Publications with Adam Phillippy, PhD


Highly-accurate long-read sequencing improves variant detection and assembly of a human genome
bioRxiv, January 23, 2019
Wenger AM … Phillippy AMKoren S … Hunkapiller MW
A chromosome-scale assembly of the major African malaria vector Anopheles funestus
bioRxiv, December 10, 2018
Ghurye J, Koren S, Small ST, Redmond S, Howell P, Phillippy AM, Besansky NJ
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
bioRxiv, December 9, 2018
Bickhart D, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, Ghurye J, Pop M, Weimer PJ, Phillippy AM, Smith TPL
High-throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Nature Communications, November 30, 2018
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S
Improved reference genome of Aedes aegypti informs arbovirus vector control
Nature, November 14, 2018
Matthews BJ … Koren SPhillippy AM, Vosshall LB
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Genome Biology, October 30, 2018
Nasko DJ, Koren S, Phillippy AM, Treangen TJ
HLA*PRG:LA - HLA typing from linearly projected graph alignments
bioRxiv, October 26, 2018
Dilthey AT, Mentzer AJ, Carapito R, Cutland C, Cereb N, Madhi SA, Rhie A, Koren S, Bahram S, McVean G, Phillippy AM
De novo assembly of haplotype-resolved genomes with trio binning
Nature Biotechnology, October 22, 2018
Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM
Leveraging evolutionary relationships to improve Anopheles genome assemblies
bioRxiv, October 4, 2018
Waterhouse RM, Aganezov S, Anselmetti Y, Lee J, Ruzzante L, Reijnders MJMF, Bèrard S, George P, Hahn MW, Howell PI, Kamali M, Koren S, Lawson D, Maslen G, Peery A, Phillippy AM, Sharakhova MV, Tannier E, Unger MF, Zhang SV, Alekseyev MA, Besansky NJ, Chauve C, Emrich SJ, Sharakhov IV
A fast adaptive algorithm for computing whole-genome homology maps
Bioinformatics, September 1, 2018
Jain C, Koren S, Dilthey A, Phillippy AM, Aluru S
Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing
Nucleic Acids Res, July 27, 2018
Kim JH, Dilthey AT, Nagaraja R, Lee HS, Koren S, Dudekula D, Wood III WH, Piao Y, Ogurtsov AY, Utani K, Noskov V, Shabalina SA, Schlessinger D, Phillippy AM, Larionov V
MetaMaps - Strain-level metagenomic assignment and compositional estimation for long reads
bioRxiv, July 20, 2018
Dilthey A, Jain C, Koren S, Phillippy AM
De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole genome duplication
bioRxiv, July 20, 2018
Chen Z, Omori Y, Koren S, Shirokiya T, Kuroda T, Miyamoto A, Wada H, Fujiyama A, Toyoda A, Zhang S, Wolfsberg TG, Kawakami K, Phillippy AM, NISC, Mullikin JC, Burgess SM
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
bioRxiv, February 7, 2018
Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S
Nanopore sequencing and assembly of a human genome with ultra-long reads
Nature Biotechnology, January 29, 2018
Jain M, Koren SDilthey ATRhie APhillippy AM … & Loose M
MUMmer4: A fast and versatile genome alignment system
PLoS Comput Biol, January 26, 2018
Marcais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A
Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation
Gigascience, January 10, 2018
Miller JR, Koren S, Dilley KA, Puri V, Brown DM, Harkins DM, Thibaud-Nissen F, Rosen BD, Chen X, Tu Z, Sharakhov IV, Sharakhova MV, Sebra R, Stockwell TB, Bergman NH, Sutton GG, Phillippy AM, Piermarini PM, Shabman RS
Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station
Genome Announcements, July 12, 2017
Venkateswaran K, Sielaff AC, Ratnayake S, Pope RK, Blank TE, Stepanov VG, Fox GE, van Tongeren SP, Torres C, Allen J, Jaing C, Pierson D, Perry J, Koren S, Phillippy AM, Klubnik J, Treangen TJ, Rosovitz MJ, Bergman NH
A fast approximate algorithm for mapping long reads to large reference databases
RECOMB 2017, May 3, 2017
Jain C, Dilthey A, Koren S, Aluru S, Phillippy AM
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
Genome Research, May 1, 2017
Schneider VA … Koren SPhillippy AM … Church DM
New advances in sequence assembly
Genome Research, May 1, 2017
Phillippy AM
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
Genome Research, May 1, 2017
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
Nature Genetics, March 16, 2017
Bickhart DM … Koren SPhillippy AM … Smith TPL
The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation
Immunogenetics, February 9, 2017
Schwartz JC, Gibson MS, Heimeier D, Koren S, Phillippy AM, Bickhart DM, Smith TPL, Medrano JF, Hammond JA
Mash: fast genome and metagenome distance estimation using MinHash
Genome Biol, June 20, 2016
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM
The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts
Nat Commun, June 2, 2016
Liu Z … Koren SPhillippy AM … Waldbieser GC
Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru
PLoS Negl Trop Dis, April 13, 2016
Treangen TJ, Schoeler G, Phillippy AM, Bergman NH, Turell MJ
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes
Proc Natl Acad Sci U S A, March 29, 2016
Hall AB … Koren SPhillippy AM … Besansky NJ
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
Nature Biotechnol, May 25, 2015
Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
Curr Opin Microbiol, December 1, 2014
Koren S, Phillippy AM
Long-read, whole-genome shotgun sequence data for five model organisms
Sci Data, November 25, 2014
Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DE, Celniker SE, Phillippy AM, Bergman CM, Landolin JM
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
Genome Biol, November 19, 2014
Treangen TJ, Ondov BD, Koren S, Phillippy AM
Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923
Genome Announc, November 6, 2014
