Publications
Journal articles, preprints, and conference proceedings
Publications are grouped by broad research area and listed in reverse chronological order within each section. For an up-to-date, complete citation record, see Google Scholar or the PubMed bibliography. Selected highlights appear on the home page.
Population Genomics and Precision Medicine
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EGP1K: Whole-Genome Sequencing of 1,024 Egyptians Characterizes Population Structure and Genetic Diversity Khaled Amer, Ahmed Moustafa, Wael A. Hassan, et al. bioRxiv. 2 April 2026 doi: 10.64898/2026.04.02.715521 |
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Whole genome sequencing identifies monogenic disease in 56.1% of families with early-onset steroid-resistant nephrotic syndrome Neveen A Soliman, Mohamed A Elmonem, Ahmed F El-Sayed, Eman Ramadan, Ahmed M Badr, Fatma M Atia, Rasha Helmy, May O Amer, Ahmed Abd El-Raouf, Fadya M El-Garhy, Omnia M Abdel-Haseb, Tokka M Hassan, Yasmeen K Farouk, Ahmed El-Hosseiny, Usama Bakry, Asmaa Ali, Sheri Saleeb, Tasnim A Ghanim, Mahynour Albarbary, Ahmed Elmahy, Tarek Elnagdy, Amira Ragheb, Wael A Hassan, Ahmed Moustafa, Khaled Amer Human Genetics. 22 May 2025 doi: 10.1007/s00439-025-02752-y | pmid: 40402239 |
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Egypt Genome: Towards an African new genomic era Khaled Amer, Neveen A Soliman, Sameh Soror, Yehia Z Gad, Ahmed Moustafa, Mohamed A Elmonem, May Amer, Ameera Ragheb, Amira Kotb, Tarek Taha, Wael Ali, Mahmoud Sakr, Khaled Abdel Ghaffar; Scientific Committee Consortium Journal of Advanced Research. 4 June 2024 doi: 10.1016/j.jare.2024.06.003 | pmid: 38844121 |
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The Egypt Genome Project Mohamed A Elmonem, Neveen A Soliman, Ahmed Moustafa, Yehia Z Gad, Wael A Hassan, Tarek Taha, Gina El-Feky, Mahmoud Sakr, Khaled Amer Nature Genetics. 29 April 2024 doi: 10.1038/s41588-024-01739-1 | pmid: 38684896 |
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New Variant With a Previously Unrecognized Mechanism of Pathogenicity in Hypertrophic Cardiomyopathy Yasmine Aguib, Mona Allouba, Roddy Walsh, Ayman M. Ibrahim, Sarah Halawa, Alaa Afify, Mohammed Hosny, Pantazis I. Theotokis, Aya Galal, Sara Elshorbagy, Mohamed Roshdy, Heba S. Kassem, Amany Ellithy, Rachel Buchan, Nicola Whiffin, Shehab Anwer, Stuart A. Cook, Ahmed Moustafa, Ahmed ElGuindy, James S. Ware, Paul J.R. Barton, Magdi H. Yacoub Circulation. 30 August 2021 doi: 10.1161/CIRCULATIONAHA.120.048295 | pmid: 34460321 |
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Toward Colorectal Cancer Biomarkers: The Role of Genetic Variation, Wnt Pathway, and Long Noncoding RNAs Amany I. Abdel-Motaleb, Hassan M. Azzazy, Ahmed Moustafa OMICS: A Journal of Integrative Biology. 22 April 2021 doi: 10.1089/omi.2020.0231 | pmid: 33891491 |
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Deep Next Generation Sequencing Identifies Somatic Mutational Signature in Egyptian Colorectal Cancer Patients Amira Youssef, Mohamed A. Abdel-Fattah, Ahmed O. Touny, Zeinab K. Hassan, Auhood Nassar, Mai M. Lotfy, Ahmed Moustafa, Mohammed Mohey Eldin, Abeer Bahnassy, Abdel-Rahman N. Zekri Research Square. 18 December 2020 doi: 10.21203/rs.3.rs-125305/v1 |
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Deep Sequencing of 10,000 Human Genomes Amalio Telenti, Levi T Pierce, William H Biggs, Julia di Iulio, Emily H.M. Wong, Martin M Fabani, Ewen F Kirkness, Ahmed Moustafa, Naisha Shah, Chao Xie, Suzanne C Brewerton, Nadeem Bulsara, Chad Garner, Gary Metzker, Efren Sandoval, Brad A Perkins, Franz J Och, Yaron Turpaz, J. Craig Venter Proceedings of the National Academy of Sciences. 4 October 2016 doi: 10.1073/pnas.1613365113 | pmid: 27702888 |
Human Microbiome, Metagenomics, and Viromes
