Adam M. Phillippy, Ph.D.

Head, Genome Informatics Section
Computational and Statistical Genomics Branch
National Human Genome Research Institute
National Institutes of Health

Email: adam.phillippy[at]nih.gov
Twitter: @aphillippy
GitHub: Maryland Bioinformatics Laboratories (MarBL)
NHGRI: Genome Informatics Section (GIS)


I have moved my lab to the NIH/NHGRI! Interested postdocs please contact me. I have several openings.

Canu assembler v1.3 released: https://github.com/marbl/canu/releases
A single-molecule assembler for genomes large and small, designed for single-molecule sequences from PacBio or Nanopore instruments.

Preprint: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while simultaneously reducing runtime by an order of magnitude on large genomes.

Preprint: Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes
We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most contiguous de novo mammalian assembly to date, with chromosome-length scaffolds and only 663 gaps.


I am interested in the design and application of efficient algorithms for the analysis of massive genomic sequencing data. My current research focuses on methods for the assembly, comparison, and exploration of large genomes and metagenomes; and the production of high-quality reference genomes to enable novel variation discovery.

Abbreviated list of my research interests:

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

I have helped develop the following software tools:

  • Canu - A single-molecule assembler for genomes large and small
  • MUMmer - Rapid whole-genome alignment and matching using suffix trees
  • Mash - Fast genome distance estimation using MinHash
  • MHAP - MinHash Alignment Process for noisy read overlapping
  • Harvest - A suite of alignment tools for thousands of microbial genomes
  • MetAMOS - A metagenomic assembly and analysis pipeline
  • Krona - Interactive visualization of hierarchical data for metagenomics
  • Insignia - DNA signature discovery for microbial detection and diagnostics
  • PanArray - Pan-genome tiling array design for rapid comparative genomics

And some older tools no longer actively supported:

  • PBcR - PacBio read correction and assembly pipeline
  • 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


Google Scholar, PubMed
  1. Mash: fast genome and metagenome distance estimation using MinHash.
    Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Genome Biol. 2016 Jun 20.
  2. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.
    Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Wang R, Zhang Y, Zhou T, Zeng Q, Fu Q, Gao S, Li N, Koren S, Jiang Y, Zimin A, Xu P, Phillippy AM, Geng X, Song L, Sun F, Li C, Wang X, Chen A, Jin Y, Yuan Z, Yang Y, Tan S, Peatman E, Lu J, Qin Z, Dunham R, Li Z, Sonstegard T, Feng J, Danzmann RG, Schroeder S, Scheffler B, Duke MV, Ballard L, Kucuktas H, Kaltenboeck L, Liu H, Armbruster J, Xie Y, Kirby ML, Tian Y, Flanagan ME, Mu W, Waldbieser GC. Nat Commun. 2016 Jun 2.
  3. Identification and genomic analysis of a novel Group C orthobunyavirus isolated from a mosquito captured near Iquitos, Peru.
    Treangen TJ, Schoeler G, Phillippy AM, Bergman NH, Turell MJ. PLoS Negl Trop Dis. 2016 Apr 13.
  4. Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes.
    Hall AB, Papathanos PA, Sharma A, Cheng C, Akbari OS, Assour L, Bergman NH, Cagnetti A, Crisanti A, Dottorini T, Fiorentini E, Galizi R, Hnath J, Jiang X, Koren S, Nolan T, Radune D, Sharakhova MV, Steele A, Timoshevskiy VA, Windbichler N, Zhang S, Hahn MW, Phillippy AM, Emrich SJ, Sharakhov IV, Tu ZJ, Besansky NJ. Proc Natl Acad Sci. 2016 Mar 29.
  5. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
    Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. Nat Biotechnol. 2015 May 25. [PDF] [SUP]
  6. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.
    Koren S, Phillippy AM. Curr Opin Microbiol. 2015 February 23.
  7. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.
    Treangen TJ, Ondov BO, Koren S, Phillippy AM. Genome Biol. 2014 November 19.
  8. Automated ensemble assembly and validation of microbial genomes.
    Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. BMC Bioinformatics. 2014 May 3.
  9. 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 Biol. 2013 September 13.
  10. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
    The Assemblathon Group. GigaScience. 2013 July 22.
  11. 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.
  12. Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone.
    Treangen TJ, Phillippy AM. Genome Biol. 2012 December 27. [PDF]
  13. The rise of a digital immune system.
    Schatz MC, Phillippy AM. GigaScience. 2012 July 12.
  14. 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.
  15. 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. Nat Biotechnol. 2012 July 1. [PDF] [SUP]
  16. 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.
  17. 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.
  18. 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.
  19. Interactive metagenomic visualization in a Web browser.
    Ondov BD, Bergman NH, Phillippy AM. BMC Bioinformatics. 2011 Sep 30;12(1):385.
  20. Assemblathon 1: A competitive assessment of de novo short read assembly methods.
    The Assemblathon Group. Genome Res. 2011 Sep 16.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. Efficient oligonucleotide probe selection for pan-genomic tiling arrays.
    Phillippy AM, Deng X, Zhang W, Salzberg SL. BMC Bioinformatics. 2009 September 16;10:293.
  28. 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.
  29. 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.
  30. Genome assembly forensics: finding the elusive mis-assembly.
    Phillippy AM, Schatz MC, Pop M. Genome Biol. 2008;9(3):R55.
  31. Evolution of genes and genomes on the Drosophila phylogeny.
    Drosophila 12 Genomes Consortium. Nature. 2007 Nov 8;450(7167):203-18.
  32. 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.
  33. 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.
  34. Hawkeye: an interactive visual analytics tool for genome assemblies.
    Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL. Genome Biol. 2007;8(3):R34.
  35. 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.
  36. Comparative genome assembly.
    Pop M, Phillippy A, Delcher AL, Salzberg SL. Brief Bioinform. 2004 Sep;5(3):237-48.
  37. 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.
  38. Using MUMmer to identify similar regions in large sequence sets.
    Delcher AL, Salzberg SL, Phillippy AM. Current Protocols in Bioinformatics. John Wiley & Sons, 2003.
  39. 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.

Data Notes

  1. Long-read, whole-genome shotgun sequence data for five model organisms.
    Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin C-S, Rapicavoli NA, Rank DR, Li J, Catcheside DEA, Celniker SE, Phillippy AM, Bergman CM, Landolin JM. Scientific Data. 2014 Nov 25.
  2. Complete genome sequence of the quality control strain Staphylococcus aureus subsp. aureus ATCC 25923.
    Treangen TJ, Maybank RA, Enke S, Friss MB, Diviak LF, Karaolis DK, Koren S, Ondov B, Phillippy AM, Bergman NH, Rosovitz MJ. Genome Announc. 2014 Nov 6.
  3. High-coverage sequencing and annotated assemblies of the budgerigar genome.
    Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, Xiong Y, Zhang Y, Zhou S, Schwartz DC, Schatz M, Aboukhalil R, Fedrigo O, Bukovnik L, Wang T, Wray G, Rasolonjatovo I, Winer R, Knight JR, Koren S, Warren WC, Zhang G, Phillippy AM, Jarvis ED. Gigascience. 2014 Jul 8.
  4. 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.
  5. 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.
  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.