國家高速網路與計算中心
  國網中心     | 生物化學資料庫服務    
 
 
回首頁    | 好站連結    | SiteMap

 三維影像國際合作

 2005識之精微

 會議展示及參訪

 好站連結
最新消息
NGS分析平台
Olfactory DB
生物知識庫
知識庫服務說明
生技新知 
生物計算服務系統
生物計算服務說明   
生物序列分析     
軟體與資料庫 
結構生物軟體 
生醫影像軟體 
關於我們
認識生物計算小組
台灣生物資訊學會
聯絡我們
 
Velvet 相關文獻
    (5666 閱讀)   友善列印

Velvet是一套用來進行次世代定序短序列組裝(de novo assembly)的工具,可以用來組裝Solexa與454的資料,此軟體利用de Bruijn graphs 的方法進行序列組裝,透過大量緊密的短字串(k-mers)來處理高度覆蓋(20-25x)以及非常短(25-50bp)的序列組,其組裝的結果有相當高的N50值,代表組裝的效率相當好,但唯一的缺點是耗用相當大量的系統記憶體,不過velvet已經有支援openMP的版本,可在單一主機內進行多緒處理,目前學界常使用他來組裝基因體大小約為真菌以下的基因體.

Velvet software has been cited by following papers:

  1. LOCAS - A Low Coverage Assembly Tool for Resequencing Projects.
    Klein JD, Ossowski S, Schneeberger K, Weigel D, Huson DH.
    PLoS One. 2011;6(8):e23455. Epub 2011 Aug 15.
  2. Drug-Resistant Genotypes and Multi-Clonality in Plasmodium falciparum Analysed by Direct Genome Sequencing from Peripheral Blood of Malaria Patients.
    Robinson T, Campino SG, Auburn S, Assefa SA, Polley SD, Manske M, Macinnis B, Rockett KA, Maslen GL, Sanders M, Quail MA, Chiodini PL, Kwiatkowski DP, Clark TG, Sutherland CJ.
    PLoS One. 2011;6(8):e23204. Epub 2011 Aug 11.
  3. Sequencing and Validation of the Genome of a Campylobacter concisus Reveals Intra-Species Diversity.
    Deshpande NP, Kaakoush NO, Mitchell H, Janitz K, Raftery MJ, Li SS, Wilkins MR.
    PLoS One. 2011;6(7):e22170. Epub 2011 Jul 29.
  4. Exploring the Zoonotic Potential of Mycobacterium avium Subspecies paratuberculosis through Comparative Genomics.
    Wynne JW, Bull TJ, Seemann T, Bulach DM, Wagner J, Kirkwood CD, Michalski WP.
    PLoS One. 2011;6(7):e22171. Epub 2011 Jul 22.
  5. Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana.
    Kemen E, Gardiner A, Schultz-Larsen T, Kemen AC, Balmuth AL, Robert-Seilaniantz A, Bailey K, Holub E, Studholme DJ, Maclean D, Jones JD.
    PLoS Biol. 2011 Jul;9(7):e1001094. Epub 2011 Jul 5.
  6. Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing.
    Wong MM, Cannon CH, Wickneswari R.
    BMC Genomics. 2011 Jul 5;12:342.
  7. Meta-IDBA: a de Novo assembler for metagenomic data.
    Peng Y, Leung HC, Yiu SM, Chin FY.
    Bioinformatics. 2011 Jul 1;27(13):i94-101.
  8. Error correction of high-throughput sequencing datasets with non-uniform coverage.
    Medvedev P, Scott E, Kakaradov B, Pevzner P.
    Bioinformatics. 2011 Jul 1;27(13):i137-41.
  9. Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance.
    Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M.
    BMC Genomics. 2011 Jun 16;12:317. doi: 10.1186/1471-2164-12-317.
  10. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139).
    Land M, Held B, Gronow S, Abt B, Lucas S, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Hauser L, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A.
    Stand Genomic Sci. 2011 Apr 29;4(2):233-43.
  11. Complete genome sequence of Cellulophaga lytica type strain (LIM-21).
    Pati A, Abt B, Teshima H, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Mavromatis K, Ovchinikova G, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Kannan KP, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N.
    Stand Genomic Sci. 2011 Apr 29;4(2):221-32.
  12. Complete genome sequence of Oceanithermus profundus type strain (506).
    Pati A, Zhang X, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Hauser L, Jeffries CD, Brambilla EM, Röhl A, Mwirichia R, Rohde M, Tindall BJ, Sikorski J, Wirth R, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M.
    Stand Genomic Sci. 2011 Apr 29;4(2):210-20.
  13. Complete genome sequence of Odoribacter splanchnicus type strain (1651/6).
    Göker M, Gronow S, Zeytun A, Nolan M, Lucas S, Lapidus A, Hammon N, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brambilla EM, Rohde M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Eisen JA, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2011 Apr 29;4(2):200-9.
  14. Complete genome sequence of Bacteroides salanitronis type strain (BL78).
    Gronow S, Held B, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Eisen JA.
    Stand Genomic Sci. 2011 Apr 29;4(2):191-9.
  15. Complete genome sequence of Desulfurococcus mucosus type strain (O7/1).
    Wirth R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ioanna P, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Bilek Y, Hader T, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2011 Apr 29;4(2):173-82.
  16. Complete genome sequence of Deinococcus maricopensis type strain (LB-34).
    Pukall R, Zeytun A, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2011 Apr 29;4(2):163-72. Epub 2011 Apr 25.
  17. Complete genome sequence of Marivirga tractuosa type strain (H-43).
    Pagani I, Chertkov O, Lapidus A, Lucas S, Del Rio TG, Tice H, Copeland A, Cheng JF, Nolan M, Saunders E, Pitluck S, Held B, Goodwin L, Liolios K, Ovchinikova G, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Han C, Tapia R, Ngatchou-Djao OD, Rohde M, Göker M, Spring S, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.
    Stand Genomic Sci. 2011 Apr 29;4(2):154-62.
  18. Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845).
    Mavromatis K, Lu M, Misra M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Göker M, Gronow S, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.
    Stand Genomic Sci. 2011 Apr 29;4(2):144-53.
  19. Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6).
    Zeytun A, Sikorski J, Nolan M, Lapidus A, Lucas S, Han J, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Ngatchou-Djao OD, Land M, Hauser L, Jeffries CD, Han C, Detter JC, Ubler S, Rohde M, Tindall BJ, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.
    Stand Genomic Sci. 2011 Apr 29;4(2):131-43.
  20. Efficient alignment of pyrosequencing reads for re-sequencing applications.
    Fernandes F, da Fonseca PG, Russo LM, Oliveira AL, Freitas AT.
    BMC Bioinformatics. 2011 May 16;12(1):163.
  21. Pathogen detection using short-RNA deep sequencing subtraction and assembly.
    Isakov O, Modai S, Shomron N.
    Bioinformatics. 2011 Aug 1;27(15):2027-30. Epub 2011 Jun 11.
  22. Identification of SNP and SSR markers in eggplant using RAD tag sequencing.
    Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL.
    BMC Genomics. 2011 Jun 10;12:304. doi: 10.1186/1471-2164-12-304.
  23. Single nucleotide polymorphism discovery in elite North American potato germplasm.
    Hamilton JP, Hansey CN, Whitty BR, Stoffel K, Massa AN, Van Deynze A, De Jong WS, Douches DS, Buell CR.
    BMC Genomics. 2011 Jun 9;12:302.
  24. Complete genome sequence of Treponema paraluiscuniculi, strain Cuniculi A: the loss of infectivity to humans is associated with genome decay.
