headshot

Adam M. Phillippy, Ph.D.

Principal Investigator, Bioinformatics
National Biodefense Analysis and Countermeasures Center

Affiliations
Center for Bioinformatics and Computational Biology
Maryland Pathogen Research Institute
University of Maryland

Email: amp[at]umiacs.umd.edu

News

Ensemble assembly
Automated ensemble assembly and validation of microbial genomes
iMetAMOS enables accurate and reproducible genome assembly via a "GAGE-in-a-box" analysis, allowing non-expert users to run multiple assemblers, validation metrics, and annotations with a single command.

PacBio assembly of Drosophila melanogaster
GenomeWeb: PacBio Demos First De Novo Animal Genome as it Plans Longer Reads, Increased Throughput
PacBio: Preliminary de novo Haploid and Diploid Assemblies of Drosophila melanogaster
PBcR Assembly of D. melanogaster
The results demonstrate that hierarchical assembly, recently demonstrated for microbial genomes, is also applicable to larger, eukaryotic genomes and can result in highly continuous assemblies, including near-fully assembled chromosome arms.

Complete assembly of microbial genomes
Reducing assembly complexity of microbial genomes with single-molecule sequencing
Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library.

Push-button metagenomics
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
...towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations.

PacBio correction and assembly
Hybrid error correction and de novo assembly of single-molecule sequencing reads
Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies.

Coverage at Nature News :
Correction algorithms extend the reach of genome sequencing
Watch Sergey and I present this work on YouTube :
NGS Leaders Webinar : Hybrid error correction and de novo assembly of single-molecule sequencing reads

GigaScience commentary
The rise of a digital immune system
With the potential to have an enormous impact on public health, it is time to integrate the necessary biotechnology, computational, and organizational systems to seed the development of a global, sequencing-based pathogen surveillance system.

Genome Biology commentary
Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone
A growing resource of methicillin-resistant Staphylococcus aureus (MRSA) genomes uncovers intriguing phylogeographic and recombination patterns and highlights challenges in identifying the source of these phenomena.

Bio

I am interested in the design and application of efficient algorithms for the assembly, alignment, and analysis of massive genomic sequencing data. Most notably, I am a primary developer of the MUMmer whole-genome alignment suite, and a founding developer of the AMOS genome assembly toolkit. My current research focuses on rapid nucleic acid diagnostics and microbial forensics using next generation sequencing.

Abbreviated list of my research interests:

  • DNA sequencing
  • Whole-genome alignment
  • Sequence assembly and validation
  • Microbial genomics and forensics
  • Metagenomics

I have developed or contributed to the following software tools:

  • MUMmer - Rapid whole-genome alignment and matching using suffix trees
  • PBcR - PacBio read correction and assembly pipeline
  • Celera Assembler - Large-genome shotgun sequence assembly
  • MetAMOS - A metagenomic assembly and analysis pipeline
  • Krona - Interactive visualization of hierarchical data for metagenomics
  • Insignia - DNA signature discovery for microbial detection and diagnostics
  • AMOS - Shotgun sequence assembly infrastructure
  • AMOScmp - Comparative genome assembly
  • AMOSvalidate - Automated genome assembly validation
  • Hawkeye - Visual analytics for genome assembly
  • PanArray - Pan-genome tiling array design for rapid comparative genomics
  • PhyloTrac - Environmental sample analysis and visualization for the Berkeley Lab PhyloChip
  • GenomeMTV - Analysis and display for tiling and expression microarrays

