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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
....01) (Supplemental Fig. S5). Genes with prostaglandin receptor activity (such as PTGER2 and PTGDR) and serine-type endopeptidase activity (including granzyme B, GZMB) were enriched in ruminant-specific EBRs; whereas pecoran-specific EBRs contained genes involved in the protein-lipid complex (CLU and PCYOX1, FDR < 0...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...of transcriptional regulation whereby approximately 200 mammalian genes are expressed monoallelically according to their parental origin. This crucial developmental process is primarily controlled by discrete cis-regulatory elements known as imprinting control regions (ICRs), which play essential roles in directing...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
....g., GTEx [The GTEx Consortium 2013], CZ CELLxGENE [CZI Cell Science Program et al. 2025]), other vertebrate model systems (e.g., mouse, rat, zebrafish), as well as phenotypic data from rare disease patients to generate hypotheses regarding molecular mechanisms of pathogenicity. In some cases...
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PERSPECTIVE: Impact of genomics on research in the rat
- Jozef Lazar,
- Carol Moreno,
- Howard J. Jacob,
- and Anne E. Kwitek
Genome Res. December 2005 15: 1717-1728; doi:10.1101/gr.3744005
...Impact of genomics on research in the rat Jozef Lazar , Carol Moreno , Howard J. Jacob , and Anne E. Kwitek 1 Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA Abstract The need to translate genes to function has...
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ARTICLE: A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids
- Daria V. Babushok,
- Kazuhiko Ohshima,
- Eric M. Ostertag,
- Xinsheng Chen,
- Yanfeng Wang,
- Prabhat K. Mandal,
- Norihiro Okada,
- Charles S. Abrams,
- and Haig H. Kazazian, Jr.
Genome Res. August 2007 17: 1129-1138; Published in Advance July 10, 2007, doi:10.1101/gr.6252107
...A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids Daria V. Babushok 1 , Kazuhiko Ohshima 2 , 6 , Eric M. Ostertag 1 , 3 , 6 , Xinsheng Chen 4 , Yanfeng Wang 4 , Prabhat K. Mandal 1...
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LETTER: MHC-Linked Olfactory Receptor Loci Exhibit Polymorphism and Contribute to Extended HLA/OR-Haplotypes
- Anke Ehlers,
- Stephan Beck,
- Simon A. Forbes,
- John Trowsdale,
- Armin Volz,
- Ruth Younger,
- and Andreas Ziegler
Genome Res. December 1, 2000 10: 1968-1978; doi:10.1101/gr.120400
..., Cambridge CB2 1QP, UK Abstract Clusters of olfactory receptor (OR) genes are found on most human chromosomes. They are one of the largest mammalian multigene families. Here, we report a systematic study of polymorphism of OR genes belonging to the largest fully sequenced OR cluster. The cluster...
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Research: Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf
- Charles Y. Feigin,
- Axel H. Newton,
- and Andrew J. Pask
Genome Res. October 2019 29: 1648-1658; Published in Advance September 18, 2019, doi:10.1101/gr.244251.118
...that TWAR-associated genes represent several components of these pathways, including receptors, ligands, modifiers of ligand availability, and mediators of downstream signaling (Fig. 2A,B; Supplemental Table S7).View larger version: In this window In a new window Figure 2. Genes involved in TGF beta...
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LETTERS: Genomic structure of the human OB receptor and identification of two novel intronic microsatellites.
- W K Chung,
- L Power-Kehoe,
- M Chua,
- R Lee,
- and R L Leibel
Genome Res. December 1996 6: 1192-1199; doi:10.1101/gr.6.12.1192
...(Lepr). Diabetes 45 : 1141 – 1143 . Chung, W.K., Power-Kehoe, L. Chua, M. and Leibel. R.L. 1996 . Mapping of the OB receptor (OBR) to 1p in a region of non-conserved gene order from mouse and rat to human. Genome Res. 6 : 431 – 438 . Cioffi, J.A., Shaper, A.W. Zupancic, T.J. Smith-Gbur, J. Mikhail, A...
- Abstract
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LETTER: Analysis of the Gene-Dense Major Histocompatibility Complex Class III Region and Its Comparison to Mouse
- Tao Xie,
- Lee Rowen,
- Begoña Aguado,
- Mary Ellen Ahearn,
- Anup Madan,
- Shizhen Qin,
- R. Duncan Campbell,
- and Leroy Hood
Genome Res. December 2003 13: 2621-2636; doi:10.1101/gr.1736803
...inherent to the use of RefSeqs for counting genes. Finally, regions such as protocadherins and T-cell receptors that contain rear-ranging gene elements strewn across hundreds of kilobases of sequence have been eliminated from the analysis as, in a sense, these can be considered to be one gene...
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LETTER: Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes
- Katsuki Tsuritani,
- Takuma Irie,
- Riu Yamashita,
- Yuta Sakakibara,
- Hiroyuki Wakaguri,
- Akinori Kanai,
- Junko Mizushima-Sugano,
- Sumio Sugano,
- Kenta Nakai,
- and Yutaka Suzuki
Genome Res. July 2007 17: 1005-1014; Published in Advance June 13, 2007, doi:10.1101/gr.6030107
...Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes Katsuki Tsuritani 1 , Takuma Irie 2 , Riu Yamashita 1 , Yuta Sakakibara 2 , Hiroyuki Wakaguri 2...

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