* indicates equal contribution. ** indicates corresponding authorship. For a full list of our publications, please visit our Google Scholar Profile

1- Helmy M, Elhalis H, Rashid MM, Selvarajoo K. Can digital twin efforts shape microorganism-based alternative food?. Current Opinion in Biotechnology. 2024 Jun 1;87:103115.

2- Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Helmy M. Drugst. One—a plug-and-play solution for online systems medicine and network-based drug repurposing. Nucleic Acids Research. 2024 May 23:gkae388.

3- Elhalis H*, Helmy M*, Ho S, Leow S, Liu Y, Selvarajoo K, Chow Y. Identifying Chlorella vulgaris and Chlorella sorokiniana as sustainable organisms to bioconvert glucosamine into valuable biomass. Biotechnology Notes. 2024 Jan 1;5:13-22.

1- Sirbu O, Helmy M, Giuliani A, Selvarajoo K. Globally invariant behavior of oncogenes and random genes at population but not at single cell level. NPJ Systems Biology and Applications. 2023 Jun 24;9(1):28.

2 -Helmy M, Elhalis H, Liu Y, Chow Y, Selvarajoo K. Perspective: multiomics and machine learning help unleash the alternative food potential of microalgae. Advances in Nutrition. 2023 Jan 1;14(1):1-1.

3- Mousbah AM, Abdullah HM, Mohammed WS, El-Refy AM, Helmy M. Buffalo Genome Projects: Current Situation and Future Perspective in Improving Breeding Programs. arXiv preprint arXiv:2304.04977. 2023 Apr 11. (Preprint).

1- Khanijou JK, Kulyk H, Bergès C, Khoo LW, Ng P, Yeo HC, Helmy M, Bellvert F, Chew W, Selvarajoo K. Metabolomics and modelling approaches for systems metabolic engineering. Metabolic Engineering Communications. 2022 Dec 1;15:e00209.

2- Smith DJ, Helmy M, Lindley ND, Selvarajoo K. The transformation of our food system using cellular agriculture: What lies ahead and who will lead it?. Trends in Food Science & Technology. 2022 Sep 1;127:368-76.

3- Dumont M, Weber-Lassalle N, Joly-Beauparlant C, Ernst C, Droit A, Feng BJ, Dubois S, Collin-Deschesnes AC, Soucy P, Vallée M, Fournier F. Uncovering the contribution of moderate-penetrance susceptibility genes to breast cancer by whole-exome sequencing and targeted enrichment sequencing of candidate genes in women of European ancestry. Cancers. 2022 Jul 11;14(14):3363.

4- Helmy M, Mee M, Ranjan A, Hao T, Vidal M, Calderwood MA, Luck K, Bader GD. OpenPIP: An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data. Journal of Molecular Biology. 2022 Jun 15;434(11):167603.

5- Giuliani A, Bui TT, Helmy M, Selvarajoo K. Identifying toggle genes from transcriptome-wide scatter: A new perspective for biological regulation. Genomics. 2022 Jan 1;114(1):215-28.

1- Helmy M, Agrawal R, Ali J, Soudy M, Bui TT, Selvarajoo K. GeneCloudOmics: a data analytic cloud platform for high-throughput gene expression analysis. Frontiers in Bioinformatics. 2021 Nov 25;1:693836.

2- Qunaibi EA, Helmy M, Basheti I, Sultan I. A high rate of COVID-19 vaccine hesitancy in a large-scale survey on Arabs. elife. 2021 May 27;10:e68038.

3- Lambourne L, Yadav A, Wang Y, Desbuleux A, Kim DK, Cafarelli T, Pons C, Kovács IA, Jailkhani N, Schlabach S, Ridder DD. Binary interactome models of innerversus outer-complexome organisation. BioRxiv, 1-89. (Preprint).

4- Helmy M, Selvarajoo K. Systems biology to understand and regulate human retroviral proinflammatory response. Frontiers in Immunology. 2021 Nov 16;12:736349.

1- Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D. A reference map of the human binary protein interactome. Nature. 2020 Apr 16;580(7803):402-8.

2- Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, Boutros PC. Sex differences in oncogenic mutational processes. Nature communications. 2020 Aug 28;11(1):4330.

3- Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature communications. 2020 Sep 21;11(1):4748.

4- Helmy M, Smith D, Selvarajoo K. Systems biology approaches integrated with artificial intelligence for optimized metabolic engineering. Metabolic engineering communications. 2020 Dec 1;11:e00149.

5- Teyra J, Kelil A, Jain S, Helmy M, Jajodia R, Hooda Y, Gu J, D’Cruz AA, Nicholson SE, Min J, Sudol M. Large‐scale survey and database of high affinity ligands for peptide recognition modules. Molecular Systems Biology. 2020 Dec;16(12):e9310.

6- Abd El-Raouf HS, Helmy M, Awad M, El-Taher AM. Pollen grains taxonomy matches DNA-barcoding taxonomy in discrimination between some Convolvulaceae taxa. Plant Archives. 2020;20(Supplement 2):2089-94.

7- Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS, Johnson R. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Communications biology. 2020 Feb 5;3(1):56.

8- Reyna MA, Haan D, Paczkowska M, Verbeke LP, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R. Pathway and network analysis of more than 2500 whole cancer genomes. Nature communications. 2020 Feb 5;11(1):729.

9- Shuai S, Gallinger S, Stein LD. Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature communications. 2020 Feb 5;11(1):734.

10- Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, Reimand J. Integrative pathway enrichment analysis of multivariate omics data. Nature communications. 2020 Feb 5;11(1):735.

11- Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 Feb 6;578(7793):102-11.

12- Pan-cancer analysis of whole genomes. Nature 578, no. 7793 (2020): 82-93.

13- Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M. The evolutionary history of 2,658 cancers. Nature. 2020 Feb 6;578(7793):122-8.

14- PCAWG Transcriptome Core Group Calabrese Claudia 2 Davidson Natalie R. 3 4 5 6 7 Demircioğlu Deniz 8 9 Fonseca Nuno A. 2 He Yao 10 Kahles André 3 4 6 7 Lehmann Kjong-Van 3 4 6 7 Liu Fenglin 10 Shiraishi Yuichi 11 Soulette Cameron M. 12 Urban Lara 2, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM. Genomic basis for RNA alterations in cancer. Nature. 2020 Feb 6;578(7793):129-36.

15- Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SA. The repertoire of mutational signatures in human cancer. Nature. 2020 Feb 6;578(7793):94-101.

16- Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M. Patterns of somatic structural variation in human cancer genomes. Nature. 2020 Feb 6;578(7793):112-21.

17- Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nature genetics. 2020 Mar 2;52(3):342-52.

1- Tong J, Helmy M, Cavalli FM, Jin L, St‐Germain J, Karisch R, Taylor P, Minden MD, Taylor MD, Neel BG, Bader GD. Integrated analysis of proteome, phosphotyrosine‐proteome, tyrosine‐kinome, and tyrosine‐phosphatome in acute myeloid leukemia. Proteomics. 2017 Mar;17(6):1600361.

2- Awad M, Fahmy RM, Mosa KA, Helmy M, El-Feky FA. Identification of effective DNA barcodes for Triticum plants through chloroplast genome-wide analysis. Computational Biology and Chemistry. 2017 Dec 1;71:20-31.

1- Mosa KA, Saadoun I, Kumar K, Helmy M, Dhankher OP. Potential biotechnological strategies for the cleanup of heavy metals and metalloids. Frontiers in plant science. 2016 Mar 15;7:303.

2- Helmy M, Awad M, Mosa KA. Limited resources of genome sequencing in developing countries: challenges and solutions. Applied & translational genomics. 2016 Jun 1;9:15-9.

3- Helmy M, Crits-Christoph A, Bader GD. Ten simple rules for developing public biological databases. PLoS computational biology. 2016 Nov 10;12(11):e1005128.

1- Awad M, Ouda O, El-Refy A, El-Feky FA, Mosa KA, Helmy M. FN‐Identify: Novel Restriction Enzymes‐Based Method for Bacterial Identification in Absence of Genome Sequencing. Advances in Bioinformatics. 2015;2015(1):303605.

1- El-Metwally S, Hamza T, Zakaria M, Helmy M. Next-generation sequence assembly: four stages of data processing and computational challenges. PLoS computational biology. 2013 Dec 12;9(12):e1003345.

1- Helmy M, Sugiyama N, Tomita M, Ishihama Y. Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics. Genes to Cells. 2012 Aug;17(8):633-44.

2- Helmy M, Sugiyama N, Tomita M, Ishihama Y. The rice proteogenomics database OryzaPG-DB: development, expansion, and new features. Frontiers in plant science. 2012 Apr 2;3:65.

3- Helmy M, Tomita M, Ishihama Y. Peptide identification by searching large-scale tandem mass spectra against large databases: bioinformatics methods in proteogenomics. Genes Genome Genomics. 2012;6:76-85.

1- Helmy M, Tomita M, Ishihama Y. OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC plant biology. 2011 Dec;11:1-9.

1- Helmy M, Sugiyama N, Tomita M, Ishihama Y. Onco-proteogenomics: a novel approach to identify cancer-specific mutations combining proteomics and transcriptome deep sequencing. Genome biology. 2010 Nov;11:1-2.

1- Helmy M, Gohda J, Inoue JI, Tomita M, Tsuchiya M, Selvarajoo K. Predicting novel features of toll-like receptor 3 signaling in macrophages. PLoS One. 2009 Mar 2;4(3):e4661.

1- Selvarajoo K, Takada Y, Gohda J, Helmy M, Akira S, Tomita M, Tsuchiya M, Inoue JI, Matsuo K. Signaling flux redistribution at toll-like receptor pathway junctions. PLoS One. 2008 Oct 17;3(10):e3430.

1- Helmy M, Selvarajoo K. Application of GeneCloudOmics: Transcriptomic Data Analytics for Synthetic Biology. InComputational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology 2022 Oct 14 (pp. 221-263). New York, NY: Springer US.

2- Ismail A, Mosa KA, Ali MA, Helmy M. Biochemical and molecular markers: unraveling their potential role in screening germplasm for thermotolerance. Heat Stress Tolerance in Plants: Physiological, Molecular and Genetic Perspectives. 2020 Mar 23:47-76.

3- Soliman S, El-Keblawy A, Mosa KA, Helmy M, Wani SH. Understanding the phytohormones biosynthetic pathways for developing engineered environmental stress-tolerant crops. Biotechnologies of Crop Improvement, Volume 2: Transgenic Approaches. 2018:417-50.

4- Mosa K. A., El-Shabrawi H., Ismail A., and Helmy, M. (2017) Plant Stress Tolerance: An Integrated Omics Approaches, Springer Briefs in Systems Biology, ISBN: 978-3-319-59377-7 (Print) 978-3-319-59379-1 (Online), Springer, PA, USA. 

5- 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.

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. ResearchGate

1- 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.

2- 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.