Publications

Google, PubMed (⇔ denotes equal contribution)
  1. Automated ensemble assembly and validation of microbial genomes.
    Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. BMC Bioinformatics. 2014 May 3.
  2. Complete closed genome sequences of three Bibersteinia trehalosi nasopharyngeal isolates from cattle with shipping Fever.
    Harhay GP, McVey DS, Koren S, Phillippy AM, Bono J, Harhay DM, Clawson ML, Heaton MP, Chitko-McKown CG, Korlach J, Smith TP. Genome Announc. 2014 Feb 13.
  3. Complete closed genome sequences of four Mannheimia varigena isolates from cattle with shipping fever.
    Harhay GP, Murray RW, Lubbers B, Griffin D, Koren S, Phillippy AM, Harhay DM, Bono J, Clawson ML, Heaton MP, Chitko-McKown CG, Smith TP. Genome Announc. 2014 Feb 13.
  4. Reducing assembly complexity of microbial genomes with single-molecule sequencing.
    Koren S, Harhay GP, Smith TPL, Bono JL, Harhay DM, McVey DS, Radune D, Bergman NH, Phillippy AM. Genome Biology. 2013 September 13.
  5. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
    The Assemblathon Group. GigaScience. 2013 July 22.
  6. Complete closed genome sequences of Mannheimia haemolytica serotypes A1 and A6, isolated from cattle.
    Harhay GP, Koren S, Phillippy AM, McVey DS, Kuszak J, Clawson ML, Harhay DM, Heaton MP, Chitko-McKown CG, Smith TPL. Genome Announc. 2013 May/June.
  7. Genome sequence of the attenuated Carbosap vaccine strain of Bacillus anthracis.
    Harrington R, Ondov BD, Radune D, Friss MB, Klubnik J, Diviak L, Hnath J, Cendrowski SR, Blank TE, Karaolis D, Friedlander AM, Burans JP, Rosovitz MJ, Treangen T, Phillippy AM, Bergman NH. Genome Announc. 2013 January/February.
  8. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.
    Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. Genome Biol. 2013 January 15.
  9. Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone.
    Treangen TJ, Phillippy AM. Genome Biol. 2012 December 27. [PDF]
  10. The rise of a digital immune system.
    Schatz MC, Phillippy AM. GigaScience. 2012 July 12.
  11. Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe.
    Price EP, Seymour ML, Sarovich DS, Latham J, Wolken R, Mason J, Vincent G, Drees KP, Beckstrom-Sternberg SM, Phillippy AM, Koren S, Okinaka RT, Chung W, Schupp JM, Wagner DM, Vipond R, Foster JT, Bergman NH, Burans J, Pearson T, Brooks T, Keim P. Emerging Infectious Diseases. 2012 July 5.
  12. Hybrid error correction and de novo assembly of single-molecule sequencing reads.
    Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy AM. Nature Biotechnol. 2012 July 1. [PDF] [SUP]
  13. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.
    Schatz MC ⇔ Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M. Brief Bioinform. 2011 Dec 23.
  14. GAGE: A critical evaluation of genome assemblies and assembly algorithms.
    Salzberg SL, Phillippy AM, Zimin AV, Puiu D, Magoc T, Koren S, Treangen T, Schatz MC, Delcher AL, Roberts M, Marcais G, Pop M, Yorke JA. Genome Res. 2011 Dec 6.
  15. Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis.
    Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW. Proc Natl Acad Sci. 2011 Nov 28.
  16. Interactive metagenomic visualization in a Web browser.
    Ondov BD, Bergman NH, Phillippy AM. BMC Bioinformatics. 2011 Sep 30;12(1):385.
  17. Assemblathon 1: A competitive assessment of de novo short read assembly methods.
    The Assemblathon Group. Genome Res. 2011 Sep 16.
  18. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.
    Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, Schatz MC, Shumway M, Sommer DD, Trapnell C, Benahmed F, Dimitrov G, Madupu R, Radune D, Sullivan S, Jha G, Ishihara H, Lee SW, Pandey A, Sharma V, Sriariyanun M, Szurek B, Vera-Cruz CM, Dorman KS, Ronald PC, Verdier V, Dow JM, Sonti RV, Tsuge S, Brendel V, Rabinowicz PD, Leach JE, White FF, Salzberg SL. J Bacteriol. 2011 Jul 22.
  19. Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity.
    Sahl JW, Johnson JK, Harris AD, Phillippy AM, Hsiao WW, Thom KA, Rasko DA. BMC Genomics. 2011 Jun 4;12(1):291.
  20. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation.
    Rasko DA, Worsham PL, Abshire TG, Stanley ST, Bannan JD, Wilson MR, Langham RJ, Decker RS, Jiang L, Read TD, Phillippy AM, Salzberg SL, Pop M, Van Ert MN, Kenefic LJ, Keim PS, Fraser-Liggett CM, Ravel J. Proc Natl Acad Sci. 2011 Mar 7.
  21. Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification.
    Deng X ⇔ Phillippy AM, Li Z, Salzberg SL, Zhang W. BMC Genomics. 2010 Sep 16;11(1):500.
  22. Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray.
    Schatz MC ⇔ Phillippy AM, Gajer P, Desantis TZ, Andersen GL, Ravel J. Appl and Environ Microbiol. 2010 June 25;AEM.00303-10.
  23. Transcriptomic response of Salmonella enterica Enteritidis and Typhimurium to chlorine based oxidative stress.
    Wang S, Phillippy AM, Deng K, Rui X, Li Z, Tortorello ML, Zhang W. Appl and Environ Microbiol. 2010 June 18;AEM.00823-10.
  24. Efficient oligonucleotide probe selection for pan-genomic tiling arrays.
    Phillippy AM, Deng X, Zhang W, Salzberg SL. BMC Bioinformatics. 2009 September 16;10:293.
  25. 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.
  26. 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.
  27. Genome assembly forensics: finding the elusive mis-assembly.
    Phillippy AM, Schatz MC, Pop M. Genome Biol. 2008;9(3):R55.
  28. Evolution of genes and genomes on the Drosophila phylogeny.
    Drosophila 12 Genomes Consortium. Nature. 2007 Nov 8;450(7167):203-18.
  29. 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.
  30. 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.
  31. Hawkeye: an interactive visual analytics tool for genome assemblies.
    Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL. Genome Biol. 2007;8(3):R34.
  32. 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.
  33. Comparative genome assembly.
    Pop M, Phillippy A, Delcher AL, Salzberg SL. Brief Bioinform. 2004 Sep;5(3):237-48.
  34. 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.
  35. Using MUMmer to identify similar regions in large sequence sets.
    Delcher AL, Salzberg SL, Phillippy AM. Current Protocols in Bioinformatics. John Wiley & Sons, 2003.
  36. 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 (since 2010)

