Prof. Samar Kamal Abdel Hameed Kassim

Awards

* جائزة جامعة عين شمس للنشر الدولي ٢٠٢٠،  ٢٠٢١.

* جائزة التميز في النشر الدولي مقدمة من النقابة العامة للأطباء بجمهورية مصر العربية 2013.

* جائزة المرحوم أ.د. ممتاز محمد الصاوى فى مجال الطب المعملى و أمراض الدم (إحدى جوائز الهيئات و الأفراد الممنوحة من أكاديمية البحث العلمى لعام 2007).

Molecular Biology Excellency Award (Interlab, Cairo, Egypt, 1998) for the manuscript: Samar K. Kassim, Ibrahim SA, Sanaa Eissa, Sahar SA Zaki, El-Begermy MA, Abdou MH, and Kalifa A.: Molecular Biologic Studies on Epstein-Barr Virus, Human Papilloma Virus, and Flowcytometric Cell Cycle Kinetics in Nasopharyngeal Carcinoma and Inverted Papilloma Among Egyptian Patients. Disease Markers, 14: 113-120, 1998.

Recent Studies

* Professional Diploma of Clinical Nutrition Diploma for Health Professionals program at the National Nutrition Institute 2014-2015.

Teaching interests

* Clinical Nutrition.

* Theoretical and practical teaching of Medical Biochemistry for under and postgraduate Medical students.

* Theoretical and practical teaching of Molecular Biology for under and postgraduate Medical students.

* Biostatistics.

Research interests

* Molecular Biology & Bioinformatics of HCV.

* Molecular Biology & Bioinformatics of epithelial tumors.

* Clinical Nutrition and Nutrigenomics.

Curricula development:

* Shared in designing the Genomic Medicine online course for nurses under the umbrella of H3Africa Education and Coordinated Training Working Group (2016).

* Shared in the development of recommended Bioinformatics curricula by H3ABioNet:

* https://training.h3abionet.org/curriculum_development_wg/?page_id=137.

* https://training.h3abionet.org/curriculum_development_wg/.

* Bioinformatics for under (Ain Shams Faculty of Computer Sciences and Information) and postgraduate students (Ain Shams Faculty of Medicine).

* Bioinformatics for postgraduate students (Faculty of Computer Sciences and Information, Helwan University).

Workshops and conferences

* Professor Samar Kamal Kassim presented “Open Data in Bioinformatics and Required Infrastructure towards achieving the SDGs” on behalf of www.h3abionet.org in the 9th BioVision Alexandria Conference, Alexandria, Egypt, 2018.

* One of the Board of the 10th conference of African Society of Human Genetics, http://afshg-cairo017.org/conference-board/, November 16th-18th, Ritz Carlton Hotel, Cairo, Egypt.

* Bioinformatics Teaching Methods by Global Organization for Learning, Education and Training (GOBLET). November 16-17th, 2015, Cape Town, South Africa.

* H3ABioNet ICIPE Train the Trainer Bioinformatics Workshop, July 8-26, 2013, Nairobi, Kenya.

* Total Quality Management for Health Care Professionals. The American University in Cairo, School of Continuing Education. March 21 – May 16, 2013.

* "Structural Bioinformatics School" held at Cairo University October 8-13, 2012.

Portal design: https://agmp.h3abionet.org/

https://doi.org/10.3390/jpm12020265

Projects

* PI of the National Network for Bioinformatics BioNetMasr, Scientific Research Academy, 2022.

* MATREX (MASRI CAncer Biobank and InTegrated Genomic solution AccRedited Center of Scientific EXcellence): Science and Technology Development (STDF) funded project at MASRI research institution, Faculty of Medicine, Ain Shams University for BioBank center accreditation.

* Co-PI, Grant # 5U24HG006941-08, National Human Genome Research Institute, 07/01/17-06/30/22: H3ABioNet: informatics solutions for H3Africa.

