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= Mohamed Helmy =
{{attachment:mhelmy.png|mhelmy.png}}
Postdoc Researcher, Bader's Lab<<BR>>The Donnelly Centre<<BR>>University of Toronto (UofT)
'''Contact Address''':[[http://maps.google.com/maps?f=q&hl=en&q=160+College+St,+Toronto+ON&om=1|Map]]<<BR>>160 College Street, Room 630<<BR>>The Donnelly Centre<<BR>>University of Toronto<<BR>>Toronto, Ontario<<BR>>Canada, M5S 3E1<<BR>>
'''Email''': helmy.sfc AT gmail.com
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=== 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, Egypt then I traveled to Japan and joined The Institute for Advanced Biosciences of Keio University. I got my MSc and PhD from Keio university 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. 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.
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=== Fields of Interest ===
Bioinformatics, Computational Biology, Proteomics, Systems Biology, Proteogenomics, Cancer Biology
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=== 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.
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=== 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
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=== 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
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=== 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.
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