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We began analyzing https://academic.oup.com/bioinformatics/article/30/11/1493/282534, but it redirected us to https://academic.oup.com/bioinformatics/article/30/11/1493/282534. The analysis below is for the second page.

Title[redir]:
Comparing DNA integration site clusters with scan statistics | Bioinformatics | Oxford Academic
Description:
Abstract. Motivation: Gene therapy with retroviral vectors can induce adverse effects when those vectors integrate in sensitive genomic regions. Retroviral

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sites, windows, regions, number, vector, clumps, integration, region, window, google, vectors, odds, scholar, false, iss, discoveries, mse, expected, worldcat, genomic, set, critical, jurkat, data, avr, vol, gene, power, discovered, versus, site, clump, cutpoints, methods, therapy, target, crossrefpubmed, bases, width, supplementary, comparison, background, discovery, dna, hiv, genome, infection, chromosome, figure, values,

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computational biology oxford academic bioinformatics mathematics books journals oxford university press hacein-bey-abina google scholar latest university press partners article sign genome-wide insertional mutagenesis search scid-x1 gene therapy volume 30 june 2014 term maryland view design wet-bench follow supplementary data show genome-wide background odds enhancing variant interpretation genome-wide variation references yield patient-specific clumps discussion single fixed-width scan recursively splits data introduction genomic data analysis clinical gene therapy comprehensive genomic access gene-corrected subjects marketing citing articles human gene therapy successful gene therapy target false discovery hiv primary isolate discovered windows results bioinformatics online access accessibility contact false discovery rate basic data form specific filter based cd4+ versus jurkat supplementary data author 2014 data collection methods vector reflect preferences avr versus mse challenges clumping methods gene therapy vectors gene therapy vectors