* Co-PI, Grant # 1U41HG006941-01 NIH. H3ABioNet: a sustainable African Bioinformatics Network for H3Africa, 08/01/12- 07/01/17.

* PI in “Development and Accreditation of Dr. Ali Khalifa Hormones and Tumor Markers Lab, Faculty of Medicine, Ain Shams University” project # LP8-002-AINawarded by Ministry of High Education, 2014.

* PI in “Development and Accreditation of Dr. Ali Khalifa Virology Lab, Faculty of Medicine, Ain Shams University” project # LP7-012-AIN awarded by Ministry of High Education, 2013.

* "Development of Curriculum for a Master Degree Program in Medical Informatics. Faculty of Computers and Information, Helwan University",Granted By: TEMPUS, 2007.

* · "Screening for Markers for Molecular Diagnosis of Schistosomal Bladder Cancer, under the program of the National Strategy for Biotechnology and Genetic Engineering", Granted By: Academy of Scientific Research and Technology, 2005.

Manuscripts of last 7 years

https://www.ncbi.nlm.nih.gov/myncbi/samar.kamal%20kassim.1/bibliography/public/

1. Judit Kumuthini, Lyndon Zass, Melek Chaouch, Faisal M Fadlelmola, Nicola Mulder, Fouzia Radouani, Verena Ras, Chaimae Samtal, Milaine SS Tchamga, Dassen Sathan, Anisah Ghoorah, Raphael Z Sangeda, Liberata A Mwita, Upendo Masamu, Samar Kamal Kassim, Zoe Gill, Zahra Mungloo-Dilmohamud, Gordon Wells: Genomic Data Sharing. In Genomics Data Sharing, Academic press publisher, 111-135. https://doi.org/10.1016/B978-0-12-819803-2.00003-1

2. HOURIIYAH TEGALLY, JAMES E. SAN., MATTHEW COTTEN, MONIKA MOIR, BRYAN TEGOMOH, GERALD MBOOWA, DARREN P. MARTIN, CHERYL BAXTER, ARNOLD W. LAMBISIA[...]EDUAN WILKINSON E+393 authorS: The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. SCIENCE, 15 Sep 2022, DOI: 10.1126/science.abq5358

3. Jongeneel C. Victor, Kotze Maritha J., Bhaw-Luximon Archana, Fadlelmola Faisal M., Fakim Yasmina J., Hamdi Yosr, Kassim Samar Kamal, Kumuthini Judit, Nembaware Victoria, Radouani Fouzia, Tiffin Nicki, Mulder Nicola: A View on Genomic Medicine Activities in Africa: Implications for Policy. Frontiers in Genetics (13), 2022. https://doi.org/10.3389/fgene.2022.769919

4. Othman H, Zass L, da Rocha JEB, Radouani F, Samtal C, Benamri I, Kumuthini J, Fakim YJ, Hamdi Y, Mezzi N, Boujemaa M, Okeke CJ, Tendwa MB, Sanak K, Chaouch M, Panji S, Kefi R, Sallam RM, Ghoorah AW, Romdhane L, Kiran A, Meintjes AP, Maturure P, Jmel H, Ksouri A, Azzouzi M, Farahat MA, Ahmed S, Sibira R, Turkson MEE, Ssekagiri A, Parker Z, Fadlelmola FM, Ghedira K, Mulder N, Kamal Kassim S. African Genomic Medicine Portal: A Web Portal for Biomedical Applications. Journal of Personalized Medicine. 2022; 12(2):265. https://doi.org/10.3390/jpm12020265. PMCID: PMC8879570.

5. Wilkinson E, Giovanetti M, Tegally H, et al.,: A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science. 2021 Oct 22;374(6566):423-431. doi: 10.1126/science.abj4336. Epub 2021 Sep 9. PubMed PMID: 34672751; PubMed Central PMCID: PMC7613315.

