Publications with Adam Phillippy, PhD

Senior Investigator

The complete sequence and comparative analysis of ape sex chromosomes
Nature, May 29, 2024
Makova KD, Pickett BDNurk SRhie ASolar SJSweeten AKoren SPhillippy AM
Parsnp 2.0: Scalable core-genome alignment for massive microbial datasets
Bioinformatics, May 9, 2024
Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ
ModDotPlot - Rapid and interactive visualization of complex repeats
bioRxiv, April 19, 2024
Sweeten AP, Schatz MC, Phillippy AM
Comparative genomics of macaques and integrated insights into genetic variation and population history
bioRxiv, April 8, 2024
Zhang S … Phillippy AM … Mao Y
The variation and evolution of complete human centromeres
Nature, April 3, 2024
Logsdon GA, Rozanski AN, Ryabov F, Potapova T, Shepelev VA, Catacchio CR, Porubsky D, Mao Y, Yoo D, Rautiainen M, Koren S, Nurk S, Lucas JK, Hoekzema K, Munson KM, Gerton JL, Phillippy AM, Ventura M, Alexandrov IA, Eichler EE
The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals
Genome Research, March 20, 2024
Schnitzler CE … Koren SPhillippy AM … Baxevanis AD
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
bioRxiv, March 17, 2024
Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautianinen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, Ware D, Schatz MC, Garrison E, Huang S, McCombie WR, Miga KH, Wittenberg AHJ, Phillippy AM
A high-quality blue whale genome, segmental duplications, and historical demography
Molecular Biology and Evolution, February 20, 2024
Bukhman YV … Rhie APhillippy AM … Stewart R
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
Nature Biotechnology, January 26, 2024
Larivière D … Pickett BDRhie APhillippy AM … Formenti G
High-quality metagenome assembly from long accurate reads with metaMDBG
Nature Biotechnology, January 2, 2024
Benoit G, Raguideau S, James R, Phillippy AM, Chikhi R, Quince C
Improved sequence mapping using a complete reference genome and lift-over
Nature Methods, November 30, 2023
Chen N-C, Paulin LF, Sedlazeck FJ, Koren S, Phillippy AM, Langmead B
Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks
Nature Communications, October 19, 2023
Sendell-Price AT, Tulenko FJ, Pettersson M, Kang D, Montandon M, Winkler S, Kulb K, Naylor GP, Phillippy A, Fedrigo O, Mountcastle J, Balacco JR, Dutra A, Dale RE, Haase B, Jarvis ED, Myers G, Burgess SM, Currie PD, Andersson L, Schartl M
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
Nature Methods, September 14, 2023
Kolmogorov M … Rhie APhillippy AM … Paten B
The complete sequence of a human Y chromosome
Nature, August 23, 2023
Rhie A, Nurk SKoren S, Rautiainen MHansen NFMc Cartney AMWalenz BPPhillippy AM
Minmers are a generalization of minimizers that enable unbiased local jaccard estimation
Bioinformatics, August 21, 2023
Kille B, Garrison E, Treangen TJ, Phillippy AM
Recombination between heterologous human acrocentric chromosomes
Nature, May 10, 2023
Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C, Human Pangenome Reference Consortium, Gerton JL, Phillippy AM, Colonna V, Garrison E
A draft human pangenome reference
Nature, May 10, 2023
Liao W-W … Koren SNurk SRautiainen MRhie AWalenz BPhillippy AM … Paten B
Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions
BMC Biology, April 3, 2023
Waldbieser GC, Liu S, Yuan Z, Older CE, Gao D, Shi C, Bosworth BG, Li N, Bao L, Kirby MA, Jin Y, Wood ML, Scheffler B, Simpson S, Youngblood RC, Duke MV, Ballard L, Phillippy A, Koren S, Liu Z
Telomere-to-telomere assembly of diploid chromosomes with Verkko
Nature Biotechnology, February 16, 2023
Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S
A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes
BMC Biology, November 8, 2022
Toh H … Rhie A, Phillippy AM … Bukhman YV
Semi-automated assembly of high-quality diploid human reference genomes
Nature, October 19, 2022
Jarvis ED … Rhie AGhurye JKoren SPhillippy AM … Human Pangenome Reference Consortium
A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L)
DNA Research, October 8, 2022
McGrath JM … Koren S, Phillippy A … Dorn K
A family of unusual immunoglobulin superfamily genes in an invertebrate histocompatibility complex
Proceedings of the National Academy of Sciences, October 4, 2022
Huene AL, Sanders SM, Ma Z, Nguyen AD, Koren S, Michaca MH, Mullikin JC, Phillippy AM, Schnitzler CE, Baxevanis AD, Nicotra ML
False gene and chromosome losses in genome assemblies caused by GC content variation and repeats
Genome Biology, September 27, 2022
Kim J, Lee C, Ko BJ, Yoo DA, Won S, Phillippy AM, Fedrigo O, Zhang G, Howe K, Wood J, Durbin R, Formenti G, Brown S, Cantin L, Mello CV, Cho S, Rhie A, Kim H, Jarvis ED
The Human Pangenome Project: a global resource to map genomic diversity
Nature, April 20, 2022
Wang T … Phillippy AM … Haussler D; Human Pangenome Reference Consortium
Epigenetic Patterns in a Complete Human Genome
