Youlian Pan

Roles and responsibilities

A Senior Research Officer in Data Science for Complex Systems, Digital Technologies Research Centre.

Responsible for data analytics with applications in environmental and life sciences.

 

 

Current research and/or projects

Youlian’s recent research interest includes big data analytics, machine learning, artificial neural networks, bioinformatics, functional genomics and systems biology. His research applications include biological, medical and environmental data analysis and numeric modeling. Specifically, his research is currently focused on (1) functional genomics related with human diseases, such as cancer and neurodegenerative diseases, particularly on discovery of human health therapeutics, (2) geospatial data analytics related with marine pollution and biotoxins, and (3) systems biology related with yield and resistance to biotic or abiotic stress of commercial crops, such as canola and wheat.
 

 

 

 

 

Research and/or project statements

Use deep learning and big genomics data for personalized early cancer diagnosis and therapeutics.

Geospatial data analytics to explore spatial and temporal distribution patterns and risk prediction of marine pollutants and biotoxins.

Study transcriptional reprograming of crop plants (e.g. wheat and canola) under biotic and abiotic stresses.

Explore differential gene expression feature patterns using machine learning approaches.

Education

Master of Computer Science, 2002

Ph.D. in Biology, 1994

Professional activities/interests

Adjunct Professor:

 

Brock University: St. Catharines, Ontario – Department of Computer Science, 2023-present

University of Victoria: Victoria, BC - Department of Mathematics & Statistics, 2021-present

Regional (Associate) Editor:

Frontiers in (2020-present) – Plant Sciences, Microbiology

MDPI (2020-present) – Biology  

Bentham – Current Bioinformatics (2005-2018), The Open Applied Informatics Journal (2007-2013)

Editorial Advisor:  

Frontiers in (2020-present) – Genetics

ScienPress (2011-present) - Journal of Computations & Modeling 

Bentham (2007-present) – Open Medical Informatics   

Science Publishing Group (2012-2015) – Health Informatics

Reviewer for:  

Springer Nature journals (2017 – present), Science Publishing Group journals (2012 – present), Elsevier Journals (1991 – present), Multidisciplinary Digital Publishing Institute (MDPI, 2020 – present), IEEE & ACM conferences, and many others.

Awards

Outstanding Research Achievement Award, NRC-IIT (2009)

General Research Achievement Award, NRC-IIT (2005)

Postdoctoral Visiting Fellowship, NRC-NSERC (1996 - 1998)

Postdoctoral Fellowship, NSERC (1996)

Graduate Scholarships, Dalhousie University (1989-94)

