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Items: 1 to 20 of 92

1.

Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource.

Peters B, Dirscherl S, Dantzer J, Nowacki J, Cross S, Li X, Cornetta K, Dinauer MC, Mooney SD.

Gene Ther. 2008 Sep;15(18):1294-8. doi: 10.1038/gt.2008.99. Epub 2008 Jun 26.

2.

Identifying viral integration sites using SeqMap 2.0.

Hawkins TB, Dantzer J, Peters B, Dinauer M, Mockaitis K, Mooney S, Cornetta K.

Bioinformatics. 2011 Mar 1;27(5):720-2. doi: 10.1093/bioinformatics/btq722. Epub 2011 Jan 17.

3.

High-throughput genomic mapping of vector integration sites in gene therapy studies.

Beard BC, Adair JE, Trobridge GD, Kiem HP.

Methods Mol Biol. 2014;1185:321-44. doi: 10.1007/978-1-4939-1133-2_22.

PMID:
25062639
4.

High efficiency restriction enzyme-free linear amplification-mediated polymerase chain reaction approach for tracking lentiviral integration sites does not abrogate retrieval bias.

Wu C, Jares A, Winkler T, Xie J, Metais JY, Dunbar CE.

Hum Gene Ther. 2013 Jan;24(1):38-47. doi: 10.1089/hum.2012.082. Epub 2012 Oct 26.

5.

QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis.

Appelt JU, Giordano FA, Ecker M, Roeder I, Grund N, Hotz-Wagenblatt A, Opelz G, Zeller WJ, Allgayer H, Fruehauf S, Laufs S.

Gene Ther. 2009 Jul;16(7):885-93. doi: 10.1038/gt.2009.37. Epub 2009 Apr 23.

PMID:
19387483
6.

VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.

Hocum JD, Battrell LR, Maynard R, Adair JE, Beard BC, Rawlings DJ, Kiem HP, Miller DG, Trobridge GD.

BMC Bioinformatics. 2015 Jul 7;16:212. doi: 10.1186/s12859-015-0653-6.

7.

Detection and direct genomic sequencing of multiple rare unknown flanking DNA in highly complex samples.

Schmidt M, Hoffmann G, Wissler M, Lemke N, Müssig A, Glimm H, Williams DA, Ragg S, Hesemann CU, von Kalle C.

Hum Gene Ther. 2001 May 1;12(7):743-9.

PMID:
11339891
8.

Detection of retroviral integration sites by linear amplification-mediated PCR and tracking of individual integration clones in different samples.

Schmidt M, Schwarzwaelder K, Bartholomae CC, Glimm H, von Kalle C.

Methods Mol Biol. 2009;506:363-72. doi: 10.1007/978-1-59745-409-4_24.

PMID:
19110638
9.

Bioinformatic clonality analysis of next-generation sequencing-derived viral vector integration sites.

Arens A, Appelt JU, Bartholomae CC, Gabriel R, Paruzynski A, Gustafson D, Cartier N, Aubourg P, Deichmann A, Glimm H, von Kalle C, Schmidt M.

Hum Gene Ther Methods. 2012 Apr;23(2):111-8. doi: 10.1089/hgtb.2011.219. Epub 2012 May 4.

10.

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes.

Shao W, Shan J, Kearney MF, Wu X, Maldarelli F, Mellors JW, Luke B, Coffin JM, Hughes SH.

Retrovirology. 2016 Jul 4;13(1):47. doi: 10.1186/s12977-016-0277-6.

11.
12.

Linear amplification mediated PCR--localization of genetic elements and characterization of unknown flanking DNA.

Gabriel R, Kutschera I, Bartholomae CC, von Kalle C, Schmidt M.

J Vis Exp. 2014 Jun 25;(88):e51543. doi: 10.3791/51543.

13.

[Approaches towards directed DNA integration by the use of retroviral integrases and transposases].

Kniazhanskaia ES, Kondrashina OV, Gottikh MB.

Mol Biol (Mosk). 2011 Nov-Dec;45(6):931-48. Review. Russian.

PMID:
22295563
14.

High-resolution insertion-site analysis by linear amplification-mediated PCR (LAM-PCR).

Schmidt M, Schwarzwaelder K, Bartholomae C, Zaoui K, Ball C, Pilz I, Braun S, Glimm H, von Kalle C.

Nat Methods. 2007 Dec;4(12):1051-7.

PMID:
18049469
15.

Integration site selection by retroviral vectors: molecular mechanism and clinical consequences.

Daniel R, Smith JA.

Hum Gene Ther. 2008 Jun;19(6):557-68. doi: 10.1089/hum.2007.148. Review.

16.

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites.

Serrao E, Cherepanov P, Engelman AN.

J Vis Exp. 2016 Mar 22;(109). doi: 10.3791/53840.

17.

A high-throughput method for cloning and sequencing human immunodeficiency virus type 1 integration sites.

Kim S, Kim Y, Liang T, Sinsheimer JS, Chow SA.

J Virol. 2006 Nov;80(22):11313-21. Epub 2006 Sep 13.

18.

Flanking-sequence exponential anchored-polymerase chain reaction amplification: a sensitive and highly specific method for detecting retroviral integrant-host-junction sequences.

Pule MA, Rousseau A, Vera J, Heslop HE, Brenner MK, Vanin EF.

Cytotherapy. 2008;10(5):526-39. doi: 10.1080/14653240802192636.

19.

Retroviral integration site analysis in hematopoietic stem cells.

Kustikova OS, Baum C, Fehse B.

Methods Mol Biol. 2008;430:255-67. doi: 10.1007/978-1-59745-182-6_18.

PMID:
18370305
20.

RTCGD: retroviral tagged cancer gene database.

Akagi K, Suzuki T, Stephens RM, Jenkins NA, Copeland NG.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D523-7.

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