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, Japa.
Keio University, Tokyo, Japa.
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.

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