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Review: Contrasting genetic architectures in different mouse reference populations used for studying complex traits
- David A. Buchner and
- Joseph H. Nadeau
Genome Res. June 2015 25: 775-791; Published in Advance May 7, 2015, doi:10.1101/gr.187450.114
...strains (Shao et al. 2010; Yazbek et al. 2011). Evidence from other species such as yeast, rats, and humans also shows that QTLs harbor multiple tightly linked sub-QTLs and causative genetic variants (Steinmetz et al. 2002; Nejentsev et al. 2007; Lango Allen et al. 2010; Ehret et al. 2012; Flister et al...
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Research: Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency
- Chan-Shuo Wu,
- Chun-Ying Yu,
- Ching-Yu Chuang,
- Michael Hsiao,
- Cheng-Fu Kao,
- Hung-Chih Kuo,
- and Trees-Juen Chuang
Genome Res. January 2014 24: 25-36; Published in Advance October 16, 2013, doi:10.1101/gr.159483.113
...experimental artifacts, candidates that satisfied any of the following in silico filters were eliminated: (1) chimeric junction sites containing short homologous sequences (SHSs) or gaps (as these tend to arise from template switching) (McManus et al. 2010); (2) sense–antisense fusion candidates containing...
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Research: The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- Santosh S. Atanur,
- İnanç Birol,
- Victor Guryev,
- Martin Hirst,
- Oliver Hummel,
- Catherine Morrissey,
- Jacques Behmoaras,
- Xose M. Fernandez-Suarez,
- Michelle D. Johnson,
- William M. McLaren,
- Giannino Patone,
- Enrico Petretto,
- Charles Plessy,
- Kathleen S. Rockland,
- Charles Rockland,
- Kathrin Saar,
- Yongjun Zhao,
- Piero Carninci,
- Paul Flicek,
- Ted Kurtz,
- Edwin Cuppen,
- Michal Pravenec,
- Norbert Hubner,
- Steven J.M. Jones,
- Ewan Birney,
- and Timothy J. Aitman
Genome Res. June 2010 20: 791-803; Published in Advance April 29, 2010, doi:10.1101/gr.103499.109
...physiological and pathophysiological phenotypes, scores of which have been mapped to the as quantitative trait loci (QTLs) (Rat Genome Database; http://rgd.mcw. edu/). For some of the QTLs, the underlying genes and nucleotide variants have been identified (Aitman et al. 2008). In the early 1980s, the SHR...
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Letter: A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains
- Yongming Wang,
- František Liška,
- Claudia Gosele,
- Lucie Šedová,
- Vladimír Křen,
- Drahomíra Křenová,
- Zoltán Ivics,
- Norbert Hubner,
- and Zsuzsanna Izsvák
Genome Res. January 2010 20: 19-27; Published in Advance November 3, 2009, doi:10.1101/gr.100073.109
...cloned a potentially autonomous RnERV-K8e element identified by in silico analysis and, using an in vitro retrotransposition assay, demonstrated that it is capable of retrotransposition. This particular element (named Rat-ρ, pronounced “retro”) encodes a retroviral envelope gene ( env ); however, env...
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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
...norvegicus. Hear. Res. 174 : 86 -92. ↵ Twigger, S.N., Nie, J., Ruotti, V., Yu, J., Chen, D., Li, D., Mathis, J., Narayanasamy, V., Gopinath, G.R., Pasko, D., et al. 2004 . Integrative genomics: In silico coupling of rat physiology and complex traits with mouse and human data. Genome Res. (this issue...
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PERSPECTIVE: Genomics of the future: Identification of quantitative trait loci in the mouse
- Lorraine Flaherty,
- Bruce Herron,
- and Derek Symula
Genome Res. December 2005 15: 1741-1745; doi:10.1101/gr.3841405
...to regions of differing haplotypes between the parental strains, and thus were strong candidates for regulatory QTLs. Like the LD studies described above, genetical genomics is a highly in silico method that has increased power to compare phenotypes from existing databases with emerging expression data...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...promoter(s) and enhancer(s) (Zhang et al. 2022). Although many tools exist for this purpose, newcomers should understand the benefits and limitations of in silico approaches. With advanced, often algorithmically opaque, machine learning tools now available, a cautious approach can save time and effort...
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Resource: The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains
- Toyoyuki Takada,
- Toshinobu Ebata,
- Hideki Noguchi,
- Thomas M. Keane,
- David J. Adams,
- Takanori Narita,
- Tadasu Shin-I,
- Hironori Fujisawa,
- Atsushi Toyoda,
- Kuniya Abe,
- Yuichi Obata,
- Yoshiyuki Sakaki,
- Kazuo Moriwaki,
- Asao Fujiyama,
- Yuji Kohara,
- and Toshihiko Shiroishi
Genome Res. August 2013 23: 1329-1338; Published in Advance April 19, 2013, doi:10.1101/gr.156497.113
.... molossinus and M. m. domesticus, respectively. We also used the sequence of SPRET/EiJ as a reference for Mus spretus and used the rat sequence as an outgroup. The WSB and SPRET/EiJ sequences were obtained from the MGP data set. The genomic regions for which a single B6/MSM topology was supported...
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Research: Adaptive selection of an incretin gene in Eurasian populations
- Chia Lin Chang,
- James J. Cai,
- Chiening Lo,
- Jorge Amigo,
- Jae-Il Park,
- and Sheau Yu Teddy Hsu
Genome Res. January 2011 21: 21-32; Published in Advance October 26, 2010, doi:10.1101/gr.110593.110
.... The right panels showed the dark field and phased contrast images of merged immunofluorescent signals (8003). The white horizontal bar in each panel represents a distance of 30 mm. (C ) GIP, GIP55G, and GIP55S suppressed exogenous glucose in fasting rats in vivo. Each of the three GIP peptides reduced...
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Letter: Ecological adaptation determines functional mammalian olfactory subgenomes
- Sara Hayden,
- Michaël Bekaert,
- Tess A. Crider,
- Stefano Mariani,
- William J. Murphy,
- and Emma C. Teeling
Genome Res. January 2010 20: 1-9; Published in Advance December 1, 2009, doi:10.1101/gr.099416.109
...values lay inside the simulated 95% CI (Supplemental Fig. 5). In silico methods OR family assignment and classification of retrieved and amplified sequences A unique probabilistic genomic search algorithmwas developed to identify theOR genes, assign their class and family, and distinguish between...

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