    Šmajs D, Zobaníková M, Strouhal M, Čejková D, Dugan-Rocha S, Pospíšilová P, Norris SJ, Albert T, Qin X, Hallsworth-Pepin K, Buhay C, Muzny DM, Chen L, Gibbs RA, Weinstock GM.
    PLoS One. 2011;6(5):e20415. Epub 2011 May 31.
  25. Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.
    Qi M, Wang P, O'Toole N, Barboza PS, Ungerfeld E, Leigh MB, Selinger LB, Butler G, Tsang A, McAllister TA, Forster RJ.
    PLoS One. 2011;6(5):e20521. Epub 2011 May 31.
  26. De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants.
    Ness RW, Siol M, Barrett SC.
    BMC Genomics. 2011 Jun 7;12:298.
  27. Reference-guided assembly of four diverse Arabidopsis thaliana genomes.
    Schneeberger K, Ossowski S, Ott F, Klein JD, Wang X, Lanz C, Smith LM, Cao J, Fitz J, Warthmann N, Henz SR, Huson DH, Weigel D.
    Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10249-54. Epub 2011 Jun 6.
  28. Phage encoded H-NS: a potential achilles heel in the bacterial defence system.
    Skennerton CT, Angly FE, Breitbart M, Bragg L, He S, McMahon KD, Hugenholtz P, Tyson GW.
    PLoS One. 2011;6(5):e20095. Epub 2011 May 18.
  29. Evaluating the fidelity of de novo short read metagenomic assembly using simulated data.
    Pignatelli M, Moya A.
    PLoS One. 2011;6(5):e19984. Epub 2011 May 23.
  30. Positional Information Resolves Structural Variations and Uncovers an Evolutionarily Divergent Genetic Locus in Accessions of Arabidopsis thaliana.
    Lai AG, Denton-Giles M, Mueller-Roeber B, Schippers JH, Dijkwel PP.
    Genome Biol Evol. 2011;3:627-40. Epub 2011 May 27.
  31. Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing.
    Durban J, Juárez P, Angulo Y, Lomonte B, Flores-Diaz M, Alape-Girón A, Sasa M, Sanz L, Gutiérrez JM, Dopazo J, Conesa A, Calvete JJ.
    BMC Genomics. 2011 May 23;12:259.
  32. Sequence-specific error profile of Illumina sequencers.
    Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M, Ogasawara N, Kanaya S.
    Nucleic Acids Res. 2011 Jul 1;39(13):e90. Epub 2011 May 16.
  33. Genome sequence of strain IMCC9480, a xanthorhodopsin-bearing betaproteobacterium isolated from the Arctic Ocean.
    Oh HM, Lee K, Jang Y, Kang I, Kim HJ, Kang TW, Kim SY, Cho JC.
    J Bacteriol. 2011 Jul;193(13):3421. Epub 2011 May 13.
  34. Comparing de novo genome assembly: the long and short of it.
    Narzisi G, Mishra B.
    PLoS One. 2011 Apr 29;6(4):e19175.
  35. Deep sequencing of organ- and stage-specific microRNAs in the evolutionarily basal insect Blattella germanica (L.) (Dictyoptera, Blattellidae).
    Cristino AS, Tanaka ED, Rubio M, Piulachs MD, Belles X.
    PLoS One. 2011 Apr 28;6(4):e19350.
  36. Genome sequence of strain IMCC3088, a proteorhodopsin-containing marine bacterium belonging to the OM60/NOR5 clade.
    Jang Y, Oh HM, Kang I, Lee K, Yang SJ, Cho JC.
    J Bacteriol. 2011 Jul;193(13):3415-6. Epub 2011 May 6.
  37. Streptococcus pneumoniae serotype 6C: an intra- and interclonal complex comparison.
    Thomas JC, Kong Y, Sabharwal V, Pelton SI, Pettigrew MM.
    J Bacteriol. 2011 Jul;193(13):3409-10. Epub 2011 May 6.
  38. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.
    Straub SC, Fishbein M, Livshultz T, Foster Z, Parks M, Weitemier K, Cronn RC, Liston A.
    BMC Genomics. 2011 May 4;12:211.
  39. Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.
    Baxter SW, Davey JW, Johnston JS, Shelton AM, Heckel DG, Jiggins CD, Blaxter ML.
    PLoS One. 2011 Apr 26;6(4):e19315.
  40. Local de novo assembly of RAD paired-end contigs using short sequencing reads.
    Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA.
    PLoS One. 2011 Apr 13;6(4):e18561.
  41. Streptococcus pneumoniae clonal complex 199: genetic diversity and tissue-specific virulence.
    Thomas JC, Figueira M, Fennie KP, Laufer AS, Kong Y, Pichichero ME, Pelton SI, Pettigrew MM.
    PLoS One. 2011 Apr 14;6(4):e18649.
  42. The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist.
    Suen G, Weimer PJ, Stevenson DM, Aylward FO, Boyum J, Deneke J, Drinkwater C, Ivanova NN, Mikhailova N, Chertkov O, Goodwin LA, Currie CR, Mead D, Brumm PJ.
    PLoS One. 2011 Apr 19;6(4):e18814.
  43. Multiple changes in peptide and lipid expression associated with regeneration in the nervous system of the medicinal leech.
    Meriaux C, Arafah K, Tasiemski A, Wisztorski M, Bruand J, Boidin-Wichlacz C, Desmons A, Debois D, Laprévote O, Brunelle A, Gaasterland T, Macagno E, Fournier I, Salzet M.
    PLoS One. 2011 Apr 22;6(4):e18359.
  44. Sequence characteristics of T4-like bacteriophage IME08 benome termini revealed by high throughput sequencing.
    Jiang X, Jiang H, Li C, Wang S, Mi Z, An X, Chen J, Tong Y.
    Virol J. 2011 Apr 27;8:194.
  45. Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient.
    Avasthi TS, Devi SH, Taylor TD, Kumar N, Baddam R, Kondo S, Suzuki Y, Lamouliatte H, Mégraud F, Ahmed N.
    J Bacteriol. 2011 Jul;193(13):3385-6. Epub 2011 Apr 22.
  46. Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore.
    Knaus BJ, Cronn R, Liston A, Pilgrim K, Schwartz MK.
    BMC Ecol. 2011 Apr 20;11:10.
  47. Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems.
    Yang SS, Tu ZJ, Cheung F, Xu WW, Lamb JF, Jung HJ, Vance CP, Gronwald JW.
    BMC Genomics. 2011 Apr 19;12:199.
  48. First complete genome sequence of infectious laryngotracheitis virus.
    Lee SW, Markham PF, Markham JF, Petermann I, Noormohammadi AH, Browning GF, Ficorilli NP, Hartley CA, Devlin JM.
    BMC Genomics. 2011 Apr 19;12:197.
  49. Analysis of quality raw data of second generation sequencers with Quality Assessment Software.
    Ramos RT, Carneiro AR, Baumbach J, Azevedo V, Schneider MP, Silva A.
    BMC Res Notes. 2011 Apr 18;4:130.
  50. Major prospects for exploring canine vector borne diseases and novel intervention methods using 'omic technologies.
    Gasser RB, Cantacessi C, Campbell BE, Hofmann A, Otranto D.
    Parasit Vectors. 2011 Apr 13;4:53.
  51. Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies.
    Wetzel J, Kingsford C, Pop M.
    BMC Bioinformatics. 2011 Apr 13;12:95.
  52. Complete genome sequence of Desulfobulbus propionicus type strain (1pr3).
    Pagani I, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Chertkov O, Davenport K, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Kannan KP, Djao OD, Rohde M, Pukall R, Spring S, Göker M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2011 Feb 20;4(1):100-10.
