Adam Phillippy - Publications

Affiliations: 
2010 Computer Science University of Maryland, College Park, College Park, MD 

90 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, ... ... Phillippy AM, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 592: 737-746. PMID 33911273 DOI: 10.1038/s41586-021-03451-0  0.52
2021 Kronenberg ZN, Rhie A, Koren S, Concepcion GT, Peluso P, Munson KM, Porubsky D, Kuhn K, Mueller KA, Low WY, Hiendleder S, Fedrigo O, Liachko I, Hall RJ, Phillippy AM, et al. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nature Communications. 12: 1935. PMID 33911078 DOI: 10.1038/s41467-020-20536-y  0.52
2021 Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R, Houde P, Koren S, Oliver K, Smith M, Skelton J, ... ... Phillippy AM, et al. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome Biology. 22: 120. PMID 33910595 DOI: 10.1186/s13059-021-02336-9  0.52
2021 Yang C, Zhou Y, Marcus S, Formenti G, Bergeron LA, Song Z, Bi X, Bergman J, Rousselle MMC, Zhou C, Zhou L, Deng Y, Fang M, Xie D, Zhu Y, ... ... Phillippy AM, et al. Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature. PMID 33910227 DOI: 10.1038/s41586-021-03535-x  0.52
2021 Logsdon GA, Vollger MR, Hsieh P, Mao Y, Liskovykh MA, Koren S, Nurk S, Mercuri L, Dishuck PC, Rhie A, de Lima LG, Dvorkina T, Porubsky D, Harvey WT, Mikheenko A, ... ... Phillippy AM, et al. The structure, function and evolution of a complete human chromosome 8. Nature. PMID 33828295 DOI: 10.1038/s41586-021-03420-7  0.52
2020 Rhie A, Walenz BP, Koren S, Phillippy AM. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology. 21: 245. PMID 32928274 DOI: 10.1186/S13059-020-02134-9  0.52
2020 Palatini U, Masri RA, Cosme LV, Koren S, Thibaud-Nissen F, Biedler JK, Krsticevic F, Johnston JS, Halbach R, Crawford JE, Antoshechkin I, Failloux AB, Pischedda E, Marconcini M, Ghurye J, ... ... Phillippy AM, et al. Improved reference genome of the arboviral vector Aedes albopictus. Genome Biology. 21: 215. PMID 32847630 DOI: 10.1186/S13059-020-02141-W  0.52
2020 Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Research. PMID 32801147 DOI: 10.1101/Gr.263566.120  0.52
2020 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, et al. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32699374 DOI: 10.1038/S41587-020-0640-Y  0.52
2020 Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, ... ... Phillippy A, et al. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology. PMID 32686750 DOI: 10.1038/S41587-020-0503-6  0.52
2020 Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, ... ... Phillippy AM, et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. PMID 32663838 DOI: 10.1038/S41586-020-2547-7  0.52
2020 Jain C, Rhie A, Zhang H, Chu C, Walenz BP, Koren S, Phillippy AM. Weighted minimizer sampling improves long read mapping. Bioinformatics (Oxford, England). 36: i111-i118. PMID 32657365 DOI: 10.1093/Bioinformatics/Btaa435  0.52
2020 Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, ... ... Phillippy AM, et al. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience. 9. PMID 32543654 DOI: 10.1093/Gigascience/Giaa051  0.52
2020 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, et al. A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32541955 DOI: 10.1038/S41587-020-0538-8  0.52
2020 Ou S, Liu J, Chougule KM, Fungtammasan A, Seetharam AS, Stein JC, Llaca V, Manchanda N, Gilbert AM, Wei S, Chin CS, Hufnagel DE, Pedersen S, Snodgrass SJ, Fengler K, ... ... Phillippy AM, et al. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications. 11: 2288. PMID 32385271 DOI: 10.1038/S41467-020-16037-7  0.52
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, ... ... Phillippy AM, et al. Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nature Communications. 11: 2071. PMID 32350247 DOI: 10.1038/S41467-020-15848-Y  0.52
