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Resource: GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis
- Robyn L. Ball,
- Molly A. Bogue,
- Hongping Liang,
- Anuj Srivastava,
- David G. Ashbrook,
- Anna Lamoureux,
- Matthew W. Gerring,
- Alexander S. Hatoum,
- Matthew J. Kim,
- Hao He,
- Jake Emerson,
- Alexander K. Berger,
- David O. Walton,
- Keith Sheppard,
- Baha El Kassaby,
- Francisco Castellanos,
- Govindarajan Kunde-Ramamoorthy,
- Lu Lu,
- John Bluis,
- Sejal Desai,
- Beth A. Sundberg,
- Gary Peltz,
- Zhuoqing Fang,
- Gary A. Churchill,
- Robert W. Williams,
- Arpana Agrawal,
- Carol J. Bult,
- Vivek M. Philip,
- and Elissa J. Chesler
Genome Res. January 2024 34: 145-159; Published in Advance January 30, 2024, doi:10.1101/gr.278157.123
...of genetic variation and phenotypic diversity in health and disease. For example, GenomeMUSter can be used for GWAS and genetic meta-analysis, used to refine genetic loci underlying trait variation across mouse strain panels (Raza et al. 2023), and used for a host of other -scale operations. The extant...
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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
...Research Institute, Seattle, Washington 98122, USA Quantitative trait loci (QTLs) are being used to study genetic networks, protein functions, and systems properties that underlie phenotypic variation and disease risk in humans, model organisms, agricultural species, and natural populations. The challenges...
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Method: Identification and dynamic quantification of regulatory elements using total RNA
- Sascha H. Duttke,
- Max W. Chang,
- Sven Heinz,
- and Christopher Benner
Genome Res. November 2019 29: 1836-1846; Published in Advance October 24, 2019, doi:10.1101/gr.253492.119
...for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSSs) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription...
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Method: High resolution mapping of modified DNA nucleobases using excision repair enzymes
- D. Suzi Bryan,
- Monica Ransom,
- Biniam Adane,
- Kerri York,
- and Jay R. Hesselberth
Genome Res. September 2014 24: 1534-1542; Published in Advance July 11, 2014, doi:10.1101/gr.174052.114
...-216-01-DMC), a Department of Defense Visionary Postdoc award (M.R.,W81XWH-12-1-0333), and an NIH Molecular Biology Training grant (D.S.B., T32 GM008730). References The 1000 Genomes Project Consortium. 2012. An integratedmap of genetic variation from 1,092 human s. Nature 491: 56–65. Agier N, Fischer G. 2012...
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Research: Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides
- Kelly M. Balmant,
- Jerald D. Noble,
- Filipe C. Alves,
- Christopher Dervinis,
- Daniel Conde,
- Henry W. Schmidt,
- Ana I. Vazquez,
- William B. Barbazuk,
- Gustavo de los Campos,
- Marcio F.R. Resende, Jr.,
- and Matias Kirst
Genome Res. August 2020 30: 1131-1143; Published in Advance August 19, 2020, doi:10.1101/gr.261438.120
..., quantitative phenotype and can be subjected to association mapping to identify polymorphisms responsible for transcript abundance variation among individuals and gene expression regulation. In this context, polymorphisms associated with gene expression are referred to as expression quantitative trait loci (e...
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Research: A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy
- Ayesha Noorani,
- Jan Bornschein,
- Andy G. Lynch,
- Maria Secrier,
- Achilleas Achilleos,
- Matthew Eldridge,
- Lawrence Bower,
- Jamie M.J. Weaver,
- Jason Crawte,
- Chin-Ann Ong,
- Nicholas Shannon,
- Shona MacRae,
- Nicola Grehan,
- Barbara Nutzinger,
- Maria O'Donovan,
- Richard Hardwick,
- Simon Tavaré,
- Rebecca C. Fitzgerald,
- and on behalf of the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium
Genome Res. June 2017 27: 902-912; Published in Advance May 2, 2017, doi:10.1101/gr.214296.116
...provided written consent for participation in this study and the staff at all participating sites. References The 1000Genomes Project Consortium. 2015. A global reference for human genetic variation. Nature 526: 68–74. Alderson D, Langley RE, Nankivell MG, Blazeby JM, Griffin M, Crellin A, Grabsch HI...
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ARTICLE: The Nuclear Receptor Superfamily Has Undergone Extensive Proliferation and Diversification in Nematodes
- Ann E. Sluder,
- Siuyien Wong Mathews,
- David Hough,
- Viravuth P. Yin,
- and Claude V. Maina
Genome Res. February 1, 1999 9: 103-120; doi:10.1101/gr.9.2.103
...Department of Cellular Biology, University of Georgia, Athens, Georgia 30602 USA; 2New England Biolabs, Beverly, Massachusetts 01915 USA Abstract The nuclear receptor (NR) superfamily is the most abundant class of transcriptional regulators encoded in the Caenorhabditis elegans genome, with &gt...
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Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- Bo Zhang,
- Yan Zhou,
- Nan Lin,
- Rebecca F. Lowdon,
- Chibo Hong,
- Raman P. Nagarajan,
- Jeffrey B. Cheng,
- Daofeng Li,
- Michael Stevens,
- Hyung Joo Lee,
- Xiaoyun Xing,
- Jia Zhou,
- Vasavi Sundaram,
- GiNell Elliott,
- Junchen Gu,
- Taoping Shi,
- Philippe Gascard,
- Mahvash Sigaroudinia,
- Thea D. Tlsty,
- Theresa Kadlecek,
- Arthur Weiss,
- Henriette O’Geen,
- Peggy J. Farnham,
- Cécile L. Maire,
- Keith L. Ligon,
- Pamela A.F. Madden,
- Angela Tam,
- Richard Moore,
- Martin Hirst,
- Marco A. Marra,
- Baoxue Zhang,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
...; CpG and MRE-site content are fixed for any Genome Research 1523 www..org Discovering DNA methylation differences with M&M specific genomic region when SNP, mutation, or copy number differences are not considered.Whengenetic variation data is available for the sample, corrections can bemade to reflect...
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Research: Evolution at two levels of gene expression in yeast
- Carlo G. Artieri and
- Hunter B. Fraser
Genome Res. March 2014 24: 411-421; Published in Advance December 6, 2013, doi:10.1101/gr.165522.113
...material is available for this article.] Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.165522.113 . Received August 20, 2013. Accepted December 5, 2013. © 2014 Artieri...

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