  53. Complete genome sequence of Truepera radiovictrix type strain (RQ-24).
    Ivanova N, Rohde C, Munk C, Nolan M, Lucas S, Del Rio TG, Tice H, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A.
    Stand Genomic Sci. 2011 Feb 22;4(1):91-9.
  54. Complete genome sequence of Weeksella virosa type strain (9751).
    Lang E, Teshima H, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Kopitz M, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.
    Stand Genomic Sci. 2011 Feb 22;4(1):81-90.
  55. Complete genome sequence of Cellulophaga algicola type strain (IC166).
    Abt B, Lu M, Misra M, Han C, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Tindall BJ, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A.
    Stand Genomic Sci. 2011 Feb 22;4(1):72-80.
  56. Complete genome sequence of Isosphaera pallida type strain (IS1B).
    Göker M, Cleland D, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Beck B, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2011 Feb 20;4(1):63-71.
  57. Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1).
    Pitluck S, Sikorski J, Zeytun A, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Djao OD, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M.
    Stand Genomic Sci. 2011 Feb 20;4(1):54-62.
  58. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108).
    Pati A, Gronow S, Zeytun A, Lapidus A, Nolan M, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S.
    Stand Genomic Sci. 2011 Feb 22;4(1):45-53.
  59. Complete genome sequence of Paludibacter propionicigenes type strain (WB4).
    Gronow S, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2011 Feb 20;4(1):36-44.
  60. Complete genome sequence of Leadbetterella byssophila type strain (4M15).
    Abt B, Teshima H, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.
    Stand Genomic Sci. 2011 Mar 4;4(1):2-12.
  61. Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant.
    Gibbons HS, Broomall SM, McNew LA, Daligault H, Chapman C, Bruce D, Karavis M, Krepps M, McGregor PA, Hong C, Park KH, Akmal A, Feldman A, Lin JS, Chang WE, Higgs BW, Demirev P, Lindquist J, Liem A, Fochler E, Read TD, Tapia R, Johnson S, Bishop-Lilly KA, Detter C, Han C, Sozhamannan S, Rosenzweig CN, Skowronski EW.
    PLoS One. 2011 Mar 25;6(3):e17836.
  62. DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI.
    Liu Y, Schmidt B, Maskell DL.
    BMC Bioinformatics. 2011 Mar 29;12:85.
  63. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies.
    Doorduin L, Gravendeel B, Lammers Y, Ariyurek Y, Chin-A-Woeng T, Vrieling K.
    DNA Res. 2011 Apr;18(2):93-105. Epub 2011 Mar 28.
  64. Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli.
    Minty JJ, Lesnefsky AA, Lin F, Chen Y, Zaroff TA, Veloso AB, Xie B, McConnell CA, Ward RJ, Schwartz DR, Rouillard JM, Gao Y, Gulari E, Lin XN.
    Microb Cell Fact. 2011 Mar 25;10:18.
  65. Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing.
    Jäger M, Ott CE, Grünhagen J, Hecht J, Schell H, Mundlos S, Duda GN, Robinson PN, Lienau J.
    BMC Genomics. 2011 Mar 24;12:158.
  66. A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.
    Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B.
    PLoS One. 2011 Mar 14;6(3):e17915.
  67. Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation.
    Galeote V, Bigey F, Beyne E, Novo M, Legras JL, Casaregola S, Dequin S.
    PLoS One. 2011 Mar 10;6(3):e17872.
  68. Repeat-aware modeling and correction of short read errors.
    Yang X, Aluru S, Dorman KS.
    BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S52.
  69. Strain-specific copy number variation in the intelectin locus on the 129 mouse chromosome 1.
    Lu ZH, di Domenico A, Wright SH, Knight PA, Whitelaw CB, Pemberton AD.
    BMC Genomics. 2011 Feb 16;12:110.
  70. RATT: Rapid Annotation Transfer Tool.
    Otto TD, Dillon GP, Degrave WS, Berriman M.
    Nucleic Acids Res. 2011 May;39(9):e57. Epub 2011 Feb 8.
  71. Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847).
    Brambilla E, Djao OD, Daligault H, Lapidus A, Lucas S, Hammon N, Nolan M, Tice H, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2010 Oct 27;3(2):203-11.
  72. Complete genome sequence of Sulfurimonas autotrophica type strain (OK10).
    Sikorski J, Munk C, Lapidus A, Ngatchou Djao OD, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Han C, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Sims D, Meincke L, Brettin T, Detter JC, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Lang E, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2010 Oct 27;3(2):194-202.
  73. Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228).
    Mavromatis K, Yasawong M, Chertkov O, Lapidus A, Lucas S, Nolan M, Del Rio TG, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Tapia R, Han C, Bruce D, Goodwin L, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Rohde M, Brambilla E, Spring S, Göker M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.
    Stand Genomic Sci. 2010 Oct 18;3(2):136-44.
  74. Complete genome sequence of Arcanobacterium haemolyticum type strain (11018).
    Yasawong M, Teshima H, Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter C, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Pukall R, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2010 Sep 28;3(2):126-35.
  75. Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P).
    Pitluck S, Yasawong M, Munk C, Nolan M, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter C, Tapia R, Han C, Goodwin L, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2010 Sep 28;3(2):108-16.
  76. Complete genome sequence of Thermaerobacter marianensis type strain (7p75a).
    Han C, Gu W, Zhang X, Lapidus A, Nolan M, Copeland A, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Schneider S, Rohde M, Göker M, Pukall R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC.
    Stand Genomic Sci. 2010 Dec 15;3(3):337-45.
  77. Complete genome sequence of Methanothermus fervidus type strain (V24S).
    Anderson I, Djao OD, Misra M, Chertkov O, Nolan M, Lucas S, Lapidus A, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Sikorski J, Spring S, Rohde M, Eichinger K, Huber H, Wirth R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.
    Stand Genomic Sci. 2010 Nov 20;3(3):315-24.
  78. Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1).
    Sikorski J, Chertkov O, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Yasawong M, Rohde M, Pukall R, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2010 Dec 15;3(3):304-14.
  79. Complete genome sequence of Intrasporangium calvum type strain (7 KIP).
    Del Rio TG, Chertkov O, Yasawong M, Lucas S, Deshpande S, Cheng JF, Detter C, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Pukall R, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A.
    Stand Genomic Sci. 2010 Nov 16;3(3):294-303.
  80. Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3).
    Pitluck S, Yasawong M, Held B, Lapidus A, Nolan M, Copeland A, Lucas S, Del Rio TG, Tice H, Cheng JF, Chertkov O, Goodwin L, Tapia R, Han C, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Pukall R, Spring S, Rohde M, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2010 Nov 20;3(3):285-93.
  81. Complete genome sequence of Desulfarculus baarsii type strain (2st14).
    Sun H, Spring S, Lapidus A, Davenport K, Del Rio TG, Tice H, Nolan M, Copeland A, Cheng JF, Lucas S, Tapia R, Goodwin L, Pitluck S, Ivanova N, Pagani I, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Han C, Rohde M, Brambilla E, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M.
    Stand Genomic Sci. 2010 Nov 20;3(3):276-84.
  82. Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1).
    Djao OD, Zhang X, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2010 Dec 15;3(3):268-75.
  83. Complete genome sequence of Arcobacter nitrofigilis type strain (CI).
    Pati A, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Chertkov O, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.
    Stand Genomic Sci. 2010 Jun 15;2(3):300-8.
  84. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24).
    Mavromatis K, Abt B, Brambilla E, Lapidus A, Copeland A, Deshpande S, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Woyke T, Goodwin L, Pitluck S, Held B, Brettin T, Tapia R, Ivanova N, Mikhailova N, Pati A, Liolios K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.
