Mohamed Helmy
Postdoc Researcher, Bader's Lab
The Donnelly Centre
University of Toronto (UofT)
Contact Address:Map
160 College Street, Room 630
The Donnelly Centre
University of Toronto
Toronto, Ontario
Canada, M5S 3E1
Email: helmy.sfc AT gmail.com
Bio
I am a Postdoc researcher at Bader's Lab, The Donnelly Centre of the University of Toronto. I got my BSc in Genetics from Al-Azhar University (Cairo, Egypt) then attended one-year course in Information Technology at the Information Technology Institute (ITI) (Giza, Egypt). Later on, I joined The Institute for Advanced Biosciences (IAB) of Keio University (Tokyo & Tsuruoka, Japan) where I got my MSc and PhD in Systems Biology working under Professor Masaru Tomita, Professor Yasushi Ishihama and Professor Kumar Selvarajoo.
During my Masters, I developed the first mathematical model simulating the Toll-Like Receptor (TLR)-3 pathway and worked in the modelling of TLR-4 pathway and the models that descries the Signalling flux Redistribution (SFR) Concept. In my PhD I developed the Mass Spectrum Sequential Subtraction (MSSS) method, the ProteoGenomics Features EVALuator (PGFeval) and the Rice Proteogenomics Database (Oryza-PG).
I did my first postdoctoral training at Professor Yasushi Ishihama's lab at the Graduate School of Pharmaceutical Sciences of Kyoto University (Kyoto, Japan). During my postdoc training, I developed the Onco-Proteogenomics methods that I was initially worked on it at the end of my PhD. In this work, I am trying to unravel novel information about the somatic mutations related to Cancer using proteogenomic approach and a Comprehensive Database Array (CDA).
I am married to Heba Magdi and I have two kids Omar and Yusof.
Fields of Interest
Bioinformatics, Computational Biology, Proteomics, Systems Biology, Proteogenomics, Cancer Biology, Next-generation Sequence data analysis
Education
A.Degrees
• 2012: Ph.D. Degree, Systems Biology Program, Institute for Advanced Biosciences (IAB), Keio University, Japan. (Supervisors: Professors Masaru Tomita, Akio Kanai and Yasushi Ishihama)
• 2009: M.Sc. Degree, on Systems Biology, Institute for Advanced Biosciences (IAB), Keio University Japan. (Supervisors: Professors Masaru Tomita, Yasushi Ishihama and Kumar Selvarajoo)
• 2000: Honours B.Sc. degree in Agricultural Sciences – Genetics department, School of Agricultur, AlAzhar University, Egypt.
B.Courses and Training
• 2007(3~9): Internship at Systems Immunology Group, Institute for Advanced Biosciences, Keio University.
• 2002: Diploma in Software Skills Development Program (SSDP) from the Information Technology Institute (ITI), Egypt.
Academic and Research Positions
• 2013(9)-Present: Postdoctoral Researcher, Bader's Lab. The Donnelly Centre, University of Toronto (UofT), Canada
• 2012(10)-2013(3): Postdoctoral Fellow, Japan Society for promotion of Science (JSPS), Japan
• 2012(10)-2013(3): Postdoctoral Researcher, G. Sch. of Pharmaceutical Sciences, Kyoto University, Japan
• 2011-2012: Research Fellow (DC2), Japan Society for promotion of Science (JSPS), Japan
• 2009-2011: Research Assistantship, the Global Centre of Excellence (G-COE), Keio University, Japan
• 2007-2012: Research Assistantship, Institute for Advanced Biosciences, Keio University, Japan
• 2002-2007: Full-Time Teaching Assistant, Botany Dept, School of Agriculture, Al-Azhar University, Egypt
Previous affiliations
• Kyoto University, Kyoto, Japan.
• Keio University, Tokyo, Japan.
• Japan Society for Promotion of Science (JSPS), Tokyo, Japan
• Institute for Advanced Biosciences (IAB), Tsuruoka, Japan.