2020 Rice ES, Koren S, Rhie A, Heaton MP, Kalbfleisch TS, Hardy T, Hackett PH, Bickhart DM, Rosen BD, Ley BV, Maurer NW, Green RE, Phillippy AM, Petersen JL, Smith TPL. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. Gigascience. 9. PMID 32242610 DOI: 10.1093/Gigascience/Giaa029  0.52
2020 Rosen BD, Bickhart DM, Schnabel RD, Koren S, Elsik CG, Tseng E, Rowan TN, Low WY, Zimin A, Couldrey C, Hall R, Li W, Rhie A, Ghurye J, McKay SD, ... ... Phillippy AM, et al. De novo assembly of the cattle reference genome with single-molecule sequencing. Gigascience. 9. PMID 32191811 DOI: 10.1093/Gigascience/Giaa021  0.52
2020 Moser KA, Drábek EF, Dwivedi A, Stucke EM, Crabtree J, Dara A, Shah Z, Adams M, Li T, Rodrigues PT, Koren S, Phillippy AM, Munro JB, Ouattara A, Sparklin BC, et al. Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential. Genome Medicine. 12: 6. PMID 31915075 DOI: 10.1186/S13073-019-0708-9  0.52
2020 Waterhouse RM, Aganezov S, Anselmetti Y, Lee J, Ruzzante L, Reijnders MJMF, Feron R, Bérard S, George P, Hahn MW, Howell PI, Kamali M, Koren S, Lawson D, Maslen G, ... ... Phillippy AM, et al. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies. Bmc Biology. 18: 1. PMID 31898513 DOI: 10.1186/S12915-019-0728-3  0.52
2019 Liachko I, Press M, Stalder T, Bickhart D, Koren S, Top E, Phillippy A, Smith T, Sullivan S. Linking the Resistome to the Microbiome: A Culture-Free Method Links Plasmid, Virus, and Antimicrobial Resistance Genes to their Hosts in Complex Microbial Populations. Journal of Biomolecular Techniques : Jbt. 30: S25. PMID 31892900  0.52
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. New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes. Bmc Genomics. 20: 1000. PMID 31856728 DOI: 10.1186/S12864-019-6364-Z  0.52
2019 Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM. Mash Screen: high-throughput sequence containment estimation for genome discovery. Genome Biology. 20: 232. PMID 31690338 DOI: 10.1186/S13059-019-1841-X  0.52
2019 Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. Plos Computational Biology. 15: e1007273. PMID 31433799 DOI: 10.1371/Journal.Pcbi.1007273  0.8
2019 Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, ... Phillippy AM, et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature Biotechnology. PMID 31406327 DOI: 10.1038/S41587-019-0217-9  0.52
2019 Bickhart DM, 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, ... ... Phillippy AM, et al. 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. 20: 153. PMID 31375138 DOI: 10.1186/S13059-019-1760-X  0.8
2019 Dilthey AT, Jain C, Koren S, Phillippy AM. Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps. Nature Communications. 10: 3066. PMID 31296857 DOI: 10.1038/S41467-019-10934-2  0.52
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, Mullikin JC, et al. De novo assembly of the goldfish () genome and the evolution of genes after whole-genome duplication. Science Advances. 5: eaav0547. PMID 31249862 DOI: 10.1126/Sciadv.Aav0547  0.52
2019 Ghurye J, Koren S, Small ST, Redmond S, Howell P, Phillippy AM, Besansky NJ. A chromosome-scale assembly of the major African malaria vector Anopheles funestus. Gigascience. 8. PMID 31157884 DOI: 10.1093/Gigascience/Giz063  0.52
2019 Dilthey AT, Mentzer AJ, Carapito R, Cutland C, Cereb N, Madhi SA, Rhie A, Koren S, Bahram S, McVean G, Phillippy AM. HLA*LA - HLA typing from linearly projected graph alignments. Bioinformatics (Oxford, England). PMID 30942877 DOI: 10.1093/Bioinformatics/Btz235  0.52
2019 Koren S, Phillippy AM, Simpson JT, Loman NJ, Loose M. Reply to 'Errors in long-read assemblies can critically affect protein prediction'. Nature Biotechnology. PMID 30670797 DOI: 10.1038/S41587-018-0005-Y  0.52
