Searching journal content for articles similar to Ihara et al. 14 (10a): 1987.

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  1. Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
    • Dmitry Antipov,
    • Mikko Rautiainen,
    • Sergey Nurk,
    • Brian P. Walenz,
    • Steven J. Solar,
    • Adam M. Phillippy,
    • and Sergey Koren
    Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
    ...the issue of Hi-C links between homologous nodes, we construct an additional set of edges on top of the ULA graph that are based on sequence similarity between the nodes, called the Match Graph. Homologous nodes in the ULA graph are identified by an all-versus-all similarity search using MashMap3 (Kille et...
    OPEN ACCESS ARTICLE
  2. Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
    • Yang Zhou,
    • Lv Yang,
    • Xiaotao Han,
    • Jiazheng Han,
    • Yan Hu,
    • Fan Li,
    • Han Xia,
    • Lingwei Peng,
    • Clarissa Boschiero,
    • Benjamin D. Rosen,
    • Derek M. Bickhart,
    • Shujun Zhang,
    • Aizhen Guo,
    • Curtis P. Van Tassell,
    • Timothy P.L. Smith,
    • Liguo Yang,
    • and George E. Liu
    Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
    ...groups and represent all SVs. The 1000 Bull Genomes Project was initiated to provide a database for the imputation of genetic variants (mainly SNP and indel) in all cattle breeds. However, the approach in that project creates a bias against SV as the regions with multiple mapped reads are generally...
  3. RESOURCE: A Cattle–Human Comparative Map Built with Cattle BAC-Ends and Human Genome Sequence
    • Denis M. Larkin,
    • Annelie Everts-van der Wind,
    • Mark Rebeiz,
    • Peter A. Schweitzer,
    • Sharon Bachman,
    • Cheryl Green,
    • Chris L. Wright,
    • Edhilvia J. Campos,
    • Leslie D. Benson,
    • Jennifer Edwards,
    • Lei Liu,
    • Kazutoyo Osoegawa,
    • James E. Womack,
    • Pieter J. de Jong,
    • and Harris A. Lewin
    Genome Res. August 2003 13: 1966-1972; doi:10.1101/gr.1560203
    ...boundaries appear to be conserved in all three species. The BAC clone-based comparative map provides a foundation for the evolutionary analysis of mammalian karyotypes and for sequencing of the cattle genome. Footnotes [Supplemental material is available online at www.genome...
  4. Commentary: Every genome sequence needs a good map
    • Harris A. Lewin,
    • Denis M. Larkin,
    • Joan Pontius,
    • and Stephen J. O'Brien
    Genome Res. November 2009 19: 1925-1928; Published in Advance July 13, 2009, doi:10.1101/gr.094557.109
    ...human microsatellite loci. Genomics 87: 30–38. Schibler L, Roig A, Mahe MF, Laurent P, Hayes H, Rodolphe F, Cribiu EP. 2006. High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian evolution. BMC Genomics 7: 194. doi: 10...
  5. Resource: Analysis of copy number variations among diverse cattle breeds
    • George E. Liu,
    • Yali Hou,
    • Bin Zhu,
    • Maria Francesca Cardone,
    • Lu Jiang,
    • Angelo Cellamare,
    • Apratim Mitra,
    • Leeson J. Alexander,
    • Luiz L. Coutinho,
    • Maria Elena Dell'Aquila,
    • Lou C. Gasbarre,
    • Gianni Lacalandra,
    • Robert W. Li,
    • Lakshmi K. Matukumalli,
    • Dan Nonneman,
    • Luciana C. de A. Regitano,
    • Tim P.L. Smith,
    • Jiuzhou Song,
    • Tad S. Sonstegard,
    • Curt P. Van Tassell,
    • Mario Ventura,
    • Evan E. Eichler,
    • Tara G. McDaneld,
    • and John W. Keele
    Genome Res. May 2010 20: 693-703; Published in Advance March 8, 2010, doi:10.1101/gr.105403.110
    ...insight into mechanisms of bovine evolution and generate a valuable resource for cattle genomics research. This high-quality cattle CNV map fills the gaps left out by the current SNP-based -wide association and selection studies.Amore comprehensiveappreciationof the full dimensionof bovine genetic...