Treangen TJ, Maybank RA, Enke S, Friss MB, Diviak LF, Karaolis DK, Koren S, Ondov B, Phillippy AM, Bergman NH, Rosovitz MJ
High-coverage sequencing and annotated assemblies of the budgerigar genome
Gigascience, July 8, 2014
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
Automated ensemble assembly and validation of microbial genomes
BMC Bioinformatics, May 3, 2014
Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM
Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever
Genome Announc, February 13, 2014
Harhay GP, McVey DS, Koren S, Phillippy AM, Bono J, Harhay DM, Clawson ML, Heaton MP, Chitko-McKown CG, Korlach J, Smith TP
Complete Closed Genome Sequences of Four Mannheimia varigena Isolates from Cattle with Shipping Fever
Genome Announc, February 13, 2014
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
Reducing assembly complexity of microbial genomes with single-molecule sequencing
Genome Biol, September 13, 2013
Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Gigascience, July 22, 2013
Bradnam KR … Koren SPhillippy AM … Korf IF
Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle
Genome Announc, May 16, 2013
Harhay GP, Koren S, Phillippy AM, McVey DS, Kuszak J, Clawson ML, Harhay DM, Heaton MP, Chitko-McKown CG, Smith TP
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
Genome Biol, January 15, 2013
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M
Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis
Genome Announc, January 15, 2013
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
Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone
Genome Biol, December 27, 2012
Treangen TJ, Phillippy AM
Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe
Emerg Infect Dis, August 1, 2012
Price EP, Seymour ML, Sarovich DS, Latham J, Wolken SR, Mason J, Vincent G, Drees KP, Beckstrom-Sternberg SM, Phillippy AM, Koren S, Okinaka RT, Chung WK, Schupp JM, Wagner DM, Vipond R, Foster JT, Bergman NH, Burans J, Pearson T, Brooks T, Keim P
The rise of a digital immune system
Gigascience, July 12, 2012
Schatz MC, Phillippy AM
Hybrid error correction and de novo assembly of single-molecule sequencing reads
Nat Biotechnol, July 1, 2012
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy AM
GAGE: A critical evaluation of genome assemblies and assembly algorithms
Genome Res, January 6, 2012
Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies
Brief Bioinform, December 23, 2011
Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M
Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis
Proc Natl Acad Sci U S A, November 28, 2011
Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW
Interactive metagenomic visualization in a Web browser
BMC Bioinformatics, September 30, 2011
Ondov BD, Bergman NH, Phillippy AM
Assemblathon 1: a competitive assessment of de novo short read assembly methods
Genome Res, September 16, 2011
Earl D … Phillippy AM, Koren S … Paten B
Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp
J Bacteriol, July 22, 2011
Bogdanove AJ … Phillippy AM … Salzberg SL
Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity
BMC Genomics, June 4, 2011
Sahl JW, Johnson JK, Harris AD, Phillippy AM, Hsiao WW, Thom KA, Rasko DA
Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation
Proc Natl Acad Sci U S A, March 7, 2011
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
Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
BMC Genomics, September 16, 2010
Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W
Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray
Appl Environ Microbiol, June 25, 2010
Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL, Ravel J
Transcriptomic responses of Salmonella enterica serovars Enteritidis and Typhimurium to chlorine-based oxidative stress
Appl Environ Microbiol, June 18, 2010
Wang S, Phillippy AM, Deng K, Rui X, Li Z, Tortorello ML, Zhang W
Efficient oligonucleotide probe selection for pan-genomic tiling arrays
BMC Bioinformatics, September 16, 2009
Phillippy AM, Deng X, Zhang W, Salzberg SL
Insignia: a DNA signature search web server for diagnostic assay development
Nucleic Acids Res, May 5, 2009
Phillippy AM, Ayanbule K, Edwards NJ, Salzberg SL
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
BMC Genomics, May 1, 2008
Salzberg SL … Phillippy AM … Bogdanove AJ
Genome assembly forensics: finding the elusive mis-assembly
Genome Biol, March 14, 2008
Phillippy AM, Schatz MC, Pop M
Evolution of genes and genomes on the Drosophila phylogeny
Nature, November 8, 2007
Drosophila 12 Genomes Consortium … Phillippy AMWalenz B … MacCallum I
Knowledge discovery using the sand spatial browser
8th annual international conference on digital government research, May 20, 2007
Samet H, Phillippy A, Sankaranarayanan J
Comprehensive DNA signature discovery and validation
PLoS Comput Biol, April 20, 2007
Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL
Hawkeye: an interactive visual analytics tool for genome assemblies
Genome Biol, March 9, 2007
Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL
Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes
Science, January 7, 2005
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
Comparative genome assembly
Brief Bioinform, September 1, 2004
Pop M, Phillippy A, Delcher AL, Salzberg SL
Versatile and open software for comparing large genomes
Genome Biol, January 30, 2004
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL
Using MUMmer to identify similar regions in large sequence sets
Curr Protoc Bioinformatics, February 1, 2003
Delcher AL, Salzberg SL, Phillippy AM
Fast algorithms for large-scale genome alignment and comparison
Nucleic Acids Res, June 1, 2002
Delcher AL, Phillippy A, Carlton J, Salzberg SL