6. Fadlelmola FM, Ghedira K, Hamdi Y, Hanachi M, Radouani F, Allali I, Kiran A, Zass L, Alsayed N, Fassatoui M, Samtal C, Ahmed S, Da Rocha J, Chaqsare S, Sallam RM, Chaouch M, Farahat M, Ssekagiri A, Parker Z, Adil M, Turkson M, Benchaalia A, Benkahla A, Panji S, Kassim S, Souiai O, Mulder N: H3ABioNet genomic medicine and microbiome data portals hackathon proceedings. Database (Oxford). 2021 Apr 17;2021:baab016. doi: 10.1093/database/baab016. PMID: 33864455

7. Hamdi Y, Zass L*, Othman H,* Radouani F, Allali I, Hanachi M, Okeke CJ, Chaouch M, Tendwa MB, Samtal C, Sallam RM, Alsayed N, Turkson M, Ahmed S, Benkahla A, Romdhane L, Souiai O, Bishop OT, Ghedira K, Fadlelmola FM, {Mulder N, Kassim SK}: Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects. OMICS A Journal of Integrative Biology 25 (4): 2021. DOI: 10.1089/omi.2021.0004. PMCID: PMC80607177.

8. Choudhury A, Aron S, Botigué LR, Sengupta D, Botha G, Bensellak T, Wells G, Kumuthini J, Shriner D, Fakim YJ, Ghoorah AW, Dareng E, Odia T, Falola O, Adebiyi E, Hazelhurst S, Mazandu G, Nyangiri OA, Mbiyavanga M, Benkahla A, Kassim SK, Mulder N, Adebamowo SN, Chimusa ER, Muzny D, Metcalf G, Gibbs RA, Rotimi C, Ramsay M, Adeyemo AA, Lombard Z, Hanchard NA. High-depth African genomes inform human migration and health. Nature. 2020 Oct;586(7831):741-748. doi: 10.1038/s41586-020-2859-7. Epub 2020 Oct 28. PubMed PMID: 33116287.

9. Aron S, Jongeneel CV, Chauke PA, Chaouch M, Kumuthini J, Zass L, Radouani F, Kassim SK, Fadlelmola FM, Mulder N. Ten simple rules for developing bioinformatics capacity at an academic institution. PLoS Comput Biol. 2021 Dec 9;17(12):e1009592. doi: 10.1371/journal.pcbi.1009592. PMID: 34882684; PMCID: PMC8659687.

10. Radouani F, Zass L, Hamdi Y, Rocha JD, Sallam R, Abdelhak S, Ahmed S, Azzouzi M, Benamri I, Benkahla A, Bouhaouala-Zahar B, Chaouch M, Jmel H, Kefi R, Ksouri A, Kumuthini J, Masilela P, Masimirembwa C, Othman H, Panji S, Romdhane L, Samtal C, Sibira R, Ghedira K, Fadlelmola F, Kassim SK, Mulder N. A review of clinical pharmacogenetics Studies in African populations. Per Med. 2020 Mar;17(2):155-170. doi: 10.2217/pme-2019-0110. Epub 2020 Mar 3. Review. PubMed PMID: 32125935.

11. Nembaware V; African Genomic Medicine Training Initiative, Mulder N.: African Genomic Medicine Training Initiative, Mulder N2.The African Genomic Medicine Training Initiative (AGMT): Showcasing a Community and Framework Driven Genomic Medicine Training for Nurses in Africa. Front Genet. 2019 Dec 20;10:1209. doi: 10.3389/fgene.2019.01209. eCollection 2019. PMID: 31921282.

12. Aron, Shaun et al. H3ABioNet: Developing Sustainable Bioinformatics Capacity in Africa. EMBnet.journal, [S.l.], v. 23, p. e886, may 2017. ISSN 2226-6089. Available at: <https://journal.embnet.org/index.php/embnetjournal/article/view/886/1342>. Date accessed: 29 aug. 2021. doi:https://doi.org/10.14806/ej.23.0.886.