    Stand Genomic Sci. 2010 Jun 15;2(3):290-9.
  85. Complete genome sequence of Aminobacterium colombiense type strain (ALA-1).
    Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Spring S, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2010 Jun 15;2(3):280-9.
  86. Complete genome sequence of Thermosphaera aggregans type strain (M11TL).
    Spring S, Rachel R, Lapidus A, Davenport K, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Brettin T, Detter JC, Tapia R, Han C, Heimerl T, Weikl F, Brambilla E, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2010 Jun 15;2(3):245-59.
  87. Complete genome sequence of Segniliparus rotundus type strain (CDC 1076).
    Sikorski J, Lapidus A, Copeland A, Misra M, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Jando M, Schneider S, Bruce D, Goodwin L, Pitluck S, Liolios K, Mikhailova N, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Chertkov O, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2010 Mar 30;2(2):203-11.
  88. Complete genome sequence of Thermocrinis albus type strain (HI 11/12).
    Wirth R, Sikorski J, Brambilla E, Misra M, Lapidus A, Copeland A, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Tapia R, Bruce D, Goodwin L, Pitluck S, Pati A, Anderson I, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Bilek Y, Hader T, Land M, Hauser L, Chang YJ, Jeffries CD, Tindall BJ, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
    Stand Genomic Sci. 2010 Mar 30;2(2):194-202.
  89. Evidence of a dominant lineage of Vibrio cholerae-specific lytic bacteriophages shed by cholera patients over a 10-year period in Dhaka, Bangladesh.
    Seed KD, Bodi KL, Kropinski AM, Ackermann HW, Calderwood SB, Qadri F, Camilli A.
    MBio. 2011 Feb 8;2(1):e00334-10. doi: 10.1128/mBio.00334-10. Print 2011.
  90. Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture.
    Kent BN, Salichos L, Gibbons JG, Rokas A, Newton IL, Clark ME, Bordenstein SR.
    Genome Biol Evol. 2011;3:209-18. Epub 2011 Feb 2.
  91. Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine.
    Magbanua ZV, Ozkan S, Bartlett BD, Chouvarine P, Saski CA, Liston A, Cronn RC, Nelson CD, Peterson DG.
    PLoS One. 2011 Jan 21;6(1):e16214.
  92. Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution.
    Suzuki H, Lefébure T, Hubisz MJ, Pavinski Bitar P, Lang P, Siepel A, Stanhope MJ.
    Genome Biol Evol. 2011;3:168-85. Epub 2011 Jan 31.
  93. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence.
    You FM, Huo N, Deal KR, Gu YQ, Luo MC, McGuire PE, Dvorak J, Anderson OD.
    BMC Genomics. 2011 Jan 25;12:59.
  94. PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals.
    Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, Futschik A, Kosiol C, Schlötterer C.
    PLoS One. 2011 Jan 6;6(1):e15925.
  95. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification.
    Garg R, Patel RK, Tyagi AK, Jain M.
    DNA Res. 2011 Feb;18(1):53-63. Epub 2011 Jan 7.
  96. Community-driven computational biology with Debian Linux.
    Möller S, Krabbenhöft HN, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C, Holland R, Belhachemi D, Plessy C.
    BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S5.
  97. Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola.
    Stukenbrock EH, Jørgensen FG, Zala M, Hansen TT, McDonald BA, Schierup MH.
    PLoS Genet. 2010 Dec 23;6(12):e1001189.
  98. Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly.
    Wong K, Keane TM, Stalker J, Adams DJ.
    Genome Biol. 2010;11(12):R128. Epub 2010 Dec 31.
  99. High-quality draft assemblies of mammalian genomes from massively parallel sequence data.
    Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB.
    Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8. Epub 2010 Dec 27.
  100. Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments.
    Sirota-Madi A, Olender T, Helman Y, Ingham C, Brainis I, Roth D, Hagi E, Brodsky L, Leshkowitz D, Galatenko V, Nikolaev V, Mugasimangalam RC, Bransburg-Zabary S, Gutnick DL, Lancet D, Ben-Jacob E.
    BMC Genomics. 2010 Dec 17;11:710.
  101. Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi.
    Subramanian S, Huynen L, Millar CD, Lambert DM.
    BMC Evol Biol. 2010 Dec 15;10:387.
  102. De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology.
    Crawford JE, Guelbeogo WM, Sanou A, Traoré A, Vernick KD, Sagnon N, Lazzaro BP.
    PLoS One. 2010 Dec 2;5(12):e14202.
  103. Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L.
    Sato S, Hirakawa H, Isobe S, Fukai E, Watanabe A, Kato M, Kawashima K, Minami C, Muraki A, Nakazaki N, Takahashi C, Nakayama S, Kishida Y, Kohara M, Yamada M, Tsuruoka H, Sasamoto S, Tabata S, Aizu T, Toyoda A, Shin-i T, Minakuchi Y, Kohara Y, Fujiyama A, Tsuchimoto S, Kajiyama S, Makigano E, Ohmido N, Shibagaki N, Cartagena JA, Wada N, Kohinata T, Atefeh A, Yuasa S, Matsunaga S, Fukui K.
    DNA Res. 2011 Feb;18(1):65-76. Epub 2010 Dec 13.
  104. SlideSort: all pairs similarity search for short reads.
    Shimizu K, Tsuda K.
    Bioinformatics. 2011 Feb 15;27(4):464-70. Epub 2010 Dec 9.
  105. BIGSdb: Scalable analysis of bacterial genome variation at the population level.
    Jolley KA, Maiden MC.
    BMC Bioinformatics. 2010 Dec 10;11:595.
  106. Directed adenovirus evolution using engineered mutator viral polymerases.
    Uil TG, Vellinga J, de Vrij J, van den Hengel SK, Rabelink MJ, Cramer SJ, Eekels JJ, Ariyurek Y, van Galen M, Hoeben RC.
    Nucleic Acids Res. 2011 Mar;39(5):e30. Epub 2010 Dec 7.
  107. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome.
    Kim MY, Lee S, Van K, Kim TH, Jeong SC, Choi IY, Kim DS, Lee YS, Park D, Ma J, Kim WY, Kim BC, Park S, Lee KA, Kim DH, Kim KH, Shin JH, Jang YE, Kim KD, Liu WX, Chaisan T, Kang YJ, Lee YH, Kim KH, Moon JK, Schmutz J, Jackson SA, Bhak J, Lee SH.
    Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22032-7. Epub 2010 Dec 3. Review.
  108. Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss.
    den Bakker HC, Cummings CA, Ferreira V, Vatta P, Orsi RH, Degoricija L, Barker M, Petrauskene O, Furtado MR, Wiedmann M.
    BMC Genomics. 2010 Dec 2;11:688.
  109. Evolutionary relationships and divergence times among the native rats of Australia.
    Robins JH, McLenachan PA, Phillips MJ, McComish BJ, Matisoo-Smith E, Ross HA.
    BMC Evol Biol. 2010 Dec 2;10:375.
  110. Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist.
    Williams LE, Wernegreen JJ.
    BMC Genomics. 2010 Dec 2;11:687.
  111. De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq.
    Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA.
    BMC Genomics. 2010 Dec 1;11:681.
  112. Quake: quality-aware detection and correction of sequencing errors.
    Kelley DR, Schatz MC, Salzberg SL.
    Genome Biol. 2010;11(11):R116. Epub 2010 Nov 29.
  113. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
    Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z.
    BMC Genomics. 2010 Nov 24;11:663.
  114. Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs.
