Ahmed Moustafa's Curriculum Vitae


Research Interests

Elucidating functional and evolutionary complexities of genomes and microbiomes using machine learning and genome analytics



Appointments

2014PresentAssociate Professor (tenured)American University in Cairo
20102014Assistant ProfessorAmerican University in Cairo
20092010Postdoctoral Research FellowJ. Craig Venter Institute
20082009Pre-Doctoral Research FellowUniversity of Iowa (NIH | NRSA)
20052008Graduate Research AssistantUniversity of Iowa
20002005Senior Software EngineerKaiser Permanente
19982000Software EngineerArab Academy for Science and Technology

Education

20052009PhD Computational GeneticsUniversity of Iowa
19931998BSc Computer ScienceAlexandria University

Teaching Experience

Professional Memberships

Publications

Effect of Radiotherapy on the Gut Microbiome in Pediatric Cancer Patients: A Pilot Study
Nourhan Sahly, Ahmed Moustafa, Mohamed Zaghloul, Tamer Z Salem
PeerJ. 2019 September 23.
pmid: 31579590 | doi: 10.7717/peerj.7683
Effect of Radiotherapy on the Gut Microbiome in Pediatric Cancer Patients: A Pilot Study  
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. 2019 July 18.
pmid: 31320727 | doi: 10.1038/s41396-019-0472-2
Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection  
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. 2019 April 24.
pmid: 31032404 | doi: 10.1126/sciadv.aav1110
An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome  
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. 2018 October.
pmid: 30598728 | doi: 10.1080/20002297.2018.1536181
Xylitol and Sorbitol effects on the microbiome of saliva and plaque  
Transcriptional Regulatory Networks in Hepatitis C Virus-induced Hepatocellular Carcinoma
Marwa Zahra, Hassan Azzazy, Ahmed Moustafa
Scientific Reports. 2018 September 24.
pmid: 30250040 | doi: 10.1038/s41598-018-32464-5
Transcriptional Regulatory Networks in Hepatitis C Virus-induced Hepatocellular Carcinoma  
Microbial metagenome of urinary tract infection Microbial metagenome of urinary tract infection [PDF]
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. 2018 March 12.
pmid: 29531289 | doi: 10.1038/s41598-018-22660-8
Microbial metagenome of urinary tract infection  
Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease [PDF]
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. 2018 January 18.
pmid: 29345635 | doi: 10.1038/ctg.2017.58
Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease  
Microbial Metagenome Of Urinary Tract Infection Microbial metagenome of urinary tract infection [PDF]
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. 2017 May 4.
doi: 10.1101/134320
Microbial Metagenome Of Urinary Tract Infection  
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. 2017 May 11.
pmid: 28611750 | doi: 10.3389/fmicb.2017.00949
Nutrient stoichiometry shapes microbial community structure in a shallow evaporitic pond  
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. 2017 March 22.
pmid: 28328962 | doi: 10.1371/journal.ppat.1006292
The blood DNA virome in 8,000 humans.  
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. 2016 October 4.
pmid: 27702888 | doi: 10.1073/pnas.1613365113
Deep Sequencing of 10,000 Human Genomes Faculty of 1000
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. 2016 October 31.
doi: 10.1016/j.orggeochem.2016.07.008
Intact polar diacylglycerol biomarker lipids isolated from suspended particulate organic matter accumulating in an ultraoligotrophic water column  
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. 2016 September 24.
pmid: 27664942 | doi: 10.1111/tpj.13383
Pre‐mRNA splicing repression triggers abiotic stress signaling in plants  
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. 2016 September 6.
pmid: 27598790 | doi: 10.1371/journal.pone.0160929
Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume  
Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge [PDF]
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. 2015 July 28.
pmid: 26221022 | doi: 10.1073/pnas.1501615112
Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge  
A Novel Protein, Ubiquitous in Marine Phytoplankton, Concentrates Iron at the Cell Surface and Facilitates Uptake A Novel Protein, Ubiquitous in Marine Phytoplankton, Concentrates Iron at the Cell Surface and Facilitates Uptake [PDF]
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. S0960-9822(14)01563-2. 2014 December 31.
pmid: 25557662 | doi: 10.1016/j.cub.2014.12.004
A Novel Protein, Ubiquitous in Marine Phytoplankton, Concentrates Iron at the Cell Surface and Facilitates Uptake  
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. 2014 October 21.
pmid: pmid: 25333462 | doi: 10.1038/ismej.2014.198
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities  
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. S0960-9822(13)01446-2. 2013 Dec 11.
pmid: 24332546 | doi: 10.1016/j.cub.2013.11.027
The Genome of the Foraminiferan Reticulomyxa filosa  
