Ahmed Moustafa

Post-Doctoral Research Fellow, Microbial & Environmental Genomics, J. Craig Venter Institute, La Jolla, California.

Education

• PhD, Genetics, Evolutionary and functional genomics of photosynthetic eukaryotes, University of Iowa (2005 - 2009) [Thesis | Talk]
• BS, Computer Science, Code mobility and intelligent software agents, Alexandria University (1993 - 1998)

Appointments

• Post-Doctoral Research Fellow, J. Craig Venter Institute (2009 - Present)
• Post-Doctoral Research Associate, Rutgers University (2009)
• Pre-Doctoral Research Fellow, NIH NRSA, University of Iowa (2008 - 2009)
• Graduate Research Assistant, University of Iowa (2005 - 2008)
• Senior Software Engineer, Kaiser Permanente (2000 - 2005)
• Software Engineer, Scientific Computation Center, Alexandria University (1998 - 2000)

Publications

• Ahmed Moustafa, Deana L. Erdner, David M. Kulis, Donald M. Anderson, Debashish Bhattacharya. Transcriptome Profiling of a Toxic Dinoflagellate Reveals a Gene-Rich Protist and a Potential Impact on Gene Expression Due to Bacterial Presence. PLoS ONE. 2010 March 12;5(3): e9688
• Adrian Reyes-Prieto, Hwan Su Yoon, Ahmed Moustafa, Eun Chan Yang, Robert A. Andersen, Sung Min Boo, Takuro Nakayama, Ken-ichiro Ishida, Debashish Bhattacharya. Differential gene retention in plastids of common recent origin. Molecular Biology and Evolution. 2010 Feb 1.
• Ahmed Moustafa, Bánk Beszteri, Uwe G. Maier, Chris Bowler, Klaus Valentin, Debashish Bhattacharya. Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science. 2009 Jun 26;324(5935):1724-6.
  • Featured and reviewed in the same issue of Science
  • Evaluated and rated as “Must Read” by Faculty of 1000 (Post-publication peer-review) [.pdf]
  • Ranked among the “Top 10” Evolutionary Biology articles by Faculty of 1000 [.pdf]
  • Ranked among the “Top 10” Microbiology articles by Faculty of 1000
  • Cited 15 times
• Ahmed Moustafa, Jeannette E. Loram, Jeremiah D. Hackett, Donald M. Anderson, F. Gerald Plumley, Debashish Bhattacharya. Origin of saxitoxin biosynthetic genes in cyanobacteria. PLoS ONE. 2009 Jun 1;4(6):e5758.
• Mary E. Rumpho, Jared M. Worful, Jungho Lee, Krishna Kannan, Mary S. Tyler, Debashish Bhattacharya, Ahmed Moustafa, James R. Manhart. Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. PNAS. 2008 Nov 18;105(46):17867-71.
  • Featured on the cover
  • Ranked among the most-read articles during November and December 2008
  • Cited 17 times
• Ahmed Moustafa, CX Chan, Megan Danforth, David Zear, Hiba Ahmed, Nagnath Jadhav, Trevor Savage, Debashish Bhattacharya. A phylogenomic approach for studying plastid endosymbiosis. Genome Informatics. 21: 165-176 (2008) 165.
• Adrian Reyes-Prieto, Ahmed Moustafa, Debashish Bhattacharya. Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic. Current Biology. 2008 Jul 8;18(13):956-62.
  • Cited 23 times
• Ahmed Moustafa, Adrian Reyes-Prieto, Debashish Bhattacharya. Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions. PLoS ONE. 2008 May 21;3(5):e2205.
  • Cited 13 times
• William Lanier, Ahmed Moustafa, Debashish Bhattacharya, Josep Comeron. EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes. PLoS ONE. 2008 May 14;3(5):e2171.
• Ahmed Moustafa, Debashish Bhattacharya. PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas. BMC Evolutionary Biology. 2008 Jan 15;8:6.
  • Ranked as highly accessed publication
  • Cited 18 times
• Naomi Phillips, Calhoun Sam, Ahmed Moustafa, Debashish Bhattacharya, Edward Braun. Genomic insights into evolutionary relationships among heterokont lineages emphasizing the phaeophyceae. Journal of Phycology. 44 (1), 15.18 (2008)
• Ahmed Moustafa. JAligner: an open-source efficient implementation of the Smith-Waterman algorithm. SourceForge. (2003)
  • Cited more than 70 times in journal articles and book chapters