Key publications

  1. You S, L Xing, M Lesperance, Y Pan, X Zhang (2024). Temporal and spatial variation of domoic acid along Canada's coast. Science of The Total Environment 993: 172817. https://doi.org/10.1016/j.scitotenv.2024.172817
  2. Ali, N.S., S Thakur, M Ye, F Monteil-Rivera, Y Pan, W Qin & TC Yang   Uncovering the lignin-degrading potential of Serratia quinivorans AORB19: insights from genomic analyses and alkaline lignin degradation. BMC Microbiol 24: 181 (2024). https://doi.org/10.1186/s12866-024-03331-3
  3. You S, L Xing, M Lesperance, Y Pan, X Zhang (2024). Longitudinal study of paralytic shellfish toxins along Canada's coast. Environmental Research 252: 118944. 10.1016/j.envres.2024.118944
  4. Freitas-Andrade M, CH Comin, PV Dyken, J Ouellette, J Raman-Nair, N Blakeley, QY Liu, S Leclerc, Y Pan, Z Liu, M Carrier, K Thakur, A Saward, GM Rurak, M-E Tremblay, N Salmaso, LDF Costa, G Coppola, B Lacoste (2023). Astroglial Hmgb1 regulates postnatal astrocyte morphogenesis and cerebrovascular maturation. Nature Communications 14: 4965. 10.1038/s41467-023-40682-3
  5. You S, X Huang, L Xing, M Lesperance, C LeBlanc, P Moccia, V Mercier, X Shao, Y Pan, X Zhang (2023). Dynamics of Fecal Coliform Bacteria along Canada’s Coast. Marine Pollution Bulletin 189:114712.  10.1016/j.marpolbul.2023.114712
  6. Pan Y, Y Li, Z Liu, J Zou, Q Li (2022). Computational genomics insights into cold acclimation in wheat. Frontiers in Genetics 13:1015673. 10.3389/fgene.2022.1015673
  7. Yang G, Y Pan, Q Zhao, J Huang, W Pan, L Cui, W Song, T Ouellet, Y Pan, X Nie (2022). Genome-wide identification and characterization of RNA-DNA differences associated with Fusarium graminearum infection in wheat. International Journal of Molecular Sciences 23(14): 7982.  10.3390/ijms23147982
  8. Liu Q, S LeClerc, Y Pan, Z Liu, F Stark, JW Conlan (2022). Novel transcriptional and translational biomarkers of tularemia vaccine efficacy in a mouse inhalation model: proof of concept. Microorganisms 10(1): 36. 10.3390/microorganisms10010036
  9. Buhrow LM, Z Liu, D Cram, T Sharma, NA Foroud, Y Pan, MC Loewen (2021). Wheat transcriptome profiling reveals abscisic and gibberellic acid treatments regulate early-stage phytohormone defense signaling, cell wall fortification, and metabolic switches following Fusarium graminearum-challenge. BMC Genomics, 22:798. 
  10. Fauteux F, A. Surendra, S McComb, Y Pan, JJ Hill (2021). Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data. Scientific Reports 11:8709.  10.1038/s41598-021-88209-4
  11. Ouellette J, X Toussay, M Ho, CH Comin, LF Costa, M Lacalle-Aurioles, QY Liu, S Leclerc, Y Pan, Z Liu, Y Truong, A Kirby, M Yin, J-F Thibodeau, PV Dyken1, M Freitas-Andrade, M Carrier, ME Tremblay, CR Kennedy, D Burger, AJ Shuhendler, DJ Stewart, B Lacoste (2020). Vascular contribution to 16p11.2 deletion autism syndrome modeled in mice. Nature Neuroscience 23:1090-1101. 10.1038/s41593-020-0663-1
  12. Fauteux F, Y Wang, H Rocheleau, Z Liu, Y Pan, G Fedak, C McCartney, T Ouellet (2019). Characterization of QTL and eQTL linked with early Fusarium graminearum infection and deoxynivalenol levels in a Wuhan 1 x Nyubai doubled-haploid wheat population. BMC Plant Biol. 19:536. 10.1186/s12870-019-2149-4
  13. Xiang D, T Quilichini, Z Liu, P Gao, Y Pan, Q Li, K Nilsen, P Venglat, E Esteban, A Pasha, Y Wang, R Wen, Z Zhang, Z Hao, E Wang, Y Wei, R Cuthbert, A Sharpe, N Provart, D Weijers, S Gillmor, C Pozniak, R Datla (2019). The transcriptional landscape of polyploid wheats and their diploid ancestors during embryogenesis and grain development. The Plant Cell 31: 2888–2911. 10.1105/tpc.19.00397
  14. Li Y, Pan Y, Liu Z (2019). Multi-class non-negative matrix factorization for comprehensive feature pattern discovery. IEEE Transactions on Neural Networks and Learning Systems 30:615-629. Appeared online July 16, 2018. https://doi.org/10.1109/TNNLS.2018.2849932. pdf
  15. Wang L, Li Q, Liu Z, Surendra A, Pan Y, Li Y, Zaharia LI, Ouellet T, Fobert PR (2018). Integrated transcriptome and hormone profiling highlight the role of multiple phytohormone pathways in wheat resistance against fusarium head blight. Plos One 13(11): e0207036. https://doi.org/10.1371/journal.pone.0207036. pdf
  16. Li Y, Fauteux F, Zou J, Nantel A, Pan Y (2018). Personalized prediction of genes with tumor-causing somatic mutations based on multi-modal deep Boltzmann machine. Neurocomputing 324:51-62. pdf
  17. Pan Y, Liu Z, Rocheleau H, Fauteux F, Wang Y, McCartney M, Ouellet T (2018). Transcriptome dynamics Associated with Resistance and Susceptibility against Fusarium Head Blight in Four Wheat Genotypes. BMC Genomics 19:642. pdf.
  18. Tchagang AB, Fauteux F, Tulpan D, Pan Y (2017). Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat. BMC Bioinformatics 18:174. pdf
  19. Wang Y, Richard R, Pan Y (2016). Prior knowledge guided eQTL mapping for identifying candidate genes. BMC Bioinformatics 17:531. pdf
  20. Fauteux F, Hill J, Jaramillo ML, Pan Y, Phan S, Famili F, O’Connor-McCourt M (2016). Computational Selection of Antibody-Drug Conjugate Targets for Breast Cancer. Oncotarget 7(3): 2555-2571, DOI: 10.18632/oncotarget.6679. pdf
  21. Tulpan D, Leger S, Tchagang A, Pan Y (2015). Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants. BMC Genomics, 16:299. pdf
  22. Wang Y and Pan Y (2014) Semi-supervised consensus clustering for gene expression data analysis. BioData Mining 7:7. pdf
  23. Tchagang AB, F. Famili, and Y Pan (2014). Subspace-clustering of DNA Microarray Data: Theory, Evaluation, and Applications. International Journal of Computational Models and Algorithms in Medicine (IJCMAM) 4(2): 1-52.
  24. Tchagang AB, S Phan, F Famili, H Shearer, P Fobert, Y Huang, J Zou, D Huang, A Cutler, Z Liu, and Y Pan (2012) Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm. BMC Bioinformatics 13:54. pdf
  25. Pan Y, S Phan, F Famili, ML Jaramillo, AEG Lenferink, and E Wang (2010). Differences in promoters of orthologous genes. The Open Bioinformatics Journal 4: 41-49. pdf

Previous work experience

1999-2001 Guest Worker - Canadian Bioinformatics Resource, National Research Council Canada (NRC), Halifax

1999-2001 Lecturer - Department of Biology, Saint Mary's University, Halifax.
1996-98 Post-doctorate (NSERC Visiting Fellow) – Institute for Marine Bioscience (IMB), NRC, Halifax
1994-96 Instructor - Department of Biology, Saint Mary's University, Halifax
1989-96 Consultant - Bedford Institute of Oceanography (BIO), DFO, Halifax
1988-89 Visiting Scientist - Bedford Institute of Oceanography, DFO, Halifax

International experience and/or work

1998-99 Research Associate – Marine Biomedicine and Environmental Sciences (MBES), Medical University of South Carolina; Center for Coastal Environmental Health and Biomolecular Research, NOAA/NOS, Charleston, South Carolina, USA

1982-88 Research Associate (87-88) and Research Assistant (82-87) - Institute of Oceanology, Chinese Academy of Sciences (中国科学院海洋研究所), Qingdao, China

Youlian Pan

Senior Research Officer
Digital Technologies
1200 Montreal Road
Ottawa, Ontario K1A 0R6
Preferred language: English
Other(s): Chinese (Mandarin)
Telephone: 613-993-0853

Expertise

Genomics, Big Data, Information Technology