    Kundeti VK, Rajasekaran S, Dinh H, Vaughn M, Thapar V.
    BMC Bioinformatics. 2010 Nov 15;11:560.
  115. Exploring molecular signaling in plant-fungal symbioses using high throughput RNA sequencing.
    Cox MP, Eaton CJ, Scott DB.
    Plant Signal Behav. 2010 Nov;5(11):1353-8. Epub 2010 Nov 1.
  116. Dindel: accurate indel calls from short-read data.
    Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R.
    Genome Res. 2011 Jun;21(6):961-73. Epub 2010 Oct 27.
  117. Scaffolding a Caenorhabditis nematode genome with RNA-seq.
    Mortazavi A, Schwarz EM, Williams B, Schaeffer L, Antoshechkin I, Wold BJ, Sternberg PW.
    Genome Res. 2010 Dec;20(12):1740-7. Epub 2010 Oct 27.
  118. The European Nucleotide Archive.
    Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D28-31. Epub 2010 Oct 23.
  119. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.
    Boisvert S, Laviolette F, Corbeil J.
    J Comput Biol. 2010 Nov;17(11):1519-33. Epub 2010 Oct 20.
  120. Genome sequence of the obligate methanotroph Methylosinus trichosporium strain OB3b.
    Stein LY, Yoon S, Semrau JD, Dispirito AA, Crombie A, Murrell JC, Vuilleumier S, Kalyuzhnaya MG, Op den Camp HJ, Bringel F, Bruce D, Cheng JF, Copeland A, Goodwin L, Han S, Hauser L, Jetten MS, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T, Zeytun A, Klotz MG.
    J Bacteriol. 2010 Dec;192(24):6497-8. Epub 2010 Oct 15.
  121. Genome of Helicobacter pylori strain 908.
    Devi SH, Taylor TD, Avasthi TS, Kondo S, Suzuki Y, Megraud F, Ahmed N.
    J Bacteriol. 2010 Dec;192(24):6488-9. Epub 2010 Oct 15.
  122. Comparing de novo assemblers for 454 transcriptome data.
    Kumar S, Blaxter ML.
    BMC Genomics. 2010 Oct 16;11:571.
  123. Tailoring enzyme-rich environmental DNA clones: a source of enzymes for generating libraries of unnatural natural products.
    Banik JJ, Craig JW, Calle PY, Brady SF.
    J Am Chem Soc. 2010 Nov 10;132(44):15661-70.
  124. Molecular and evolutionary bases of within-patient genotypic and phenotypic diversity in Escherichia coli extraintestinal infections.
    Levert M, Zamfir O, Clermont O, Bouvet O, Lespinats S, Hipeaux MC, Branger C, Picard B, Saint-Ruf C, Norel F, Balliau T, Zivy M, Le Nagard H, Cruveiller S, Chane-Woon-Ming B, Nilsson S, Gudelj I, Phan K, Ferenci T, Tenaillon O, Denamur E.
    PLoS Pathog. 2010 Sep 30;6(9). pii: e1001125. Erratum in: PLoS Pathog. 2011 Jun;7(6). doi:10.1371/annotation/700dcb3b-3475-49a1-9064-d9d070cda7be. Cruvellier, Stéphane[corrected to Cruveiller, Stéphane].
  125. Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform.
    Atherton RA, McComish BJ, Shepherd LD, Berry LA, Albert NW, Lockhart PJ.
    Plant Methods. 2010 Sep 28;6:22.
  126. An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6.
    Kimbrel JA, Givan SA, Halgren AB, Creason AL, Mills DI, Banowetz GM, Armstrong DJ, Chang JH.
    BMC Genomics. 2010 Sep 28;11:522.
  127. Studying bacterial transcriptomes using RNA-seq.
    Croucher NJ, Thomson NR.
    Curr Opin Microbiol. 2010 Oct;13(5):619-24. Epub 2010 Sep 29. Review.
  128. Reference-free validation of short read data.
    Schröder J, Bailey J, Conway T, Zobel J.
    PLoS One. 2010 Sep 22;5(9):e12681.
  129. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data.
    Cox MP, Peterson DA, Biggs PJ.
    BMC Bioinformatics. 2010 Sep 27;11:485.
  130. A Brassica exon array for whole-transcript gene expression profiling.
    Love CG, Graham NS, O Lochlainn S, Bowen HC, May ST, White PJ, Broadley MR, Hammond JP, King GJ.
    PLoS One. 2010 Sep 16;5(9). pii: e12812.
  131. Colistin resistance in Acinetobacter baumannii is mediated by complete loss of lipopolysaccharide production.
    Moffatt JH, Harper M, Harrison P, Hale JD, Vinogradov E, Seemann T, Henry R, Crane B, St Michael F, Cox AD, Adler B, Nation RL, Li J, Boyce JD.
    Antimicrob Agents Chemother. 2010 Dec;54(12):4971-7. Epub 2010 Sep 20.
  132. Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T.
    Elkins JG, Lochner A, Hamilton-Brehm SD, Davenport KW, Podar M, Brown SD, Land ML, Hauser LJ, Klingeman DM, Raman B, Goodwin LA, Tapia R, Meincke LJ, Detter JC, Bruce DC, Han CS, Palumbo AV, Cottingham RW, Keller M, Graham DE.
    J Bacteriol. 2010 Nov;192(22):6099-100. Epub 2010 Sep 17.
  133. The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis.
    Nishant KT, Wei W, Mancera E, Argueso JL, Schlattl A, Delhomme N, Ma X, Bustamante CD, Korbel JO, Gu Z, Steinmetz LM, Alani E.
    PLoS Genet. 2010 Sep 9;6(9). pii: e1001109.
  134. An algorithm for automated closure during assembly.
    Koren S, Miller JR, Walenz BP, Sutton G.
    BMC Bioinformatics. 2010 Sep 10;11:457.
  135. Functional convergence in reduced genomes of bacterial symbionts spanning 200 My of evolution.
    McCutcheon JP, Moran NA.
    Genome Biol Evol. 2010;2:708-18. Epub 2010 Sep 9.
  136. Integrating genome assemblies with MAIA.
    Nijkamp J, Winterbach W, van den Broek M, Daran JM, Reinders M, de Ridder D.
    Bioinformatics. 2010 Sep 15;26(18):i433-9.
  137. A major role for mammals in the ecology of Mycobacterium ulcerans.
    Fyfe JA, Lavender CJ, Handasyde KA, Legione AR, O'Brien CR, Stinear TP, Pidot SJ, Seemann T, Benbow ME, Wallace JR, McCowan C, Johnson PD.
    PLoS Negl Trop Dis. 2010 Aug 10;4(8):e791.
  138. High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing.
    Matsumura H, Yoshida K, Luo S, Kimura E, Fujibe T, Albertyn Z, Barrero RA, Krüger DH, Kahl G, Schroth GP, Terauchi R.
    PLoS One. 2010 Aug 6;5(8):e12010.
  139. Optimization of de novo transcriptome assembly from next-generation sequencing data.
    Surget-Groba Y, Montoya-Burgos JI.
    Genome Res. 2010 Oct;20(10):1432-40. Epub 2010 Aug 6.
  140. Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept.
    Lefébure T, Bitar PD, Suzuki H, Stanhope MJ.
    Genome Biol Evol. 2010;2:646-55. Epub 2010 Aug 4.
  141. Genome sequencing reveals widespread virulence gene exchange among human Neisseria species.
    Marri PR, Paniscus M, Weyand NJ, Rendón MA, Calton CM, Hernández DR, Higashi DL, Sodergren E, Weinstock GM, Rounsley SD, So M.