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Association between the subcellular localization of host proteins and gut microbiome and metabolome in metabolic dysfunction-associated steatotic liver disease: a pilot study Shereen A. El Sobky, Nada El-Ekiaby, Injie O. Fawzy, Amira Khaled Abdelhamid, Heba Attia, Ibrahim H. Fayed, Yasser Badr, Mohammed Emadeldeen, Ahmed Nagy, Mohamed Negm, Mohamed Sherif Negm, Ahmed Moustafa, Mohamed El-Kassas, Mohamed A. Farag, Ramy K. Aziz, Ahmed I. Abdelaziz Frontiers in Molecular Biosciences. 2 July 2026 doi: 10.3389/fmolb.2026.1703547 |
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Metagenomic profiling of gut microbiome signatures across liver disease stages and HCV-related hepatocellular carcinoma in Egyptian patients Marwa Zahra, Amged Ouf, Hassan M. E. Azzazy, Ahmed Moustafa Frontiers in Microbiology. 28 April 2026 doi: 10.3389/fmicb.2026.1758563 | pmid: 42131203 |
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Gut microbial shifts toward inflammation in Parkinson’s disease: Insights from pilot shotgun metagenomics Egyptian cohort Ali Shalash, Shahd Ezzeldin, Sara Hashish, Yara Salah, Noha L. Dawood, Ahmed Moustafa, Mohamed Salama Journal of Parkinson’s Disease. 17 September 2025 doi: 10.1177/1877718x251370156 | pmid: 40961238 |
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SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021 Andrew D. Marques, Scott Sherrill-Mix, John K. Everett, Shantan Reddy, Pascha Hokama, Aoife M. Roche, Young Hwang, Abigail Glascock, Samantha A. Whiteside, Jevon Graham-Wooten, Layla A. Khatib, Ayannah S. Fitzgerald, Ahmed M. Moustafa, Colleen Bianco, Swetha Rajagopal, Jenna Helton, Regan Deming, Lidiya Denu, Azad Ahmed, Eimear Kitt, Susan E. Coffin, Claire Newbern, Josh Chang Mell, Paul J. Planet, Nitika Badjatia, Bonnie Richards, Zi-Xuan Wang, Carolyn C. Cannuscio, Katherine M. Strelau, Anne Jaskowiak-Barr, Leigh Cressman, Sean Loughrey, Arupa Ganguly, Michael D. Feldman, Ronald G. Collman, Kyle G. Rodino, Brendan J. Kelly, Frederic D. Bushman mBio. 8 February 2022 doi: 10.1128/mbio.03788-21 | pmid: 35130727 |
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Traces of SARS-CoV-2 RNA in Peripheral Blood Cells of Patients with COVID-19 Ahmed Moustafa, Rana Salah Khalel, Ramy K. Aziz OMICS: A Journal of Integrative Biology. 19 July 2021 doi: 10.1089/omi.2021.0068 | pmid: 34280038 |
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Gut microbiome differences between amyotrophic lateral sclerosis patients and spouse controls Vicki S. Hertzberg, Harinder Singh, Christina N. Fournier, Ahmed Moustafa, Meraida Polak,Claire A. Kuelbs, Manolito G. Torralba, Malú G. Tansey, Karen E. Nelson, Jonathan D. Glass Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration. 5 April 2021 doi: 10.1080/21678421.2021.1904994 | pmid: 33818222 |
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Traces of SARS-CoV-2 RNA in the Blood of COVID-19 Patients Ahmed Moustafa, Ramy K Aziz medRxiv. 18 May 2020 doi: 10.1101/2020.05.10.20097055 |
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Longitudinal Study of Oral Microbiome Variation in Twins Marcelo Freire, Ahmed Moustafa, Derek M. Harkins, Manolito G. Torralba, Yun Zhang, Pamela Leong, Richard Saffery, Michelle Bockmann, Claire Kuelbs, Toby Hughes, Jeffrey M. Craig, Karen E. Nelson Scientific Reports. 14 May 2020 doi: 10.1038/s41598-020-64747-1 | pmid: 32409670 |
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Effect of Radiotherapy on the Gut Microbiome in Pediatric Cancer Patients: A Pilot Study Nourhan Sahly, Ahmed Moustafa, Mohamed Zaghloul, Tamer Z Salem PeerJ. 23 September 2019 doi: 10.7717/peerj.7683 | pmid: 31579590 |
