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    Results: 1 to 20 of 72

    1.

    Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.

    Brady A, Salzberg SL.

    Nat Methods. 2009 Sep;6(9):673-6. Epub 2009 Aug 2.PMID: 19648916 [PubMed - indexed for MEDLINE]Related articles

    2.

    Sim4cc: a cross-species spliced alignment program.

    Zhou L, Pertea M, Delcher AL, Florea L.

    Nucleic Acids Res. 2009 Jun;37(11):e80. Epub 2009 May 8.PMID: 19429899 [PubMed - indexed for MEDLINE]Related articlesFree article

    3.

    A whole-genome assembly of the domestic cow, Bos taurus.

    Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL.

    Genome Biol. 2009;10(4):R42. Epub 2009 Apr 24.PMID: 19393038 [PubMed - indexed for MEDLINE]Related articlesFree article

    4.

    CloudBurst: highly sensitive read mapping with MapReduce.

    Schatz MC.

    Bioinformatics. 2009 Jun 1;25(11):1363-9. Epub 2009 Apr 8.PMID: 19357099 [PubMed - indexed for MEDLINE]Related articlesFree article

    5.

    TopHat: discovering splice junctions with RNA-Seq.

    Trapnell C, Pachter L, Salzberg SL.

    Bioinformatics. 2009 May 1;25(9):1105-11. Epub 2009 Mar 16.PMID: 19289445 [PubMed - indexed for MEDLINE]Related articlesFree article

    6.

    Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

    Langmead B, Trapnell C, Pop M, Salzberg SL.

    Genome Biol. 2009;10(3):R25. Epub 2009 Mar 4.PMID: 19261174 [PubMed - indexed for MEDLINE]Related articlesFree article

    7.

    Genome sequence of the Wolbachia endosymbiont of Culex quinquefasciatus JHB.

    Salzberg SL, Puiu D, Sommer DD, Nene V, Lee NH.

    J Bacteriol. 2009 Mar;191(5):1725. Epub 2008 Dec 29.PMID: 19114486 [PubMed - indexed for MEDLINE]Related articlesFree article

    8.

    Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas.

    Lu H, Patil P, Van Sluys MA, White FF, Ryan RP, Dow JM, Rabinowicz P, Salzberg SL, Leach JE, Sonti R, Brendel V, Bogdanove AJ.

    PLoS One. 2008;3(11):e3828. Epub 2008 Nov 27.PMID: 19043590 [PubMed - indexed for MEDLINE]Related articlesFree article

    9.

    The complete genome sequence of Bacillus anthracis Ames "Ancestor".

    Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD, Worsham P, Keim PS, Salzberg SL, Fraser-Liggett CM, Rasko DA.

    J Bacteriol. 2009 Jan;191(1):445-6. Epub 2008 Oct 24.PMID: 18952800 [PubMed - indexed for MEDLINE]Related articlesFree article

    10.

    OperonDB: a comprehensive database of predicted operons in microbial genomes.

    Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL.

    Nucleic Acids Res. 2009 Jan;37(Database issue):D479-82. Epub 2008 Oct 23.PMID: 18948284 [PubMed - indexed for MEDLINE]Related articlesFree article

    11.

    Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18.

    Puiu D, Salzberg SL.

    PLoS One. 2008;3(10):e3427. Epub 2008 Oct 17.PMID: 18927608 [PubMed - indexed for MEDLINE]Related articlesFree article

    12.

    Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

    Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV, Fernandez-Becerra C, Gilson PR, Gueye AH, Guo X, Kang'a S, Kooij TW, Korsinczky M, Meyer EV, Nene V, Paulsen I, White O, Ralph SA, Ren Q, Sargeant TJ, Salzberg SL, Stoeckert CJ, Sullivan SA, Yamamoto MM, Hoffman SL, Wortman JR, Gardner MJ, Galinski MR, Barnwell JW, Fraser-Liggett CM.

    Nature. 2008 Oct 9;455(7214):757-63.PMID: 18843361 [PubMed - indexed for MEDLINE]Related articlesFree article

    13.

    Gene-boosted assembly of a novel bacterial genome from very short reads.

    Salzberg SL, Sommer DD, Puiu D, Lee VT.

    PLoS Comput Biol. 2008 Sep 26;4(9):e1000186.PMID: 18818729 [PubMed - indexed for MEDLINE]Related articlesFree article

    14.

    Using GlimmerM to find genes in eukaryotic genomes.

    Pertea M, Salzberg SL.

    Curr Protoc Bioinformatics. 2002 Nov;Chapter 4:Unit 4.4.PMID: 18792941 [PubMed - indexed for MEDLINE]Related articles

    15.

    What are decision trees?

    Kingsford C, Salzberg SL.

    Nat Biotechnol. 2008 Sep;26(9):1011-3. Review.PMID: 18779814 [PubMed - indexed for MEDLINE]Related articlesFree article

    16.

    The contents of the syringe.

    Salzberg S.

    Nature. 2008 Jul 10;454(7201):160-1. No abstract available. PMID: 18615063 [PubMed - indexed for MEDLINE]Related articlesFree article

    17.

    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, Won Lee S, Seo YS, Sriariyanum M, Ronald PC, Sonti RV, Van Sluys MA, Leach JE, White FF, Bogdanove AJ.

    BMC Genomics. 2008 May 1;9:204. Erratum in: BMC Genomics. 2008;9:534.. Seo, Young-Su [added]; Sriariyanum, Malinee [added]. PMID: 18452608 [PubMed - indexed for MEDLINE]Related articlesFree article

    18.

    The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

    Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M.

    Nature. 2008 Apr 24;452(7190):991-6.PMID: 18432245 [PubMed - indexed for MEDLINE]Related articles

    19.

    Genome assembly forensics: finding the elusive mis-assembly.

    Phillippy AM, Schatz MC, Pop M.

    Genome Biol. 2008;9(3):R55. Epub 2008 Mar 14.PMID: 18341692 [PubMed - indexed for MEDLINE]Related articlesFree article

    20.

    Bioinformatics challenges of new sequencing technology.

    Pop M, Salzberg SL.

    Trends Genet. 2008 Mar;24(3):142-9. Epub 2008 Feb 11. Review.PMID: 18262676 [PubMed - indexed for MEDLINE]Related articlesFree article

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