13. Ahmed MY, Salah MM, Kassim SK, Elayat WM, Mohamed DA and Zahra FA: Evaluation of the diagnostic and therapeutic roles of non-coding RNA and cell proliferation related gene association in hepatocellular carcinoma. Gene (706): Available online April 26, 2019. https://doi.org/10.1016/j.gene.2019.04.054

14. Ibrahim H. Borai, Ahmed F. Soliman, Hadeer M. Ahmed, Gihan F. Ahmed, and Samar K. Kassim (2018): Association of MTHFR C677T and ABCA1 G656A polymorphisms with obesity among Egyptian children. Gene Reports, 11: 143-149. 10.1016/j.genrep.2018.03.011

15. Sawsan Aboul-Fotouh, Mohamed Habib, Tarek Asaad, Samar K. Kassim and Mohamed H. Ghanem (2018): Behavioral effects of toll-like receptor-4 antagonist ‘eritoran’ in an experimental model of depression: role of prefrontal and hippocampal neurogenesis and γ-aminobutyric acid/glutamate balance. Behavioural Pharmacology, 29 :413-425. PMID: 29561292, DOI: 10.1097/FBP.0000000000000390

16. S El Sayed, E Khairy, AR Basheer, WS Zaki, GF Ahmad, SK Kassim (2018): Evaluation of leptin and MMP2 genes methylation in childhood obesity. Gene Reports 11: 79-86. 10.1016/j.genrep.2018.02.006

17. Hamdy M, Kassim SK, Khairy E, Maher M, Mansour KA, Albreedy AM. (2018): Ghrelin gene polymorphism as a genetic biomarker for prediction of therapy induced clearance in Egyptian chronic HCV patients. Gene. 2018 Jan 25. pii: S0378-1119(18)30098-2. doi: 10.1016/j.gene. 2018.01.077. [Epub ahead of print]. PMID: 29374597.

18. Aboul-Fotouh S, Hassan D, Habib M, Amin AI, Kassim SK, and Mohamed AS (2018): Biochemical studies of hippocampal gene expression of brain-derived neurotropic factor and toll-like receptor-4 in diabetic rats exposed to chronic stress: effects of antidepressant drugs. Asian J of Pharmaceutical and Clinical Research; (11): 271-7. 10.22159/ajpcr.2018.v11i1.21593

19. S.K. Kassim, S.M. Kamal, H.H. Shehata, M.M. Salib, M.L. Louka, M.M. Sallam, L.M. Nabegh (2017): Evaluation of serum fibrotic markers; CTGF, IL-17and TGF-β1 versus liver biopsy for detection of hepatic fibrosis in Egyptian patients with chronic hepatitis C. Meta Gene (13): 63-69. https://doi.org/10.1016/j.mgene.2017.05.003

20. Nicola J. Mulder Correspondence information about the author Nicola J. Mulder Email the author Nicola J. Mulder, Ezekiel Adebiyi, Marion Adebiyi, Seun Adeyemi, Azza Ahmed, Rehab Ahmed, Bola Akanle, Mohamed Alibi, Don L. Armstrong, Shaun Aron, Efejiro Ashano, Shakuntala Baichoo, Alia Benkahla, David K. Brown, Emile R. Chimusa, Faisal M. Fadlelmola, Dare Falola, Segun Fatumo, Kais Ghedira, Amel Ghouila, Scott Hazelhurst, Itunuoluwa Isewon, Segun Jung, Samar Kamal Kassim, Jonathan K. Kayondo, Mamana Mbiyavanga, Ayton Meintjes, Somia Mohammed, Abayomi Mosaku, Ahmed Moussa, Mustafa Muhammd, Zahra Mungloo-Dilmohamud, Oyekanmi Nashiru, Trust Odia, Adaobi Okafor, Olaleye Oladipo, Victor Osamor, Jellili Oyelade, Khalid Sadki, Samson Pandam Salifu, Jumoke Soyemi, Sumir Panji, Fouzia Radouani, Oussama Souiai, Özlem Tastan Bishop, and The H3ABioNet Consortium, as members of the H3Africa Consortium (2017): Development of Bioinformatics Infrastructure for Genomics Research in H3Africa. Global Heart; 12: 91-98. DOI: http://dx.doi.org/10.1016/j.gheart.2017.01.005