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Xylitol and Sorbitol effects on the microbiome of saliva and plaque Reisha Rafeek, Christine V. F. Carrington, Andres Gomez, Derek Harkins, Manolito Torralba, Claire Kuelbs, Jonas Addae, Ahmed Moustafa, Karen E. Nelson Journal of Oral Microbiology. 23 October 2018 doi: 10.1080/20002297.2018.1536181 | pmid: 30598728 |
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Microbial metagenome of urinary tract infection Ahmed Moustafa, Weizhong Li, Harinder Singh, Kelvin J. Moncera, Manolito G. Torralba, Yanbao Yu, Oriol Manuel, William Biggs, J. Craig Venter, Karen E. Nelson, Rembert Pieper, Amalio Telenti Scientific Reports. 12 March 2018 doi: 10.1038/s41598-018-22660-8 | pmid: 29531289 |
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Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease Ahmed Moustafa, Brigid S. Boland, Weizhong Li, Ericka L. Anderson, Emily H. M. Wong, Parambir S. Dulai, William J. Sandborn, William Biggs, J. Craig Venter, Karen E. Nelson, Amalio Telenti, John T. Chang Clinical and Translational Gastroenterology. 18 January 2018 doi: 10.1038/ctg.2017.58 | pmid: 29345635 |
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Microbial Metagenome Of Urinary Tract Infection Ahmed Moustafa, Harinder Singh, Weizhong Li, Kelvin Moncera, Manolito Torralba, Yanbao Yu, Oriol Manuel, William Biggs, J. Craig Venter, Karen Nelson, Rembert Pieper, Amalio Telenti bioRxiv. 4 May 2017 doi: 10.1101/134320 |
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The blood DNA virome in 8,000 humans Ahmed Moustafa, Chao Xie, Ewen Kirkness, William Biggs, Emily Wong, Yaron Turpaz, Kenneth Bloom, Eric Delwart, Karen E. Nelson, J. Craig Venter, Amalio Telenti PLOS Pathogens. 22 March 2017 doi: 10.1371/journal.ppat.1006292 | pmid: 28328962 |
Microbial, Environmental, and Marine Genomics
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A Pan-Biome Metagenomic Atlas of the Brazilian Rhizosphere, Root, and Soil Microbiomes Luisa Mayumi Arake de Tacca, Rayane Nunes Lima, Patrícia Verdugo Pascoal, Deborah Bambil, Marco Antônio de Oliveira, Ahmed Moustafa, Helena Ipê Pinheiro Guimarães, Carlos Alexandre Azevedo, Paula Mizote, Grácia Maria Soares Rosinha, Daniela Carvalho Bittencourt, Diana Signor, Magna Soelma Beserra de Moura, José Pedro Pereira Trindade, Leandro Bochi da Silva Volk, Fernando Antônio Fernandes, Ricardo Lopes, Jean Luiz Simões-Araújo, Marcelo Freire, Elibio Rech Research Square. 9 March 2026 doi: 10.21203/rs.3.rs-8948634/v1 |
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The coral microbiome: Towards an understanding of the molecular mechanisms of coral-microbiota interactions Amin Mohamed, Michael Ochsenkuhn, Ahmed Kazlak, Ahmed Moustafa, Shady Amin FEMS Microbiology Reviews. 7 March 2023 doi: 10.1093/femsre/fuad005 | pmid: 36882224 |
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Gene Networks and Pathways Involved in Escherichia coli Response to Multiple Stressors Eman K. Abdelwahed, Nahla A. Hussein, Ahmed Moustafa, Nayera A. Moneib, Ramy K. Aziz Microorganisms. 6 September 2022 doi: 10.3390/microorganisms10091793 | pmid: 36144394 |
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Nitrogen and Iron Availability Drive Metabolic Remodeling and Natural Selection of Diverse Phytoplankton during Experimental Upwelling B C Kolody, S R Smith, L Zeigler Allen, J P McCrow, Ahmed Moustafa, D Shi, B M Hopkinson, F M M Morel, B B Ward, A E Allen mSystems. 29 August 2022 doi: 10.1128/msystems.00729-22 | pmid: 36036504 |
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Genetic variation of staphylococcal LukAB toxin determines receptor tropism Sofya S. Perelman, David B. A. James, Kristina M. Boguslawski, Chase W. Nelson, Juliana K. Ilmain, Erin E. Zwack, Rachel A. Prescott, Adil Mohamed, Kayan Tam, Rita Chan, Apurva Narechania, Miranda B. Pawline, Nikollaq Vozhilla, Ahmed M. Moustafa, Sang Y. Kim, Meike Dittmann, Damian C. Ekiert, Gira Bhabha, Bo Shopsin, Paul J. Planet, Sergei B. Koralov, Victor J. Torres Nature Microbiology. 19 April 2021 doi: 10.1038/s41564-021-00890-3 | pmid: 33875847 |
