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Items: 1 to 50 of 57

1.

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.

Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S.

Nat Commun. 2018 Nov 30;9(1):5114. doi: 10.1038/s41467-018-07641-9.

2.

Improved reference genome of Aedes aegypti informs arbovirus vector control.

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, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašić G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC 4th, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB.

Nature. 2018 Nov;563(7732):501-507. doi: 10.1038/s41586-018-0692-z. Epub 2018 Nov 14.

PMID:
30429615
3.

A fast adaptive algorithm for computing whole-genome homology maps.

Jain C, Koren S, Dilthey A, Phillippy AM, Aluru S.

Bioinformatics. 2018 Sep 1;34(17):i748-i756. doi: 10.1093/bioinformatics/bty597.

4.

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification.

Nasko DJ, Koren S, Phillippy AM, Treangen TJ.

Genome Biol. 2018 Oct 30;19(1):165. doi: 10.1186/s13059-018-1554-6.

5.

De novo assembly of haplotype-resolved genomes with trio binning.

Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM.

Nat Biotechnol. 2018 Oct 22. doi: 10.1038/nbt.4277. [Epub ahead of print]

PMID:
30346939
6.

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing.

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.

Nucleic Acids Res. 2018 Jul 27;46(13):6712-6725. doi: 10.1093/nar/gky442.

7.

A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.

Jain C, Dilthey A, Koren S, Aluru S, Phillippy AM.

J Comput Biol. 2018 Jul;25(7):766-779. doi: 10.1089/cmb.2018.0036. Epub 2018 Apr 30.

PMID:
29708767
8.

Nanopore sequencing and assembly of a human genome with ultra-long reads.

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, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M.

Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29.

9.

MUMmer4: A fast and versatile genome alignment system.

Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A.

PLoS Comput Biol. 2018 Jan 26;14(1):e1005944. doi: 10.1371/journal.pcbi.1005944. eCollection 2018 Jan.

10.

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation.

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, Sutton GG, Phillippy AM, Piermarini PM, Shabman RS.

Gigascience. 2018 Mar 1;7(3):1-13. doi: 10.1093/gigascience/gix135.

11.

New advances in sequence assembly.

Phillippy AM.

Genome Res. 2017 May;27(5):xi-xiii. doi: 10.1101/gr.223057.117. No abstract available.

12.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

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, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM.

Genome Res. 2017 May;27(5):849-864. doi: 10.1101/gr.213611.116. Epub 2017 Apr 10.

13.

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.

Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM.

Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15.

14.

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.

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, Zhou Y, Sun J, Crisà A, Ponce de León FA, Schwartz JC, Hammond JA, Waldbieser GC, Schroeder SG, Liu GE, Dunham MJ, Shendure J, Sonstegard TS, Phillippy AM, Van Tassell CP, Smith TP.

Nat Genet. 2017 Apr;49(4):643-650. doi: 10.1038/ng.3802. Epub 2017 Mar 6.

15.

The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation.

Schwartz JC, Gibson MS, Heimeier D, Koren S, Phillippy AM, Bickhart DM, Smith TP, Medrano JF, Hammond JA.

Immunogenetics. 2017 Apr;69(4):255-269. doi: 10.1007/s00251-017-0973-y. Epub 2017 Feb 9.

16.

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;17(1):132. doi: 10.1186/s13059-016-0997-x.

17.

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;7:11757. doi: 10.1038/ncomms11757.

18.

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;10(4):e0004440. doi: 10.1371/journal.pntd.0004440. eCollection 2016 Apr.

19.

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 U S A. 2016 Apr 12;113(15):E2114-23. doi: 10.1073/pnas.1525164113. Epub 2016 Mar 29.

20.

Corrigendum: 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 Oct;33(10):1109. doi: 10.1038/nbt1015-1109c. No abstract available.

PMID:
26448093
21.

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 Jun;33(6):623-30. doi: 10.1038/nbt.3238. Epub 2015 May 25. Erratum in: Nat Biotechnol. 2015 Oct;33(10):1109.

PMID:
26006009
22.

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.

Koren S, Phillippy AM.

Curr Opin Microbiol. 2015 Feb;23:110-20. doi: 10.1016/j.mib.2014.11.014. Epub 2014 Dec 1. Review.

23.
24.

