Sameh El-Sayed Ibrahim Hassanein

Head of Bioinformatics and Functional Genomics Dept.

Professor, Head of Bioinformatics and Functional Genomics Dept. College of Biotechnology, Misr University for Science and Technology (MUST). Instructor and Coordinator for many undergraduate and postgraduate courses. Supervised many M.Sc. and Ph.D. theses in many national universities and institutes. Published more than 40 papers in National and International Scientific Journals.


As a Bioinformatician, I have experience in many Bioinformatics applications, databases, and software packages aided in a wide range of bioinformatics, genomics, and proteomics research topics, e.g. similarity searching, phylogenetic analysis and constructions, epitope prediction, molecular modeling, secondary structure prediction, primer design, big data analysis (clustering, normalization, …), 3D structure prediction, gene finding (motif finding and prediction), genomic analysis, transcriptome analysis, pathways, and networks analysis and prediction.

My goal is to reveal new insights and principles in life sciences, manage and analyze biological data, especially genomic, transcriptomic metabolomic, and proteomic research data such as sequence analysis, interpretation, and annotation. Study tremendous details of biological processes (such as diseases) using the tools of bioinformatics.


Biomedical Bioinformatics Diploma  Jul. 2011

Helwan Univ. College of Computers and Information Sciences

PhD  Aug. 2008

Ain Shams Univ., Faculty of Agriculture, Genetics Dept.

Dissertation title: “Improvement of wheat plants for environmental stress tolerance by genetic engineering methods”

Major Field: “Genetic Engineering”

M. Sc.  Feb. 2002

Ain Shams Univ., Faculty of Agriculture, Genetics Dept.

Dissertation title: “Physiological genetic studies on some inbred lines and hybrids of maize (Zea mays L.)”

Major Field: “Molecular Genetics”

B.Sc.   Jun. 1996

Ain Shams Univ., Faculty of Agriculture, Genetics Dept.

Major Field: “Genetics”


Abdel-Tawab, F.M., Eman M. Fahmy, M. A. Rashed, Gh. A. Gad El-karim, S. H. Abdel-aziz, and S. E. Hassanein (2002). Development of Molecular Markers for Salt and Drought Tolerance in Maize (Zea mays, L.). Egypt. J. Genet. Cytol., 31:355-371, July, 2002.

Eissa, H.F., A. Shokry, O.M. Saleh, S. E. Hassanein, A.M. Ramadan, A. Bahieldin and W. E. Dyer (2006). Genomic characterization of stress-related genes from wild barley. Second International Conference of Genetic Engineering and its applications. Sharm El-Sheikh, Egypt.

Gadalla, N.O., Eman M. Fahmy; A. Bahieldin, A.I. Abdel-Sattar, S. Edris, A. Shokry and S.E. Hassanein (2008). Functional genomics for Orobanche tolerance in faba bean (Vicia faba L.). Journal of Genetics Engineering and Biotechnology, 2008, 6(1): 1-10

Hassanein, S.E., F.M. Abdel-tawab, E.M. Fahmy, Gh.A. Gad El-karim, Th. Alniemi, M. Abdelsalam, S. Mostafa, A.M. Ramadan, O.M. Saleh, Hala F. Eissa and A. Bahieldin (2009). Molecular assessment of chitinase activity in transgenic wheat. Egypt. J. Genet. Cytol., 38: 207-220, July, 2009.

Hassanein, S.E., A.Z. Abdel Azeiz, A.M. Ramadan and Afaf Z. El-Meneisy (2012). Screening for Pectinase and Cellulase inhibitors from the root exudates and protein contents of five plants against six phytopathogenic fungi. J. Biol. Chem. Environ. Sci., (2012), Vol. 7(3): 454-553.

Khaled M.A. Ramadan, Abdel Azeiz A., Hassanein S. E. and Eissa H.F. (2012). Biodegradation of used lubricating and diesel oils by a new yeast strain Candida viswanathii KA-2011. African Journal of Biotechnology Vol. 11(77), pp. 14166-14174.

F.M. El-Domyati, A.M. Ramadan, N.O. Gadalla, S. Edris, A.M. Shokry, S.M. Hassan, S.E. Hassanein, M.N. Baeshen, N.H. Hajrah, M.A. Al-Kordy, O.A. Abuzinadah, A.S.M. Al- Hajar, C.C. Akoh and A. Bahieldin (2012). Identification of molecular markers for flower characteristics in Catharanthus roseus producing anticancer compounds. Life Science Journal 2012; 9 (4), pp. 5949-5960.