Science, April 1, 2022
Gershman A, Sauria ME, Hook PW, Hoyt SJ, Razaghi R, Koren S, Altemose N, Caldas GV, Vollger MR, Logsdon GA, Rhie A, Eichler EE, Schatz MC, O’Neill RJ, Phillippy AM, Miga KH, Timp W
The complete sequence of a human genome
Science, April 1, 2022
Nurk S, Koren S, Rhie A, Rautiainen MHansen NFJain CMc Cartney AMWalenz BPPhillippy AM
Complete genomic and epigenetic maps of human centromeres
Science, April 1, 2022
Altemose N … Rhie A, McCartney AMNurk S, Koren SPhillippy AM … Miga KH
Long-read mapping to repetitive reference sequences using Winnowmap2
Nature Methods, April 1, 2022
Jain C, Rhie A, Hansen N, Koren S, Phillippy AM
From telomere to telomere: the transcriptional and epigenetic state of human repeat elements
Science, April 1, 2022
Hoyt SJ … Phillippy AM … O’Neill RJ
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Nature Methods, April 1, 2022
Mc Cartney AM, Shafin K, Alonge M, Bzikadze AV, Formenti G, Fungtammasan A, Howe K, Jain C, Koren S, Logsdon GA, Miga KH, Mikheenko A, Paten B, Shumate A, Soto DC, Sović I, Wood JM, Zook JM, Phillippy AM, Rhie A
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Nature Methods, April 1, 2022
Formenti G, Rhie A, Walenz BP, Thibaud-Nissen F, Shafin K, Koren S, Myers EW, Jarvis ED, Phillippy AM
Segmental duplications and their variation in a complete human genome
Science, April 1, 2022
Vollger MR, Guitart X, Dishuck PC, Mercuri L, Harvey WT, Gershman A, Diekhans M, Sulovari A, Munson KM, Lewis AM, Hoekzema K, Porubsky D, Li R, Nurk S, Koren S, Miga KH, Phillippy AM, Timp W, Ventura M, Eichler EE
Standards recommendations for the Earth BioGenome Project
Proc Natl Acad Sci USA, January 25, 2022
Lawniczak MKN … Phillippy AMRhie A … Richards S
Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life
Proc Natl Acad Sci USA, January 25, 2022
Mc Cartney AM, Anderson J, Liggins L, Hudson ML, Anderson MZ, TeAika B, Geary J, Cook-Deegan R, Patel HR, Phillippy AM
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps
Bioinformatics, January 10, 2022
Vollger MR, Kerpedjiev P, Phillippy AM, Eichler EE
Population genomics of the critically endangered kākāpō
Cell Genomics, October 13, 2021
Dussex N … Rhie A, Phillippy AM … Dalén L
The whale shark genome reveals patterns of vertebrate gene family evolution
eLife, August 19, 2021
Tan M, Redmond AK, Dooley H, Nozu R, Sato K, Kuraku S, Koren S, Phillippy AM, Dove ADM, and Read TD
Reference genome and demographic history of the most endangered marine mammal, the vaquita
Molecular Ecology Resources, May 21, 2021
Morin PA … Phillippy A, Rhie A … Jarvis ED
Complete vertebrate mitogenomes reveal widespread gene duplications and repeats
Genome Biology, April 29, 2021
Formenti G, Rhie AKoren SPhillippy AM … The Vertebrate Genomes Project Consortium
Extended haplotype phasing of long-read de novo genome assemblies using Hi-C
Nature Communications, April 28, 2021
Kronenberg ZN, Rhie A, Koren S, Concepcion G, Peluso P, Munson K, Porubsky D, Kuhn K, Mueller KA, Low WY, Hiendleder S, Fedrigo O, Liachko I, Hall RJ, Phillippy AM, Eichler EE, Williams JL, Smith TPL, Jarvis ED, Sullivan ST, Kingan SB
Towards complete and error-free genome assemblies of all vertebrate species
Nature, April 28, 2021
Rhie AKoren SGhurye JWalenz BPPhillippy AM, Jarvis ED
Evolutionary and biomedical insights from a marmoset diploid genome assembly
Nature, April 12, 2021
Yang C … Rhie AKoren SPhillippy AM … Zhang G
The structure, function and evolution of a complete human chromosome 8
Nature, April 7, 2021
Logsdon GA … Koren S, Nurk SRhie AJain CPhillippy AM, Eichler EE
A complete reference genome improves analysis of human genetic variation
Science, April 1, 2021
Aganezov S … Avdeyev PRhie AKoren SHansen NFPhillippy AM … Schatz MC
The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning
Scientific reports, February 4, 2021
Kim JH, Noskov VN, Ogurtsov AY, Nagaraja R, Petrov N, Liskovykh M, Walenz BP, Lee HS, Kouprina N, Phillippy AM, Shabalina SA, Schlessinger D, Larionov V
Platypus and echidna genomes reveal mammalian biology and evolution
Nature, January 6, 2021
Zhou Y … Rhie APhillippy AM … Zhang G
Strategic vision for improving human health at The Forefront of Genomics
Nature, October 28, 2020
Green ED … Phillippy AM … Manolio TA
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Genome Biology, September 14, 2020
Rhie A, Walenz BP, Koren S, Phillippy AM
Improved reference genome of the arboviral vector Aedes albopictus
Genome Biology, August 26, 2020
Palatini U … Koren SGhurye J, Rhie APhillippy AM, Bonizzoni M
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Genome Research, August 14, 2020
Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S
Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs
Communications biology, August 4, 2020
