Differences between revisions 8 and 11 (spanning 3 versions)

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

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

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

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-|| {{attachment:mhelmy2.png|mhelmy.png}} <<BR>> Postdoc Researcher, Bader Lab<<BR>>The Donnelly Centre,<<BR>>University of Toronto (UofT)<<BR>><<BR>>'''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>><<BR>>'''Email''': mohamed.attiashahata AT utoronto.ca||<<BR>><<BR>>''' __Publications__ ''' [[http://scholar.google.com/citations?hl=en&user=Ccx_2agAAAAJ&view_op=list_works|Google Scholar Profile]]<<BR>><<BR>>'''A. Journals'''<<BR>><<BR>>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).<<BR>>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.<<BR>>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.<<BR>>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.<<BR>>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.<<BR>>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.<<BR>>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.<<BR>>'''B. Books'''<<BR>><<BR>>1- 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.<<BR>><<BR>>'''C. Proceedings'''<<BR>><<BR>>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.<<BR>>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.<<BR>><<BR>>||
+|| {{attachment:mhelmy2.png|mhelmy.png}} <<BR>> Postdoc Researcher, Bader Lab<<BR>>The Donnelly Centre,<<BR>>University of Toronto (UofT)<<BR>><<BR>>'''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>><<BR>>'''Email''': mohamed.attiashahata AT utoronto.ca||<<BR>><<BR>>''' __Publications__ '''  [[http://scholar.google.com/citations?hl=en&user=Ccx_2agAAAAJ&view_op=list_works|{{attachment:gs.png|target="_blank"}}]]<<BR>><<BR>>'''A. Journals'''<<BR>><<BR>>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).<<BR>>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.<<BR>>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.<<BR>>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.<<BR>>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.<<BR>>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.<<BR>>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.<<BR>>'''B. Books'''<<BR>><<BR>>1- 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.<<BR>><<BR>>'''C. Proceedings'''<<BR>><<BR>>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.<<BR>>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.<<BR>><<BR>>||