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Items: 1 to 20 of 96

1.

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C.

Nat Commun. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z.

2.

A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing.

Kingan SB, Heaton H, Cudini J, Lambert CC, Baybayan P, Galvin BD, Durbin R, Korlach J, Lawniczak MKN.

Genes (Basel). 2019 Jan 18;10(1). pii: E62. doi: 10.3390/genes10010062.

3.

Porous Zero-Mode Waveguides for Picogram-Level DNA Capture.

Jadhav V, Hoogerheide DP, Korlach J, Wanunu M.

Nano Lett. 2019 Feb 13;19(2):921-929. doi: 10.1021/acs.nanolett.8b04170. Epub 2018 Dec 3.

PMID:
30484321
4.

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.

5.

Author Correction: Comprehensive analysis of single molecule sequencing-derived complete genome and whole transcriptome of Hyposidra talaca nuclear polyhedrosis virus.

Nguyen TT, Suryamohan K, Kuriakose B, Janakiraman V, Reichelt M, Chaudhuri S, Guillory J, Divakaran N, Rabins PE, Goel R, Deka B, Sarkar S, Ekka P, Tsai YC, Vargas D, Santhosh S, Mohan S, Chin CS, Korlach J, Thomas G, Babu A, Seshagiri S.

Sci Rep. 2018 Aug 31;8(1):13274. doi: 10.1038/s41598-018-31454-x.

6.

A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaii's Last Remaining Crow Species.

Sutton JT, Helmkampf M, Steiner CC, Bellinger MR, Korlach J, Hall R, Baybayan P, Muehling J, Gu J, Kingan S, Masuda BM, Ryder OA.

Genes (Basel). 2018 Aug 1;9(8). pii: E393. doi: 10.3390/genes9080393.

7.

Comprehensive analysis of single molecule sequencing-derived complete genome and whole transcriptome of Hyposidra talaca nuclear polyhedrosis virus.

Nguyen TT, Suryamohan K, Kuriakose B, Janakiraman V, Reichelt M, Chaudhuri S, Guillory J, Divakaran N, Rabins PE, Goel R, Deka B, Sarkar S, Ekka P, Tsai YC, Vargas D, Santhosh S, Mohan S, Chin CS, Korlach J, Thomas G, Babu A, Seshagiri S.

Sci Rep. 2018 Jun 12;8(1):8924. doi: 10.1038/s41598-018-27084-y. Erratum in: Sci Rep. 2018 Aug 31;8(1):13274.

8.

Pacific Biosciences Sequencing and IMGT/HighV-QUEST Analysis of Full-Length Single Chain Fragment Variable from an In Vivo Selected Phage-Display Combinatorial Library.

Hemadou A, Giudicelli V, Smith ML, Lefranc MP, Duroux P, Kossida S, Heiner C, Hepler NL, Kuijpers J, Groppi A, Korlach J, Mondon P, Ottones F, Jacobin-Valat MJ, Laroche-Traineau J, Clofent-Sanchez G.

Front Immunol. 2017 Dec 20;8:1796. doi: 10.3389/fimmu.2017.01796. eCollection 2017.

9.

Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data.

Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin CS, Korlach J, Wilson RK, Eichler EE.

Genome Res. 2018 Jan;28(1):144. doi: 10.1101/gr.233007.117. No abstract available.

10.

Methylomic and phenotypic analysis of the ModH5 phasevarion of Helicobacter pylori.

Srikhanta YN, Gorrell RJ, Power PM, Tsyganov K, Boitano M, Clark TA, Korlach J, Hartland EL, Jennings MP, Kwok T.

Sci Rep. 2017 Nov 23;7(1):16140. doi: 10.1038/s41598-017-15721-x.

11.

Genome and Methylome Variation in Helicobacter pylori With a cag Pathogenicity Island During Early Stages of Human Infection.

Nell S, Estibariz I, Krebes J, Bunk B, Graham DY, Overmann J, Song Y, Spröer C, Yang I, Wex T, Korlach J, Malfertheiner P, Suerbaum S.

Gastroenterology. 2018 Feb;154(3):612-623.e7. doi: 10.1053/j.gastro.2017.10.014. Epub 2017 Oct 21.

PMID:
29066327
12.

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads.

Korlach J, Gedman G, Kingan SB, Chin CS, Howard JT, Audet JN, Cantin L, Jarvis ED.

Gigascience. 2017 Oct 1;6(10):1-16. doi: 10.1093/gigascience/gix085.

13.

Length-independent DNA packing into nanopore zero-mode waveguides for low-input DNA sequencing.

Larkin J, Henley RY, Jadhav V, Korlach J, Wanunu M.

Nat Nanotechnol. 2017 Dec;12(12):1169-1175. doi: 10.1038/nnano.2017.176. Epub 2017 Sep 11.

14.

Long-read genome sequencing identifies causal structural variation in a Mendelian disease.

Merker JD, Wenger AM, Sneddon T, Grove M, Zappala Z, Fresard L, Waggott D, Utiramerur S, Hou Y, Smith KS, Montgomery SB, Wheeler M, Buchan JG, Lambert CC, Eng KS, Hickey L, Korlach J, Ford J, Ashley EA.

Genet Med. 2018 Jan;20(1):159-163. doi: 10.1038/gim.2017.86. Epub 2017 Jun 22.

15.

Complete Genome Sequence of Moraxella catarrhalis Strain CCRI-195ME, Isolated from the Middle Ear.

Tan A, Blakeway LV, Bakaletz LO, Boitano M, Clark TA, Korlach J, Jennings MP, Peak IR, Seib KL.

Genome Announc. 2017 May 25;5(21). pii: e00384-17. doi: 10.1128/genomeA.00384-17.

16.

Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing.

Kong N, Ng W, Thao K, Agulto R, Weis A, Kim KS, Korlach J, Hickey L, Kelly L, Lappin S, Weimer BC.

Stand Genomic Sci. 2017 Mar 23;12:27. doi: 10.1186/s40793-017-0239-1. eCollection 2017.

17.

Identification of a Pseudomonas aeruginosa PAO1 DNA Methyltransferase, Its Targets, and Physiological Roles.

Doberenz S, Eckweiler D, Reichert O, Jensen V, Bunk B, Spröer C, Kordes A, Frangipani E, Luong K, Korlach J, Heeb S, Overmann J, Kaever V, Häussler S.

MBio. 2017 Feb 21;8(1). pii: e02312-16. doi: 10.1128/mBio.02312-16.

18.

Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Katneni VK, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L.

PLoS Genet. 2016 Dec 9;12(12):e1006500. doi: 10.1371/journal.pgen.1006500. eCollection 2016 Dec.

19.

Discovery and genotyping of structural variation from long-read haploid genome sequence data.

Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin CS, Korlach J, Wilson RK, Eichler EE.

Genome Res. 2017 May;27(5):677-685. doi: 10.1101/gr.214007.116. Epub 2016 Nov 28. Erratum in: Genome Res. 2018 Jan;28(1):144.

20.

Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes.

Chen P, den Bakker HC, Korlach J, Kong N, Storey DB, Paxinos EE, Ashby M, Clark T, Luong K, Wiedmann M, Weimer BC.

Appl Environ Microbiol. 2017 Jan 17;83(3). pii: e02091-16. doi: 10.1128/AEM.02091-16. Print 2017 Feb 1.

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