2018 Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, ... ... Phillippy AM, et al. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature. PMID 30429615 DOI: 10.1038/S41586-018-0692-Z  0.52
2018 Jain C, Koren S, Dilthey A, Phillippy AM, Aluru S. A fast adaptive algorithm for computing whole-genome homology maps. Bioinformatics (Oxford, England). 34: i748-i756. PMID 30423094 DOI: 10.1093/Bioinformatics/Bty597  0.52
2018 Nasko DJ, Koren S, Phillippy AM, Treangen TJ. RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification. Genome Biology. 19: 165. PMID 30373669 DOI: 10.1186/S13059-018-1554-6  0.96
2018 Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM. De novo assembly of haplotype-resolved genomes with trio binning. Nature Biotechnology. PMID 30346939 DOI: 10.1038/Nbt.4277  0.52
2018 Kim JH, Dilthey AT, Nagaraja R, Lee HS, Koren S, Dudekula D, Wood Iii WH, Piao Y, Ogurtsov AY, Utani K, Noskov VN, Shabalina SA, Schlessinger D, Phillippy AM, Larionov V. Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing. Nucleic Acids Research. PMID 29788454 DOI: 10.1093/Nar/Gky442  0.52
2018 Jain C, Dilthey A, Koren S, Aluru S, Phillippy AM. A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 29708767 DOI: 10.1089/cmb.2018.0036  0.52
2018 Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, ... ... Phillippy AM, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology. PMID 29431738 DOI: 10.1038/Nbt.4060  0.52
2018 Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome alignment system. Plos Computational Biology. 14: e1005944. PMID 29373581 DOI: 10.1371/Journal.Pcbi.1005944  0.8
2018 Miller JR, Koren S, Dilley KA, Puri V, Brown DM, Harkins DM, Thibaud-Nissen F, Rosen B, Chen XG, Tu Z, Sharakhov IV, Sharakhova MV, Sebra R, Stockwell TB, Bergman NH, ... ... Phillippy AM, et al. Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation. Gigascience. PMID 29329394 DOI: 10.1093/Gigascience/Gix135  0.52
2017 Venkateswaran K, Checinska Sielaff A, 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 A, et al. Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station. Genome Announcements. 5. PMID 28798168 DOI: 10.1128/Genomea.00680-17  0.96
2017 Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, ... ... Phillippy AM, et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Research. PMID 28396521 DOI: 10.1101/Gr.213611.116  0.52
2017 Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research. PMID 28298431 DOI: 10.1101/Gr.215087.116  0.52
2017 Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, Lee J, Lam ET, Liachko I, Sullivan ST, Burton JN, Huson HJ, Nystrom JC, Kelley CM, Hutchison JL, ... ... Phillippy AM, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nature Genetics. PMID 28263316 DOI: 10.1038/Ng.3802  0.52
2017 Schwartz JC, Gibson MS, Heimeier D, Koren S, Phillippy AM, Bickhart DM, Smith TP, Medrano JF, Hammond JA. The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation. Immunogenetics. PMID 28180967 DOI: 10.1007/S00251-017-0973-Y  0.52
2017 Ondov B, Phillippy A. Juxtaposition of hierarchical quantities with bipartite Krona charts F1000research. 6. DOI: 10.7490/F1000Research.1114802.1  0.48
2016 Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology. 17: 132. PMID 27323842 DOI: 10.1186/S13059-016-0997-X  0.8
2016 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, ... ... Phillippy AM, et al. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature Communications. 7: 11757. PMID 27249958 DOI: 10.1038/Ncomms11757  0.8
2016 Treangen TJ, Schoeler G, Phillippy AM, Bergman NH, Turell MJ. Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru. Plos Neglected Tropical Diseases. 10: e0004440. PMID 27074162 DOI: 10.1371/Journal.Pntd.0004440  0.96