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Draft Genome Sequences and Antimicrobial Profiles of Three Staphylococcus epidermidis Strains from Neonatal Blood Samples Innocent Afeke, Ahmed Moustafa, Misa Hirose, Mareike Becker, Hauke Busch, Axel Kuenstner, Anke Faehnrich, Anthony S. Ablordey, Christoph Haertel, Kokou Hefoume Amega-Aho, Mohamed Tarek Badr, Jan Rupp, Saleh Ibrahim Microbiology Resource Announcements. 1 April 2021 doi: 10.1128/MRA.00170-21 | pmid: 33795343 |
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Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection B. C. Kolody, J. P. McCrow, L. Zeigler Allen, F. O. Aylward, K. M. Fontanez, A. Moustafa, M. Moniruzzaman, F. P. Chavez, C. A. Scholin, E. E. Allen, A. Z. Worden, E. F. Delong & A. E. Allen The ISME Journal. 18 July 2019 doi: 10.1038/s41396-019-0472-2 | pmid: 31320727 |
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Nutrient stoichiometry shapes microbial community structure in a shallow evaporitic pond Zarraz M. Lee, Amisha T. Poret-Peterson, Janet L. Siefert, Drishti Kaul, Ahmed Moustafa, Andrew E. Allen, Chris L. Dupont, Luis E. Eguiarte, Valeria Souza, James J. Elser Frontiers in Microbiology. 30 May 2017 doi: 10.3389/fmicb.2017.00949 | pmid: 28611750 |
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Intact polar diacylglycerol biomarker lipids isolated from suspended particulate organic matter accumulating in an ultraoligotrophic water column Jenan J Kharbush, Andrew E Allen, Ahmed Moustafa, Pieter C Dorrestein, Lihini I Aluwihare Organic Geochemistry. 31 October 2016 doi: 10.1016/j.orggeochem.2016.07.008 |
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Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume Brian L Zielinski, Andrew E Allen, Edward J Carpenter, Victoria J Coles, Byron C Crump, Mary Doherty, Rachel A Foster, Joaquim I Goes, Helga R Gomes, Raleigh R Hood, John P McCrow, Joseph P Montoya, Ahmed Moustafa, Brandon M Satinsky, Shalabh Sharma, Christa B Smith, Patricia L Yager, John H Paul PloS one. 6 September 2016 doi: 10.1371/journal.pone.0160929 | pmid: 27598790 |
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Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge Erin M Bertrand, John P McCrow, Ahmed Moustafa, Hong Zheng, Jeffrey B McQuaid, Tom O Delmont, Anton F Post, Rachel E Sipler, Jenna L Spackeen, Kai Xu, Deborah A Bronk, David A Hutchins, Andrew E Allen Proceedings of the National Academy of Sciences. 28 July 2015 doi: 10.1073/pnas.1501615112 | pmid: 26221022 |
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A Novel Protein, Ubiquitous in Marine Phytoplankton, Concentrates Iron at the Cell Surface and Facilitates Uptake Joe Morrissey, Robert Sutak, Javier Paz-Yepes, Atsuko Tanaka, Ahmed Moustafa, Alaguraj Veluchamy, Yann Thomas, Hugo Botebol, François-Yves Bouget, Jeffrey B. McQuaid, Leila Tirichine, Andrew E Allen, Emmanuel Lesuisse, Chris Bowler Current Biology. 31 December 2014 doi: 10.1016/j.cub.2014.12.004 | pmid: 25557662 |
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Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities Chris L Dupont, John P McCrow, Ruben Valas, Ahmed Moustafa, Nathan Walworth, Ursula Goodenough, Robyn Roth, Shane L Hogle, Jing Bai, Zackary I Johnson, Elizabeth Mann, Brian Palenik, Katherine A Barbeau, J Craig Venter, Andrew E Allen The ISME Journal. 21 October 2014 doi: 10.1038/ismej.2014.198 | pmid: 25333462 |