    PLoS One. 2010 Jul 28;5(7):e11835.
  142. Whole-genome sequencing reveals distinct mutational patterns in closely related laboratory and naturally propagated Francisella tularensis strains.
    Sjödin A, Svensson K, Lindgren M, Forsman M, Larsson P.
    PLoS One. 2010 Jul 19;5(7):e11556.
  143. Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.
    Cahill MJ, Köser CU, Ross NE, Archer JA.
    PLoS One. 2010 Jul 12;5(7):e11518.
  144. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data.
    Novák P, Neumann P, Macas J.
    BMC Bioinformatics. 2010 Jul 15;11:378.
  145. Uncovering the complexity of transcriptomes with RNA-Seq.
    Costa V, Angelini C, De Feis I, Ciccodicola A.
    J Biomed Biotechnol. 2010;2010:853916. Epub 2010 Jun 27. Review.
  146. Index-free de novo assembly and deconvolution of mixed mitochondrial genomes.
    McComish BJ, Hills SF, Biggs PJ, Penny D.
    Genome Biol Evol. 2010 Jul 12;2:410-24. Print 2010.
  147. Combining next-generation sequencing strategies for rapid molecular resource development from an invasive aphid species, Aphis glycines.
    Bai X, Zhang W, Orantes L, Jun TH, Mittapalli O, Mian MA, Michel AP.
    PLoS One. 2010 Jun 29;5(6):e11370.
  148. Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems.
    Nowrousian M.
    Eukaryot Cell. 2010 Sep;9(9):1300-10. Epub 2010 Jul 2. Review.
  149. SOPRA: Scaffolding algorithm for paired reads via statistical optimization.
    Dayarian A, Michael TP, Sengupta AM.
    BMC Bioinformatics. 2010 Jun 24;11:345.
  150. Two novel point mutations in clinical Staphylococcus aureus reduce linezolid susceptibility and switch on the stringent response to promote persistent infection.
    Gao W, Chua K, Davies JK, Newton HJ, Seemann T, Harrison PF, Holmes NE, Rhee HW, Hong JI, Hartland EL, Stinear TP, Howden BP.
    PLoS Pathog. 2010 Jun 10;6(6):e1000944.
  151. De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
    Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR, Barrett CL.
    PLoS One. 2010 Jun 8;5(6):e10922.
  152. Identification of novel pathogenicity loci in Clostridium perfringens strains that cause avian necrotic enteritis.
    Lepp D, Roxas B, Parreira VR, Marri PR, Rosey EL, Gong J, Songer JG, Vedantam G, Prescott JF.
    PLoS One. 2010 May 24;5(5):e10795. Erratum in: PLoS One. 2010;5(6). doi: 10.1371/annotation/501e5656-71ac-420f-a194-80141f6381e5.
  153. Genomewide analysis of divergence of antibiotic resistance determinants in closely related isolates of Acinetobacter baumannii.
    Adams MD, Chan ER, Molyneaux ND, Bonomo RA.
    Antimicrob Agents Chemother. 2010 Sep;54(9):3569-77. Epub 2010 Jun 7.
  154. Efficient construction of an assembly string graph using the FM-index.
    Simpson JT, Durbin R.
    Bioinformatics. 2010 Jun 15;26(12):i367-73.
  155. Complete genome sequence of the electricity-producing "Thermincola potens" strain JR.
    Byrne-Bailey KG, Wrighton KC, Melnyk RA, Agbo P, Hazen TC, Coates JD.
    J Bacteriol. 2010 Aug;192(15):4078-9. Epub 2010 Jun 4.
  156. A computational genomics pipeline for prokaryotic sequencing projects.
    Kislyuk AO, Katz LS, Agrawal S, Hagen MS, Conley AB, Jayaraman P, Nelakuditi V, Humphrey JC, Sammons SA, Govil D, Mair RD, Tatti KM, Tondella ML, Harcourt BH, Mayer LW, Jordan IK.
    Bioinformatics. 2010 Aug 1;26(15):1819-26. Epub 2010 Jun 2.
  157. Assembly of large genomes using second-generation sequencing.
    Schatz MC, Delcher AL, Salzberg SL.
    Genome Res. 2010 Sep;20(9):1165-73. Epub 2010 May 27.
  158. Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae.
    Wenger JW, Schwartz K, Sherlock G.
    PLoS Genet. 2010 May 13;6(5):e1000942.
  159. Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.
    Kuroshu RM, Watanabe J, Sugano S, Morishita S, Suzuki Y, Kasahara M.
    PLoS One. 2010 May 7;5(5):e10517.
  160. Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-generation DNA sequencer.
    Kuroda M, Katano H, Nakajima N, Tobiume M, Ainai A, Sekizuka T, Hasegawa H, Tashiro M, Sasaki Y, Arakawa Y, Hata S, Watanabe M, Sata T.
    PLoS One. 2010 Apr 23;5(4):e10256.
  161. Comparative genome analysis provides insights into the evolution and adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum.
    Green S, Studholme DJ, Laue BE, Dorati F, Lovell H, Arnold D, Cottrell JE, Bridgett S, Blaxter M, Huitema E, Thwaites R, Sharp PM, Jackson RW, Kamoun S.
    PLoS One. 2010 Apr 19;5(4):e10224.
  162. Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data.
    Nishito Y, Osana Y, Hachiya T, Popendorf K, Toyoda A, Fujiyama A, Itaya M, Sakakibara Y.
    BMC Genomics. 2010 Apr 16;11:243.
  163. Quinol-cytochrome c oxidoreductase and cytochrome c4 mediate electron transfer during selenate respiration in Thauera selenatis.
    Lowe EC, Bydder S, Hartshorne RS, Tape HL, Dridge EJ, Debieux CM, Paszkiewicz K, Singleton I, Lewis RJ, Santini JM, Richardson DJ, Butler CS.
    J Biol Chem. 2010 Jun 11;285(24):18433-42. Epub 2010 Apr 13.
  164. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.
    Tsai IJ, Otto TD, Berriman M.
    Genome Biol. 2010;11(4):R41. Epub 2010 Apr 13.
  165. The next generation becomes the now generation.
    Martinez DA, Nelson MA.
    PLoS Genet. 2010 Apr 8;6(4):e1000906. No abstract available.
  166. De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.
    Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, Halliday K, Kamerewerd J, Kempken F, Knab B, Kuo HC, Osiewacz HD, Pöggeler S, Read ND, Seiler S, Smith KM, Zickler D, Kück U, Freitag M.
    PLoS Genet. 2010 Apr 8;6(4):e1000891.
  167. High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis.
    Chen XS, Collins LJ, Biggs PJ, Penny D.
    Genome Biol Evol. 2009 Jul 6;1:165-75.
  168. Genome assembly quality: assessment and improvement using the neutral indel model.
    Meader S, Hillier LW, Locke D, Ponting CP, Lunter G.
    Genome Res. 2010 May;20(5):675-84. Epub 2010 Mar 19.
  169. Calling SNPs without a reference sequence.
    Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W.
    BMC Bioinformatics. 2010 Mar 15;11:130.
  170. Detection and correction of false segmental duplications caused by genome mis-assembly.
    Kelley DR, Salzberg SL.
    Genome Biol. 2010;11(3):R28. Epub 2010 Mar 10.
  171. Assembly algorithms for next-generation sequencing data.
    Miller JR, Koren S, Sutton G.
    Genomics. 2010 Jun;95(6):315-27. Epub 2010 Mar 6. Review.
  172. A primer on metagenomics.
    Wooley JC, Godzik A, Friedberg I.
    PLoS Comput Biol. 2010 Feb 26;6(2):e1000667. Review.
