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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
...and Kaessmann 2014). Therefore, comparative gene expression studiesmay provide unique insights into the functional evolution of both old and new (duplicate) genes. High-throughput RNA sequencing (RNA-seq) enables detailed cross-species transcriptome comparisons (Necsulea and Kaessmann 2014). However, while...
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PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
- Paul B. Samollow
Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
...and the functional attributes of their components. Comparative analyses using the opossum genome have already provided a wealth of new evidence regarding the importance of noncoding elements in the evolution of mammalian genomes, the role of transposable elements in driving genomic innovation, and the relationships...
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Research: A quantitative framework for characterizing the evolutionary history of mammalian gene expression
- Jenny Chen,
- Ross Swofford,
- Jeremy Johnson,
- Beryl B. Cummings,
- Noga Rogel,
- Kerstin Lindblad-Toh,
- Wilfried Haerty,
- Federica di Palma,
- and Aviv Regev
Genome Res. January 2019 29: 53-63; Published in Advance December 14, 2018, doi:10.1101/gr.237636.118
...RNAs. As shown by our analysis, characterizations of expression across additional tissue types and species under varied developmental and environmental contexts will provide increased power and further insight into the evolution of gene expression and the relationship between genotype and phenotype...
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Research: Birth and expression evolution of mammalian microRNA genes
- Julien Meunier,
- Frédéric Lemoine,
- Magali Soumillon,
- Angélica Liechti,
- Manuela Weier,
- Katerina Guschanski,
- Haiyang Hu,
- Philipp Khaitovich,
- and Henrik Kaessmann
Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
...processes. Overall, our study thus provides detailed insights into the birth and evolution of mammalian miRNA genes and the associated selective forces. [Supplemental material is available for this article.] Understanding the molecular basis of phenotypic differences amongmammals has been a central topic...
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Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
- Yi Shao,
- Chunyan Chen,
- Hao Shen,
- Bin Z. He,
- Daqi Yu,
- Shuai Jiang,
- Shilei Zhao,
- Zhiqiang Gao,
- Zhenglin Zhu,
- Xi Chen,
- Yan Fu,
- Hua Chen,
- Ge Gao,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
...a novel pattern, that is, the enrichment of PSGs implicated in the defense response (Fig. 8; Supplemental Fig. S15), which is not surprising given the rapid gene family evolution in immune response (Demuth and Hahn 2009). Thus, new genes are either recruited to processes under tremendous selection...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...and other mammalian species remains to be characterized. Here, we address the global contribution of TEs to mammalian NF-kB binding by performing a comparative genomic analysis of TNF-induced NF-kB binding in primary human, mouse, and cow aortic endothelial cells.ResultsTransposable elements contribute...
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REVIEW: Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
- Victoria P. Belancio,
- Dale J. Hedges,
- and Prescott Deininger
Genome Res. March 2008 18: 343-358; Published in Advance February 6, 2008, doi:10.1101/gr.5558208
.... Insertions and disease Host impact Insights from comparative genomic studies The ever-increasing availability of large-scale genomic sequence data has provided considerable insight concerning the important role TEs have played in building and shaping eukaryotic s. The sequence from a representative...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Corresponding authors: jianhaichen@uchicago.edu, mlong@uchicago.edu, bairong.shen@scu.edu.cnAbstractNew genes (or young genes) are genetic novelties pivotal in mammalian evolution. However, their phenotypic...
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Platypus Special/Letter: Defensins and the convergent evolution of platypus and reptile venom genes
- Camilla M. Whittington,
- Anthony T. Papenfuss,
- Paramjit Bansal,
- Allan M. Torres,
- Emily S.W. Wong,
- Janine E. Deakin,
- Tina Graves,
- Amber Alsop,
- Kyriena Schatzkamer,
- Colin Kremitzki,
- Chris P. Ponting,
- Peter Temple-Smith,
- Wesley C. Warren,
- Philip W. Kuchel,
- and Katherine Belov
Genome Res. June 2008 18: 986-994; Published in Advance May 7, 2008, doi:10.1101/gr.7149808
...(short-beaked echidna) Comp Biochem Physiol A Comp Physiol 136 811 - 819 ↵ Belov, K. , Sanderson, C. , Deakin, J. , Wong, E. , Assange, D. , McColl, K. , Gout, A. , de Bono, B. , Barrow, A. , Speed, T. , et al. ( 2007 ) Characterization of the opossum immune provides insights into the evolution...
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LETTER: An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes
- Leo Goodstadt,
- Andreas Heger,
- Caleb Webber,
- and Chris P. Ponting
Genome Res. July 2007 17: 969-981; Published in Advance May 10, 2007, doi:10.1101/gr.6093907
..., University of Oxford, Department of Physiology, Anatomy, and Genetics, South Parks Road, Oxford OX1 3QX, UK Abstract The newly sequenced genome of Monodelphis domestica not only provides the out-group necessary to better understand our own eutherian lineage, but it enables insights...

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