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;2(6). pii: e01110-14. doi: 10.1128/genomeA.01110-14.

25.

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;3:11. doi: 10.1186/2047-217X-3-11. eCollection 2014.

26.

Automated ensemble assembly and validation of microbial genomes.

Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM.

BMC Bioinformatics. 2014 May 3;15:126. doi: 10.1186/1471-2105-15-126.

27.

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;2(1). pii: e00088-14. doi: 10.1128/genomeA.00088-14.

28.

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;2(1). pii: e00084-14. doi: 10.1128/genomeA.00084-14.

29.

Long-read, whole-genome shotgun sequence data for five model organisms.

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.

Sci Data. 2014 Nov 25;1:140045. doi: 10.1038/sdata.2014.45. eCollection 2014.

30.

Reducing assembly complexity of microbial genomes with single-molecule sequencing.

Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM.

Genome Biol. 2013;14(9):R101.

31.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

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, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

32.

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 TP.

Genome Announc. 2013 May 16;1(3). pii: e00188-13. doi: 10.1128/genomeA.00188-13.

33.

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 Jan;1(1). pii: e00067-12. doi: 10.1128/genomeA.00067-12. Epub 2013 Jan 15.

34.

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 Jan 15;14(1):R2. doi: 10.1186/gb-2013-14-1-r2.

35.

Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone.

Treangen TJ, Phillippy AM.

Genome Biol. 2012 Dec 27;13(12):181. doi: 10.1186/gb-2012-13-12-181.

36.

Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe.

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.

Emerg Infect Dis. 2012 Aug;18(8):1307-13. doi: 10.3201/eid1808.111343.

37.

The rise of a digital immune system.

Schatz MC, Phillippy AM.

Gigascience. 2012 Jul 12;1(1):4. doi: 10.1186/2047-217X-1-4.

38.

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. 2013 Mar;14(2):213-24. doi: 10.1093/bib/bbr074. Epub 2011 Dec 23.

39.

GAGE: A critical evaluation of genome assemblies and assembly algorithms.

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.

Genome Res. 2012 Mar;22(3):557-67. doi: 10.1101/gr.131383.111. Epub 2012 Jan 6. Erratum in: Genome Res. 2012 Jun;22(6):1196.

40.

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 U S A. 2011 Dec 20;108(51):E1423-32. doi: 10.1073/pnas.1111712108. Epub 2011 Nov 28.

41.

Interactive metagenomic visualization in a Web browser.

Ondov BD, Bergman NH, Phillippy AM.

BMC Bioinformatics. 2011 Sep 30;12:385. doi: 10.1186/1471-2105-12-385.

42.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

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, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.

Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.

43.

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 VP, Rabinowicz PD, Leach JE, White FF, Salzberg SL.

J Bacteriol. 2011 Oct;193(19):5450-64. doi: 10.1128/JB.05262-11. Epub 2011 Jul 22.

44.

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;12:291. doi: 10.1186/1471-2164-12-291.

45.

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 U S A. 2011 Mar 22;108(12):5027-32. doi: 10.1073/pnas.1016657108. Epub 2011 Mar 7.

46.

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;11:500. doi: 10.1186/1471-2164-11-500.

47.

Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray.

Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL, Ravel J.

Appl Environ Microbiol. 2010 Aug;76(16):5636-8. doi: 10.1128/AEM.00303-10. Epub 2010 Jun 25.

48.

Transcriptomic responses of Salmonella enterica serovars Enteritidis and Typhimurium to chlorine-based oxidative stress.

Wang S, Phillippy AM, Deng K, Rui X, Li Z, Tortorello ML, Zhang W.

Appl Environ Microbiol. 2010 Aug;76(15):5013-24. doi: 10.1128/AEM.00823-10. Epub 2010 Jun 18.

49.

Efficient oligonucleotide probe selection for pan-genomic tiling arrays.

Phillippy AM, Deng X, Zhang W, Salzberg SL.

BMC Bioinformatics. 2009 Sep 16;10:293. doi: 10.1186/1471-2105-10-293.

50.

Insignia: a DNA signature search web server for diagnostic assay development.

Phillippy AM, Ayanbule K, Edwards NJ, Salzberg SL.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W229-34. doi: 10.1093/nar/gkp286. Epub 2009 May 5.

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