  173. Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing.
    Birzele F, Schaub J, Rust W, Clemens C, Baum P, Kaufmann H, Weith A, Schulz TW, Hildebrandt T.
    Nucleic Acids Res. 2010 Jul;38(12):3999-4010. Epub 2010 Mar 1.
  174. Analysis of the Legionella longbeachae genome and transcriptome uncovers unique strategies to cause Legionnaires' disease.
    Cazalet C, Gomez-Valero L, Rusniok C, Lomma M, Dervins-Ravault D, Newton HJ, Sansom FM, Jarraud S, Zidane N, Ma L, Bouchier C, Etienne J, Hartland EL, Buchrieser C.
    PLoS Genet. 2010 Feb 19;6(2):e1000851.
  175. Remarkably ancient balanced polymorphisms in a multi-locus gene network.
    Hittinger CT, Gonçalves P, Sampaio JP, Dover J, Johnston M, Rokas A.
    Nature. 2010 Mar 4;464(7285):54-8. Epub 2010 Feb 17.
  176. Fis is essential for capsule production in Pasteurella multocida and regulates expression of other important virulence factors.
    Steen JA, Steen JA, Harrison P, Seemann T, Wilkie I, Harper M, Adler B, Boyce JD.
    PLoS Pathog. 2010 Feb 5;6(2):e1000750.
  177. Assembling genomes using short-read sequencing technology.
    Jackman SD, Birol I.
    Genome Biol. 2010 Jan 28;11(1):202. Review.
  178. Whole-genome sequencing of a laboratory-evolved yeast strain.
    Araya CL, Payen C, Dunham MJ, Fields S.
    BMC Genomics. 2010 Feb 3;11:88.
  179. A new strategy for genome assembly using short sequence reads and reduced representation libraries.
    Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH.
    Genome Res. 2010 Feb;20(2):249-56.
  180. Expanded multilocus sequence typing and comparative genomic hybridization of Campylobacter coli isolates from multiple hosts.
    Lang P, Lefebure T, Wang W, Pavinski Bitar P, Meinersmann RJ, Kaya K, Stanhope MJ.
    Appl Environ Microbiol. 2010 Mar;76(6):1913-25. Epub 2010 Jan 22.
  181. Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene.
    Becker D, Tetens J, Brunner A, Bürstel D, Ganter M, Kijas J; International Sheep Genomics Consortium, Drögemüller C.
    PLoS One. 2010 Jan 13;5(1):e8689.
  182. Parallel, tag-directed assembly of locally derived short sequence reads.
    Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J.
    Nat Methods. 2010 Feb;7(2):119-22. Epub 2010 Jan 17.
  183. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs.
    Wu Q, Luo Y, Lu R, Lau N, Lai EC, Li WX, Ding SW.
    Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1606-11. Epub 2010 Jan 4.
  184. Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life.
    Hittinger CT, Johnston M, Tossberg JT, Rokas A.
    Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1476-81. Epub 2010 Jan 4.
  185. Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction.
    Palmer LE, Dejori M, Bolanos R, Fasulo D.
    BMC Bioinformatics. 2010 Jan 15;11:33.
  186. Population genetic inference from genomic sequence variation.
    Pool JE, Hellmann I, Jensen JD, Nielsen R.
    Genome Res. 2010 Mar;20(3):291-300. Epub 2010 Jan 12. Review.
  187. Assembly complexity of prokaryotic genomes using short reads.
    Kingsford C, Schatz MC, Pop M.
    BMC Bioinformatics. 2010 Jan 12;11:21.
  188. Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates.
    Blakesley RW, Hansen NF, Gupta J, McDowell JC, Maskeri B, Barnabas BB, Brooks SY, Coleman H, Haghighi P, Ho SL, Schandler K, Stantripop S, Vogt JL, Thomas PJ; NISC Comparative Sequencing Program, Bouffard GG, Green ED.
    BMC Genomics. 2010 Jan 11;11:21.
  189. Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.
    Zerbino DR, McEwen GK, Margulies EH, Birney E.
    PLoS One. 2009 Dec 22;4(12):e8407.
  190. Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strains.
    Klockgether J, Munder A, Neugebauer J, Davenport CF, Stanke F, Larbig KD, Heeb S, Schöck U, Pohl TM, Wiehlmann L, Tümmler B.
    J Bacteriol. 2010 Feb;192(4):1113-21. Epub 2009 Dec 18.
  191. De novo assembly of human genomes with massively parallel short read sequencing.
    Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J.
    Genome Res. 2010 Feb;20(2):265-72. Epub 2009 Dec 17.
  192. A comprehensive catalogue of somatic mutations from a human cancer genome.
    Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A, Mudie LJ, Ning Z, Royce T, Schulz-Trieglaff OB, Spiridou A, Stebbings LA, Szajkowski L, Teague J, Williamson D, Chin L, Ross MT, Campbell PJ, Bentley DR, Futreal PA, Stratton MR.
    Nature. 2010 Jan 14;463(7278):191-6. Epub 2009 Dec 16.
  193. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.
    Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM.
    Nucleic Acids Res. 2010 Apr;38(6):1767-71. Epub 2009 Dec 16. Review.
  194. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes.
    Parks M, Cronn R, Liston A.
    BMC Biol. 2009 Dec 2;7:84.
  195. Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library.
    Sánchez CC, Smith TP, Wiedmann RT, Vallejo RL, Salem M, Yao J, Rexroad CE 3rd.
    BMC Genomics. 2009 Nov 25;10:559.
  196. Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens.
    Cunningham C, Gatherer D, Hilfrich B, Baluchova K, Dargan DJ, Thomson M, Griffiths PD, Wilkinson GW, Schulz TF, Davison AJ.
    J Gen Virol. 2010 Mar;91(Pt 3):605-15. Epub 2009 Nov 11.
  197. Improvements to services at the European Nucleotide Archive.
    Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M, Cheng Y, Demiralp F, Faruque N, Goodgame N, Gibson R, Hoad G, Hunter C, Jang M, Leonard S, Lin Q, Lopez R, Maguire M, McWilliam H, Plaister S, Radhakrishnan R, Sobhany S, Slater G, Ten Hoopen P, Valentin F, Vaughan R, Zalunin V, Zerbino D, Cochrane G.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D39-45. Epub 2009 Nov 11.
  198. RNA-seq: from technology to biology.
    Marguerat S, Bähler J.
    Cell Mol Life Sci. 2010 Feb;67(4):569-79. Epub 2009 Oct 27. Review.
  199. NGSView: an extensible open source editor for next-generation sequencing data.
    Arner E, Hayashizaki Y, Daub CO.
    Bioinformatics. 2010 Jan 1;26(1):125-6. Epub 2009 Oct 24.
  200. Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey.
    Kerstens HH, Crooijmans RP, Veenendaal A, Dibbits BW, Chin-A-Woeng TF, den Dunnen JT, Groenen MA.
    BMC Genomics. 2009 Oct 16;10:479.
  201. Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels.
    Sudbery I, Stalker J, Simpson JT, Keane T, Rust AG, Hurles ME, Walter K, Lynch D, Teboul L, Brown SD, Li H, Ning Z, Nadeau JH, Croniger CM, Durbin R, Adams DJ.
    Genome Biol. 2009;10(10):R112. Epub 2009 Oct 13.
  202. Emergence of single-molecule sequencing and potential for molecular diagnostic applications.
    Milos PM.
    Expert Rev Mol Diagn. 2009 Oct;9(7):659-66.
  203. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.
    Maccallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, Gnirke A, Malek J, McKernan K, Ranade S, Shea TP, Williams L, Young S, Nusbaum C, Jaffe DB.