2016 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, ... ... Phillippy AM, et al. Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. Proceedings of the National Academy of Sciences of the United States of America. PMID 27035980 DOI: 10.1073/Pnas.1525164113  0.8
2015 Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. Corrigendum: Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature Biotechnology. 33: 1109. PMID 26448093 DOI: 10.1038/Nbt1015-1109C  0.52
2015 Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature Biotechnology. 33: 623-30. PMID 26006009 DOI: 10.1038/Nbt.3238  0.8
2015 Koren S, Phillippy AM. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Current Opinion in Microbiology. 23: 110-20. PMID 25461581 DOI: 10.1016/J.Mib.2014.11.014  0.52
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. Long-read, whole-genome shotgun sequence data for five model organisms. Scientific Data. 1: 140045. PMID 25977796 DOI: 10.1038/Sdata.2014.45  0.8
2014 Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology. 15: 524. PMID 25410596 DOI: 10.1186/S13059-014-0524-X  0.96
2014 Treangen TJ, Maybank RA, Enke S, Friss MB, Diviak LF, Karaolis DK, Koren S, Ondov B, Phillippy AM, Bergman NH, Rosovitz MJ. Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923. Genome Announcements. 2. PMID 25377701 DOI: 10.1128/Genomea.01110-14  0.96
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, ... ... Phillippy AM, et al. High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience. 3: 11. PMID 25061512 DOI: 10.1186/2047-217X-3-11  0.8
2014 Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. Automated ensemble assembly and validation of microbial genomes. Bmc Bioinformatics. 15: 126. PMID 24884846 DOI: 10.1186/1471-2105-15-126  0.8
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. Complete Closed Genome Sequences of Four Mannheimia varigena Isolates from Cattle with Shipping Fever. Genome Announcements. 2. PMID 24526648 DOI: 10.1128/Genomea.00088-14  0.52
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 Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever. Genome Announcements. 2. PMID 24526647 DOI: 10.1128/Genomea.00084-14  0.52
2013 Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology. 14: R101. PMID 24034426 DOI: 10.1186/Gb-2013-14-9-R101  0.52
2013 Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, ... ... Phillippy AM, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2: 10. PMID 23870653 DOI: 10.1186/2047-217X-2-10  0.52
2013 Harhay GP, Koren S, Phillippy AM, McVey DS, Kuszak J, Clawson ML, Harhay DM, Heaton MP, Chitko-McKown CG, Smith TP. Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle. Genome Announcements. 1. PMID 23682137 DOI: 10.1128/Genomea.00188-13  0.52
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, et al. Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis. Genome Announcements. 1. PMID 23405332 DOI: 10.1128/Genomea.00067-12  0.52
2013 Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biology. 14: R2. PMID 23320958 DOI: 10.1186/Gb-2013-14-1-R2  0.8
2013 Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings in Bioinformatics. 14: 213-24. PMID 22199379 DOI: 10.1093/Bib/Bbr074  0.8
2012 Schatz MC, Phillippy AM. The rise of a digital immune system. Gigascience. 1: 4. PMID 23587178 DOI: 10.1186/2047-217X-1-4  0.52
2012 Treangen TJ, Phillippy AM. Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone. Genome Biology. 13: 181. PMID 23270611 DOI: 10.1186/gb-2012-13-12-181  0.96
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, et al. Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe. Emerging Infectious Diseases. 18: 1307-13. PMID 22840345 DOI: 10.3201/Eid1808.111343  0.8
2012 Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Adam M Phillippy. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology. 30: 693-700. PMID 22750884 DOI: 10.1038/Nbt.2280  0.8
