Adam M. Phillippy

Research Publications Presentations Service Education Honors

Research

I am currently a PhD candidate in Computer Science at the University of Maryland with an expected graduation date of Spring 2010. My research has focused on computational biology since about 2000 when I began as an undergraduate research assistant for Art Delcher at Loyola College. From there I moved to TIGR (now JCVI) and worked closely with Mihai Pop until 2005, before arriving at the University of Maryland to begin my PhD work under Steven Salzberg. I spend the majority of my time working on my thesis research at the CBCB, but also work part-time developing bioinformatics tools for Jacques Ravel at the UMD Institute for Genome Sciences.

My primary research area has been sequence analysis and alignment. Most notably, I am a primary developer of the MUMmer genome alignment suite, and the sole developer of the Nucmer and Promer whole-genome alignment programs. While at TIGR, I also consulted on a number of sequencing projects, aiding in the assembly, closure, and analysis of numerous whole genomes, including multiple Bacillus anthracis genomes related to the investigation of the 2001 anthrax attacks. More recently, my research has expanded to include microbial diagnostics and metagenomics using both microarray and short-read sequencing.

Abbreviated list of my research interests:

• Whole genome alignment
• Sequence assembly and validation
• DNA sequence signatures for microbial diagnostics
• Comparative genomics
• Metagenomics and microbial ecology

I have developed or co-developed the following software tools:

• MUMmer - Rapid whole genome alignment and matching using suffix trees
• Insignia - DNA signature discovery for microbial detection and diagnostics
• PanArray - Pan-genome tiling array design for rapid comparative genomics
• AMOS - Shotgun sequence assembly infrastructure
• AMOScmp - Comparative genome assembly
• AMOSvalidate - Automated genome assembly validation
• Hawkeye - Visual analytics for genome assembly
• PhyloTrac - Environmental sample analysis and visualization for the Berkeley Lab PhyloChip
• GenomeMTV - Analysis and display for tiling and expression microarrays

Publications

1. Efficient oligonucleotide probe selection for pan-genomic tiling arrays.
   Phillippy AM, Deng X, Zhang W, Salzberg SL. BMC Bioinformatics. 2009 September 16;10:293.
2. Insignia: a DNA signature search web server for diagnostic assay development.
   Phillippy AM, Ayanbule K, Edwards, NJ, Salzberg SL. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W229-34.
3. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.
   Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, Aparna G, Jha G, Pandey A, Patil PB, Ishihara H, Meyer DF, Szurek B, Verdier V, Koebnik R, Dow JM, Ryan RP, Hirata H, Tsuyumu S, Lee SW, Ronald PC, Sonti RV, Van Sluys MA, Leach JE, White FF, Bogdanove AJ. BMC Genomics. 2008 May 1;9(1):204.
4. Genome assembly forensics: finding the elusive mis-assembly.
   Phillippy AM, Schatz MC, Pop M. Genome Biol. 2008;9(3):R55.
5. Evolution of genes and genomes on the Drosophila phylogeny.
   Drosophila 12 Genomes Consortium. Nature. 2007 Nov 8;450(7167):203-18.
6. Comprehensive DNA Signature Discovery and Validation.
   Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL. PLoS Comput Biol. 2007 May 18;3(5):e98.
7. Knowledge discovery using the sand spatial browser.
   Samet H, Phillippy A, Sankaranarayanan J. Proceedings of the 7th National Conference on Digital Government Research. 2007 May pages 284-285, Philadelphia, PA.
8. Hawkeye: an interactive visual analytics tool for genome assemblies.
   Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL. Genome Biol. 2007;8(3):R34.
9. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes.
   Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF. Science. 2005 Jan 7;307(5706):105-8.
10. Comparative genome assembly.
    Pop M, Phillippy A, Delcher AL, Salzberg SL. Brief Bioinform. 2004 Sep;5(3):237-48.
11. Versatile and open software for comparing large genomes.
    Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Genome Biol. 2004;5(2):R12.
12. Using MUMmer to identify similar regions in large sequence sets.
    Delcher AL, Salzberg SL, Phillippy AM. Current Protocols in Bioinformatics. John Wiley & Sons, 2003.
13. Fast algorithms for large-scale genome alignment and comparison.
    Delcher AL, Phillippy A, Carlton J, Salzberg SL. Nucleic Acids Res. 2002 Jun 1;30(11):2478-83.