Manuscripts in Progress

• Ahmed Moustafa, Jonathan Badger, Micaela S. Parker, E. Virginia Armbrust, Andrew Allen. Metatranscriptomics profiling of Puget Sound microbial communities
• Ahmed Moustafa, Debashish Bhattacharya. iTree: Phylogenomic Pipeline with Sequencing Biased Correction
• Ahmed Moustafa, Adrian Reyes-Prieto, Alexandra Z. Worden, Debashish Bhattacharya. Genome reduction and its impact on endosymbiotic transferred genes
• Ahmed Moustafa, Aurora M. Nedelcu, Debashish Bhattacharya. Estimating the contribution of photosynthetic microbes to the choanoflagellate Monosiga brevicollis
• Adrian Reyes-Prieto, Ahmed Moustafa, Debashish Bhattacharya. Green algae contributed to the chromalveolate membrane transporter repertoire
• Mary E. Rumpho, Karen A. Pelletreau, Ahmed Moustafa, Debashish Bhattacharya. The making of a photosynthetic animal
• CX Chan, Marcelo B. Soares, Maria F. Bonaldo, Ahmed Moustafa, Donald M. Anderson, Deana L. Erdner, Debashish Bhattacharya. Extensive horizontal gene transfer in microbial eukaryotes

Teaching Experience

• Teaching Fellow, Molecular Phylogenetics, University of Iowa (Spring 2009)
• Teaching Assistant, Statistics for Bioinformatics, University of Iowa (Spring 2008)
• Teaching Assistant, Bioinformatics, University of Iowa (Fall 2006)
• Teaching Assistant, Introduction to Programming, Alexandria University (Fall 2000)

Awards

• Received a predoctoral fellowship in Genetics from the National Institute of Health (July 2008)
• Received a grant from the Marine Genomics Europe to talk at the Marine Environmental Genomics and Gene Expression workshop, Germany (May 2008)
• Received a grant from the Woods Hole Center for Oceans and Human Health to talk at the Fourth Symposium on Harmful Algae in the US (October 2007)
• Received a membership to the American Association for the Advancement of Science/Science Program for Excellence in Science (February 2007)
• Awarded the first place for developing a graphical HTML Editor using C++ in an international programming contest supervised by the Egyptian Cabinet Information and Decision Support Center (September 1997)

Memberships & Professional Activities

• Member, American Society for Microbiology
• Member, American Association for the Advancement of Science
• Member, International Society for Computational Biology
• Member, IEEE Computer Society
• Journal peer-reviewer, BMC Genomics
• Journal peer-reviewer, BMC Evolutionary Biology
• Journal peer-reviewer, Molecular Biology and Evolution
• Journal peer-reviewer, PLoS ONE
• Journal peer-reviewer, Evolutionary Bioinformatics
• Journal peer-reviewer, Genomics Insights
• Conference peer-reviewer, 4th International Symposium on Biomedical Informatics & Cybernetics

Computational Skills

• Programming languages: Java/J2EE, Perl, Tcl, C/C++, Ruby, Python
• Web development: HTML/XHTML/DHTML, CSS, JavaScript, AJAX, PHP
• Development tools: Eclipse, NetBeans, WebSphere, Emacs, Visual Studio
• Database systems: MySQL, PostgreSQL, DB2, Oracle
• Operating systems: Linux, Unix, Mac OS, Windows, Mainframe
• Biological and statistical platforms: BioPerl, BioRuby, BioSQL, R, MATLAB

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).
  • Cited more than 70 times in journal articles and book chapters
  • Downloaded more than 10,000 times with a monthly average of 150 downloads
  • Accepted by the National Institute of Standards and Technology as a model implementation of the Smith-Waterman algorithm
  • Rated Top “25%” by JARS
• 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).
  • Rated Top “25%” by JARS
• Participated in porting packages from ArsDigita Community System (ACS) to OpenACS.

Talks

• Ahmed Moustafa, Jonathan Badger, Micaela S. Parker, E. Virginia Armbrust, Andrew 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)