Mohamed Helmy, PhD

Postdoctoral Researcher, Bader Lab
The Donnelly Centre
University of Toronto

Contact Information

160 College Street, Room 630
The Donnelly Centre
University of Toronto
Toronto, Ontario
Canada, M5S 3E1
Map
Email: mohamed.attiashahata[AT]utoronto.ca

Publications

Google Scholar Profile

PUBLICATIONS

* Corresponding author, ** Equal first author

A. Journals

17- Helmy, M., Wagih O., Jain S., Kuang K. Bader G.D. Cancer high-resolution domain-based interaction networks with integrated mutation impacts.
Under preparation

16- Helmy, M., Mee M., Bader G.D. openPIP: The Open Source Protein Interactions Platform.
Under preparation

15- Shah, M., Helmy, M., Bader G.D. Utilizing biological data in conjunction with supervised machine learning to identify potential regulatory regions and their sizes throughout the human genome.
Under preparation

14- Helmy, M., Crits-Christoph A., Wagih O., Bader G.D DV-Impact: An Online Resource and Data Standard for Reporting Disease Variants Impact on Domain-based Protein Interactions.
Under preparation

13- Awad, M., Fahmy R.M., Mosa K. A., Helmy, M., El-Feky F. A. Identification of Effective DNA Barcodes for Triticum Plants through Chloroplast Genome-wide Analysis.
In revision

12- Tong J., Helmy, M.^**., et al,. Systems level analysis of the protein-phosphotyrosine landscape in acute myeloid leukemia as a product of activated tyrosine kinases and phosphotyrosine phosphatases.
In revision

11- Helmy, M., Crits-Christoph A., Bader G.D. (2016) Ten Simple Rules for Developing Biological Database.PLOS Computational Biology, 12(11): e1005128.
PubMed Abstract - DOI - PDF

10- Helmy, M., Awad M., Mosa K. A. (2016) Limited resources of genome sequencing in developing countries: Challenges and solutions. Applied & Translational Genomics, 9,15:19.
PubMed Abstract - DOI - PDF

9- Mosa K. A., , Saadoun I., Kumar K., Helmy, M., Dhankher O. P. (2016) Potential Biotechnological Strategies for the Cleanup of Heavy Metals and Metalloids. Frontiers in Plant Science 7, 303.
PubMed Abstract - DOI - PDF

8- 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.
PubMed Abstract - DOI - PDF

7- El-Metwally, S, Hamza, T, Zakarya, M and Helmy, M.^*. (2013)Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges, PLOS Computational Biology, 9 (12), e1003345.
PubMed Abstract - DOI - PDF

6- 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.
ResearchGate - PDF

5- 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.
PubMed Abstract - DOI - PDF

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.
PubMed Abstract - DOI - PDF

3- 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.
PubMed Abstract - DOI - PDF

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.
PubMed Abstract - DOI - PDF

1- 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.
PubMed Abstract - DOI - PDF

B. Books

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.

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.
Springer, Amazon, Request free copy

C. Proceedings

2- 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.
ResearchGate

1- 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.
ResearchGate

D. Thesis

2- PhD thesis: Helmy, M. (2012) Systems biology approaches to improve genome annotations through development of bioinformatics pipeline for large-scale mass spectrometry-based proteogenomics. Supervisors: Professor Masaru Tomita, Peofessor Yasushi Isgihama, Professor Akio Kanai, Keio University, Tokyo, Japan.
full Text PDF

1- Master's thesis: Helmy, M. (2009) Systems biology research on: 1) Computational analysis of Toll-like receptor 3 signaling pathway, and 2) Exploiting proteogenomics for improving Oryzae sativa genome annotation. Supervisors: Professor Masaru Tomita, Peofessor Yasushi Isgihama, Professor Kumar Selvarajoo, Keio University, Tokyo, Japan.
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