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  1. The increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only prov...

    Authors: Chantal B. F. Vogels, Verity Hill, Mallery I. Breban, Chrispin Chaguza, Lauren M. Paul, Afeez Sodeinde, Emma Taylor-Salmon, Isabel M. Ott, Mary E. Petrone, Dennis Dijk, Marcel Jonges, Matthijs R. A. Welkers, Timothy Locksmith, Yibo Dong, Namratha Tarigopula, Omer Tekin…
    Citation: BMC Genomics 2024 25:433
  2. Ophthalmic manifestations have recently been observed in acute and post-acute complications of COVID-19 caused by SARS-CoV-2 infection. Our precious study has shown that host RNA editing is linked to RNA viral...

    Authors: Yun-Yun Jin, Ya-Ping Liang, Wen-Hao Huang, Liang Guo, Li-Li Cheng, Tian-Tian Ran, Jin-Ping Yao, Lin Zhu and Jian-Huan Chen
    Citation: BMC Genomics 2024 25:431
  3. Although multiple chicken genomes have been assembled and annotated, the numbers of protein-coding genes in chicken genomes and their variation among breeds are still uncertain due to the low quality of these ...

    Authors: Siwen Wu, Tengfei Dou, Sisi Yuan, Shixiong Yan, Zhiqiang Xu, Yong Liu, Zonghui Jian, Jingying Zhao, Rouhan Zhao, Xiannian Zi, Dahai Gu, Lixian Liu, Qihua Li, Dong-Dong Wu, Junjing Jia, Changrong Ge…
    Citation: BMC Genomics 2024 25:430
  4. Expression quantitative trait loci (eQTL) studies aim to understand the influence of genetic variants on gene expression. The colocalization of eQTL mapping and GWAS strategy could help identify essential cand...

    Authors: Wentao Cai, Jian Hu, Yunsheng Zhang, Zhanbao Guo, Zhengkui Zhou and Shuisheng Hou
    Citation: BMC Genomics 2024 25:429
  5. Although many studies have been done to reveal artificial selection signatures in commercial and indigenous chickens, a limited number of genes have been linked to specific traits. To identify more trait-relat...

    Authors: Siwen Wu, Tengfei Dou, Kun Wang, Sisi Yuan, Shixiong Yan, Zhiqiang Xu, Yong Liu, Zonghui Jian, Jingying Zhao, Rouhan Zhao, Hao Wu, Dahai Gu, Lixian Liu, Qihua Li, Dong-Dong Wu, Changrong Ge…
    Citation: BMC Genomics 2024 25:428
  6. Current approaches to profile the single-cell transcriptomics of human pancreatic endocrine cells almost exclusively rely on freshly isolated islets. However, human islets are limited in availability. Furtherm...

    Authors: Gengqiang Xie, Maria Pilar Toledo, Xue Hu, Hyo Jeong Yong, Pamela Sandoval Sanchez, Chengyang Liu, Ali Naji, Jerome Irianto and Yue J. Wang
    Citation: BMC Genomics 2024 25:427
  7. In the beef industry, bull calves are usually castrated to improve flavor and meat quality; however, this can reduce their growth and slaughter performance. The gut microbiota is known to exert a significant i...

    Authors: Jinping Shi, Zemin Li, Li Jia, Yue Ma, Yongliang Huang, Pengjia He, Tao Ran, Wangjing Liu, Wangdong Zhang, Qiang Cheng, Zhao Zhang and Zhaomin Lei
    Citation: BMC Genomics 2024 25:426
  8. Purple non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis] has become popular because of its richness in anthocyanin. However, anthocyanin only accumulates in the upper epidermis...

    Authors: Qian Zhou, Xinfeng Xu, Mengjie Li, Xiaoxue Yang, Meiyun Wang, Ying Li, Xilin Hou and Tongkun Liu
    Citation: BMC Genomics 2024 25:425
  9. Salinity impacts crop growth and productivity and lowers the activities of rhizosphere microbiota. The identification and utilization of habitat-specific salinity-adapted plant growth-promoting rhizobacteria (...

