Searching journal content for articles similar to Brody et al. 28 (12): 1901.

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  1. Research: Somatic retrotransposition in the developing rhesus macaque brain
    • Victor Billon,
    • Francisco J. Sanchez-Luque,
    • Jay Rasmussen,
    • Gabriela O. Bodea,
    • Daniel J. Gerhardt,
    • Patricia Gerdes,
    • Seth W. Cheetham,
    • Stephanie N. Schauer,
    • Prabha Ajjikuttira,
    • Thomas J. Meyer,
    • Cora E. Layman,
    • Kimberly A. Nevonen,
    • Natasha Jansz,
    • Jose L. Garcia-Perez,
    • Sandra R. Richardson,
    • Adam D. Ewing,
    • Lucia Carbone,
    • and Geoffrey J. Faulkner
    Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
    ...et al. 2017; Feusier et al. 2019) and before the complete establishment of L1 methylation (Macia et al. 2017; Sanchez-Luque et al. 2019). Single-cell whole- sequencing (scWGS) of postmitotic neurons (Evrony et al. 2015; Sanchez-Luque et al. 2019) has uncovered somatic retrotransposition events traced...
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  2. Research: Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling
    • Lu Liu,
    • He Chen,
    • Cheng Sun,
    • Jianyun Zhang,
    • Juncheng Wang,
    • Meijie Du,
    • Jie Li,
    • Lin Di,
    • Jie Shen,
    • Shuang Geng,
    • Yuhong Pang,
    • Yingying Luo,
    • Chen Wu,
    • Yusi Fu,
    • Zhe Zheng,
    • Jianbin Wang,
    • and Yanyi Huang
    Genome Res. January 2022 32: 44-54; Published in Advance December 28, 2021, doi:10.1101/gr.275453.121
    ...- sequencing method, we sequenced over 20,000 single lymphocytes from 16 individuals. Then, with the scale increased to a few thousand single cells per individual, we found that about 7.5% of the cells had large-size copy number alterations. Trisomy 21 was the most prevalent aneuploid event among all autosomal...
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  3. Method: Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq
    • Pete H. Taylor,
    • Amanda Cinquin,
    • and Olivier Cinquin
    Genome Res. November 2016 26: 1600-1611; Published in Advance October 19, 2016, doi:10.1101/gr.200501.115
    ...by differentiated cells, which have a higher mutation rate—quantification of stem cell DNA damage and DNA mutations is thus best performed from small, well-defined cell populations. Here we report a mutation detection technique, based on the “duplex sequencing” principle, with an error rate below ∼10...
  4. Method: Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing
    • Renato Salazar,
    • Barbara Arbeithuber,
    • Maja Ivankovic,
    • Monika Heinzl,
    • Sofia Moura,
    • Ingrid Hartl,
    • Theresa Mair,
    • Angelika Lahnsteiner,
    • Thomas Ebner,
    • Omar Shebl,
    • Johannes Pröll,
    • and Irene Tiemann-Boege
    Genome Res. March 2022 32: 499-511; Published in Advance February 24, 2022, doi:10.1101/gr.275695.121
    ...different genomic positions in the exonic FGFR3 sequence (exons 3–15 without exon 11). Of those, 20 have been reported in other databases to be associated with congenital disorders (Human Gene Mutation database [HGMD]) and/or tumors (Catalog Of Somatic Mutations in Cancer [COSMIC]), 13 were unique...
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  5. Method: Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
    • Keyi Geng,
    • Lara G. Merino,
    • Linda Wedemann,
    • Aniek Martens,
    • Małgorzata Sobota,
    • Yerma P. Sanchez,
    • Jonas Nørskov Søndergaard,
    • Robert J. White,
    • and Claudia Kutter
    Genome Res. October 2022 32: 1876-1891; Published in Advance September 30, 2022, doi:10.1101/gr.276901.122
    ...to a protospacer adjacent motif (PAM), the expressed Cas9 endonuclease induces a double-strand break (DSB) at a specific genomic site. If an exogenous homologous DNA template is supplied, the DSB is repaired by the homology-directed repair to introduce specific mutations or insertions of desired sequences (Greene...