A.M. Ramadan, H.F. Eissa, S.E. Hassanein, A.Z. Abdel Azeiz, O.M. Saleh, H.T. Mahfouz, F.M. El-Domyati, M.A. Madkour and A. Bahieldin (2013). Increased salt stress tolerance and modified sugar content of bread wheat stably expressing the mtlD gene. Life Science Journal 2013; Vol. 10 (2), pp. 2757-2770

Rasha, A. Mohammed, Kh. M.A. Ramadan, S.E. Hassanein, R.R. Francis and A.Z. Abdel Azeiz (2013). Butyl-Iso-butyl phthalate as an Orobanche crenata seed germination activator secreted by roots of Vicia faba. J. Biol. Chem. Environ. Sci., (2013), Vol. 8(4): 157-167.

El Banna, M. N.; H. M. F. El-Wakil.; A. A. Abd-Allah; Hala F. Eissa; S. E. Hassanein and R. A. Sallam. (2013). Identification of drought tolerant molecular markers in rice (Oryza sativa L.): I-Assessment of F1 genotypes under normal and drought condition. J. Plant Production. Mansoura Univ., Vol. 4(1) :79-105. ISSN 1110-0346.

Hassanein, S.E., A.M. Ramadan, A.Z. Abdel Azeiz, R.A. Mohammed, S.M. Hassan, A. Atef, K.B.H. Kamal, S. Rabah, J.S.M. Sabir, O.A. Abuzinadah, F.M. El-Domyati, G.B. Martin and Ahmed Bahieldin (2013). Thymoquinone causes multiple effects, including cell death, on dividing plant cells. C. R. Biologies Nov-Dec;336(11-12):546-56. doi: 10.1016/j.crvi.2013.10.007. Epub 2013 Nov 19.

Heba E. Ghareb, Basita A. Hussein, Hala F. Eissa, A.M. Shokry, S. E. Hassanein, Mahdia F. Gaber and Naglaa A. Abdallah (2014). Isolation of some drought stress related cDNAs from Rhus tripartite plant via differential display. Arab J. Biotech., Vol. 17, No. (1) January (2014): 43-58.

A.M. Ramadan and S.E. Hassanein (2014). Characterization of P5CS gene in Calotropis procera plant from the de novo assembled transcriptome contigs of the high-throughput sequencing dataset. C. R. Biologies Dec;337(12):683-90. doi: 10.1016/j.crvi.2014.09.002. Epub 2014 Oct 7.

Sameh E. Hassanein (2014). Characterization of ATP gene in Calotropis procera Mitochondrial Genome. Egypt. J. Genet. Cytol., 43: 257 – 269. July 2014

Heba H Abouseadaa, Gamal H Osman, Ahmed M Ramadan, Sameh E Hassanein, Mohamed T Abdelsattar, Yasser B Morsy, Hussien F Alameldin, Doaa K El-Ghareeb, Hanan A Nour-Eldin, Reda Salem, Adel A Gad, Soheir E Elkhodary, Maher M Shehata, Hala M Mahfouz, Hala F Eissa and Ahmed Bahieldin (2015). Development of transgenic wheat (Triticum aestivum L.) expressing avidin gene conferring resistance to stored product insects. BMC Plant Biology 15:183 (2015) 1-8.

Donia K. Hanafi, Sameh E. Hassanein and Ahmed Z. Abdel Azeiza (2015). Identification of a new antifungal oligoacetal derivative produced by Streptomyces toxytricini against Candida albicans. Natural Product Research: Formerly Natural Product Letters. doi:10.1080/14786419.2015

Lobna A. Moussa, Ahmed Z. Abdel Azeiz and Sameh E. Hassanein (2017). Microbial Biodegradation of Crude Petroleum Oil as Affected by Salinity. J. Biol. Chem. Environ. Sci., 2017, Vol. 12(1): 545-558.