    Authors: V. S. Sunithakumari, Rahul R. Menon, Gayathri G. Suresh, Ramya Krishnan and N. Rameshkumar
    Citation: BMC Genomics 2024 25:424
  10. Single-cell clustering has played an important role in exploring the molecular mechanisms about cell differentiation and human diseases. Due to highly-stochastic transcriptomics data, accurate detection of cel...

    Authors: Wei Zhang, Ruochen Yu, Zeqi Xu, Junnan Li, Wenhao Gao, Mingfeng Jiang and Qi Dai
    Citation: BMC Genomics 2024 25:423
  11. Brasenia schreberi, a plant species traditionally utilized in Chinese medicine and cuisine, represents an early evolutionary stage among flowering plants (angiosperms). While the plastid genome of this species ha...

    Authors: Yuanyu Shan, Jingling Li, Xinmei Duan, Xue Zhang and Jie Yu
    Citation: BMC Genomics 2024 25:422
  12. Herpetospermum pedunculosum (Ser.) C. B. Clarke is a traditional Chinese herbal medicine that heavily relies on the lignans found in its dried ripe seeds (Herpetospermum caudigerum), which have antioxidant and h...

    Authors: Ziwei Zhu, Daihan Chen, Min Sun, Maotao Xiao, Peng Huang, Dongsheng Ren, Yixi Yang, Zhen Zhang, Qi Zhao and Rui Li
    Citation: BMC Genomics 2024 25:421
  13. Goats have achieved global prominence as essential livestock since their initial domestication, primarily owing to their remarkable adaptability to diverse environmental and production systems. Differential se...

    Authors: Weifeng Peng, Yiyuan Zhang, Lei Gao, Wanlu Shi, Zi Liu, Xinyu Guo, Yunxia Zhang, Bing Li, Guoyin Li, Jingya Cao and Mingsheng Yang
    Citation: BMC Genomics 2024 25:420
  14. The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type ...

    Authors: Yan Li, Tingyan Guo, Liqin Sun, En-Tao Wang, J. Peter W. Young and Chang-Fu Tian
    Citation: BMC Genomics 2024 25:419
  15. Plant specialized (or secondary) metabolites (PSM), also known as phytochemicals, natural products, or plant constituents, play essential roles in interactions between plants and environment. Although many res...

    Authors: Wenhui Bai, Cheng Li, Wei Li, Hai Wang, Xiaohong Han, Peipei Wang and Li Wang
    Citation: BMC Genomics 2024 25:418
  16. Between 2020 and 2022, eight calves in a Nebraska herd (composite Simmental, Red Angus, Gelbvieh) displayed exercise intolerance during forced activity. In some cases, the calves collapsed and did not recover....

    Authors: Mackenzie C. Batt, Leila G. Venzor, Keri Gardner, Rachel R. Reith, Kelsey A. Roberts, Nicolas J. Herrera, Anna M. Fuller, Gary A. Sullivan, J. Travis Mulliniks, Matthew L. Spangler, Stephanie J. Valberg, David J. Steffen and Jessica L. Petersen
    Citation: BMC Genomics 2024 25:417
  17. Admixture occurs between different ethnic human populations. The global colonization in recent centuries by Europeans led to the most significant admixture in human history. While admixture may enhance genetic...

    Authors: Stephanie Andaluz, Bojin Zhao, Siddharth Sinha, Philip Naderev Panuringan Lagniton, Diogo Alpuim Costa, Xiaofan Ding, Miguel Brito and San Ming Wang
    Citation: BMC Genomics 2024 25:416
  18. Oxygen-induced retinopathy (OIR) animal model is widely used for retinopathy of prematurity (ROP) researches. The purpose of this study was to identify proteins and related pathways of OIR with or without anti...

    Authors: Zhaokai Xu, Yubo Wu, Jianbo Mao, Yiqi Chen, Huan Chen, Shian Zhang, Jiafeng Yu, Xinyi Deng and Lijun Shen
    Citation: BMC Genomics 2024 25:415
  19. Growth rate is a crucial economic trait for farmed animals, but the genetic regulation of this trait is largely unknown in non-model organisms such as shrimp.