  1. "Complete genome assembly with long reads." Invited seminar. PacBio Symposium. University of Liverpool. Liverpool, UK. April 2014.
  2. "Microbial forensics and interdisciplinary science." Invited seminar. NICBR Exploring Careers in a Scientific Enviornment Symposium. National Cancer Institute. Frederick, MD. February 2014.
  3. "Genome assembly, microbial forensics, and the digital immune system." Invited seminar. Johns Hopkins University. Baltimore, MD. October 2013.
  4. "Assembly of complete microbial genomes and metagenomes." Invited seminar. CDC. Atlanta, GA. June 2013.
  5. "Low-cost finished genomes: what's possible?" Invited talk. PacBio User Group Meeting. Baltimore, MD. June 2013.
  6. "Reducing assembly complexity with single-molecule sequencing." Selected talk. Sequencing, Finishing and Analysis in the Future. Santa Fe, NM. May 2013.
  7. "Sequence and analysis standards for microbial forensics." Selected talk. GSC 15. Bethesda, MD. April 2013.
  8. "Where are standards in genomics most needed now?" Panel discussion. GSC 15. Bethesda, MD. April 2013.
  9. "Genomics and informatics at the National Bioforensic Analysis Center." Invited seminar. FDA. White Oak, MD. March 2013.
  10. "Genome assembly and microbial forensics." Invited seminar. Johns Hopkins University. Baltimore, MD. March 2013.
  11. "Whole genome alignment, microbial genomics, and the digital immune system." Invited seminar. Northern Arizona University. Flagstaff, AZ. October 2012.
  12. "One-step bacterial genome closure with single-molecule hybrid assembly." Invited talk. Pacific Biosciences User Group Meeting. Menlo Park, CA. October 2012.
  13. "Algorithms for the digital immune system." Invited talk. Disease Outbreak Detection in the Genomics Era. NCBI. Bethesda, MD. September 2012.
  14. "Hybrid error correction and de novo assembly of single-molecule sequencing reads." Invited talk. NGS Leaders Featured Webinar. August 2012. (YouTube link)
  15. "Sequencing alchemy: turning single-molecule reads to gold using hybrid error correction." Invited talk. Advances in Genome Biology and Technology. Marco Island, FL. February 2012.
  16. "The future of fighting infectious disease." Panel discussion. Advances in Genome Biology and Technology. Marco Island, FL. February 2012.
  17. "Embracing next generation technologies in outbreak investigations: assessing the needs and bottlenecks." Panel discussion. Microbial Evolution and Cutting Edge Tools for Outbreak Investigations. Centers for Disease Control and Prevention. Atlanta, GA. September 2011.
  18. "Of parrots and pathogens: benchmarking of short and long read sequencing." Invited talk. Sequencing, Finishing, and Analysis in the Future. Santa Fe, NM. June 2011.
  19. "The bioinformatics of microbial forensics." Invited seminar. University of Notre Dame. September 2010.
  20. "Bioinformatics for real-time pathogen detection and characterization." Invited seminar. NCBI Computational Biology Brach. April 2010.
  21. "Bioinformatics for nucleic acid diagnostics." Invited seminar. National Biodefense Analysis and Countermeasures Center. February 2010.
  22. "Comparative genomics of Listeria monocytogenes." Invited seminar. University of Notre Dame. January 2010.

Posters (since 2010)

  1. "One-step bacterial genome closure with single-molecule hybrid assembly." Koren S, et al. Microbial Genomics. Lake Arrowhead, CA. September 2012.
  2. "Hybrid error correction and de novo assembly of single-molecule sequencing reads." Koren S, et al. Advances in Genome Biology and Technology. Marco Island, FL. February 2012.
  3. "Krona: Interactive visualization of taxonomic abundance." Ondov B, et al. Genome Informatics. Cold Spring Harbor, NY. November 2011.
  4. "Evaluation of genetic variation and virulence in Yersinia spp." Salvador BK, et al. ASM General Meeting. New Orleans, LA. May 2011.
  5. "Interactive visualization of taxonomic abundance." Ondov B, et al. Rocky Mountain Bioinformatics Conference. Snowmass, CO. December 2010.
  6. "Pan-genomic analysis of Listeria monocytogenes." Deng X, et al. ASM General Meeting. San Diego, CA. June 2010.

Education