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Method: A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission
- Mikhail Liskovykh,
- Nikolay V. Goncharov,
- Nikolai Petrov,
- Vasilisa Aksenova,
- Gianluca Pegoraro,
- Laurent L. Ozbun,
- William C. Reinhold,
- Sudhir Varma,
- Mary Dasso,
- Vadim Kumeiko,
- Hiroshi Masumoto,
- William C. Earnshaw,
- Vladimir Larionov,
- and Natalay Kouprina
Genome Res. October 2019 29: 1719-1732; Published in Advance September 12, 2019, doi:10.1101/gr.254276.119
...completing the annotation of genetic loci controlling chromosome transmission.Genome-wide siRNA screens have been used to interrogate a variety of molecular mechanisms related to increased sensitivity to ionizing radiation or spontaneous gamma H2AX (phosphorylated histone H2AX at serine 139) (Paulsen et al...
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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
...rearrangements were predicted by identifying BACs that reliably mapped by four- or three-pool indices to two distinct loci within a human chromosome. Only the loci that were &gt;200 kbp apart were considered. Simulating detection of rearrangements A total of 540 BACs were generated by using randomly selected...
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LETTER: Genetic Variation in Coding Regions Between and Within Commonly Used Inbred Rat Strains
- Bart M.G. Smits,
- Bert F.M. van Zutphen,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1285-1290; doi:10.1101/gr.2155004
...1999 ). Pharmacogenomic approaches in model organisms are expected to contribute considerably to the understanding of the function of specific genes in relation to drug response ( Watters and McLeod 2002 ). Characterization of the naturally occurring genetic variation at such loci, for example...
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Methods: Decoding the fine-scale structure of a breast cancer genome and transcriptome
- Stanislav Volik,
- Benjamin J. Raphael,
- Guiqing Huang,
- Michael R. Stratton,
- Graham Bignel,
- John Murnane,
- John H. Brebner,
- Krystyna Bajsarowicz,
- Pamela L. Paris,
- Quanzhou Tao,
- David Kowbel,
- Anna Lapuk,
- Dmitri A. Shagin,
- Irina A. Shagina,
- Joe W. Gray,
- Jan-Fang Cheng,
- Pieter J. de Jong,
- Pavel Pevzner,
- and Colin Collins
Genome Res. March 2006 16: 394-404; Published in Advance February 3, 2006, doi:10.1101/gr.4247306
...directions using the breast cancer cell line MCF-7. First, targeted ESP is applied to multiple amplified loci, revealing a complex process of rearrangement and coamplification in these regions reminiscent of breakage/fusion/bridge cycles. Second, breakpoints identified by ESP are confirmed using...
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PERSPECTIVE: The mouse genome
- Jean Louis Guénet
Genome Res. December 2005 15: 1729-1740; doi:10.1101/gr.3728305
...made with this small mammal have regularly contributed to enrich our knowledge of mammalian biology and pathology, ranging from embryonic development to metabolic disease, histocompatibility, immunology, behavior, and cancer. Over the past two decades, a number of large-scale integrated and concerted...
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LETTER: Novel patterns of genome rearrangement and their association with survival in breast cancer
- James Hicks,
- Alexander Krasnitz,
- B. Lakshmi,
- Nicholas E. Navin,
- Michael Riggs,
- Evan Leibu,
- Diane Esposito,
- Joan Alexander,
- Jen Troge,
- Vladimir Grubor,
- Seungtai Yoon,
- Michael Wigler,
- Kenny Ye,
- Anne-Lise Børresen-Dale,
- Bjørn Naume,
- Ellen Schlicting,
- Larry Norton,
- Torsten Hägerström,
- Lambert Skoog,
- Gert Auer,
- Susanne Månér,
- Pär Lundin,
- and Anders Zetterberg
Genome Res. December 2006 16: 1465-1479; doi:10.1101/gr.5460106
..., as studied by fluorescence in situ hybridization (FISH) or Q-PCR, has been clinically useful ( van de Vijver et al. 1987 ; Slamon et al. 1989 ; Menard et al. 2001 ). ROMA provides an extra measure of resolution in genomic analysis that might be useful in clinical evaluation, as well as delineating loci...
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ARTICLE: Extensive and breed-specific linkage disequilibrium in Canis familiaris
- Nathan B. Sutter,
- Michael A. Eberle,
- Heidi G. Parker,
- Barbara J. Pullar,
- Ewen F. Kirkness,
- Leonid Kruglyak,
- and Elaine A. Ostrander
Genome Res. December 2004 14: 2388-2396; Published in Advance November 15, 2004, doi:10.1101/gr.3147604
...for most of the gene pool. The only other study of LD in dogs focused on a purpose-bred pedigree of Labrador Retrievers and Greyhounds managed at Cornell Veterinary College. This cross was designed to identify genes for hip dysplasia ( Lou et al. 2003 ). In that study, again using microsatellites, LD...
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RESOURCE: Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics
- Matthew L. Rise,
- Kristian R. von Schalburg,
- Gordon D. Brown,
- Melanie A. Mawer,
- Robert H. Devlin,
- Nathanael Kuipers,
- Maura Busby,
- Marianne Beetz-Sargent,
- Roberto Alberto,
- A. Ross Gibbs,
- Peter Hunt,
- Robert Shukin,
- Jeffrey A. Zeznik,
- Colleen Nelson,
- Simon R.M. Jones,
- Duane E. Smailus,
- Steven J.M. Jones,
- Jacqueline E. Schein,
- Marco A. Marra,
- Yaron S.N. Butterfield,
- Jeff M. Stott,
- Siemon H.S. Ng,
- William S. Davidson,
- and Ben F. Koop
Genome Res. March 2004 14: 478-490; Published in Advance February 12, 2004, doi:10.1101/gr.1687304
...Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics Matthew L. Rise 1 , Kristian R. von Schalburg 1 , Gordon D. Brown 1 , Melanie A. Mawer 1 , Robert H. Devlin 3...

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