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Results: 1 to 20 of 63

1.

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.

PMID:
25061512
[PubMed]
Free PMC Article
2.

An improved genome release (version Mt4.0) for the model legume Medicago truncatula.

Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, Gentzbittel L, Childs KL, Yandell M, Gundlach H, Mayer KF, Schwartz DC, Town CD.

BMC Genomics. 2014 Apr 27;15:312. doi: 10.1186/1471-2164-15-312.

PMID:
24767513
[PubMed - in process]
Free PMC Article
3.

Presentation of large DNA molecules for analysis as nanoconfined dumbbells.

Kounovsky-Shafer KL, Hernández-Ortiz JP, Jo K, Odijk T, de Pablo JJ, Schwartz DC.

Macromolecules. 2013 Oct 22;46(20):8356-8368.

PMID:
24683272
[PubMed]
Free PMC Article
4.

Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis.

Ray M, Goldstein S, Zhou S, Potamousis K, Sarkar D, Newton MA, Esterberg E, Kendziorski C, Bogler O, Schwartz DC.

BMC Genomics. 2013 Jul 26;14:505. doi: 10.1186/1471-2164-14-505.

PMID:
23885787
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
23870653
[PubMed]
Free PMC Article
6.

Comparative genomics of cryptosporidium.

Mazurie AJ, Alves JM, Ozaki LS, Zhou S, Schwartz DC, Buck GA.

Int J Genomics. 2013;2013:832756. doi: 10.1155/2013/832756. Epub 2013 May 2.

PMID:
23738321
[PubMed]
Free PMC Article
7.

Using latent class analysis to model prescription medications in the measurement of falling among a community elderly population.

Hardigan PC, Schwartz DC, Hardigan WD.

BMC Med Inform Decis Mak. 2013 May 25;13:60. doi: 10.1186/1472-6947-13-60.

PMID:
23705639
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.

van Heesch S, Kloosterman WP, Lansu N, Ruzius FP, Levandowsky E, Lee CC, Zhou S, Goldstein S, Schwartz DC, Harkins TT, Guryev V, Cuppen E.

BMC Genomics. 2013 Apr 16;14:257. doi: 10.1186/1471-2164-14-257.

PMID:
23590730
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence.

Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, Holman WH, Kodira CD, Martin J, Oliver RP, Robbertse B, Schackwitz W, Schwartz DC, Spatafora JW, Turgeon BG, Yandava C, Young S, Zhou S, Zeng Q, Grigoriev IV, Ma LJ, Ciuffetti LM.

G3 (Bethesda). 2013 Jan;3(1):41-63. doi: 10.1534/g3.112.004044. Epub 2013 Jan 1.

PMID:
23316438
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

AGORA: Assembly Guided by Optical Restriction Alignment.

Lin HC, Goldstein S, Mendelowitz L, Zhou S, Wetzel J, Schwartz DC, Pop M.

BMC Bioinformatics. 2012 Aug 2;13:189. doi: 10.1186/1471-2105-13-189.

PMID:
22856673
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Genome sequence of the model medicinal mushroom Ganoderma lucidum.

Chen S, Xu J, Liu C, Zhu Y, Nelson DR, Zhou S, Li C, Wang L, Guo X, Sun Y, Luo H, Li Y, Song J, Henrissat B, Levasseur A, Qian J, Li J, Luo X, Shi L, He L, Xiang L, Xu X, Niu Y, Li Q, Han MV, Yan H, Zhang J, Chen H, Lv A, Wang Z, Liu M, Schwartz DC, Sun C.

Nat Commun. 2012 Jun 26;3:913. doi: 10.1038/ncomms1923.

PMID:
22735441
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Statistical significance of optical map alignments.

Sarkar D, Goldstein S, Schwartz DC, Newton MA.

J Comput Biol. 2012 May;19(5):478-92. doi: 10.1089/cmb.2011.0221. Epub 2012 Apr 16.

PMID:
22506568
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association.

Bannantine JP, Wu CW, Hsu C, Zhou S, Schwartz DC, Bayles DO, Paustian ML, Alt DP, Sreevatsan S, Kapur V, Talaat AM.

BMC Genomics. 2012 Mar 12;13:89. doi: 10.1186/1471-2164-13-89.

PMID:
22409516
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The Medicago genome provides insight into the evolution of rhizobial symbioses.

Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA.

Nature. 2011 Nov 16;480(7378):520-4. doi: 10.1038/nature10625.

PMID:
22089132
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Complete genome sequence of Rhodospirillum rubrum type strain (S1).

Munk AC, Copeland A, Lucas S, Lapidus A, Del Rio TG, Barry K, Detter JC, Hammon N, Israni S, Pitluck S, Brettin T, Bruce D, Han C, Tapia R, Gilna P, Schmutz J, Larimer F, Land M, Kyrpides NC, Mavromatis K, Richardson P, Rohde M, Göker M, Klenk HP, Zhang Y, Roberts GP, Reslewic S, Schwartz DC.

Stand Genomic Sci. 2011 Jul 1;4(3):293-302. doi: 10.4056/sigs.1804360. Epub 2011 Jun 30.

PMID:
21886856
[PubMed]
Free PMC Article
16.

Nanochannel confinement: DNA stretch approaching full contour length.

Kim Y, Kim KS, Kounovsky KL, Chang R, Jung GY, dePablo JJ, Jo K, Schwartz DC.

Lab Chip. 2011 May 21;11(10):1721-9. doi: 10.1039/c0lc00680g. Epub 2011 Mar 23.

PMID:
21431167
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk.

Antonacci F, Kidd JM, Marques-Bonet T, Teague B, Ventura M, Girirajan S, Alkan C, Campbell CD, Vives L, Malig M, Rosenfeld JA, Ballif BC, Shaffer LG, Graves TA, Wilson RK, Schwartz DC, Eichler EE.

Nat Genet. 2010 Sep;42(9):745-50. doi: 10.1038/ng.643. Epub 2010 Aug 22.

PMID:
20729854
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

High-resolution human genome structure by single-molecule analysis.

Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, Sarkar D, Valouev A, Churas C, Kidd JM, Kohn S, Runnheim R, Lamers C, Forrest D, Newton MA, Eichler EE, Kent-First M, Surti U, Livny M, Schwartz DC.

Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10848-53. doi: 10.1073/pnas.0914638107. Epub 2010 Jun 1.

PMID:
20534489
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.

Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M.

Nature. 2010 Mar 18;464(7287):367-73. doi: 10.1038/nature08850.

PMID:
20237561
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

New Generations: Sequencing Machines and Their Computational Challenges.

Schwartz DC, Waterman MS.

J Comput Sci Technol. 2010 Jan 1;25(1):3-9.

PMID:
22121326
[PubMed]
Free PMC Article

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