Scott MJ, Benoit JB, Davis RJ, Bailey ST, Varga V, Martinson EO, Hickner PV, Syed Z, Cardoso GA, Torres TT, Weirauch MT, Scholl EH, Phillippy AM, Sagel A, Vasquez M, Quintero G, Skoda SR
Telomere-to-telomere assembly of a complete human X chromosome
Nature, July 14, 2020
Miga KH, Koren S, Rhie AChang AM, Hansen NFPhillippy AM
Weighted minimizer sampling improves long read mapping
Bioinformatics, July 13, 2020
Jain C, Rhie A, Zhang H, Chu C, Koren S, Phillippy A
An improved pig reference genome sequence to enable pig genetics and genomics research
Gigascience, June 16, 2020
Warr A … Koren SPhillippy AM … Archibald AL
A robust benchmark for detection of germline large deletions and insertions
Nature Biotechnology, June 15, 2020
Zook JM, Hansen NFKoren S, Phillippy AM … Salit M
Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358
Nature Communications, May 8, 2020
Ou S, Liu J, Chougule KM, Fungtammasan A, Seetharam A, Stein J, Llaca V, Manchanda N, Gilbert AM, Wei X, Chin C, Hufnagel DE, Pedersen S, Snodgrass S, Fengler K, Woodhouse M, Walenz BP, Koren S, Phillippy AM, Hannigan B, Kelly DR, Hirsch CN, Hufford MB, Ware D
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
Nature Biotechnology, May 4, 2020
Shafin K … Koren SPhillippy AM … Paten B
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle
Nature Communications, April 29, 2020
Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, Lee J, Pang AW, Heaton MP, Phillippy AM, Hiendleder S, Smith TP, Williams JL
Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle
Gigascience, April 3, 2020
Rice ES, Koren S, Rhie A, Heaton MP, Kalbfleisch TS, Hardy T, Hackett PH, Bickhart DM, Rosen BD, Vander LB, Maurer NW, Green RE, Phillippy AM, Petersen JL, Smith TP
De novo assembly of the cattle reference genome with single-molecule sequencing
Gigascience, March 19, 2020
Rosen BD … Koren SRhie A, Ghurye JPhillippy AM … Medrano JF
Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential
Genome medicine, January 8, 2020
Moser KA … Koren S, Phillippy AM … Silva JC
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
BMC Biology, January 2, 2020
Waterhouse RM … Koren SPhillippy AM … Sharakhov IV
New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes
BMC Genomics, December 19, 2019
Liu R, Low WY, Tearle R, Koren S, Ghurye J, Rhie A, Phillippy AM, Rosen BD, Bickhart DM, Smith TPL, Hiendleder S, Williams JL
Mash Screen: high-throughput sequence containment estimation for genome discovery
Genome biology, November 5, 2019
Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
PLoS Computational Biology, August 21, 2019
Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S
Accurate Circular Consensus Long-Read Sequencing Improves Variant Detection and Assembly of a Human Genome
Nature Biotechnology, August 12, 2019
Wenger AM … Phillippy AMKoren S … Hunkapiller MW
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
Genome Biology, August 2, 2019
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
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
Nature Communications, July 11, 2019
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
Science Advances, June 26, 2019
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
A chromosome-scale assembly of the major African malaria vector Anopheles funestus
Gigascience, June 3, 2019
Ghurye J, Koren S, Small ST, Redmond S, Howell P, Phillippy AM, Besansky NJ
HLA*LA - HLA typing from linearly projected graph alignments
Bioinformatics, April 3, 2019
Dilthey AT, Mentzer AJ, Carapito R, Cutland C, Cereb N, Madhi SA, Rhie A, Koren S, Bahram S, McVean G, Phillippy AM
Reply to 'Errors in long-read assemblies can critically affect protein prediction'
Nature Biotechnology, February 1, 2019
Koren S, Phillippy AM, Simpson JT, Loman NJ, Loose M
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
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
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
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
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
New advances in sequence assembly
Genome Research, May 1, 2017
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 USA, 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
Krona: interactive metagenomic visualization in a web browser
Encyclopedia of Metagenomics, January 1, 2015
Ondov BD, Bergman NH, 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
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
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
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
Nature Biotechnology, 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 USA, 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 USA, 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
Whole-genome sequence analysis for pathogen detection and diagnostics
Thesis, January 1, 2010
Phillippy AM
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