Searching journal content for articles similar to Taylor et al. 14 (4): 555.

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  1. Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
    • Chong Li,
    • Marc Jan Bonder,
    • Sabriya Syed,
    • Matthew Jensen,
    • Human Genome Structural Variation Consortium (HGSVC),
    • HGSVC Functional Analysis Working Group,
    • Mark B. Gerstein,
    • Michael C. Zody,
    • Mark J.P. Chaisson,
    • Michael E. Talkowski,
    • Tobias Marschall,
    • Jan O. Korbel,
    • Evan E. Eichler,
    • Charles Lee,
    • and Xinghua Shi
    Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
    ...associating domains (TADs), and loops. TAD boundaries, separating adjacent TADs, have been found to be well conserved across mammalian species and more evolutionarily constrained than TADs themselves. Recent studies show that structural variants (SVs) can modify 3D s through the disruption of TADs, which play...
  2. Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
    • Yu-Chi Chen,
    • David L.J. Vendrami,
    • Maximilian L. Huber,
    • Luisa E.Y. Handel,
    • Christopher R. Cooney,
    • Joseph I. Hoffman,
    • and Toni I. Gossmann
    Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
    ...impact of NUMT integration, we identified mitochondrial insertions in the nuclear s of more than 1000 mammalian and avian species. Specifically, we analyzed 680 mammalian and 458 avian s with both nuclear and mitochondrial assemblies available from public databases. Using a previously published...
  3. Research: Natural genetic variation caused by small insertions and deletions in the human genome
    • Ryan E. Mills,
    • W. Stephen Pittard,
    • Julienne M. Mullaney,
    • Umar Farooq,
    • Todd H. Creasy,
    • Anup A. Mahurkar,
    • David M. Kemeza,
    • Daniel S. Strassler,
    • Chris P. Ponting,
    • Caleb Webber,
    • and Scott E. Devine
    Genome Res. June 2011 21: 830-839; Published in Advance April 1, 2011, doi:10.1101/gr.115907.110
    ...Natural genetic variation caused by small insertions and deletions in the human genome Ryan E. Mills 1 , 8 , W. Stephen Pittard 2 , Julienne M. Mullaney 3 , 4 , Umar Farooq 3 , Todd H. Creasy 3 , Anup A. Mahurkar 3 , David...
  4. Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
    • Jianghan Qu,
    • Emily Hodges,
    • Antoine Molaro,
    • Pascal Gagneux,
    • Matthew D. Dean,
    • Gregory J. Hannon,
    • and Andrew D. Smith
    Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
    ...methylation has substantially impacted the large-scale evolution of mammalian s. Spontaneous deamination elevates the mutation rate at methylated cytosines (Bird 1980). Consequently, germline DNA methylation profiles have shaped the CpG landscape of mammalian s (Cohen et al. 2011), resulting in the CpG island...
  5. Letter: Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions
    • Erika M. Kvikstad,
    • Francesca Chiaromonte,
    • and Kateryna D. Makova
    Genome Res. July 2009 19: 1153-1164; Published in Advance June 5, 2009, doi:10.1101/gr.088922.108
    ...Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions Erika M. Kvikstad 1 , 2 , Francesca Chiaromonte 1 , 3 and Kateryna D. Makova 1 , 2 , 4 1 Center for Comparative Genomics and Bioinformatics...
  6. Method: Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
    • Adrian Viehweger,
    • Sebastian Krautwurst,
    • Kevin Lamkiewicz,
    • Ramakanth Madhugiri,
    • John Ziebuhr,
    • Martin Hölzer,
    • and Manja Marz
    Genome Res. September 2019 29: 1545-1554; Published in Advance August 22, 2019, doi:10.1101/gr.247064.118
    ...haplotypes.Coronaviruses (subfamily Coronavirinae, family Coronaviridae, order Nidovirales) are enveloped positive-sense (+) single-stranded (ss) RNA viruses that infect a variety of mammalian and avian hosts and are of significant medical and economic importance, as illustrated by recent zoonotic...
