Searching journal content for articles similar to Pevzner 11 (9): 1461.

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  1. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    ...in Drosophila. Third, in the human (the only one with extensive T2T assemblies), the bias is much milder and largely restricted to PacBio HiFi, allowing gaps to be closed with ONT reads (Nurk et al. 2022).This mildness initially puzzled us. One possible explanation is the small size of the satellite block...
  2. Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
    • Marta Farré,
    • Jaebum Kim,
    • Anastasia A. Proskuryakova,
    • Yang Zhang,
    • Anastasia I. Kulemzina,
    • Qiye Li,
    • Yang Zhou,
    • Yingqi Xiong,
    • Jennifer L. Johnson,
    • Polina L. Perelman,
    • Warren E. Johnson,
    • Wesley C. Warren,
    • Anna V. Kukekova,
    • Guojie Zhang,
    • Stephen J. O'Brien,
    • Oliver A. Ryder,
    • Alexander S. Graphodatsky,
    • Jian Ma,
    • Harris A. Lewin,
    • and Denis M. Larkin
    Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
    ...synteny blocks [HSBs]), often demarcated by evolutionary breakpoint regions (EBRs) where the order of orthologous sequences differs among species. Several studies have shown that HSBs are enriched for evolutionary conserved sequences and genes related to basic organismal development (Larkin et al. 2009...
  3. Research: Neurospora chromosomes are organized by blocks of importin alpha-dependent heterochromatin that are largely independent of H3K9me3
    • Jonathan M. Galazka,
    • Andrew D. Klocko,
    • Miki Uesaka,
    • Shinji Honda,
    • Eric U. Selker,
    • and Michael Freitag
    Genome Res. August 2016 26: 1069-1080; Published in Advance June 3, 2016, doi:10.1101/gr.203182.115
    ...Neurospora chromosomes are organized by blocks of importin alpha-dependent heterochromatin that are largely independent of H3K9me3 Jonathan M. Galazka 1 , 4 , 5 , Andrew D. Klocko 2 , 4 , Miki Uesaka 3 , Shinji Honda 3 , Eric U. Selker 2...
  4. Research: Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition
    • Dan E. Webster,
    • Brook Barajas,
    • Rose T. Bussat,
    • Karen J. Yan,
    • Poornima H. Neela,
    • Ross J. Flockhart,
    • Joanna Kovalski,
    • Ashley Zehnder,
    • and Paul A. Khavari
    Genome Res. May 2014 24: 751-760; Published in Advance January 17, 2014, doi:10.1101/gr.166231.113
    ...Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition Dan E. Webster , Brook Barajas 1 , Rose T. Bussat 1 , Karen J. Yan , Poornima H. Neela , Ross J. Flockhart , Joanna Kovalski...
  5. Research: Large-scale hypomethylated blocks associated with Epstein-Barr virus–induced B-cell immortalization
    • Kasper D. Hansen,
    • Sarven Sabunciyan,
    • Ben Langmead,
    • Noemi Nagy,
    • Rebecca Curley,
    • Georg Klein,
    • Eva Klein,
    • Daniel Salamon,
    • and Andrew P. Feinberg
    Genome Res. February 2014 24: 177-184; Published in Advance September 25, 2013, doi:10.1101/gr.157743.113
    ...Large-scale hypomethylated blocks associated with Epstein-Barr virus–induced B-cell immortalization Kasper D. Hansen 1 , 2 , 3 , 8 , Sarven Sabunciyan 2 , 4 , 8 , Ben Langmead 2 , 5 , Noemi Nagy 6 , Rebecca Curley 2 , 7...
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  6. Research: Core promoter T-blocks correlate with gene expression levels in C. elegans
    • Vladislav Grishkevich,
    • Tamar Hashimshony,
    • and Itai Yanai
    Genome Res. May 2011 21: 707-717; Published in Advance March 2, 2011, doi:10.1101/gr.113381.110
    ...-related genes and genes involved in nucleosome assembly (six GO terms from 15) (Supplemental Table S3). Consistently, an association of the TATA box with stress-related genes in Saccharomyces cerevisiae has been reported (Basehoar et al. 2004). We next asked whether genes with the T-blocks–SL1 supramotif show...
  7. Method: Highly accurate assembly polishing with DeepPolisher
    • Mira Mastoras,
    • Mobin Asri,
    • Lucas Brambrink,
    • Prajna Hebbar,
    • Alexey Kolesnikov,
    • Daniel E. Cook,
    • Maria Nattestad,
    • Julian Lucas,
    • Taylor S. Won,
    • Pi-Chuan Chang,
    • Andrew Carroll,
    • Benedict Paten,
    • Kishwar Shafin,
    • and and the Human Pangenome Reference Consortium
    Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
    ...to the assembly sequence) covered by that phase block. Secphase then retains the variants with alternative alleles in the selected haplotype of the phase block. Next, a variant block is created around each selected variant. The minimum block size can be set as a parameter (default = 100), and the actual size...
  8. Method: Partitioned multi-MUM finding for scalable pangenomics with MumemtoM
    • Vikram S. Shivakumar and
    • Ben Langmead
    Genome Res. February 2026 36: 397-404; Published in Advance November 7, 2025, doi:10.1101/gr.280940.125
    ...diverse s can be used to identify regions of evolutionary conservation. We identified collinear blocks from multi-MUMs present across 29 primate assemblies (including GRCh38 and CHM13). We considered all collinear blocks (with maximum space between MUMs of 100 bp) and noncollinear MUMs longer than 50 bp...
  9. Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
    • Xinghua Li,
    • Judith E. Mank,
    • and Liping Ban
    Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
    ..., Vancouver V6T 1Z4, Canada Corresponding author: liping_ban@163.comAbstractWe present the first chromosome-level assembly of the grasshopper, Locusta migratoria, one of the largest insect s. We use coverage differences between females (XX) and males (X0) to identify the X Chromosome gene content, and find...
  10. Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
    • Mari B. Gornitzka,
    • Egil Røsjø,
    • Uddalok Jana,
    • Easton E. Ford,
    • Alan Tourancheau,
    • William D. Lees,
    • Zachary Vanwinkle,
    • Melissa L. Smith,
    • Corey T. Watson,
    • and Andreas Lossius
    Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
    ...with a recent paper that found a low number of recombination events in HG002 using data from the Human Pan Reference Consortium (Lin et al. 2025).Our method successfully assembled all IGH haplotypes from four donors and one cell line into single-phase blocks and resolved novel structural variants. To achieve...
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