Ahmed Moustafa : Curriculum Vitae

Assistant Professor, Department of Biology & Graduate Program in Biotechnology, American University in Cairo
Adjunct Graduate Faculty, Department of Molecular and Biomedical Sciences, University of Maine
Academic Editor, PLoS ONE, Public Library of Science

Address: AUC Avenue, P.O. Box 74, New Cairo 11835, Egypt
Email: amoustafa@aucegypt.edu

Research Interests

Evolutionary and Ecological Genomics, Phylogenomics, Metagenomics, and Visualization of Biological Data

Education

2005 - 2009	PhD, Genetics, University of Iowa, Iowa City, Iowa, USA
1993 - 1998	BS, Computer Science, Alexandria University, Alexandria, Egypt

Appointments

2011 - Present	Adjunct Graduate Faculty, University of Maine, Orono, Maine, USA
2010 - Present	Assistant Professor, American University in Cairo, Cairo, Egypt
2009 - 2010	Post-Doctoral Research Fellow, J. Craig Venter Institute, San Diego, California, USA
2008 - 2009	Pre-Doctoral Research Fellow, NIH NRSA, University of Iowa, Iowa City, Iowa, USA
2005 - 2008	Graduate Research Assistant, University of Iowa, Iowa City, Iowa, USA
2000 - 2005	Senior Software Engineer, Kaiser Permanente, Pasadena, California, USA
1998 - 2000	Software Engineer, Scientific Computation Center, Alexandria, Egypt

Publications

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	pmid:21903677 doi:10.1093/molbev/msr223
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
iTree: a high-throughput phylogenomic pipeline 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
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
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
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
When Algae Misbehave: Plastid-Loss as a Window into Endosymbiosis and Genome Evolution Adrian Reyes-Prieto, Ahmed Moustafa, Debashish Bhattacharya *Darwin Evolution and Life*.
Genomic footprints of a cryptic plastid endosymbiosis in diatoms 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 Cited 92 times
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 Cited 18 times
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
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 PNAS cover story Cited 79 times
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 Cited 51 times
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 Cited 43 times
*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
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 Highly accessed
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)	doi:10.1111/j.1529-8817.2007.00435.x
JAligner: an open-source efficient implementation of the Smith-Waterman algorithm Ahmed Moustafa *SourceForge*. (2003)	url:jaligner.sf.net Cited > 100 times

Grants and Fellowships

Department of Energy - Joint Genome Institute, “Metagenomics and metatranscriptomics of eukaryotic phytoplankton communities in the Arctic Ocean”. Co-PI. 2011
National Institutes of Health, Pre-Doctoral Genetics Fellowship, 2008-2009

Awards and Honor

Travel award from the Marine Genomics Europe to talk at the Marine Environmental Genomics and Gene Expression workshop, Germany (2008)
Travel award from the Woods Hole Center for Oceans and Human Health to talk at the Fourth Symposium on Harmful Algae in the US (2007)
Honorary membership in the American Association for the Advancement of Science/Science Program for Excellence in Science (2007)
Best student oral presentation, 6th Annual Bioinformatics Symposium. Iowa State University (2006)

Editorial Board and Peer-reviewing

Academic Editor for PLoS ONE
Ad hoc Peer-reviewer for Molecular Biology and Evolution, PLoS ONE, BMC Genomics, BMC Evolutionary Biology, Evolutionary Bioinformatics
Ad hoc Grant Reviewer for the Natural Environment Research Council (NERC, UK)

Professional Memberships

Open-Source Activities

Designed and developed the open source JAligner for biological local pairwise sequence alignment. JAligner has been incorporated into many academic, open-source and commercial applications such as STRAP (structure-based sequence alignment), Argo (genome browser), BioWeka (biological data mining framework), SeqFEATURE (structure-based function prediction), and ApolloRNA (non-coding RNA identification). JAligner was accepted by the National Institute of Standards and Technology as a model implementation of the Smith-Waterman algorithm. Since its release, JAligner has been cited more than 100 times in journals and books and downloaded more than 15,000 times with a monthly average of 150 downloads.
Designed and developed the open source PhyloSort to sort phylogenetic trees by searching for subtrees that contain a monophyletic group of interest defined by operational taxonomic units. PhyloSort has been incorporated into PhyloGena (phylogenomic pipeline).
Designed and developed the open source iTree, a scalable multithreaded phylogenomic pipeline.