    Genome Biol. 2009;10(10):R103. Epub 2009 Oct 1.
  204. Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.
    Stabler RA, He M, Dawson L, Martin M, Valiente E, Corton C, Lawley TD, Sebaihia M, Quail MA, Rose G, Gerding DN, Gibert M, Popoff MR, Parkhill J, Dougan G, Wren BW.
    Genome Biol. 2009;10(9):R102. Epub 2009 Sep 25.
  205. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data.
    Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJ.
    Genome Biol. 2009;10(9):R94. Epub 2009 Sep 11.
  206. Whole genome amplification and de novo assembly of single bacterial cells.
    Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW.
    PLoS One. 2009 Sep 2;4(9):e6864.
  207. Response of gastric epithelial progenitors to Helicobacter pylori Isolates obtained from Swedish patients with chronic atrophic gastritis.
    Giannakis M, Bäckhed HK, Chen SL, Faith JJ, Wu M, Guruge JL, Engstrand L, Gordon JI.
    J Biol Chem. 2009 Oct 30;284(44):30383-94. Epub 2009 Sep 1.
  208. PAVE: program for assembling and viewing ESTs.
    Soderlund C, Johnson E, Bomhoff M, Descour A.
    BMC Genomics. 2009 Aug 26;10:400.
  209. A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528.
    Studholme DJ, Ibanez SG, MacLean D, Dangl JL, Chang JH, Rathjen JP.
    BMC Genomics. 2009 Aug 24;10:395. Erratum in: BMC Genomics. 2009;10:569.
  210. An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs.
    Parker HG, VonHoldt BM, Quignon P, Margulies EH, Shao S, Mosher DS, Spady TC, Elkahloun A, Cargill M, Jones PG, Maslen CL, Acland GM, Sutter NB, Kuroki K, Bustamante CD, Wayne RK, Ostrander EA.
    Science. 2009 Aug 21;325(5943):995-8. Epub 2009 Jul 16.
  211. A compartmentalized approach to the assembly of physical maps.
    Bozdag S, Close TJ, Lonardi S.
    BMC Bioinformatics. 2009 Jul 15;10:217.
  212. Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.
    Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB.
    PLoS Comput Biol. 2009 Jul;5(7):e1000432. Epub 2009 Jul 10.
  213. SNP-o-matic.
    Manske HM, Kwiatkowski DP.
    Bioinformatics. 2009 Sep 15;25(18):2434-5. Epub 2009 Jul 2.
  214. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
    Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.
    Bioinformatics. 2009 Nov 1;25(21):2865-71. Epub 2009 Jun 26.
  215. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.
    Dutilh BE, Huynen MA, Strous M.
    Bioinformatics. 2009 Nov 1;25(21):2878-81. Epub 2009 Jun 19.
  216. Directed evolution of ionizing radiation resistance in Escherichia coli.
    Harris DR, Pollock SV, Wood EA, Goiffon RJ, Klingele AJ, Cabot EL, Schackwitz W, Martin J, Eggington J, Durfee TJ, Middle CM, Norton JE, Popelars MC, Li H, Klugman SA, Hamilton LL, Bane LB, Pennacchio LA, Albert TJ, Perna NT, Cox MM, Battista JR.
    J Bacteriol. 2009 Aug;191(16):5240-52. Epub 2009 Jun 5.
  217. Genome assembly reborn: recent computational challenges.
    Pop M.
    Brief Bioinform. 2009 Jul;10(4):354-66. Epub 2009 May 29.
  218. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.
    Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C, Park D, Lee YS, Kim S, Reja R, Jho S, Kim CG, Cha JY, Kim KH, Lee B, Bhak J, Kim SJ.
    Genome Res. 2009 Sep;19(9):1622-9. Epub 2009 May 26.
  219. Next-generation sequencing of vertebrate experimental organisms.
    Turner DJ, Keane TM, Sudbery I, Adams DJ.
    Mamm Genome. 2009 Jun;20(6):327-38. Epub 2009 May 19. Review.
  220. 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.
  221. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes.
    Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ.
    Nat Methods. 2009 Apr;6(4):291-5. Epub 2009 Mar 15.
  222. ABySS: a parallel assembler for short read sequence data.
    Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
    Genome Res. 2009 Jun;19(6):1117-23. Epub 2009 Feb 27.
  223. QSRA: a quality-value guided de novo short read assembler.
    Bryant DW Jr, Wong WK, Mockler TC.
    BMC Bioinformatics. 2009 Feb 24;10:69.
  224. Crystallizing short-read assemblies around seeds.
    Hossain MS, Azimi N, Skiena S.
    BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S16.
  225. Parallel short sequence assembly of transcriptomes.
    Jackson BG, Schnable PS, Aluru S.
    BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S14.
  226. Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases.
    Kell DB.
    BMC Med Genomics. 2009 Jan 8;2:2.
  227. Annotating genomes with massive-scale RNA sequencing.
    Denoeud F, Aury JM, Da Silva C, Noel B, Rogier O, Delledonne M, Morgante M, Valle G, Wincker P, Scarpelli C, Jaillon O, Artiguenave F.
    Genome Biol. 2008;9(12):R175. Epub 2008 Dec 16.
  228. De novo fragment assembly with short mate-paired reads: Does the read length matter?
    Chaisson MJ, Brinza D, Pevzner PA.
    Genome Res. 2009 Feb;19(2):336-46. Epub 2008 Dec 3.
  229. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae.
    Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL.
    Genome Res. 2009 Feb;19(2):294-305. Epub 2008 Nov 17.
  230. The diploid genome sequence of an Asian individual.
    Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, Li G, Yang Z, Zhang G, Yang B, Yu C, Liang F, Li W, Li S, Li D, Ni P, Ruan J, Li Q, Zhu H, Liu D, Lu Z, Li N, Guo G, Zhang J, Ye J, Fang L, Hao Q, Chen Q, Liang Y, Su Y, San A, Ping C, Yang S, Chen F, Li L, Zhou K, Zheng H, Ren Y, Yang L, Gao Y, Yang G, Li Z, Feng X, Kristiansen K, Wong GK, Nielsen R, Durbin R, Bolund L, Zhang X, Li S, Yang H, Wang J.
    Nature. 2008 Nov 6;456(7218):60-5.
  231. Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009.
    Wakaguri H, Suzuki Y, Katayama T, Kawashima S, Kibukawa E, Hiranuka K, Sasaki M, Sugano S, Watanabe J.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D520-5. Epub 2008 Nov 4.
  232. Aggressive assembly of pyrosequencing reads with mates.
    Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G.
    Bioinformatics. 2008 Dec 15;24(24):2818-24. Epub 2008 Oct 24.
  233. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes.
    Noguchi H, Taniguchi T, Itoh T.
    DNA Res. 2008 Dec;15(6):387-96. Epub 2008 Oct 21.
  234. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
    Paten B, Herrero J, Beal K, Fitzgerald S, Birney E.
    Genome Res. 2008 Nov;18(11):1814-28. Epub 2008 Oct 10.
  235. 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.
  236. Sequencing of natural strains of Arabidopsis thaliana with short reads.
    Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D.
    Genome Res. 2008 Dec;18(12):2024-33. Epub 2008 Sep 25.
  237. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology.
    Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T.
    Nucleic Acids Res. 2008 Nov;36(19):e122. Epub 2008 Aug 27.
  238. Mapping short DNA sequencing reads and calling variants using mapping quality scores.
    Li H, Ruan J, Durbin R.
    Genome Res. 2008 Nov;18(11):1851-8. Epub 2008 Aug 19.

 

  

[ 回到 軟體文獻收集 | 專欄索引 ]