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Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses Ari J. S. Ferreira, Rania Siam, João C. Setubal, Ahmed Moustafa, Ahmed Sayed, Felipe S. Chambergo, Adam S. Dawe, Mohamed A. Ghazy, Hazem Sharaf, Amged Ouf, Intikhab Alam, Alyaa M. Abdel-Haleem, Heikki Lehvaslaiho, Eman Ramadan, André Antunes, Ulrich Stingl, John A. C. Archer, Boris R. Jankovic, Mitchell Sogin, Vladimir B. Bajic, Hamza El-Dorry PLoS ONE. 12 June 2014 doi: 10.1371/journal.pone.0097338 | pmid: 24921648 |
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Unique Prokaryotic Consortia in Geochemically Distinct Sediments from Red Sea Atlantis II and Discovery Deep Brine Pools Rania Siam, Ghada Moustafa, Hazem Sharaf, Ahmed Moustafa, Adham Ramadan, Andre Antunes, Vladimir Bajic, Uli Stingl, Nardine Marsis, Marco Coolen, Mitchell Sogin, Ari Ferreira, and Hamza El-Dorry PLoS ONE. 20 August 2012 doi: 10.1371/journal.pone.0042872 | pmid: 22916172 |
Machine Learning, Computational Biology, and Bioinformatics Tools
Comparative and Evolutionary Genomics
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Deciphering patterns of adaptation and acclimation in the transcriptome of Phaeocystis antarctica to changing iron conditions Mariam R. Rizkallah, Stephan Frickenhaus, Scarlett Trimborn, Lars Harms, Ahmed Moustafa, Vladimir Benes, Steffi Gäbler‐Schwarz, Sara Beszteri Journal of Phycology. 15 April 2020 doi: 10.1111/jpy.12979 | pmid: 32068264 |
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An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome Uwe John, Yameng Lu, Sylke Wohlrab, Marco Groth, Jan Janouškovec, Gurjeet S. Kohli, Felix C. Mark, Ulf Bickmeyer, Sarah Farhat, Marius Felder, Stephan Frickenhaus, Laure Guillou, Patrick J. Keeling, Ahmed Moustafa, Betina M. Porcel, Klaus Valentin, Gernot Glöckner Science Advances. 24 April 2019 doi: 10.1126/sciadv.aav1110 | pmid: 31032404 |
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Pre‐mRNA splicing repression triggers abiotic stress signaling in plants Yu Ling, Sahar Alshareef, Haroon Butt, Jorge Lozano‐Juste, Lixin Li, Aya A Galal, Ahmed Moustafa, Afaque Ahmad Momin, Manal Tashkandi, Dale N Richardson, Hiroaki Fujii, Stefan Arold, Pedro L Rodriguez, Paula Duque, Magdy M Mahfouz The Plant Journal. 24 September 2016 doi: 10.1111/tpj.13383 | pmid: 27664942 |
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The Genome of the Foraminiferan Reticulomyxa filosa Gernot Glöckner, Norbert Hülsmann, Michael Schleicher, Angelika A Noegel, Ludwig Eichinger, Christoph Gallinger, Jan Pawlowski, Roberto Sierra, Ursula Euteneuer, Loic Pillet, Ahmed Moustafa, Matthias Platzer, Marco Groth, Karol Szafranski, Manfred Schliwa Current Biology. 12 December 2013 doi: 10.1016/j.cub.2013.11.027 | pmid: 24332546 |
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Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida Jonas Collén, Betina Porcel, Wilfrid Carré, Steven G Ball, Cristian Chaparro, Thierry Tonon, Tristan Barbeyron, Gurvan Michel, Benjamin Noel, Klaus Valentin, Marek Elias, François Artiguenave, Alok Arun, Jean-Marc Aury, José F Barbosa-Neto, John H Bothwell, François-Yves Bouget, Loraine Brillet, Francisco Cabello-Hurtado, Salvador Capella-Gutiérrez, Bénédicte Charrier, Lionel Cladière, J Mark Cock, Susana M Coelho, Christophe Colleoni, Mirjam Czjzek, Corinne Da Silva, Ludovic Delage, France Denoeud, Philippe Deschamps, Simon M Dittami, Toni Gabaldón, Claire M M Gachon, Agnès Groisillier, Cécile Hervé, Kamel Jabbari, Michael Katinka, Bernard Kloareg, Nathalie Kowalczyk, Karine Labadie, Catherine Leblanc, Pascal J Lopez, Deirdre H McLachlan, Laurence Meslet-Cladiere, Ahmed Moustafa, Zofia Nehr, Pi Nyvall Collén, Olivier Panaud, Frédéric Partensky, Julie Poulain, Stefan A Rensing, Sylvie Rousvoal, Gaelle Samson, Aikaterini Symeonidi, Jean Weissenbach, Antonios Zambounisb, Patrick Wincker, Catherine Boyena Proceedings of the National Academy of Sciences. 15 March 2013 doi: 10.1073/pnas.1221259110 | pmid: 23503846 |