Hala F Eissa, Sameh E Hassanien, Ahmed M Ramadan, Moustafa M El-Shamy, Osama M Saleh, Ahmed M Shokry, Mohamed Abdelsattar, Yasser B Morsy, Maher A El-Maghraby, Hussien F Alameldin, Sabah M Hassan, Gamal H Osman, Hesham T Mahfouz, Gharib A Gad El-Karim, Magdy A Madkour and Ahmed Bahieldin (2017). Developing transgenic wheat to encounter rusts and powdery mildew by overexpressing barley chi26 gene for fungal resistance. Plant Methods (2017) 13:41

Morsy Y.B., Abdel-Tawab F.M., Eman M. Fahmy, Hala F. Eissa and S.E. Hassanein (2017). Functional Genomic Profiling of Drought Responsive Micro-RNA In Wheat. Egypt. J. Genet. Cytol. 2017, 46(2): 363-370.

Ahmed M Ramadan, Ahmed Abdel Azeiz, Saeed Baabad, Sameh E. Hassanein, Nour O Gadalla, Sabah Hassan, Mardi Algandaby, Salwa Bakr, Thana Khan, Heba H Abouseadaa, Hani Mohammed Ali, Areej Al-Ghamdi, Gamal Osman, Sherif Edris, Hala Eissa, Ahmed Bahieldin (2019). Control of β-sitosterol biosynthesis under light and watering in desert plant Calotropis procera. Steroids 141 (2019) 1–8.

Sameh E. Hassanein, A. M. Shokry, Hala F. Eissa, A. M. Ramadan, H. F. Alameldin, Y. B. Morsy, A. M. K. Nada, A. Bahieldin, M. Al-Shamy and Gh. A. Gad El-Karim (2019). Bread Wheat Comparative Expression Analysis in Response to Leaf Rust (Puccinia triticina) Using Microarray Techniques. Egypt. J. Genet. Cytol. 48(2): 139-154, July, 2019.

Rania M. I. Abou Ali, Warda A. M. Hashim, Eman I. Ibrahim, Inas F. Fahmy, S. E. Hassanein and A. M. K. Nada (2019). Enhancement of Drought Tolerance in Rice (Oriza sativa L.) Using Oxo-Phytodienoate Reductase7 (OPR7) Gene. Egypt. J. Genet. Cytol. 48(2): 155-177, July, 2019.

Ahmed Z. Abdel Azeiz, Abeer Elhalwagi, Sameh E. Hassanein and Lobna A. Moussa (2019). Microbial water source for the desert plants. Journal of Agricultural Science and Technology A 9 (2019) 71-80. doi:10.17265/2161-6256/2019.02.001

Rasha A. Mohamed; K.M., Ramadan; S. E. Hassanein; R. R. Francis; A. Z. Abdel Azeiz. (2019). “Chemoinformatic Analysis of Some Fungal Pectinases Inhibitors”. Arab Universities Journal of Agricultural Sciences, 27, 3, 2019, 1803-1818. doi: 10.21608/ajs.2019.76089

Nermin G. Mohamed, Rashed M.A., Hassanein S.E., El-Orabey W., Morsy Y., Samir O. and Hala F. Eissa (2019). Comparative Studies on Gene Expression of Rice and Wheat in Response to Fungal Infection. AUJASCI, Arab Univ. J. Agric. Sci., 27(2), 1529-1539, 2019.

Habib PT, Alsamman AM, Hassanein SE, Ghada A. Shereif and Aladdin Hamwieh (2019). SNPector: SNP inspection tool for diagnosing gene pathogenicity and drug response in a naked sequence. F1000Research 2019, 8:2133 (

Habib PT, Alsamman AM, Hassanein SE, Kerolos M. Yousef and Aladdin Hamwieh (2020). Pharmosome: an integrative and collective database for exploration and analysis of single nucleotide polymorphisms associated with disease [version 1; peer review: awaiting peer review] F1000Research 2020, 9:14 (

Habib PT, Alsamman AM, Hassanein SE, and Aladdin Hamwieh (2020). TarDict: Random Forest Classifier-based software predict Drug-Tartget interaction. BioRxiv (2020). doi:

Habib P.T., Alsamman A.M., Hassanein S.E., and Hamwieh A. (2020). Developing Convolutional Neural Networks-Based System for Predicting Pneumonia Using X-Radiography Image. Highlights in BioScience, 3.3 (2020): n. pag. Web. 23 Mar. 2020

Wasimah B Alshammari, Huda Alhamdan, Thana Khan, Sameh E. Hassanein, Ahmed M Ramadan (2020). Differential RNA editing of ATP complex in different tissues of Catharanthus roseus plastid. Advances in Environmental Biology. 2020 January; 14(1): pages 48-55. DOI: 10.22587/aeb.2020.14.1.8