  7. Research: Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals
    • Ulrike Böhme,
    • Thomas D. Otto,
    • James A. Cotton,
    • Sascha Steinbiss,
    • Mandy Sanders,
    • Samuel O. Oyola,
    • Antoine Nicot,
    • Sylvain Gandon,
    • Kailash P. Patra,
    • Colin Herd,
    • Ellen Bushell,
    • Katarzyna K. Modrzynska,
    • Oliver Billker,
    • Joseph M. Vinetz,
    • Ana Rivero,
    • Chris I. Newbold,
    • and Matthew Berriman
    Genome Res. April 2018 28: 547-560; Published in Advance March 2, 2018, doi:10.1101/gr.218123.116
    ...—with their richer metabolism and transport—is easier to evolve than development in enucleated mammalian erythrocytes, it is tempting to speculate that these parasites more closely resemble the ancestral state.In this study, we describe the sequence, annotation, and comparative genomics of Plasmodium relictum SGS1...
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  8. Research: Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes
    • Vedran Franke,
    • Sravya Ganesh,
    • Rosa Karlic,
    • Radek Malik,
    • Josef Pasulka,
    • Filip Horvat,
    • Maja Kuzman,
    • Helena Fulka,
    • Marketa Cernohorska,
    • Jana Urbanova,
    • Eliska Svobodova,
    • Jun Ma,
    • Yutaka Suzuki,
    • Fugaku Aoki,
    • Richard M. Schultz,
    • Kristian Vlahovicek,
    • and Petr Svoboda
    Genome Res. August 2017 27: 1384-1394; Published in Advance May 18, 2017, doi:10.1101/gr.216150.116
    ...Retrotransposons are “copy-and-paste” insertional mutagens that substantially contribute to mammalian content. Retrotransposons often carry long terminal repeats (LTRs) for retrovirus-like reverse transcription and integration into the . We report an extraordinary impact of a group of LTRs from the mammalian...
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  9. Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
    • David Thybert,
    • Maša Roller,
    • Fábio C.P. Navarro,
    • Ian Fiddes,
    • Ian Streeter,
    • Christine Feig,
    • David Martin-Galvez,
    • Mikhail Kolmogorov,
    • Václav Janoušek,
    • Wasiu Akanni,
    • Bronwen Aken,
    • Sarah Aldridge,
    • Varshith Chakrapani,
    • William Chow,
    • Laura Clarke,
    • Carla Cummins,
    • Anthony Doran,
    • Matthew Dunn,
    • Leo Goodstadt,
    • Kerstin Howe,
    • Matthew Howell,
    • Ambre-Aurore Josselin,
    • Robert C. Karn,
    • Christina M. Laukaitis,
    • Lilue Jingtao,
    • Fergal Martin,
    • Matthieu Muffato,
    • Stefanie Nachtweide,
    • Michael A. Quail,
    • Cristina Sisu,
    • Mario Stanke,
    • Klara Stefflova,
    • Cock Van Oosterhout,
    • Frederic Veyrunes,
    • Ben Ward,
    • Fengtang Yang,
    • Golbahar Yazdanifar,
    • Amonida Zadissa,
    • David J. Adams,
    • Alvis Brazma,
    • Mark Gerstein,
    • Benedict Paten,
    • Son Pham,
    • Thomas M. Keane,
    • Duncan T. Odom,
    • and Paul Flicek
    Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
    ...species can exhibit large-scale structural changes ranging from lineage-specific retrotransposon insertions to karyotype differences. The mechanisms driving these changes may vary between mammalian lineages, and the reasons for these differences remain mostly unknown. For example, the rate of chromosomal...
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  10. Research: Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation
    • Christine Roden,
    • Jonathan Gaillard,
    • Shaveta Kanoria,
    • William Rennie,
    • Syndi Barish,
    • Jijun Cheng,
    • Wen Pan,
    • Jun Liu,
    • Chris Cotsapas,
    • Ye Ding,
    • and Jun Lu
    Genome Res. March 2017 27: 374-384; Published in Advance January 13, 2017, doi:10.1101/gr.208900.116
    ...in the are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem...
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