Searching journal content for articles similar to Harr 16 (10): 1193.

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  1. Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
    • Leandros Boukas,
    • Teresa Romeo Luperchio,
    • Afrooz Razi,
    • Kasper D. Hansen,
    • and Hans T. Bjornsson
    Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
    ...in KS1 and KS2 = 60.01 and 1508.9, respectively.Aging-related regions show preferentially disrupted chromatin accessibility in KS1 and KS2 neurons but not in B or T cellsOur findings yield insights into (1) the genomic distribution of the chromatin defects in KS1 and KS2 and (2) the cell type...
  2. Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
    • DongAhn Yoo,
    • Katherine M. Munson,
    • and Evan E. Eichler
    Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
    ...of these regions in chimpanzees and gorillas. Detailed analyses of the composition of the associated terminal 32 bp satellite array from chimpanzee (termed pCht) and intervening segmental duplication (SD) spacers confirm two independent origins in the Pan and gorilla lineages. In chimpanzee and bonobo, we estimate...
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  3. Research: Gene amplification as double minutes or homogeneously staining regions in solid tumors: Origin and structure
    • Clelia Tiziana Storlazzi,
    • Angelo Lonoce,
    • Maria C. Guastadisegni,
    • Domenico Trombetta,
    • Pietro D'Addabbo,
    • Giulia Daniele,
    • Alberto L'Abbate,
    • Gemma Macchia,
    • Cecilia Surace,
    • Klaas Kok,
    • Reinhard Ullmann,
    • Stefania Purgato,
    • Orazio Palumbo,
    • Massimo Carella,
    • Peter F. Ambros,
    • and Mariano Rocchi
    Genome Res. September 2010 20: 1198-1206; Published in Advance July 14, 2010, doi:10.1101/gr.106252.110
    ...Gene amplification as double minutes or homogeneously staining regions in solid tumors: Origin and structure Clelia Tiziana Storlazzi 1 , Angelo Lonoce 1 , Maria C. Guastadisegni 1 , Domenico Trombetta 1 , Pietro D'Addabbo 1 , Giulia...
  4. Method: spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model
    • Tianyu Liu,
    • Tinglin Huang,
    • Wengong Jin,
    • Tinyi Chu,
    • Rex Ying,
    • and Hongyu Zhao
    Genome Res. April 2026 36: 754-768; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
    ...with the classification of cell type. Therefore, we recommend checking the predefined number of clusters in the testing data sets before using spRefine as a pretraining framework.Predicting survival and disease states for cancer patients from imputed profilesThe imputed gene expression profiles not only provide enriched...
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  5. Method: Accurate short-read alignment through r-index-based pangenome indexing
    • Rahul Varki,
    • Massimiliano Rossi,
    • Eddie Ferro,
    • Marco Oliva,
    • Erik Garrison,
    • Ben Langmead,
    • and Christina Boucher
    Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
    ...regions across multiple s. Common regions in the pan are collapsed into single nodes and single edges, making the representation efficient for pans with a lot of shared DNA. For collections of highly repetitive s, graphs can efficiently compress the pan. However, there are downsides to graph-based pan...
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  6. Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
    • Sudeshna Majumdar,
    • Lakshmi Sowjanya Bammidi,
    • Hemant C. Naik,
    • Avinchal Manhas,
    • Runumi Baro,
    • Akash Kalita,
    • Amlan Jyoti Naskar,
    • Sundarraj Nidharshan,
    • Girija S. Bariha,
    • Dimple Notani,
    • and Srimonta Gayen
    Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
    ...and autosomes. Finally, we show -wide alterations of the occupancy of architectural proteins CTCF/RAD21, including at many loci of the inactive X such as the Xist upstream regions and the Firre locus, which is critical for maintaining inactive X conformation. Taken together, we demonstrate that the Xist...
  7. RESOURCE: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
    • Vardhman K. Rakyan,
    • Thomas A. Down,
    • Natalie P. Thorne,
    • Paul Flicek,
    • Eugene Kulesha,
    • Stefan Gräf,
    • Eleni M. Tomazou,
    • Liselotte Bäckdahl,
    • Nathan Johnson,
    • Marlis Herberth,
    • Kevin L. Howe,
    • David K. Jackson,
    • Marcos M. Miretti,
    • Heike Fiegler,
    • John C. Marioni,
    • Ewan Birney,
    • Tim J.P. Hubbard,
    • Nigel P. Carter,
    • Simon Tavaré,
    • and Stephan Beck
    Genome Res. September 2008 18: 1518-1529; Published in Advance June 24, 2008, doi:10.1101/gr.077479.108
    ...An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) Vardhman K. Rakyan 1 , 9 , 10 , Thomas A. Down 2 , 9 , Natalie P. Thorne 3 , 9 , Paul Flicek 4 , 9...
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  8. Resource: Epigenomics of embryogenesis in turbot
    • Oscar Aramburu,
    • Belen G Pardo,
    • Ada Jimenez-Gonzalez,
    • Andrés Blanco-Hortas,
    • Daniel Macqueen,
    • Carmen Bouza,
    • and Paulino Martinez
    Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
    ...-egg recognition, along with more 228 generalist functions associated with cell-cell recognition, cell cycle progress, 229 DNA replication and RNA processing. 230 Chromatin accessibility and histone mark mapping 231 Open chromatin regions (ATAC-seq) and those including histone epigenetic 232 marks (ChIP-seq) for H...
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  9. Method: Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes
    • Meng Chen,
    • Ran Wei,
    • Gang Wei,
    • Mingqing Xu,
    • Zhixi Su,
    • Chen Zhao,
    • and Ting Ni
    Genome Res. May 2021 31: 890-899; Published in Advance April 19, 2021, doi:10.1101/gr.270256.120
    ....Genome-wide association studies (GWASs) have reported that a large proportion of human disease-associated single nucleotide variants (SNVs) are located in noncoding regions, including enhancer, promoter, 5′ untranslated region (5′ UTR), intron, 3′ untranslated region (3′ UTR), and intergenic regions (Lawrenson et al...
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  10. Research: Genotype imputation from low-coverage data for medical and population genetic analyses
    • Simone Andrea Biagini,
    • Sara Becelaere,
    • Mio Aerden,
    • Tatjana Jatsenko,
    • Laurens Hannes,
    • Philip Van Damme,
    • Jeroen Breckpot,
    • Koenraad Devriendt,
    • Bernard Thienpont,
    • Joris Robert Vermeesch,
    • Isabelle Cleynen,
    • and Toomas Kivisild
    Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
    ...members of the same family are within the same healthcare system (Johnson et al. 2022). However, we applied a stricter threshold, considering any pair of individuals with a kinship coefficient above 0.044 (up to third-degree relatives) as related. Notably, when cross-checking our results with additional...
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