• Information Technology Institute, Giza, Egypt.
• Al-Azhar University, Cairo, Egypt.
Grants, Honors, Scholarships and Fellowships
• 2012: Postdoctoral fellowship from Japan Society for Promotion of Science (JSPS), 2012(10)~2013(3), Japan
• 2011: DC2 Research fellowship from Japan Society for Promotion of Science (JSPS), 2011(4)~2012(9), Japan
• 2010: Student Publication Award (Life Sciences) from Misr Elkhir Foundation, Cairo, Egypt
• 2010: Traveling grant from The Human Proteome Organization (HUPO'10), Australia
• 2010: Taikichiro Mori memorial research grants (2010), Japan
• 2009: Taikichiro Mori memorial research grants (2009), Japan
• 2009: RA-Ship, Global Center of Excellence (G-COE), Keio University, Japan
• 2008: Taikichiro Mori memorial research grants (2008), Japan
• 2008: Taikichiro Mori memorial travel grants (2008), Japan
• 2008: RA-Ship, Institute for Advanced Biosciences, Keio University, Japan
• 2007: RA-Ship, Institute for Advanced Biosciences, Keio University, Japan
• 2007~2011: Scholarship Masters and PhD studying abroad from Ministry of Higher Education, Egypt
• 1998: Top Student Award from 6th of October University, Egypt
Publications
A. Journals
1- Elmtwally, S, Hamza, T, Zakarya, M and Helmy, M. Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges, PLOS Computational Biology, (In Press)
2- Helmy, M., Gohda, J., Inoue, J., Tomita, M., Tsuchiya, M. and Selvarajoo, K. (2009) Predicting novel features of Toll-like Receptor 3 signalling in macrophages, PLoS ONE, 4(3): e4661. doi:10.1371/journal.pone.0004661
3- Selvarajoo, K., Takabe, Y., Gohda, J., Helmy, M., Akira, S., Tomita, M., Tsuchiya, M., Inoue, J. and Matsuo, K. (2008) Signalling Flux Redistribution at Toll-like Receptor Pathway Junctions. , PLoS ONE , 3(10) , e3430, doi:10.1371/journal.pone.0003430
4- Helmy, M., Tomita, M., Ishihama Y. (2011) OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics, BMC Plant Biology, 11,63, 2011. doi:10.1186/1471-2229-11-63.
5- Helmy, M, Tomita M, Ishihama Y. (2012) Peptide identification by searching large-scale tandem mass spectra against large databases: bioinformatics methods in proteogenomics. Genes, Genomes and Genomics, 6(SI1), 76-85.
6- Helmy, M, Sugiyama N, Tomita M, Ishihama Y. (2012) The rice proteogenomics database OryzaPGDB: development, expansion and new features. Frontiers of Plant Sciences, 3:65, doi: 10.3389/fpls.2012.00065.
7- Helmy, M, Sugiyama N, Tomita M, Ishihama Y. (2012) Mass Spectrum Sequential Subtraction: bioinformatics method facilitates searching large dataset of peptide MS/MS spectra against large nucleotide databases for proteogenomics. Genes to Cells, 17(8), 633-644, doi: 10.1111/j.1365-2443.2012.01615.
B. Books
Next Generation Sequencing Challenges in Technologies and Sequence Assembly, El-Metwally S., Ouda O, and Helmy M, Under preparation and expected to be published by the end of 2013 by Springer.
C. Proceedings
1- Helmy M., Tomita M., Tsuchiya M., Selvarajoo K. (2008) In silico analysis of Toll-Like receptor 3 pathways. Proceedings of Bioinformatica Indica ’08. India 2008.
2- Selvarajoo K., Helmy M., Tomita M., Tsuchiya M. (2008) Inferring the mechanistic basis for the dynamic response ofthe MyD88-dependent and –independent pathways. 10 on Molecular Systems Biology 2008 (ICMSB’08).Philippine 2008.