Talks

Ahmed Moustafa. Evolutionary genomics of marine phytoplankton. Endosymbiosis and Genome Evolution Workshop. Alfred Wegener Institute, Bremerhaven, Germany (December 2010) (Invited Talk)
Ahmed Moustafa, Jonathan Badger, Micaela S. Parker, E. Virginia Armbrust, Andrew E. Allen. Transcript profiling of a large phytoplankton bloom in Puget Sound. The 13th International Symposium on Microbial Ecology. Seattle, Washington, USA (August 22, 2010)
Ahmed Moustafa, Deana L. Erdner, David M. Kulis, Donald M. Anderson, Debashish Bhattacharya. Deep transcriptomics of toxic red tide dinoflagellate Alexandrium tamarense. Fifth Symposium on Harmful Algae in the US. Ocean Shores, Washington, USA (November 15, 2009)
Debashish Bhattacharya, Adrian Reyes-Prieto, Ahmed Moustafa, Hwan Su Yoon, Robert A. Andersen, CX Chan, Jeferson Gross. The evolution of photosynthesis on the tree of life. Plant Biology 2009. Honolulu, Hawaii, USA (July 18, 2009)
Mary E. Rumpho, Jared M. Worful, Karen N. Pelletreau, Kara M. Soule, Debashish Bhattacharya, Ahmed Moustafa, Susan Devine, Helen Mattsson, James R. Manhart. Sea slug-algal chloroplast symbiosis: is horizontal gene transfer driving the evolution of photosynthesis in an animal? Plant Biology 2009. Honolulu, Hawaii, USA (July 18, 2009)
Naomi Phillips, Edward Braun, Ahmed Moustafa, Debashish Bhattacharya, Donald Kapraun, Samantha Calhoun, Teresa Coaxum. Comparative genomics of photosynthetic Heterokonts. Plant Biology 2009. Honolulu, Hawaii, USA (July 18, 2009)
Ahmed Moustafa, Jeannette E. Loram, David M. Kulis, Jeremiah D. Hackett, Deana L. Erdner, Donald M. Anderson, F. Gerald Plumley, Debashish Bhattacharya. Harmful algal blooms: origin of the saxitoxin biosynthetic pathway and high throughput transcriptomics of a toxic dinoflagellate. Annual retreat of the Genetics Program. University of Iowa, Iowa City, Iowa, USA (November 10, 2008)
Naomi Phillips, Edward Braun, Ahmed Moustafa, Debashish Bhattacharya. Phylogenomic investigations within Brown Algae. Combined Meeting of the International Society of Protistologists and the International Society for Evolutionary Protistology. Dalhousie University, Halifax, Canada (July 25, 2008)
Ahmed Moustafa, Debashish Bhattacharya. Phylogenomics and insights into algal genome evolution. Marine Environmental Genomics and Gene Expression Workshop. Alfred Wegener Institute, Bremerhaven, Germany (June 6, 2008) (Awarded a travel voucher)
Klaus Valentin, Bánk Beszteri, Ahmed Moustafa, Debashish Bhattacharya. Two primary and one secondary endosymbiosis and the origin of the diatoms. 56^th British Phycological Society Annual Meeting Bristol. UK (January 3, 2008)
Jeannette E. Loram, Ahmed Moustafa, Debashish Bhattacharya, Jeremiah D. Hackett, Shelly Brandsrud, Deana L. Erdner, Donald M. Anderson, F. Gerald Plumley. A genomic approach for identifying the saxitoxin synthesis genes. Fourth Symposium on Harmful Algae in the US. Woods Hole, Massachusetts, USA (October 30, 2007)
Ahmed Moustafa, Debashish Bhattacharya. Computational tools to facilitate the understanding of genome evolution of microalgae and the formation of toxic red tides. Fourth Symposium on Harmful Algae in the US, Woods Hole. Massachusetts, USA (October 30, 2007) (Awarded a travel voucher)
Debashish Bhattacharya, Ahmed Moustafa, Tetyana Nosenko, Adrian Reyes-Prieto. Using comparative genomic approaches to unravel the complex evolutionary history of chromalveolates. German Botanical Society Annual Meeting Hamburg, Germany (September 2007)
Naomi Phillips, Calhoun Sam, Ahmed Moustafa, Debashish Bhattacharya, Edward Braun. Genomic insights into evolutionary relationships among Heterokont lineages. Botany & Plant Biology Joint Congress. Chicago, Illinois, USA (July 7, 2007)
Ahmed Moustafa, Nicholas Rorick, Akira Kinoshita, Margaret I. Malik, Brian C. Schutte. Computational approach to predict Interferon regulatory factor 6 (Irf6) targets. Sixth annual Joint Bioinformatics Symposium. Iowa State University, Ames, Iowa, USA (July 14, 2006)