Huda Alhamdan, Wasimah B Alshammari, Thana Khan, Sherif Edris, Sameh E. Hassanein and Ahmed M Ramadan (2020). Differential RNA editing of mitochondrial atp1 gene in Catharanthus 

roseus tissues. Advances in Environmental Biology, 2020 March; 14(3): pages 1-9. DOI: 10.22587/aeb.2020.14.3.1

Mai M. Labib, M.K. Amin, A.M. Alzohairy, M.M.A. Elashtokhy, O. Samir, I. Saleh, I.A. Arif,G.H. Osman and S.E. Hassanein (2020). In silico Targeting, inhibition and analysis of polyketide synthase enzyme in Aspergillus ssp. Saudi Journal of Biological Sciences 27 (2020) 3187–3198.

Mai M. Labib, M. K. Amin, A. M. Alzohairy, M. M. A. Elashtokhy, O. Samir and S. E. Hassanein (2020). Inhibition analysis of aflatoxin by in silico targeting the thioesterase domain of polyketide synthase enzyme in Aspergillus ssp. Journal of Biomolecular Structure and Dynamics,

Suliman Khan, Huseyin Tombuloglu, Sameh E. Hassanein, Surya Rehman, Ayhan Bozkurt, Emre Cevik, Shaimaa Abdel-Ghany, Ghulam Nabi, Ashaq Ali, Hussein Sabit (2020). Coronavirus diseases 2019: Current biological situation and potential therapeutic perspective. European Journal of Pharmacology 886 (2020) 173447.

El-Sayed, A.S., Shindia, A.A., AbouZeid, A., Koura, A., Hassanein, S.E., and Rania M. Ahmed. (2021). Triggering the biosynthetic machinery of Taxol by Aspergillus flavipes via cocultivation with Bacillus subtilis: proteomic analyses emphasize the chromatin remodeling upon fungal-bacterial interaction. Environ Sci Pollut Res (2021).

Conference Posters & Presentations

Mohamed Teima, F.M. Abdel-Tawab, Eman M. Fahmy, A.M. Ramadan, H.F. Eissa, A.M. Shokry, S. E. Hassanein, H.F. Alameldin, A.Z. Abdel Aziez, M.A. Madkour, and A. Bahieldin. (2014). Development of Transgenic Wheat Plants Tolerant to Abiotic Stress Using MDAR Gene. Poster Presentation, BioVision Alexandria 2014.

Hala F. Eissa, Sameh E. Hassanien, Ahmed M. Ramadan, Moustafa M. El-Shamy, Osama M. Saleh, Ahmed M. Shokry, Mohamed Abdelsattar, Yasser B. Morsy, Maher A. El-Maghraby, Hussien F. Alameldin, Sabah M. Hassan, Gamal H. Osman, Hesham T. Mahfouz, Gharib A. Gad El-Karim, Magdy A. Madkour, and Ahmed Bahieldin (2018). Developing Transgenic Wheat to Facing Rusts and Powdery Mildew by Chi26 Gene for Fungal Resistance. Poster Presentation, BioVision Alexandria 2018.

Sameh E. Hassanein, Omar Samir (2019). De novo transcriptome assembly and Functional Annotation of Calotropis procera reveals understanding about Extreme Climate adaptation. Theme: Conservation and Use of Agrobiodiversity in Drylands, Developing Adapted Cultivars. 13th International Conference on Development of Drylands, Converting Dryland Areas from Grey into Green. February 11-14, 2019, Jodhpur, India.

Omar Samir, Omar S. Keshk, Nesma S. Shafie, Sameh E. Hassanein, Yasser Morsy, Asmaa A. El Leithy and Marwa Amer (2021). A Comprehensive Genome and Transcriptome Profiling for Oncoviruses. EMBO | EMBL Symposium: Multiomics to Mechanisms: Challenges in Data Integration. Poster Presentation, Online Symposium 15th – 17th Sep 2021.

Mohamed Abdo, Omar Amin, Moataz El-Safoury, Youssef Tawfik, Omar Samir, Sameh E. Hassanein, and Marwa Amer (2021). Meta-comparative analysis of the gut microbiome studies illustrates the differences between stool and biopsy samples in IBD patients. EMBO | EMBL Symposium: Multiomics to Mechanisms: Challenges in Data Integration. Poster Presentation, Online Symposium 15th – 17th Sep 2021.