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Metabolic Effectors Secreted by Bacterial Pathogens: Essential Facilitators of Plastid Endosymbiosis Steven G. Ball, Agathe Subtil, Debashish Bhattacharya, Ahmed Moustafa, Andreas P.M. Weber, Lena Gehre, Christophe Colleoni, Maria-Cecilia Arias, Ugo Cenci, David Dauvilléea The Plant Cell. 31 January 2013 doi: 10.1105/tpc.112.101329 | pmid: 23371946 |
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Plastid-localized amino acid biosynthetic pathways of Plantae are predominantly composed of non-cyanobacterial enzymes Adrian Reyes-Prieto, Ahmed Moustafa Scientific Reports. 11 December 2012 doi: 10.1038/srep00955 | pmid: 23233874 |
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Evolution and Functional Diversification of Fructose Bisphosphate Aldolase Genes in Photosynthetic Marine Diatoms Andrew E. Allen, Ahmed Moustafa, Anton Montsant, Angelika Eckert, Peter G. Kroth, Chris Bowler Molecular Biology and Evolution. 8 September 2011 doi: 10.1093/molbev/msr223 | pmid: 21903677 |
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Sea slug kleptoplasty and plastid maintenance in a metazoan Karen N. Pelletreau, Debashish Bhattacharya, Dana C. Price, Jared M. Worful, Ahmed Moustafa, Mary E. Rumpho Plant Physiology. 23 February 2011 doi: 10.1104/pp.111.174078 | pmid: 21346171 |
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The making of a photosynthetic animal Mary E. Rumpho, Karen N. Pelletreau, Ahmed Moustafa, Debashish Bhattacharya Journal of Experimental Biology. 15 January 2011 doi: 10.1242/jeb.046540 | pmid: 21177950 |
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Transcriptome Profiling of a Toxic Dinoflagellate Reveals a Gene-Rich Protist and a Potential Impact on Gene Expression Due to Bacterial Presence Ahmed Moustafa, Andrew N. Evans, Deana L. Erdner, David M. Kulis, Donald M. Anderson, Debashish Bhattacharya PLoS ONE. 12 March 2010 doi: 10.1371/journal.pone.0009688 | pmid: 20300646 |
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Differential gene retention in plastids of common recent origin Adrian Reyes-Prieto, Hwan Su Yoon, Ahmed Moustafa, Eun Chan Yang, Robert A. Andersen, Sung Min Boo, Takuro Nakayama, Ken-ichiro Ishida, Debashish Bhattacharya. Molecular Biology and Evolution. 1 February 2010 doi: 10.1093/molbev/msq032 | pmid: 20123796 |
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Genomic footprints of a cryptic plastid endosymbiosis in diatoms Ahmed Moustafa, Bánk Beszteri, Uwe G. Maier, Chris Bowler, Klaus Valentin, Debashish Bhattacharya Science. 26 June 2009 doi: 10.1126/science.1172983 | pmid: 19556510 |
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Origin of saxitoxin biosynthetic genes in cyanobacteria Ahmed Moustafa, Jeannette E. Loram, Jeremiah D. Hackett, Donald M. Anderson, F. Gerald Plumley, Debashish Bhattacharya. PLoS ONE. 1 June 2009 doi: 10.1371/journal.pone.0005758 | pmid: 19484122 |
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Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica Mary E. Rumpho, Jared M. Worful, Jungho Lee, Krishna Kannan, Mary S. Tyler, Debashish Bhattacharya, Ahmed Moustafa, James R. Manhart Proceedings of the National Academy of Sciences. 11 November 2008 doi: 10.1073/pnas.0804968105 | pmid: 19004808 |
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A phylogenomic approach for studying plastid endosymbiosis Ahmed Moustafa, CX Chan, Megan Danforth, David Zear, Hiba Ahmed, Nagnath Jadhav, Trevor Savage, Debashish Bhattacharya Genome Informatics. November 2008 doi: 10.1142/9781848163324_0014 | pmid: 19425156 |
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Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic Adrian Reyes-Prieto, Ahmed Moustafa, Debashish Bhattacharya Current Biology. 8 July 2008 doi: 10.1016/j.cub.2008.05.042 | pmid: 18595706 |
