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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. Koren S, et al. Among authors: walenz bp. Nat Biotechnol. 2018 Oct 22:10.1038/nbt.4277. doi: 10.1038/nbt.4277. Online ahead of print. Nat Biotechnol. 2018. PMID: 30346939 Free PMC article.
Evolution of genes and genomes on the Drosophila phylogeny.
Drosophila 12 Genomes Consortium; Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Ka… See abstract for full author list ➔ Drosophila 12 Genomes Consortium, et al. Among authors: walenz b. Nature. 2007 Nov 8;450(7167):203-18. doi: 10.1038/nature06341. Nature. 2007. PMID: 17994087
An algorithm for automated closure during assembly.
Koren S, Miller JR, Walenz BP, Sutton G. Koren S, et al. Among authors: walenz bp. BMC Bioinformatics. 2010 Sep 10;11:457. doi: 10.1186/1471-2105-11-457. BMC Bioinformatics. 2010. PMID: 20831800 Free PMC article.
The bonobo genome compared with the chimpanzee and human genomes.
Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S. Prüfer K, et al. Nature. 2012 Jun 28;486(7404):527-31. doi: 10.1038/nature11128. Nature. 2012. PMID: 22722832 Free PMC article.
Genomic insights into the Ixodes scapularis tick vector of Lyme disease.
Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SMS, Kim D, Kocan KM, Koči J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJP, Park Y, Rozas J, Benton R, Pedra JHF, Nelson DR, Unger MF, Tubio JMC, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA. Gulia-Nuss M, et al. Among authors: walenz bp. Nat Commun. 2016 Feb 9;7:10507. doi: 10.1038/ncomms10507. Nat Commun. 2016. PMID: 26856261 Free PMC article.
Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S. Ghurye J, et al. Among authors: walenz bp. PLoS Comput Biol. 2019 Aug 21;15(8):e1007273. doi: 10.1371/journal.pcbi.1007273. eCollection 2019 Aug. PLoS Comput Biol. 2019. PMID: 31433799 Free PMC article.
Effect of sequence depth and length in long-read assembly of the maize inbred NC358.
Ou S, Liu J, Chougule KM, Fungtammasan A, Seetharam AS, Stein JC, Llaca V, Manchanda N, Gilbert AM, Wei S, Chin CS, Hufnagel DE, Pedersen S, Snodgrass SJ, Fengler K, Woodhouse M, Walenz BP, Koren S, Phillippy AM, Hannigan BT, Dawe RK, Hirsch CN, Hufford MB, Ware D. Ou S, et al. Among authors: walenz bp. Nat Commun. 2020 May 8;11(1):2288. doi: 10.1038/s41467-020-16037-7. Nat Commun. 2020. PMID: 32385271 Free PMC article.
Weighted minimizer sampling improves long read mapping.
Jain C, Rhie A, Zhang H, Chu C, Walenz BP, Koren S, Phillippy AM. Jain C, et al. Among authors: walenz bp. Bioinformatics. 2020 Jul 1;36(Suppl_1):i111-i118. doi: 10.1093/bioinformatics/btaa435. Bioinformatics. 2020. PMID: 32657365 Free PMC article.
50 results