machine learning and statistical algorithms for various topics related to bioinformatics and statistical genetics. We also collaborate very closely with local, national and international life science scientists and clinicians on different transcriptomic, genetic and proteomic projects. We are actively working in the following three research areas.


Deep Learning and Visual Analytics Algorithms for  Omics Data, Imaging and Electronic Medical Records


References

  • P Hu, S Bull, H Jiang (2012). Gene network modular-based classification of microarray samples. BMC Bioinformatics13 (Suppl 10): S17.
  • P Hu, H Jiang, A Emili (2010). Predicting protein functions by relaxation labeling protein interaction network. BMC Bioinformatics 11(Suppl):S64.
  • 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.
  • P Hu, G Bader, DA Wigle, A Emili (2007). Computational Prediction of cancer gene function. Nature Reviews Cancer 7:23-34.


Integrative Analysis Frameworks for Omics Data, Imaging and Electronic Medical Records

References

  • 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.
  • 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.
  • P Hu, CMT Greenwood, J Beyene (2005). Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models. BMC Bioinformatics 6:128.



Translational Medicine and Precision Health


References

  • 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  (2014). Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder. Nature Genetics 46: 742-747.
  • 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 (2013). Metaphyseal dysplasia with maxillary hypoplasia and brachydactyly is caused by a duplication in RUNX2. American Journal of Human Genetics 92:252-258.
  • 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.
  • 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 (2012). Markers of survival and metastatic potential in childhood CNS primitive neuro-ectodermal brain tumors: an integrative genomic analysis. Lancet Oncology 13:838-848.
  • 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 (2010). PRKAR1A is an Osteosarcoma tumor suppressor and defines a molecular subclass in mice. Journal of Clinical Investigation120:3310-3325.