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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
...loci associated with the response to hypoxia among heart enhancer shifts in both ancestral and naked mole-rat branches (Fig. 4A,E). Protein levels of HIF1A are thought to be increased in mole-rats (Kim et al. 2011), and we detected Up enhancers in the ancestral mole-rat branch for both core regulators...
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Resource: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
- Jacob C. Kimmel,
- Lolita Penland,
- Nimrod D. Rubinstein,
- David G. Hendrickson,
- David R. Kelley,
- and Adam Z. Rosenthal
Genome Res. December 2019 29: 2088-2103; Published in Advance November 21, 2019, doi:10.1101/gr.253880.119
...and molecular players that cause aging or how they differ between biological contexts. Both the fundamental nature of aging and its negative effects provide motivation to enumerate these players and establish causal relationships among aging phenotypes.Mammalian aging phenotypes manifest at the organismal...
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Perspective: Insights into neural crest development and evolution from genomic analysis
- Marcos Simões-Costa and
- Marianne E. Bronner
Genome Res. July 2013 23: 1069-1080; doi:10.1101/gr.157586.113
...patterns and functional studies obtained from several model organisms (Meulemans and Bronner-Fraser 2004). Although this approach provided a conceptual framework for investigating neural crest identity, further resolution of the GRN requires the identification of direct epistatic interactions among its...
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Method: Defining cell-type specificity at the transcriptional level in human disease
- Wenjun Ju,
- Casey S. Greene,
- Felix Eichinger,
- Viji Nair,
- Jeffrey B. Hodgin,
- Markus Bitzer,
- Young-suk Lee,
- Qian Zhu,
- Masami Kehata,
- Min Li,
- Song Jiang,
- Maria Pia Rastaldi,
- Clemens D. Cohen,
- Olga G. Troyanskaya,
- and Matthias Kretzler
Genome Res. November 2013 23: 1862-1873; Published in Advance August 15, 2013, doi:10.1101/gr.155697.113
...all non–gold-standard genes among the top 150 predictions. The selected genes are the set with the maximum F-measure (Supplemental Methods) as assessed by cross-validation where precision was weighted five times as much as recall and resulted in a number of genes practical for systematic verification...
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LETTER: Reduced purifying selection prevails over positive selection in human copy number variant evolution
- Duc-Quang Nguyen,
- Caleb Webber,
- Jayne Hehir-Kwa,
- Rolph Pfundt,
- Joris Veltman,
- and Chris P. Ponting
Genome Res. November 2008 18: 1711-1723; Published in Advance August 7, 2008, doi:10.1101/gr.077289.108
...found that essential and disease genes have been preferentially retained as single copies in four lineages (those of human, mouse, dog, and opossum; see Methods) since their last common ancestor. More specifically, we found that among those genes that have remained unduplicated over a total of 485...
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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
...to the Xq arm of MDOX (M. Breen and P. Water, pers. comm.). Substitution rates and G+C content are elevated in the metatherian X chromosome We investigated G+C content since this strongly covaries with d S among eutheria ( Matassi et al. 1999 ; Lander et al. 2001 ; Hardison et al. 2003 ; Webber and Ponting...
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REVIEW: A Phenotype Map of the Mouse X Chromosome: Models for Human X-linked Disease
- Yvonne Boyd,
- Helen J. Blair,
- Pamela Cunliffe,
- Walter K. Masson,
- and Vivienne Reed
Genome Res. March 1, 2000 10: 277-292; doi:10.1101/gr.10.3.277
...Traits Thirty-eight X-linked mouse-independent visible phenotypes covering a wide range of traits are reported in the literature (Table 2; Fig. 2). Most of these phenotypes have arisen spontaneously in mouse colonies or among the large numbers of mice used in mutagenesis experiments (George et al. 1994...
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Research: Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways
- Blair W. Perry,
- Siddharth S. Gopalan,
- Giulia I.M. Pasquesi,
- Drew R. Schield,
- Aundrea K. Westfall,
- Cara F. Smith,
- Ivan Koludarov,
- Paul T. Chippindale,
- Mark W. Pellegrino,
- Edward B. Chuong,
- Stephen P. Mackessy,
- and Todd A. Castoe
Genome Res. June 2022 32: 1058-1073; Published in Advance June 1, 2022, doi:10.1101/gr.276251.121
...among gene family members, suggesting that TFBSs are conserved to a degree among paralogs within VG clusters (Supplemental Fig. S5).Only three of the “other” VGs have an ATAC-seq peak within their inferred promoter region (CTL, VEGF1, and VEGF2) (Supplemental Fig. S6). Because these genes do not inhabit...
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Research: Plasma cell-free RNA characteristics in COVID-19 patients
- Yanqun Wang,
- Jie Li,
- Lu Zhang,
- Hai-Xi Sun,
- Zhaoyong Zhang,
- Jinjin Xu,
- Yonghao Xu,
- Yu Lin,
- Airu Zhu,
- Yuxue Luo,
- Haibo Zhou,
- Yan Wu,
- Shanwen Lin,
- Yuzhe Sun,
- Fei Xiao,
- Ruiying Chen,
- Liyan Wen,
- Wei Chen,
- Fang Li,
- Rijing Ou,
- Yanjun Zhang,
- Tingyou Kuo,
- Yuming Li,
- Lingguo Li,
- Jing Sun,
- Kun Sun,
- Zhen Zhuang,
- Haorong Lu,
- Zhao Chen,
- Guoqiang Mai,
- Jianfen Zhuo,
- Puyi Qian,
- Jiayu Chen,
- Huanming Yang,
- Jian Wang,
- Xun Xu,
- Nanshan Zhong,
- Jingxian Zhao,
- Junhua Li,
- Jincun Zhao,
- and Xin Jin
Genome Res. February 2022 32: 228-241; Published in Advance January 21, 2022, doi:10.1101/gr.276175.121
...microorganisms, especially pathogenic bacteria under SARS-CoV-2 infection, may aggravate the lung injury and lead to an exacerbated inflammatory response, according to previous studies. Meanwhile, distinct signatures of microbial profiles among COVID-19 patients can be related to disease severity, according...
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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
...et al. 2021). Among the variety of methodological approaches, Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT) is widely used to identify ortholog candidates across multiple species, including flies and humans (see Supplemental Text 1; Hu et al. 2011). It is notable...

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