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. 110(13):5247-52, 2013 Mar 26
pmid: 23503846 | doi: 10.1073/pnas.1221259110
Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida  
Metabolic Effectors Secreted by Bacterial Pathogens: Essential Facilitators of Plastid Endosymbiosis Metabolic Effectors Secreted by Bacterial Pathogens: Essential Facilitators of Plastid Endosymbiosis [PDF]
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. Vol. 25: 1–15, January 2013
pmid: 23371946 | doi: 10.1105/tpc.112.101329
Metabolic Effectors Secreted by Bacterial Pathogens: Essential Facilitators of Plastid Endosymbiosis  
Plastid-localized amino acid biosynthetic pathways of Plantae are predominantly composed of non-cyanobacterial enzymes
Adrian Reyes-Prieto, Ahmed Moustafa
Scientific Reports. 2012;2:955. 2012 Dec 11
pmid: 23233874 | doi: 10.1038/srep00955
Plastid-localized amino acid biosynthetic pathways of Plantae are predominantly composed of non-cyanobacterial enzymes  
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. 2012;7(8):e42872. 2012 Aug 20
pmid: pmid: 22916172 | doi: 10.1371/journal.pone.0042872
Unique Prokaryotic Consortia in Geochemically Distinct Sediments from Red Sea Atlantis II and Discovery Deep Brine Pools  
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. 2011 Nov 4;(2012) 29 (1): 367-379
doi: 21903677 | doi: 10.1093/molbev/msr223
Evolution and Functional Diversification of Fructose Bisphosphate Aldolase Genes in Photosynthetic Marine Diatoms  
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. 2011 Apr;155(4):1561-5.
pmid: 21346171 | doi: 10.1104/pp.111.174078
Sea slug kleptoplasty and plastid maintenance in a metazoan  
iTree: a high-throughput phylogenomic pipeline iTree: a high-throughput phylogenomic pipeline [PDF]
Ahmed Moustafa, Debashish Bhattacharya, Andrew E. Allen
5th Cairo International Biomedical Engineering Conference. 2011 Feb 17; pp.103-107
doi: 10.1109/CIBEC.2010.5716071
iTree: a high-throughput phylogenomic pipeline  
The making of a photosynthetic animal
Mary E. Rumpho, Karen N. Pelletreau, Ahmed Moustafa, Debashish Bhattacharya
Journal of Experimental Biology. 2011 Jan 15;214(Pt 2):303-11
pmid: 21177950 | doi: 10.1242/jeb.046540
The making of a photosynthetic animal  
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. 2010 Jul;27(7):1530-7.
pmid: 20123796 | doi: 10.1093/molbev/msq032
Differential gene retention in plastids of common recent origin  
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. 2010 March 12;5(3): e9688.
pmid: 20300646 | doi: 10.1371/journal.pone.0009688
Transcriptome Profiling of a Toxic Dinoflagellate Reveals a Gene-Rich Protist and a Potential Impact on Gene Expression Due to Bacterial Presence  
Genomic footprints of a cryptic plastid endosymbiosis in diatoms Genomic footprints of a cryptic plastid endosymbiosis in diatoms [PDF]
Ahmed Moustafa, Bánk Beszteri, Uwe G. Maier, Chris Bowler, Klaus Valentin, Debashish Bhattacharya
Science. 2009 Jun 26;324(5935):1724-6
pmid: 19556510 | doi: 10.1126/science.1172983
Genomic footprints of a cryptic plastid endosymbiosis in diatoms Faculty of 1000
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. 2009 Jun 1;4(6):e5758.
pmid: 19484122 | doi: 10.1371/journal.pone.0005758
Origin of saxitoxin biosynthetic genes in cyanobacteria  
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. 21: 165-176 (2008) 165.
pmid: 19425156 | doi: 10.1142/9781848163324_0014
A phylogenomic approach for studying plastid endosymbiosis  
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. 2008 Nov 18;105(46):17867-71.
pmid: 19004808 | doi: 10.1073/pnas.0804968105
Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica Faculty of 1000
Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic
Adrian Reyes-Prieto, Ahmed Moustafa, Debashish Bhattacharya
Current Biology. 2008 Jul 8;18(13):956-62.
pmid: 18595706 | doi: 10.1016/j.cub.2008.05.042
Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic  
Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions
Ahmed Moustafa, Adrian Reyes-Prieto, Debashish Bhattacharya
PLoS ONE. 2008 May 21;3(5):e2205.
pmid: 18493612 | doi: 10.1371/journal.pone.0002205
Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions  
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. 2008 May 14;3(5):e2171.
pmid: 18478122 | doi: 10.1371/journal.pone.0002171
EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes  
PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas
Ahmed Moustafa, Debashish Bhattacharya
BMC Evolutionary Biology. 2008 Jan 15;8:6.
pmid: 18194581 | doi: 10.1186/1471-2148-8-6
PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas  
Genomic insights into evolutionary relationships among heterokont lineages emphasizing the phaeophyceae
Naomi Phillips, Calhoun Sam, Ahmed Moustafa, Debashish Bhattacharya, Edward Braun
Journal of Phycology. 44 (1), 15.18 (2008)
pmid: 27041034 | doi: 10.1111/j.1529-8817.2007.00435.x
Genomic insights into evolutionary relationships among heterokont lineages emphasizing the phaeophyceae  

