Mohamed Helmy, PhD

Postdoc Researcher, Bader 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: mohamed.attiashahata AT utoronto.ca

Publications

A. Journals

* Corresponding author, ** Equal first author

1- Helmy, M., Crits-Christoph A., Wagih O., Bader G. (Under preparation) Can-VD: Database and Proposed standard for Reporting Mutations Impact on Protein Interaction Networks in Cancer.
2- Helmy, M., Bader G. (In revision) Ten Simple Rules for Developing Biological Database.
3- Tong J., Helmy, M**., et al, (In revision) Systems level analysis of the protein-phosphotyrosine landscape in acute myeloid leukemia as a product of activated tyrosine kinases and phosphotyrosine phosphatases, Science Signalling.
4- Helmy, M., Awad M., Mosa K. A. (Accepted) Limited resources of genome sequencing in developing countries: Challenges and solutions. Applied & Translational Genomics.
5- Mosa K. A., , Saadoun I., Kumar K., Helmy, M., Dhankher O. P. (Accepted) Potential Biotechnological Strategies for the Cleanup of Heavy Metals and Metalloids. Frontiers in Plant Science 7, 303.
6- Awad M., Ouda O., El-Rifi A., El-Fiki F., Mosa K. A., Helmy, M*., (2015) FN-Identify: Novel Restriction Enzymes-Based Method for Bacterial Identification in Absence of Genome Sequencing. Advances in Bioinformatics Article ID 303605, doi.org/10.1155/2015/303605.
7- El-Metwally, S, Hamza, T, Zakarya, M and Helmy, M*. Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges, PLOS Computational Biology, 9 (12), e1003345.
8- 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.
9- 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.
10- 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.
11- 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.
12- 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.
13- 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

1- El-Metwally S., Ouda O, and Helmy M.* (2014) Next Generation Sequencing Challenges in Technologies and Sequence Assembly, Springer Briefs in Systems Biology, (7) ISBN: 978-1-4939-0714-4 (Print) 978-1-4939-0715-1 (Online), Springer, PA, USA.
2- Mosa K. A., El-Shabrawi H., Ismail A., and Helmy, M. (In Press) Plant Stress Tolerance: An Integrated Omics Approaches, Springer Briefs in Systems Biology, Springer, PA, USA.

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 of the MyD88-dependent and –independent pathways. 10 on Molecular Systems Biology 2008 (ICMSB’08).Philippine 2008.