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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...The grasshopper reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution Xinghua Li1,2, Judith E. Mank3 and Liping Ban1 1Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University...
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Research: Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells
- Bingxiang Xu,
- Xiaomeng Gao,
- Xiaoli Li,
- Yan Jia,
- Feifei Li,
- and Zhihua Zhang
Genome Res. July 2022 32: 1285-1297; Published in Advance July 14, 2022, doi:10.1101/gr.276554.122
...and chromatin accessibility respond differently in short- and long-term heat shock in human K562 cells. We found that chromatin conformation in K562 cells was largely stable in response to short-term heat shock, whereas it showed clear and characteristic changes after long-term heat treatment with little...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...mays L.) nested association mapping (NAM) population (McMullen et al. 2009; Gage et al. 2020) provides a valuable resource to link genotypic variation with phenotypic variation using computationally folded protein structures with affordable computing resources. The s of 26 NAM founder lines have been...
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Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
- Gage S. Black,
- Xiaomeng Huang,
- Yi Qiao,
- Philip Moos,
- Deepa Sampath,
- Deborah M. Stephens,
- Jennifer A. Woyach,
- and Gabor T. Marth
Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
...and visualization of single-cell genotypesWe have recently published a novel computational method, scBayes, to study cancer subclone-specific expression phenotypes by combining scRNA-seq and bulk DNA sequencing-based subclone structures (Fig. 3A; Qiao et al. 2024). This approach enables genotype inference...
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Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...and its implications in primary cancer cells is scarce. Here, we conducted a -wide comparison of high-resolution nucleosome maps in peripheral blood B cells from patients with chronic lymphocytic leukemia (CLL) and healthy individuals at single-base-pair resolution. Our investigation uncovered significant...
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Research: Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice
- Arikuni Uchimura,
- Mayumi Higuchi,
- Yohei Minakuchi,
- Mizuki Ohno,
- Atsushi Toyoda,
- Asao Fujiyama,
- Ikuo Miura,
- Shigeharu Wakana,
- Jo Nishino,
- and Takeshi Yagi
Genome Res. August 2015 25: 1125-1134; Published in Advance June 30, 2015, doi:10.1101/gr.186148.114
..., has become clear (Yauk et al. 2015). However, only limited information about the long-term effects of mutation-rate differences is currently available. For example, we know that an increased mutation rate will increase the frequency of congenital disease. However, the overall phenotypic effects...
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Resource: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
- Laura E. Tibbs-Cortes,
- Tingting Guo,
- Carson M. Andorf,
- Xianran Li,
- and Jianming Yu
Genome Res. August 2024 34: 1253-1263; Published in Advance September 13, 2024, doi:10.1101/gr.279027.124
...(Li et al. 2021).Phenotypic plasticity occurs when a genotype produces different phenotype values in response to differing environments (Via et al. 1995). This plasticity is ubiquitous, present in staple crops including maize, wheat, and rice, and affecting traits ranging from yield to plant height...
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Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
- Xin Li,
- San-Gang He,
- Wen-Rong Li,
- Ling-Yun Luo,
- Ze Yan,
- Dong-Xin Mo,
- Xing Wan,
- Feng-Hua Lv,
- Ji Yang,
- Ya-Xi Xu,
- Juan Deng,
- Qiang-Hui Zhu,
- Xing-Long Xie,
- Song-Song Xu,
- Chen-Xi Liu,
- Xin-Rong Peng,
- Bin Han,
- Zhong-Hui Li,
- Lei Chen,
- Jian-Lin Han,
- Xue-Zhi Ding,
- Renqing Dingkao,
- Yue-Feng Chu,
- Jin-Yan Wu,
- Li-Min Wang,
- Ping Zhou,
- Ming-Jun Liu,
- and Meng-Hua Li
Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
...to the conversion of glycine to tryptophan. Phenotypic data indicated that individuals with the homozygous reference genotype (CC) had a significantly (Mann–Whitney U test, P < 0.001) longer tail length than individuals with the heterozygous variant genotype (CA), whereas individuals with the homozygous variant...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...cause serious infections of the lungs, sinuses, and skin, as well as a central nervous system disease called granulomatous amoebic encephalitis (Visvesvara et al. 2007). The species Acanthamoeba castellanii was first isolated in 1930 by Castellani (1930) as a contaminant of a yeast culture...
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Research: Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants
- Roshan Vaid,
- Akram Mendez,
- Ketan Thombare,
- Rebeca Burgos-Panadero,
- Rémy Robinot,
- Barbara F. Fonseca,
- Nikhil R. Gandasi,
- Johan Ringlander,
- Mohammad Hassan Baig,
- Jae-June Dong,
- Jae Yong Cho,
- Björn Reinius,
- Lisa A. Chakrabarti,
- Kristina Nystrom,
- and Tanmoy Mondal
Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
..., Gothenburg 41345, Sweden ↵9 These authors contributed equally to this work. Corresponding author: tanmoy.mondal@gu.seAbstractInsights into host–virus interactions during SARS-CoV-2 infection are needed to understand COVID-19 pathogenesis and may help to guide the design of novel antiviral therapeutics. N6...
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