    Authors: Xiuli Chen, Min Peng, Chunling Yang, Qiangyong Li, Pengfei Feng, Weilin Zhu, Yongde Zhang, Digang Zeng and Yongzhen Zhao
    Citation: BMC Genomics 2024 25:414
  20. Disulfidptosis is a novel form of programmed cell death induced by high SLC7A11 expression under glucose starvation conditions, unlike other known forms of cell death. However, the roles of disulfidptosis in c...

    Authors: Lei Ren, Jinwen Liu, Qingyuan Lin, Tianyi He, Guankai Huang, Weifeng Wang, Xunhao Zhan, Yu He, Bin Huang and Xiaopeng Mao
    Citation: BMC Genomics 2024 25:413
  21. Solanum aculeatissimum and Solanum torvum belong to the Solanum species, and they are essential plants known for their high resistance to diseases and adverse conditions. They are frequently used as rootstocks fo...

    Authors: Longhao Zhang, Chengqi Yi, Xin Xia, Zheng Jiang, Lihui Du, Shixin Yang and Xu Yang
    Citation: BMC Genomics 2024 25:412
  22. Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on genomes, there is a huge variability of genomic...

    Authors: Carles Galià-Camps, Cinta Pegueroles, Xavier Turon, Carlos Carreras and Marta Pascual
    Citation: BMC Genomics 2024 25:410

    The Correction to this article has been published in BMC Genomics 2024 25:457

  23. To evaluate the contribution of germline genetics to regulating the briskness and diversity of T cell responses in CRC, we conducted a genome-wide association study to examine the associations between germline...

    Authors: Stephanie L. Schmit, Ya-Yu Tsai, Joseph D. Bonner, Rebeca Sanz-Pamplona, Amit D. Joshi, Tomotaka Ugai, Sidney S. Lindsey, Marilena Melas, Kevin J. McDonnell, Gregory E. Idos, Christopher P. Walker, Chenxu Qu, W. Martin Kast, Diane M. Da Silva, Jonathan N. Glickman, Andrew T. Chan…
    Citation: BMC Genomics 2024 25:409
  24. Klebsiella pneumoniae, a notorious pathogen for causing nosocomial infections has become a major cause of neonatal septicemia, leading to high morbidity and mortality worldwide. This opportunistic bacterium has ...

    Authors: Sidra Rahmat Ullah, Sidra Irum, Iqra Mahnoor, Humaira Ismatullah, Mariam Mumtaz, Saadia Andleeb, Abdur Rahman and Muhsin Jamal
    Citation: BMC Genomics 2024 25:408
  25. Unraveling the intricate and tightly regulated process of adipogenesis, involving coordinated activation of transcription factors and signaling pathways, is essential for addressing obesity and related metabol...

    Authors: Siriluck Ponsuksili, Puntita Siengdee, Shuaichen Li, Wannapimol Kriangwanich, Michael Oster, Henry Reyer and Klaus Wimmers
    Citation: BMC Genomics 2024 25:407
  26. Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especia...

    Authors: Mingwei Liu, Fan Zhang, Huimin Lu, Hongzhang Xue, Xiaorui Dong, Zhikang Li, Jianlong Xu, Wensheng Wang and Chaochun Wei
    Citation: BMC Genomics 2024 25:405
  27. Transposable elements (TEs) are a major force in the evolution of plant genomes. Differences in the transposition activities and landscapes of TEs can vary substantially, even in closely related species. Inter...

    Authors: Pavel Merkulov, Melania Serganova, Georgy Petrov, Vladislav Mityukov and Ilya Kirov
    Citation: BMC Genomics 2024 25:404
  28. Recent studies have found a link between deep vein thrombosis and inflammatory reactions. N6-methyladenosine (m6A), a crucial element in immunological regulation, is believed to contribute to the pathophysiolo...

