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  1. Article

    Open Access

    An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs

    Neuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression program contributes to chemotherapy resistance. However, clinical outcomes remain poor, imp...

    Richard H. Chapple, Xueying Liu, Sivaraman Natarajan in Genome Biology (2024)

  2. Article

    Open Access

    LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA

    Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical application. Most assays necessitate substantial DNA inputs, po...

    **ao-Long Cui, Ji Nie, Houxiang Zhu, Krissana Kowitwanich in Genome Biology (2024)

  3. Article

    Open Access

    Structural variant landscapes reveal convergent signatures of evolution in sheep and goats

    Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level refere...

    Ji Yang, Dong-Feng Wang, Jia-Hui Huang, Qiang-Hui Zhu, Ling-Yun Luo in Genome Biology (2024)

  4. No Access

    Article

    Assessing the causal relationship between immune cells and prostatitis: evidence from bidirectional mendelian randomization analysis

    Prostatitis represents a common disease of the male genitourinary system, significantly impacting the physical and mental health of male patients. While numerous studies have suggested a potential link between...

    Genyi Qu, Weimin Jiang, Zhaohui Long, **ng Zhou, Yijie Wang, Guang Yang in Mammalian Genome (2024)

  5. No Access

    Article

    Environmental Effects on Nocturnal Encounters of Two Sympatric Bushbabies, Galago moholi and Otolemur crassicaudatus, in a High-Altitude South African Northern Mistbelt Montane Habitat

    Temperate living primates cope with a variety of environmental stressors, which may vary by body mass. We studied two sympatric galagos, the thick-tailed greater galago, Otolemur crassicaudatus (1.5 kg) and the s...

    Michelle L. Sauther, James B. Millette in International Journal of Primatology (2024)

  6. Article

    Open Access

    Pancreatitis affects gut microbiota via metabolites and inflammatory cytokines: an exploratory two-step Mendelian randomisation study

    Previous studies have observed relationships between pancreatitis and gut microbiota; however, specific changes in gut microbiota abundance and underlying mechanisms in pancreatitis remain unknown. Metabolites...

    Yi-Fan Qiu, Jun Ye, **-** **e, **ao-Tong Mao in Molecular Genetics and Genomics (2024)

  7. Article

    Open Access

    Undetectable off-target effects induced by FokI catalytic domain in mouse embryos

    The FokI catalytic domain can be fused to various DNA binding architectures to improve the precision of genome editing tools. However, evaluation of off-target effects is essential for develo** these tools. ...

    Long **e, Hu Feng, Zhifang Li, Di Li, **ali Yang, Tanglong Yuan, Nana Yan in Genome Biology (2024)

  8. No Access

    Article

    Integration of genome-wide association studies reveal loci associated with salt tolerance score of rice at the seedling stage

    Salt threatens rice cultivation in many countries. Hence, breeding new varieties with high salt tolerance is important.

    Nhung Thi Hong Phan, Cuong Van Pham, Hanh Thi Tang in Journal of Applied Genetics (2023)

  9. No Access

    Article

    Ongoing Bidirectional Introgression and the Maintenance of Species Boundaries in Hemiculter Hybrid Zone

    The proper delimitation of species plays an important role in taxonomy as well as in studies related to speciation. However, introgressive hybridization can confuse our ability to accurately construct phylogen...

    **aofan **ong, Leilei Feng, Mingrong Wang, Haoran **ng, **angju Li in Evolutionary Biology (2023)

  10. Article

    Open Access

    Seasonal Effects on the Fecal Microbial Composition of Wild Greater Thick-Tailed Galagos (Otolemur crassicaudatus)

    Bacterial communities present in the host digestive tract are important for the breakdown and absorption of nutrients required by the host. Changes in diet and the environment are major factors affecting the c...