  6. Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
    • Bo Zhang,
    • Yan Zhou,
    • Nan Lin,
    • Rebecca F. Lowdon,
    • Chibo Hong,
    • Raman P. Nagarajan,
    • Jeffrey B. Cheng,
    • Daofeng Li,
    • Michael Stevens,
    • Hyung Joo Lee,
    • Xiaoyun Xing,
    • Jia Zhou,
    • Vasavi Sundaram,
    • GiNell Elliott,
    • Junchen Gu,
    • Taoping Shi,
    • Philippe Gascard,
    • Mahvash Sigaroudinia,
    • Thea D. Tlsty,
    • Theresa Kadlecek,
    • Arthur Weiss,
    • Henriette O’Geen,
    • Peggy J. Farnham,
    • Cécile L. Maire,
    • Keith L. Ligon,
    • Pamela A.F. Madden,
    • Angela Tam,
    • Richard Moore,
    • Martin Hirst,
    • Marco A. Marra,
    • Baoxue Zhang,
    • Joseph F. Costello,
    • and Ting Wang
    Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
    ...Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm Bo Zhang 1 , 16 , Yan Zhou 2 , 3 , 16 , Nan Lin 4 , 16 , Rebecca F. Lowdon 1 , 16 , Chibo Hong 5...
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  7. Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
    • Michelle Kudron,
    • Louis Gevirtzman,
    • Alec Victorsen,
    • Bridget C. Lear,
    • Jiahao Gao,
    • Jinrui Xu,
    • Swapna Samanta,
    • Emily Frink,
    • Adri Tran-Pearson,
    • Chau Huynh,
    • Dionne Vafeados,
    • Ann Hammonds,
    • William Fisher,
    • Martha Wall,
    • Greg Wesseling,
    • Vanessa Hernandez,
    • Zhichun Lin,
    • Mary Kasparian,
    • Kevin White,
    • Ravi Allada,
    • Mark Gerstein,
    • LaDeana Hillier,
    • Susan E. Celniker,
    • Valerie Reinke,
    • and Robert H. Waterston
    Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
    ...sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.Precise deployment of gene expression across space...
  8. Research: Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia
    • Lili Wang,
    • Jean Fan,
    • Joshua M. Francis,
    • George Georghiou,
    • Sarah Hergert,
    • Shuqiang Li,
    • Rutendo Gambe,
    • Chensheng W. Zhou,
    • Chunxiao Yang,
    • Sheng Xiao,
    • Paola Dal Cin,
    • Michaela Bowden,
    • Dylan Kotliar,
    • Sachet A. Shukla,
    • Jennifer R. Brown,
    • Donna Neuberg,
    • Dario R. Alessi,
    • Cheng-Zhong Zhang,
    • Peter V. Kharchenko,
    • Kenneth J. Livak,
    • and Catherine J. Wu
    Genome Res. August 2017 27: 1300-1311; Published in Advance July 5, 2017, doi:10.1101/gr.217331.116
    ...to increased understanding of driving events in malignancy. [Supplemental material is available for this article.] The unbiased characterization of mutational landscapes by massively parallel sequencing of bulk tumor samples has been transformative across cancers (Garraway and Lander 2013). For chronic...
  9. Research: Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells
    • Parijat Senapati,
    • Masaru Miyano,
    • Rosalyn W. Sayaman,
    • Mudaser Basam,
    • Amy Leung,
    • Mark A. LaBarge,
    • and Dustin E. Schones
    Genome Res. August 2023 33: 1229-1241; Published in Advance July 18, 2023, doi:10.1101/gr.277511.122
    ...scrambled sequences are listed. (F) Bar plots show the percentage of hypomethylated TE sequences (<30% methylation) that contain indicated TF binding motifs.Age-dependent methylation changes occur at TE subfamilies that contain lineage-specific transcription factor binding sitesHaving established...
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  10. Research: Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes
    • Geoffrey J. Maher,
    • Hannah K. Ralph,
    • Zhihao Ding,
    • Nils Koelling,
    • Hana Mlcochova,
    • Eleni Giannoulatou,
    • Pawan Dhami,
    • Dirk S. Paul,
    • Stefan H. Stricker,
    • Stephan Beck,
    • Gilean McVean,
    • Andrew O.M. Wilkie,
    • and Anne Goriely
    Genome Res. December 2018 28: 1779-1790; Published in Advance October 24, 2018, doi:10.1101/gr.239186.118
    ...of occurrence characterized by an extended geographical distribution across about one-third of the testis from individual Tes4, raising the possibility of an early post-zygotic (as opposed to adult-onset) mutational event (Supplemental Fig. S5). Although this NF1 variant exhibits a high CADD score (24.6), has...
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