Datasets

Phylogenomic Revisit for Green Contribution to Diatoms
Ahmed Moustafa, Klaus Valentin, Debashish Bhattacharya
figshare.
doi: 10.6084/m9.figshare.735804
Phylogenomic Revisit for Green Contribution to Diatoms  
The Chromalveolate Hypothesis
Ahmed Moustafa, Debashish Bhattacharya, Adrian Reyes-Prieto
figshare.
doi: 10.6084/m9.figshare.97283
The Chromalveolate Hypothesis  

Popular Press and Media Coverage

The 2019 Science Advances DNA-lacking mitochondria paper was featured in many science news outlets including Science News, EurekAlert!, Scoop Empire, Al Jazeera (الجزيرة‎), and Shorouk News (الشروق).  
The 2018 Scientific Reports urinary tract infection paper was featured in a YouTube video 
The 2017 PLOS Pathogens blood virome paper was discussed in several blogs including Virology Blog and npj Biofilms and Microbiomes and in different languages including Basque and Chinese 
The 2016 PNAS paper was featured in Nature Reviews Genetics and PNAS and many other scientific blogs and science news portals. 
The 2015 PNAS paper was featured in many popular science news bulletins and blogosphere such as Science Daily. 
The 2013 PNAS paper was featured in a “Research highlight” in Nature Middle East. 
The 2013 The Plant Cell (TPC) paper was featured in a “Commentary” in TPC. 
The 2012 expedition of my former graduate student, Mariam Reyad Rizkallah, to the Arctic Ocean was featured in the Egyptian news portals Al-Ahram and Al-Bawaba and the Egyptian TV channel Nile Life. 
The 2009 Science paper was featured in a “Perspective” in Science. 
The 2008 PNAS paper was featured in many popular science news bulletins and blogosphere such as National Geographic and Science Daily. It was also featured on the PNAS cover.Elysia chlorotica - PNAS Cover