    Channen Long, Juan Scheun, Michelle Linda Sauther in International Journal of Primatology (2023)

  11. No Access

    Article

    Characterization and diversity of CRISPR/Cas systems in Klebsiella oxytoca

    CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated protein) system is a crucial adaptive immune system for bacteria to resist foreign DNA infection. In this study, we inv...

    Jiaxue Zhao, Yanyan **, Jiangfeng Zhang, Yuefei ** in Molecular Genetics and Genomics (2023)

  12. No Access

    Article

    Allometric brain reduction in an insular, dwarfed population of black-tailed deer

    Insular populations of mammals have been shown to undergo drastic morphological changes relative to mainland counterparts, and these adaptations can provide insight into the evolutionary effects of predation a...

    Claire O. Geiman, Eric S. Long in Journal of Mammalian Evolution (2023)

  13. Article

    Open Access

    Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes

    RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the composition of tissues a...

    Francisco Avila Cobos, Mohammad Javad Najaf Panah, Jessica Epps in Genome Biology (2023)

  14. Article

    Open Access

    Plasma cell-free DNA promise monitoring and tissue injury assessment of COVID-19

    Coronavirus 2019 (COVID-19) is a complex disease that affects billions of people worldwide. Currently, effective etiological treatment of COVID-19 is still lacking; COVID-19 also causes damages to various orga...

    **n **, Yanqun Wang, **** Xu, Yimin Li, Fanjun Cheng in Molecular Genetics and Genomics (2023)

  15. Article

    Open Access

    Characterization of novel loci controlling seed oil content in Brassica napus by marker metabolite-based multi-omics analysis

    Seed oil content is an important agronomic trait of Brassica napus (B. napus), and metabolites are considered as the bridge between genotype and phenotype for physical traits.

    Long Li, Zhitao Tian, Jie Chen, Zengdong Tan, Yuting Zhang, Hu Zhao in Genome Biology (2023)

  16. No Access

    Article

    Transcriptomic profiling of the cold stress and recovery responsiveness of two contrasting Guizhou HE rice genotypes

    At the seed germination stage, rice is sensitive to cold stress, which adversely affects its growth and development. Guizhou HE rice comprises several different landraces, most of which are cold tolerant.

    Zhongni Wang, **an Wu, Yuxuan Chen, Chaoxin Wu, Wuhua Long, Susong Zhu in Genes & Genomics (2023)

  17. No Access

    Article

    Comparative transcriptome analysis to reveal key ethylene genes involved in a Lonicera macranthoides mutant

    Lonicera macranthoides Hand.-Mazz. is an important medicinal plant. **anglei-type (XL) L. macranthoides was formed after many years of cultivation by researchers on the basis of the natural mutant. The corolla of...

    YuQing Long, Juan Zeng, Min Yang, **nRu Zhou, Mei Zeng, ChangYu Liu in Genes & Genomics (2023)

  18. No Access

    Article

    Deubiquitinating enzyme Josephin-2 stabilizes PHGDH to promote a cancer stem cell phenotype in hepatocellular carcinoma

    Deubiquitinating enzymes (DUBs) have been shown to be possible targets for hepatocellular carcinoma (HCC) treatment.

    Ying Wang, Ze-**n Li, Jian-Guo Wang, Lu-Hao Li, Wen-Long Shen in Genes & Genomics (2023)

  19. No Access

    Article

    Methylophiopogonanone a Inhibits LPS/ATP-Induced Macrophage Pyroptosis via ROS/NLRP3 Pathway

    As a byproduct of mitochondrial respiration or metabolism, reactive oxygen species (ROS) can act as a signaling molecule to activate NLR family pyrin domain containing 3 (NLRP3) inflammasome, thereby triggerin...

    H. B. Zeng, L. H. Zhang, D. P. Yuan, W. Wang, X. M. Su, W. X. Weng in Molecular Biology (2023)

  20. Article

    Open Access

    Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat

    Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain ...

    Long Zhao, Yiman Yang, **chao Chen, Xuelei Lin, Hao Zhang, Hao Wang in Genome Biology (2023)

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