Presentations

Talks

1. "Comparative genomics of Listeria monocytogenes." Invited seminar. University of Notre Dame. January 2010.
2. "Bioinformatics for nucleic acid diagnostics." JHU/UMD Joint Sequencing Meeting. Johns Hopkins University. December 2009.
3. "Computational DNA signature identification for pathogen detection and diagnostics." Invited seminar. University of Notre Dame. November 2009.
4. "Bioinformatics for nucleic acid diagnostics." Invited seminar. National Center for Food Saftey and Technology, Summit IL. November 2009.
5. "Bioinformatics for nucleic acid diagnostics." Invited seminar. Food and Drug Administration. July 2009.
6. "Whole-genome sequence analysis for pathogen detection and diagnostics." CBCB Seminar Series. University of Maryland. April 2009.
7. "Design and analysis of a pan-genomic tiling array for Listeria monocytogenes." MPRI Works in Progress. University of Maryland. April 2009.
8. "Pan-genome tiling array design for Listeria monocytogenes." CBCB Seminar Series. University of Maryland. July 2008.
9. "To catch a pathogen." Dean's Fellows lecture series. University of Maryland. October 2007.
10. "DNA signature identification, with applications to real time pathogen detection." Computational Genomics conference. Baltimore, MD. October 2006.
11. "Whole genome alignment." Guest lecture. Johns Hopkins University. August 2006.
12. "Comparative genome assembly." Seminar series. The Institute for Genomic Research. 2005.
13. "Whole genome alignment using MUMmer." Yearly tutorial seminar. The Institute for Genomic Research. 2006, 2005, 2004.

Posters

1. "Computational DNA signature identification for pathogen detection and diagnostics." Phillippy AM, et al. Microbial Genomics. Rocky Gap, MD. October 2009.
2. "The marine symbiotic microbiome of Lissoclinum patella, a marine sea squirt." Fricke WF, et al. Microbial Genomics. Rocky Gap, MD. October 2009.
3. "Comparative genomic hybridization of Listeria monocytogenes using pan-genome microarrays." Deng X, Phillippy AM, et al. ASM General Meeting. Philadelphia, PA. May 2009.
4. "Detection of Burkholderia pseudomallei and Burkholderia mallei Using a Large-Scale, Comparative Genomics Approach." Cai M, Phillippy AM, et al. ASM General Meeting. Philadelphia, PA. May 2009.
5. "Improving the genome sequence of D. simulans via co-assembly of multiple strains." Phillippy AM, et al. Biology of Genomes. Cold Spring Harbor, NY. May 2009.
6. "Comparison of Transcriptomic Profiles of Salmonella enterica Enteritidis and Typhimurium under Oxidative Stress." Wang S, Phillippy AM, et al. ASM General Meeting. Boston, MA. June 2008.
7. "Detection and Screening of Francisella tularensis and its Subspecies Using a Large-Scale, Comparative Genomics Approach." Jiang L, Phillippy AM, et al. ASM General Meeting. Boston, MA. June 2008.
8. "Genome Assembly Forensics: Finding the Elusive Mis-assembly." Schatz MC, Phillippy AM, Pop M. Biology of Genomes. Cold Spring Harbor, NY. May 2008.
9. "Development of qPCR Assays for Vibrio cholerae Using Insignia, a Novel Comprehensive DNA Signature Discovery System." Mason JA, Phillippy AM, et al. ASM General Meeting. Toronto, Canada. May 2007.
10. "Comprehensive DNA signature identification." Phillippy AM, et al. Genome Informatics. Hinxton, UK. September 2006.
11. "The efficient computation of conserved amino acid sequences using MUMmer." Phillippy AM, et al. Computational Genomics. Baltimore, MD. November 2001.

Service

• Peer reviewer: Bioinformatics, BMC Bioinformatics, Genome Research, Nucleic Acids Research, Journal of Clinical Microbiology
• Associate Faculty Member: Faculty of 1000 Biology. (My reviews and papers).
• Teaching assistant: Computational Gene Finding and Genome Assembly
• Seminar instructor: Whole genome alignment using MUMmer

Education

Degrees

• Ph.D. Computer Science, University of Maryland. Expected 2010.
• M.S. Computer Science, University of Maryland. December 2008.
• B.S. Summa Cum Laude, Computer Science, Loyola College in Maryland. May 2002.
• Mathematical Sciences Minor, Loyola College in Maryland.

Ph.D. Classwork

• Algorithms for Biosequence Analysis: Mihai Pop
• Computational Gene Finding and Genome Assembly: Steven Salzberg
• Graphs and Networks in Computational Biology: Carl Kingsford
• Information Visualization: Ben Shneiderman
• Geographical Information Systems and Spatial Databases: Hanan Samet
• Link Mining: Lise Getoor
• Machine Learning: James Reggia
• Computational Geometry: Dave Mount
• Creativity Support Tools: Vibha Sazawal
• Computer Networks: Neil Spring

Honors

• Fellowships - University of Maryland Verizon Fellowship (06), The Institute for Genomic Research Summer Fellow (01), Loyola College Hauber Summer Fellow (00).
• Honor Societies - Phi Beta Kappa (02), Upsilon Pi Epsilon (00).
• Scholarships - Loyola College in Maryland Presidential Scholarship (98-02), The Federated Women's Club of Hershey Scholarship (98).
• Miscellaneous - Loyola College James D. Rozics Computer Science Medal (02), Mid Penn Conference Scholar/Athlete Award (98).