  6. LETTER: An Ordered Comparative Map of the Cattle and Human Genomes
    • Mark R. Band,
    • Joshua H. Larson,
    • Mark Rebeiz,
    • Cheryl A. Green,
    • D. Wayne Heyen,
    • Jena Donovan,
    • Ryan Windish,
    • Chad Steining,
    • Prapti Mahyuddin,
    • James E. Womack,
    • and Harris A. Lewin
    Genome Res. September 1, 2000 10: 1359-1368; doi:10.1101/gr.145900
    ...An Ordered Comparative Map of the Cattle and Human Genomes Mark R. Band 1 , 3 , Joshua H. Larson 1 , 3 , Mark Rebeiz 1 , Cheryl A. Green 1 , D. Wayne Heyen 1 , Jena Donovan 1 , Ryan Windish 1 , Chad Steining 1...
  7. RESOURCE: A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates
    • Annelie Everts-van der Wind,
    • Srinivas R. Kata,
    • Mark R. Band,
    • Mark Rebeiz,
    • Denis M. Larkin,
    • Robin E. Everts,
    • Cheryl A. Green,
    • Lei Liu,
    • Shreedhar Natarajan,
    • Tom Goldammer,
    • Jun Heon Lee,
    • Stephanie McKay,
    • James E. Womack,
    • and Harris A. Lewin
    Genome Res. July 2004 14: 1424-1437; doi:10.1101/gr.2554404
    ...A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates Annelie Everts-van der Wind 1 , Srinivas R. Kata 3 , Mark R. Band 2 , Mark Rebeiz 1 , Denis M. Larkin 1 , Robin E. Everts 1...
  8. REVIEW: A comprehensive map of the porcine genome.
    • G A Rohrer,
    • L J Alexander,
    • Z Hu,
    • T P Smith,
    • J W Keele,
    • and C W Beattie
    Genome Res. May 1996 6: 371-391; doi:10.1101/gr.6.5.371
    ...A comprehensive map of the porcine genome. G A Rohrer , L J Alexander , Z Hu , T P Smith , J W Keele , and C W Beattie U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research...
  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
    ...Gen platform. The OpGen Genome-Builder software was used to assemble the NGS scaffolds into super scaffolds based on the optical map. Super scaffolds and scaffolds were assembled into pseudochromosomes with Ragout (Kolmogorov et al. 2016). To guide the assembly, Ragout used a multiple alignment constructed...
    OPEN ACCESS ARTICLE
  10. RESOURCE: An Enhanced Linkage Map of the Sheep Genome Comprising More Than 1000 Loci
    • Jillian F. Maddox,
    • Kizanne P. Davies,
    • Allan M. Crawford,
    • Dennis J. Hulme,
    • Daniel Vaiman,
    • Edmond P. Cribiu,
    • Bradley A. Freking,
    • Ken J. Beh,
    • Noelle E. Cockett,
    • Nina Kang,
    • Christopher D. Riffkin,
    • Roger Drinkwater,
    • Stephen S. Moore,
    • Ken G. Dodds,
    • Joanne M. Lumsden,
    • Tracey C. van Stijn,
    • Sin H. Phua,
    • David L. Adelson,
    • Heather R. Burkin,
    • Judith E. Broom,
    • Johannes Buitkamp,
    • Lisa Cambridge,
    • William T. Cushwa,
    • Emily Gerard,
    • Susan M. Galloway,
    • Blair Harrison,
    • Rachel J. Hawken,
    • Stefan Hiendleder,
    • Hannah M. Henry,
    • Juan F. Medrano,
    • Korena A. Paterson,
    • Laurent Schibler,
    • Roger T. Stone,
    • and Beryl van Hest
    Genome Res. July 1, 2001 11: 1275-1289; Published in Advance June 12, 2001, doi:10.1101/gr.135001
    ...map have also been mapped by linkage analysis in cattle, and 209 of the loci mapped on the sheep linkage map have also been placed on the goat linkage map. Inspection of ruminant linkage maps indicates that the genomic coverage by the current sheep linkage map is comparable to that of the available...
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