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Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions Ahmed Moustafa, Adrian Reyes-Prieto, Debashish Bhattacharya PLoS ONE. 21 May 2008 doi: 10.1371/journal.pone.0002205 | pmid: 18493612 |
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EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes William Lanier, Ahmed Moustafa, Debashish Bhattacharya, Josep Comeron PLoS ONE. 14 May 2008 doi: 10.1371/journal.pone.0002171 | pmid: 18478122 |
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Genomic insights into evolutionary relationships among heterokont lineages emphasizing the phaeophyceae Naomi Phillips, Calhoun Sam, Ahmed Moustafa, Debashish Bhattacharya, Edward Braun Journal of Phycology. 9 January 2008 doi: 10.1111/j.1529-8817.2007.00435.x | pmid: 27041034 |
Biomedical and Translational Genomics
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Efficacy of cost-effective UV-light for Salmonella elimination Sara Mohamed, Ahmed Kreta, Heba Refaat, Shaimaa F. Ahmed, Amany Khalifa, C. Tharwat, Ahmed Moustafa, Mohamed A. Swillam Photonic Diagnosis, Monitoring, Prevention, and Treatment of Infections and Inflammatory Diseases 2026. 5 March 2026 doi: 10.1117/12.3081802 |
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Pilot study: predicting the interplay between FOXO1 and its downstream long non-coding RNAs in HCC Rowan Abdelbary, Sherine K. Saber, Fabian Rose, Kai Breuhahn, Shereen A. El Sobky, Injie Omar Fawzy, Ahmed Moustafa, Nada El-Ekiaby, Ahmed Ihab Abdelaziz Frontiers in Oncology. 16 February 2026 doi: 10.3389/fonc.2026.1692980 | pmid: 41777650 |
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Identification of Skin Multicellular Reprogramming Factors as Potential Treatment for Nonhealing Diabetic Foot Ulcers Ahmed S. Abouhashem, Sherine K. Saber, Sara Abouzekry, Mohammed Elkholy, Ahmed Moustafa, Ahmed Abdellatif, Hassan M.E. Azzazy, Ahmed A. Elbaz, Kanhaiya Singh, Chandan K. Sen, Hossam Sharara Advances in Wound Care. 26 December 2025 doi: 10.1177/21621918251376348 | pmid: 41027406 |
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LncRNA RMRP knockdown upregulates PD-1 expression in natural killer cells Sarah Abouhegaziah, Doris Urlaub, Ahmed Moustafa, Maha Mostafa, Amged Ouf, Khaled Abou-Aisha, Carsten Watzl, Mona Rady Scientific Reports. 3 October 2025 doi: 10.1038/s41598-025-20720-4 | pmid: 41044334 |
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Assessing the influence of isolation techniques on NK cell transcriptomic profiles Rana ElNouty, Ahmed Moustafa, Maha Mostafa, Amged Ouf, Khaled Abou-Aisha, Mona Rady Transplant Immunology. 14 September 2025 doi: 10.1016/j.trim.2025.102298 | pmid: 40957502 |
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Surface Plasmon Resonance Detection of Staphylococcus Aureus Pathogen Sara Mohamed, Ahmed Kreta, Karim El-Seherawy, Mostafa Hassan, Baraah Hasanin, Heba Refaa, Shaimaa F. Ahmed, Ahmed Moustafa, Mohamed A. Swillam 2025 42nd National Radio Science Conference (NRSC). 6 May 2025 doi: 10.1109/nrsc65659.2025.11018577 |
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Detection of Escherichia coli bacteria using surface plasmon resonance-wavelength interrogation setup Sara Mohamed, Karim El-Seherawy, Mostafa Hassan, Ahmed Kreta, Baraah Hasanin, Yasmine Elbagoury, Heba Refaat, Shaimaa F. Ahmed, Mai Mostafa, Ahmed Moustafa, Mohamed A. Swillam Proceedings Volume 13356, High-Power Laser Materials Processing: Applications, Diagnostics, and Systems XIV. 19 March 2025 doi: 10.1117/12.3044165 |
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Photo-degradation of water and food pathogens using cheap handheld laser Sara Mohamed, C Tharwat, Amany Khalifa, Yasmine Elbagoury, Heba Refaat, Shaimaa F Ahmed, Ahmed Moustafa, Mohamed A Swillam Proceedings Volume 13356, High-Power Laser Materials Processing: Applications, Diagnostics, and Systems XIV. 19 March 2025 doi: 10.1117/12.3043613 |
