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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
..., Schweitzer PA, Bachman S, Green C, Wright CL, Campos EJ, Benson LD, Edwards J, et al. 2003. A cattle-human comparative map built with cattle BAC-ends and human sequence. Genome Res 13: 1966–1972. Larkin DM, Pape G, Donthu R, Auvil L, Welge M, Lewin HA. 2009. Breakpoint regions and homologous synteny blocks...
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RESOURCE: A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites
- Naoya Ihara,
- Akiko Takasuga,
- Kazunori Mizoshita,
- Haruko Takeda,
- Mayumi Sugimoto,
- Yasushi Mizoguchi,
- Takashi Hirano,
- Tomohito Itoh,
- Toshio Watanabe,
- Kent M. Reed,
- Warren M. Snelling,
- Steven M. Kappes,
- Craig W. Beattie,
- Gary L. Bennett,
- and Yoshikazu Sugimoto
Genome Res. October 2004 14: 1987-1998; doi:10.1101/gr.2741704
...., Schweitzer, P.A., Bachman, S., Green, C., Wright, C.L., Campos, E.J., Benson, L.D., Edwards, J., et al. 2003 . A cattle-human comparative map built with cattle BAC-ends and human sequence. Genome Res. 13 : 1966 -1972. ↵ Maddox, J.F., Davies, K.P., Crawford, A.M., Hulme, D.J., Vaiman, D., Cribiu, E...
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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
...in mammals: The shrew map. Acta Theriologica 2000 45 : 131 –142. ↵ Larkin, D.M., Everts-van der Wind, A., Rebeiz, M., Schweitzer, P.A., Bachman, S., Green, C.A., Wright, C.L., Campos, E.J., Benson, L.D., Edwards, J., et al. 2003 . A cattle–human comparative map built with cattle BAC-ends and human sequence...
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Resource: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Joana Damas,
- Rebecca O'Connor,
- Marta Farré,
- Vasileios Panagiotis E. Lenis,
- Henry J. Martell,
- Anjali Mandawala,
- Katie Fowler,
- Sunitha Joseph,
- Martin T. Swain,
- Darren K. Griffin,
- and Denis M. Larkin
Genome Res. May 2017 27: 875-884; Published in Advance November 30, 2016, doi:10.1101/gr.213660.116
...). Assembling s using next-generation sequencing (NGS) technologies, however, typically relies on integration of theNGSdatawith a pre-existing chromosome-level reference assembly built with previous sequencing/ mapping technologies (Larkin et al. 2012). Indeed, use of shortread NGS data rarely produces...
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RESOURCE: High-Density Rat Radiation Hybrid Maps Containing Over 24,000 SSLPs, Genes, and ESTs Provide a Direct Link to the Rat Genome Sequence
- Anne E. Kwitek,
- Jo Gullings-Handley,
- Jiaming Yu,
- Danilo C. Carlos,
- Kimberly Orlebeke,
- Jeff Nie,
- Jeffrey Eckert,
- Angela Lemke,
- Jaime Wendt Andrae,
- Susan Bromberg,
- Dean Pasko,
- Dan Chen,
- Todd E. Scheetz,
- Thomas L. Casavant,
- M. Bento Soares,
- Val C. Sheffield,
- Peter J. Tonellato,
- and Howard J. Jacob
Genome Res. April 2004 14: 750-757; doi:10.1101/gr.1968704
..., and mouse. Genome Res. 11 : 1935 -1943. ↵ Larkin, D., Wind, A.E.-v.d., Rebeiz, M., Schweitzer, P., Bachman, S., Green, C., Wright, C., Campos, E., Benson, L., Edwards, J., et al. 2003 . A cattle–human comparative map built with cattle BAC-ends and human sequence. Genome Res. 13 : 1966 -1972. ↵ McCarthy, L...
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Methods: Pooled genomic indexing of rhesus macaque
- Aleksandar Milosavljevic,
- Ronald A. Harris,
- Erica J. Sodergren,
- Andrew R. Jackson,
- Ken J. Kalafus,
- Anne Hodgson,
- Andrew Cree,
- Weilie Dai,
- Miklos Csuros,
- Baoli Zhu,
- Pieter J. de Jong,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. February 2005 15: 292-301; doi:10.1101/gr.3162505
...to a cancer cell's adaptive response to therapy. The key limitation of all BAC-end sequence mapping methods such as STC, BES, and ESP is their exclusive reliance on the BAC-end sequences. Specifically, BES has limited efficiency even across relatively closely related species such as mammals. About 10...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...inversions evolved to maintain these long-range physical interactions.MethodsBAC clone sequencing, assembly, and annotationWe conducted sequencing and assembly of BAC clones from the Felis catus female BAC library FSCC from Amplicon Express. Clones were chosen based on the mapping location of the BAC end...
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Letter: Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories
- Denis M. Larkin,
- Greg Pape,
- Ravikiran Donthu,
- Loretta Auvil,
- Michael Welge,
- and Harris A. Lewin
Genome Res. May 2009 19: 770-777; Published in Advance April 2, 2009, doi:10.1101/gr.086546.108
...., Wright, C.L., Campos, E.J., Benson, L.D., Edwards, J., et al. 2003. A cattle-human comparative map built with cattle BAC-ends and human sequence. Genome Res. 13: 1966– 1972. Li, M.O. and Flavell, R.A. 2008. Contextual regulation of inflammation: A duet by transforming growth factor-beta and interleukin...

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