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. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research. 22: 557-67. PMID 22147368 DOI: 10.1101/Gr.131383.111  0.8
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. Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proceedings of the National Academy of Sciences of the United States of America. 108: E1423-32. PMID 22123943 DOI: 10.1073/Pnas.1111712108  0.52
2011 Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. Bmc Bioinformatics. 12: 385. PMID 21961884 DOI: 10.1186/1471-2105-12-385  0.52
2011 Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, ... ... Phillippy AM, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21: 2224-41. PMID 21926179 DOI: 10.1101/Gr.126599.111  0.8
2011 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, et al. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology. 193: 5450-64. PMID 21784931 DOI: 10.1128/Jb.05262-11  0.8
2011 Sahl JW, Johnson JK, Harris AD, Phillippy AM, Hsiao WW, Thom KA, Rasko DA. Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity. Bmc Genomics. 12: 291. PMID 21639920 DOI: 10.1186/1471-2164-12-291  0.8
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, et al. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of Sciences of the United States of America. 108: 5027-32. PMID 21383169 DOI: 10.1073/Pnas.1016657108  0.8
2010 Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W. Probing the pan-genome of Listeria monocytogenes: New insights into intraspecific niche expansion and genomic diversification Bmc Genomics. 11. PMID 20846431 DOI: 10.1186/1471-2164-11-500  0.8
2010 Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL, Ravel J. Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray. Applied and Environmental Microbiology. 76: 5636-8. PMID 20581189 DOI: 10.1128/Aem.00303-10  0.52
2009 Phillippy AM, Deng X, Zhang W, Salzberg SL. Efficient oligonucleotide probe selection for pan-genomic tiling arrays Bmc Bioinformatics. 10: 293. PMID 19758451 DOI: 10.1186/1471-2105-10-293  0.8
2009 Phillippy AM, Ayanbule K, Edwards NJ, Salzberg SL. Insignia: a DNA signature search web server for diagnostic assay development. Nucleic Acids Research. 37: W229-34. PMID 19417071 DOI: 10.1093/Nar/Gkp286  0.8
2008 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, et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. Bmc Genomics. 9: 204. PMID 18452608 DOI: 10.1186/1471-2164-9-204  0.8
2008 Phillippy AM, Schatz MC, Pop M. Genome assembly forensics: finding the elusive mis-assembly. Genome Biology. 9: R55. PMID 18341692 DOI: 10.1186/Gb-2008-9-3-R55  0.8
2007 Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL. Comprehensive DNA signature discovery and validation. Plos Computational Biology. 3: e98. PMID 17511514 DOI: 10.1371/Journal.Pcbi.0030098  0.8
2007 Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL. Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biology. 8: R34. PMID 17349036 DOI: 10.1186/Gb-2007-8-3-R34  0.8
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, et al. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science (New York, N.Y.). 307: 105-8. PMID 15637277 DOI: 10.1126/Science.1102226  0.8
2004 Pop M, Phillippy A, Delcher AL, Salzberg SL. Comparative genome assembly. Briefings in Bioinformatics. 5: 237-48. PMID 15383210 DOI: 10.1093/Bib/5.3.237  0.8
2004 Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biology. 5: R12. PMID 14759262 DOI: 10.1186/Gb-2004-5-2-R12  0.8
2003 Delcher AL, Salzberg SL, Phillippy AM. Using MUMmer to identify similar regions in large sequence sets. Current Protocols in Bioinformatics. Unit 10.3. PMID 18428693 DOI: 10.1002/0471250953.bi1003s00  0.8
2002 Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Research. 30: 2478-83. PMID 12034836 DOI: 10.1093/Nar/30.11.2478  0.8
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