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MiR-216a-3p inhibits the cytotoxicity of primary natural killer cells Rowan Abdelbary, Manon Ragheb, Shereen A. El Sobky, Nagwa El-Badri, Nourhan Aboud, Ahmed Tawheed, Asmaa Gomaa, Mona Zidan, Ramy K. Aziz, Abd Elrahman Abouzid, Radwa Ayman Salah, Mohamed El-Kassas, Imam Waked, Ahmed Moustafa, Injie Omar Fawzy, Nada El-Ekiaby, Ahmed Ihab Abdelaziz Frontiers in Oncology. 21 January 2025 doi: 10.3389/fonc.2024.1523068 | pmid: 39906666 |
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UV-VIs Spectrophotometry Study of Escherichia coli Bacteria and Microfluidic Channel Chip Fabrication For Optical Biosensing Application Sara Mohamed, Amira AM Ahmed, Ahmed Kreta, Amany Khalifa, Mai Mostafa, Shaimaa Ahmed, Heba Refaat, AM Faramawy, Ahmed Moustafa, Mohamed A Swillam 41st National Radio Science Conference (NRSC). 16 April 2024 doi: 10.1109/NRSC61581.2024.10510517 |
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Patterned PCL/PGS Nanofibrous Hyaluronic Acid-Coated Scaffolds Promote Cellular Response and Modulate Gene Expression Profiles Shrouk M. Abdou, Ahmed Moustafa, Nageh K. Allam ACS Applied Bio Materials. 3 April 2024 doi: 10.1021/acsabm.4c00196 | pmid: 38570335 |
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Beyond acute infection: molecular mechanisms underpinning cardiovascular complications in long COVID Roba Hamed Mostafa, Ahmed Moustafa Frontiers in Cardiovascular Medicine. 14 February 2024 doi: 10.3389/fcvm.2024.1268571 | pmid: 38495940 |
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Exploring the Regulatory Role of miRNA in Connecting Parkinson’s Disease with Pesticide Exposure in an Egyptian Cohort Fatma Galal, Shaimaa El-Jafaary, Nourhan Shebl, Nehal AB Elsayed, Jaidaa Mekky, Lobna A. Mohamed, Ahmed Moustafa, Mohamed Salama Research Square. 29 January 2024 doi: 10.21203/rs.3.rs-3873111/v1 |
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The State of Play of Parkinson’s Disease in Africa: A Systematic Review and Point of View Olaitan Okunoye, Yared Z. Zewde, Jihan Azar, Biniyam A. Ayele, Saiesha Dindayal, Ahmed Moustafa, Mosab Abdulkarim, Funmilola T. Taiwo, Daniel Gams Massi, Mohamed Salama, Abenet T. Mengesha, Yohannes D. Gelan, Dereje M. Oda, Fikru T. Kelemu, Charles Achoru, Vida Obese, Zeinab Kone, Momodou Cham, Maouly Fall, Abdoulaye Bocoum, Foksouna Sakadi, Philip Adebayo, Eric Guemekane Bila Lamou, Lorraine Chishimba, Aiysha Chaudhry, Ali Shalash, Eman Hamid, Musa Watila, Omotola Thomas, Oluwadamilola Ojo, Njideka U. Okubadejo, Mie Rizig bioRxiv. 8 July 2023 doi: 10.1101/2023.07.07.23292392 |
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Profiling Genome-Wide DNA Methylation Patterns in Human Aortic and Mitral Valves Sarah Halawa, Najma Latif, Yuan-Tsan Tseng, Ayman M. Ibrahim, Adrian H. Chester, Ahmed Moustafa, Yasmine Aguib, Magdi H. Yacoub Frontiers in Cardiovascular Medicine. 6 April 2022 doi: 10.3389/fcvm.2022.840647 | pmid: 35463757 |
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Neonatal and Young Infant Sepsis in a Regional Hospital in Ghana Innocent Afeke, Misa Hirose, Kokou Hefoume Amegan-Aho, Christoph Haertel, Mareike Becker, Ahmed Moustafa, Paul Schilf, Mohamed Tarek Badr, Graceful Lord Mensah, Hintermann Kobina Mbroh, Jan Rupp, Saleh Ibrahim Open Journal of Pediatrics. 22 June 2021 doi: 10.4236/ojped.2021.112027 |
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Transcriptional Regulatory Networks in Hepatitis C Virus-induced Hepatocellular Carcinoma Marwa Zahra, Hassan Azzazy, Ahmed Moustafa Scientific Reports. 24 September 2018 doi: 10.1038/s41598-018-32464-5 | pmid: 30250040 |