21. Nicola J Mulder, Ezekiel Adebiyi, Raouf Alami, Alia Benkahla, James Brandful, Seydou Doumbia, Dean Everett, Faisal M Fadlelmola, Fatima Gaboun, Simani Gaseitsiwe, Hassan Ghazal, Scott Hazelhurst, Azeddine Ibrahimi, Winston Hide, Yasmina Jaufeerally Fakim, Victor Jongeneel, Fourie Joubert, Samar Kassim, Jonathan Kayondo, Judit Kumuthini, Sylvester Lyantagaye, Julie Makani, Ahmed Mansour Alzohairy, Daniel Masiga, Ahmed Moussa, Oyekanmi Nash, Odile Ouwe Missi Oukem-Boyer, Ellis Owusu-Dabo, Sumir Panji, Hugh Patterton, Fouzia Radouani, Khalid Sadki, Fouad Seghrouchni, Özlem Tastan Bishop, Nicki Tiffin, Nzovu Ulenga, and H3ABioNet Consortium (2016): H3ABioNet, a sustainable Pan-African Bioinformatics Network for Human Heredity and Health in Africa. Genome Res. 26: 271-7, doi: 10.1101/gr.196295.115. Epub 2015 Dec 1.

22. H3Africa Consortium (2014): Enabling the genomic revolution in Africa. Science.;344 (6190):1346-8. doi: 10.1126/science.1251546.

http://www.ncbi.nlm.nih.gov/pubmed/?term=Enabling+the+genomic+revolution+in+Africa.

23. Islam Ibrahim Amin, Aboul Ella Hassanien, Samar K. Kassim, Hesham A. Hefny (2014): Visualizing and Identifying the DNA Methylation Markers in Breast Cancer Tumor Subtypes. In: Proceedings of the Fifth International Conference on Innovations in Bio-Inspired Computing and Applications IBICA 2014 Advances in Intelligent Systems and Computing, At VSB-Technical University of Ostrava, Ostrava, Czech republic, Springer; 303, 161-171. http://link.springer.com/chapter/10.1007/978-3-319-08156-4_17

24. Kamal SM, Kassim SK, Ahmed AI, Mahmoud S, Bahnasy KA, Hafez TA, Aziz IA, Fathelbab IF, Mansour HM. (2014): Host and viral determinants of the outcome of exposure to HCV infection genotype 4: a large longitudinal study. Am J Gastroenter; 109(2):199-211. doi: 10.1038/ajg.2013.427. Epub 2014 Jan 21.

Books & Book Chapters

1. Judit Kumuthini, Lyndon Zass, Melek Chaouch, Faisal M Fadlelmola, Nicola Mulder, Fouzia Radouani, Verena Ras, Chaimae Samtal, Milaine SS Tchamga, Dassen Sathan, Anisah Ghoorah, Raphael Z Sangeda, Liberata A Mwita, Upendo Masamu, Samar Kamal Kassim, Zoe Gill, Zahra Mungloo-Dilmohamud, Gordon Wells: Genomic Data Sharing. In Genomics Data Sharing, Academic press publisher, 111-135. https://doi.org/10.1016/B978-0-12-819803-2.00003-1

2. Mohammed A. Farahat, A. Abdo, Samar Kamal Kassim: A Systematic Literature Review of DNA-Based Steganography Techniques: Research Trends, Data Sets, Methods, and Frameworks. In: Magdi D.A., Helmy Y.K., Mamdouh M., Joshi A. (eds) Digital Transformation Technology. Lecture Notes in Networks and Systems, vol 224. Springer, Singapore. https://doi.org/10.1007/978-981-16-2275-5_31.