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ScholarlyArticle:
      context:https://schema.org
      id:https://academic.oup.com/bioinformatics/article/30/11/1493/282534
      name:Comparing DNA integration site clusters with scan statistics
      datePublished:2014-01-30
      isPartOf:
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         type:PublicationIssue
         issueNumber:11
         datePublished:2014-06-01
         isPartOf:
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            type:Periodical
            name:Bioinformatics
            issn:
               1367-4811
      url:https://dx.doi.org/10.1093/bioinformatics/btu035
      inLanguage:en
      copyrightHolder:Oxford University Press
      copyrightYear:2025
      publisher:Oxford University Press
      author:
            name:Berry, Charles C.
            affiliation:Division of Biostatistics and BioInformatics, Department of Family and Preventive Medicine, University of California at San Diego, La Jolla, CA 92093-0901 and Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, Philadelphia, PA 19104-6076, USA
            type:Person
            name:Ocwieja, Karen E.
            affiliation:Division of Biostatistics and BioInformatics, Department of Family and Preventive Medicine, University of California at San Diego, La Jolla, CA 92093-0901 and Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, Philadelphia, PA 19104-6076, USA
            type:Person
            name:Malani, Nirav
            affiliation:Division of Biostatistics and BioInformatics, Department of Family and Preventive Medicine, University of California at San Diego, La Jolla, CA 92093-0901 and Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, Philadelphia, PA 19104-6076, USA
            type:Person
            name:Bushman, Frederic D.
            affiliation:Division of Biostatistics and BioInformatics, Department of Family and Preventive Medicine, University of California at San Diego, La Jolla, CA 92093-0901 and Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, Philadelphia, PA 19104-6076, USA
            type:Person
      description:Abstract. Motivation: Gene therapy with retroviral vectors can induce adverse effects when those vectors integrate in sensitive genomic regions. Retroviral
      pageStart:1493
      pageEnd:1500
      siteName:OUP Academic
      thumbnailURL:https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/30/11/10.1093_bioinformatics_btu035/2/m_bioinformatics_30_11_1493_f2.gif?Expires=1813974148&Signature=wDcYfdR0nSihEA2IX0YfhZL~2QHYyVi2rfecY3An8vC6WmbRywVdmC2UITTVWHFAuNy~S6bMn4Wo72uYG4uKnTTj-17hlCeraBGthGbwzbjbd7TzKE20L~cbFqkYXPvET0Voe5ShE5PFTEnc5puOaqgxW-w0ZpnWPeIzjQ389T7krzKrxDDr2UaEitia-wSxyACy865NFjrjnmjRF~AycJb2B2QSdVOC9GslqL1WgwvGE0xA0IJ4WkYfFv125~Y59jokw7MeBdY0M-SIbGegdTxvD9uJaeybmZ3ImgBehpRD~Hp2rbv1iG0HYZUszucaDMXVMoWFc1QmHlb1B~mUgQ__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA
      headline:Comparing DNA integration site clusters with scan statistics
      image:https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/30/11/10.1093_bioinformatics_btu035/2/m_bioinformatics_30_11_1493_f2.gif?Expires=1813974148&Signature=wDcYfdR0nSihEA2IX0YfhZL~2QHYyVi2rfecY3An8vC6WmbRywVdmC2UITTVWHFAuNy~S6bMn4Wo72uYG4uKnTTj-17hlCeraBGthGbwzbjbd7TzKE20L~cbFqkYXPvET0Voe5ShE5PFTEnc5puOaqgxW-w0ZpnWPeIzjQ389T7krzKrxDDr2UaEitia-wSxyACy865NFjrjnmjRF~AycJb2B2QSdVOC9GslqL1WgwvGE0xA0IJ4WkYfFv125~Y59jokw7MeBdY0M-SIbGegdTxvD9uJaeybmZ3ImgBehpRD~Hp2rbv1iG0HYZUszucaDMXVMoWFc1QmHlb1B~mUgQ__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA
      image:alt:Clustering of ISs by recovery method. A region of chromosome 17 is shown and marked by locations of HIV vector ISs recovered by each of two methods (see Section 3.3 for details). Sites recovered after cleavage of genomic DNA with Mse are marked with circles; those recovered after cleavage with the Avr cocktail are shown by the triangles. The circles and triangles are shown evenly spaced along the x-axis (lower middle) for ease of visualization, then connected by lines to the chromosome scaffold (bottom) to show their distribution on the chromosome. A clump, or genomic interval enriched for a recovery method, is discovered as follows: Windows containing between 15 and 75 sites were tested for enrichment of Avr or Mse, but only those passing the enrichment test are shown. Each horizontal bar (upper section of figure) represents a window that spans the x-values for a group of sites that show enrichment for Mse. (In this region, no such group shows enrichment for Avr.) The bars are grouped together according to the number of sites spanned and the number of Mse sites required to declare enrichment (see text for details of how the cutpoints were chosen). Those numbers are given just above the right edge of each group as a fraction (required/spanned). The depth, i.e. number of different window size groups over a site, is indicated at the top. Sites with greatest depth are always included in the final clump, but sites at the edges are screened using a likelihood criterion; in this case several sites on each side are excluded. Dashed vertical lines enclose the sites that were ultimately assigned to the clump
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      issueNumber:11
      datePublished:2014-06-01
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Person:
      name:Berry, Charles C.
      affiliation:Division of Biostatistics and BioInformatics, Department of Family and Preventive Medicine, University of California at San Diego, La Jolla, CA 92093-0901 and Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, Philadelphia, PA 19104-6076, USA
      name:Ocwieja, Karen E.
      affiliation:Division of Biostatistics and BioInformatics, Department of Family and Preventive Medicine, University of California at San Diego, La Jolla, CA 92093-0901 and Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, Philadelphia, PA 19104-6076, USA
      name:Malani, Nirav
      affiliation:Division of Biostatistics and BioInformatics, Department of Family and Preventive Medicine, University of California at San Diego, La Jolla, CA 92093-0901 and Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, Philadelphia, PA 19104-6076, USA
      name:Bushman, Frederic D.
      affiliation:Division of Biostatistics and BioInformatics, Department of Family and Preventive Medicine, University of California at San Diego, La Jolla, CA 92093-0901 and Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, Philadelphia, PA 19104-6076, USA

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