Searching journal content for articles similar to Gunderson et al. 14 (5): 870.

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  1. Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
    • Gianluca Mattei,
    • Marta Baragli,
    • Barbara Gega,
    • Alessandra Mingrino,
    • Martina Chieca,
    • Tommaso Ducci,
    • Gianmaria Frigè,
    • Luca Mazzarella,
    • Romina D'Aurizio,
    • Francesco De Logu,
    • Romina Nassini,
    • Pier Giuseppe Pelicci,
    • and Alberto Magi
    Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
    ...) that is capable of identifying DMRs by segmenting methylation frequency differences (Δβ) inferred from ONT data (Magi et al. 2023b).In this work, we expand the PoreMeth tool to include epiallelic diversity changes. The diversity of DNA methylation patterns in a cell population can be measured by using the Shannon...
  2. Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
    • W.H. Adrian Tsui,
    • Spencer C. Ding,
    • Peiyong Jiang,
    • and Y.M. Dennis Lo
    Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
    ...also been parameterized in the “window protection score” for nucleosome footprinting (Snyder et al. 2016; Straver et al. 2016). Together, these studies highlight that patterns of cfDNA fragmentation are intimately linked to chromatin architecture, such as nucleosome arrays, sites of other DNA...
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  3. Methods: High-throughput DNA methylation profiling using universal bead arrays
    • Marina Bibikova,
    • Zhenwu Lin,
    • Lixin Zhou,
    • Eugene Chudin,
    • Eliza Wickham Garcia,
    • Bonnie Wu,
    • Dennis Doucet,
    • Neal J. Thomas,
    • Yunhua Wang,
    • Ekkehard Vollmer,
    • Torsten Goldmann,
    • Carola Seifart,
    • Wei Jiang,
    • David L. Barker,
    • Mark S. Chee,
    • Joanna Floros,
    • and Jian-Bing Fan
    Genome Res. March 2006 16: 383-393; Published in Advance January 31, 2006, doi:10.1101/gr.4410706
    ...High-throughput DNA methylation profiling using universal bead arrays Marina Bibikova 1 , Zhenwu Lin 2 , Lixin Zhou 1 , Eugene Chudin 1 , Eliza Wickham Garcia 1 , Bonnie Wu 1 , Dennis Doucet 1 , Neal J. Thomas 3...
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  4. LETTER: Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas
    • Neerja Karnani,
    • Christopher Taylor,
    • Ankit Malhotra,
    • and Anindya Dutta
    Genome Res. June 2007 17: 865-876; doi:10.1101/gr.5427007
    ...). Purified DNA from each time interval was hybridized to the high-density -tiling Affymetrix array comprising unique 25-mer oligonucleotides in the ENCODE-selected chromosomal loci covering 1% of the human (∼30 Mb) (see Methods for details of the ENCODE regions). Segregation of chromosomal regions...
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  5. Methods: Decoding the fine-scale structure of a breast cancer genome and transcriptome
    • Stanislav Volik,
    • Benjamin J. Raphael,
    • Guiqing Huang,
    • Michael R. Stratton,
    • Graham Bignel,
    • John Murnane,
    • John H. Brebner,
    • Krystyna Bajsarowicz,
    • Pamela L. Paris,
    • Quanzhou Tao,
    • David Kowbel,
    • Anna Lapuk,
    • Dmitri A. Shagin,
    • Irina A. Shagina,
    • Joe W. Gray,
    • Jan-Fang Cheng,
    • Pieter J. de Jong,
    • Pavel Pevzner,
    • and Colin Collins
    Genome Res. March 2006 16: 394-404; Published in Advance February 3, 2006, doi:10.1101/gr.4247306
    ...total MCF-7 RNA ( Fig. 3A ). We arrayed and end sequenced 5089 recombinant cDNA clones (clones are available from C.C. laboratory). We were able to map both ends of 2700 cDNA clones; of these, 44 clones had ends mapping to different chromosomes and 56 had ends mapping in the wrong orientation. ESP...
  6. Methods: DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen analysis
    • Yaniv Erlich,
    • Kenneth Chang,
    • Assaf Gordon,
    • Roy Ronen,
    • Oron Navon,
    • Michelle Rooks,
    • and Gregory J. Hannon
    Genome Res. July 2009 19: 1243-1253; Published in Advance May 15, 2009, doi:10.1101/gr.092957.109
    ...the sequencing run are fed to a decoder, which solves the DNA Sudoku and generates a list of individual specimens and their corresponding inferred sequences. The ability to achieve a solution in DNA Sudoku requires tracking specimens within the context of each pooling pattern and relating results generated...
  7. Research: Epigenetic characterization of pseudogenes across human tissues
    • Yunzhe Jiang,
    • Beatrice Borsari,
    • and Mark Gerstein
    Genome Res. April 15, 2026 gr.280768.125; Published in Advance April 15, 2026, doi:10.1101/gr.280768.125
    ...across transcripts and tissues for each biotype. Additionally, we obtained tissue-specific DNA methylation profiling by array assay across the same tissues. To ensure consistency across donors and technical replicates for each tissue, we used BEDTools merge (v2.30.0) (Quinlan and Hall 2010) with the -c 5...
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  8. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...looping and high-order chromatin structure (Panigrahi and O'Malley 2021; Karr et al. 2022; Chen et al. 2024b). Furthermore, the DNA interactome at a particular gene locus is controlled by the availability of the transcription machinery, its correct localization, transcriptional complex formation...
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  9. Method: Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
    • Prashant S. Emani,
    • Maya N. Geradi,
    • Gamze Gürsoy,
    • Monica R. Grasty,
    • Andrew Miranker,
    • and Mark B. Gerstein
    Genome Res. December 2023 33: 2156-2173; Published in Advance December 14, 2023, doi:10.1101/gr.278322.123
    ...rare ones) to identify individuals has been repeatedly shown, the availability of small sets of noisy genotypes, from environmental DNA samples or functional genomics data, motivated us to quantify their informativeness. We present a computational tool suite, termed Privacy Leakage by Inference across...
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  10. Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
    • Anna Grandchamp,
    • Lucas Kühl,
    • Marie Lebherz,
    • Kathrin Brüggemann,
    • John Parsch,
    • and Erich Bornberg-Bauer
    Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
    ..., multiple studies across many taxa showed that some novel genes arise de novo, that is, from previously noncoding DNA. To characterize the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within noncoding sequences in closely related...
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