3. Islam Ibrahim Amin, Aboul Ella Hassanien, Samar K. Kassim, Hesham A. Hefny: Big DNA Methylation Data Analysis and Visualizing in a Common Form of Breast Cancer. In Big Data in Complex Systems: Challenges and Opportunities, pp: 275-391. Publisher: Springer-Verlag, Germany, Editors: Aboul Ella Hassanien, Ahmad Taher Azar, Vaclav Snasel, Janusz Kacprzyk, Jemal H. Abawajy, 2014.http://www.springer.com/gp/book/9783319110554

4. Sanaa Eissa, Lilian Ramzy, Samar Kassim. Methylation of APC tumor suppressor gene In bladder cancer : Molecular Screening for Bladder Cancer Project PI: Prof Sanaa Eissa, Medical Biochemistry & Molecular biology department. First edited by Sanaa Eissa, 01/2012; LAP Lambert Academic Publishing AG & Co KG. ISBN: 978-3-8484-1376-8.https://www.exlibris.ch/de/buecher-buch/english-books/ramzy-lilian/methylation-of-apc-tumor-suppressor-gene-in-bladder-cancer/id/9783848413768

5. A. Sharaf Eldin, , S. AbdelGaber, , T. Soliman, , S. Kassim and , A. Abdo:A Comparative Study of Protein Sequence Clustering Algorithms. In “Innovations in Computing Sciences and Software Engineering”. pp 373-378. Eds.: Sobh TareK and Ellaithy Khaled, 2010. Published by: Springer Netherlands, Copyright holder: Springer Science+Business Media B.V. http://link.springer.com/chapter/10.1007%2F978-90-481-9112-3_63. Doi>10.1007/978-90-481-9112-3_63, Print ISBN: 978-90-481-9111-6, Online ESBN: 978-90-481-9112-3.

6. Bast, R.C. et al. (1995). Cell growth regulation in ovarian cancer: tyrosine kinases, tyrosine phosphatases and tumour necrosis factor-α . In: Sharp, F., Mason, P., Blackett, T., Berek, J. (eds) Ovarian Cancer 3. Springer, Boston, MA. https://doi.org/10.1007/978-1-4757-0136-4_11، https://doi.org/10.1007/978-1-4757-0136-4_11

Abstracts

1. Wiener, S.K. Kassim, A. Berchuck, R.C. Bast, Jr. 1993. Role of Protein Tyrosine Kinases and Protein Tyrosine Phophatases in Human Ovarian and Mammary Cancer Cell Growth. 2nd International Symposium on Cancer Molecular Biology. Cairo, Egypt.

2. Wiener, S.K. Kassim, A. Berchuck, R.C. Bast, Jr. 1994. Differential Expression of Protein Tyrosine Phosphatases in Human Ovarian Adenocarcinomas. American Association for Cancer Research. San Francisco, CA, USA.

3. Bast, Jr., Jon Wiener, S.K. Kassim, S. Wu, C. Boyer, K. DeSombre, J. Hurteau, G. Rodriguez, G. Mills, and A. Berchuck.Cell Growth Regulation in Ovarian Cancer: Tyrosine Kinases, Tyrosine Phosphatases and Tumor Necrosis Factor-a. Helene Harris symposium, Toronto, Canada.

Review Activity

* Scientific Reviewer at Misr ElKhair Organization.

* Reviewer for the National Encouraging Award of Academy of Science and Research, 2014.

* Reviewer for many International Scientific Journals e.g. Liver International, Gene, Clinical Biochemistry, Chemotherapy, IUBMB Life, and the International Journal of Gynecological Cancer, and regional Journals as the Egyptian Journal of Biochemistry and Molecular Biology and the Arab Journal of Biochemistry.

* Chosen by the "Merit scholarship programme of the Islamic Development Bank" as an external reviewer to evaluate the Ph.D. and post-doctoral applications for the Islamic Development Bank fellowships for the year 1429H.

* Reviewer for joint projects of Research Academy of Science and Research (Swedish MENA and Amnhotob).