    Authors: Deshuai Zhang, Wenxia Fu, Shiwei Zhu, Yitong Pan and Ruogu Li
    Citation: BMC Genomics 2024 25:403
  29. Most of the important biological mechanisms and functions of transmembrane proteins (TMPs) are realized through their interactions with non-transmembrane proteins(nonTMPs). The interactions between TMPs and no...

    Authors: Chang Lu, Jiuhong Jiang, Qiufen Chen, Huanhuan Liu, Xingda Ju and Han Wang
    Citation: BMC Genomics 2024 25(Suppl 1):401

    This article is part of a Supplement: Volume 25 Supplement 1

  30. Skeletal muscle is composed of muscle fibers with different physiological characteristics, which plays an important role in regulating skeletal muscle metabolism, movement and body homeostasis. The type of ske...

    Authors: Chenchen Li, Yinuo Wang, Xiaohui Sun, Jinjin Yang, Yingchun Ren, Jinrui Jia, Gongshe Yang, Mingzhi Liao, Jianjun Jin and Xin’e Shi
    Citation: BMC Genomics 2024 25:400
  31. Endophytic bacteria possess a range of unique characteristics that enable them to successfully interact with their host and survive in adverse environments. This study employed in silico analysis to identify gene...

    Authors: Pfariso Maumela, Adivhaho Khwathisi, Ntakadzeni Edwin Madala and Mahloro Hope Serepa-Dlamini
    Citation: BMC Genomics 2024 25:399
  32. Pinellia ternata (Thunb.) Briet., a valuable herb native to China, is susceptible to the “sprout tumble” phenomenon because of high temperatures, resulting in a significant yield reduction. However, the molecular...

    Authors: Chen Bo, Mengmeng Liu, Qian You, Xiao Liu, Yanfang Zhu, Yongbo Duan, Dexin Wang, Tao Xue and Jianping Xue
    Citation: BMC Genomics 2024 25:398
  33. Jasmonate (JA) is the important phytohormone to regulate plant growth and adaption to stress signals. MYC2, an bHLH transcription factor, is the master regulator of JA signaling. Although MYC2 in maize has bee...

    Authors: Lijun Liu, Yuhan Zhang, Chen Tang, Jine Wu, Jingye Fu and Qiang Wang
    Citation: BMC Genomics 2024 25:397

    The Correction to this article has been published in BMC Genomics 2024 25:491

  34. While the size of chloroplast genomes (cpDNAs) is often influenced by the expansion and contraction of inverted repeat regions and the enrichment of repeats, it is the intergenic spacers (IGSs) that appear to ...

    Authors: Xiaolin Gu, Lingling Li, Xiaona Zhong, Yingjuan Su and Ting Wang
    Citation: BMC Genomics 2024 25:396
  35. Untargeted metabolomics and proteomics were employed to investigate the intracellular response of yak rumen epithelial cells (YRECs) to conditions mimicking subacute rumen acidosis (SARA) etiology, including e...

    Authors: JunMei Wang, Liyuan Shi, Xiaohong Zhang, Rui Hu, Ziqi Yue, Huawei Zou, Quanhui Peng, Yahui Jiang and Zhisheng Wang
    Citation: BMC Genomics 2024 25:394
  36. Accurately deciphering clonal copy number substructure can provide insights into the evolutionary mechanism of cancer, and clustering single-cell copy number profiles has become an effective means to unmask in...

    Authors: Ruixiang Li, Fangyuan Shi, Lijuan Song and Zhenhua Yu
    Citation: BMC Genomics 2024 25:393
  37. The pituitary directly regulates the reproductive process through follicle-stimulating hormone (FSH) and luteinizing hormone (LH). Transcriptomic research on the pituitaries of ewes with different FecB (fecundity...

    Authors: Jianqi Yang, Jishun Tang, Xiaoyun He, Ran Di, Xiaosheng Zhang, Jinlong Zhang, Xiaofei Guo, Wenping Hu and Mingxing Chu
    Citation: BMC Genomics 2024 25:392
  38. Developmental delay (DD), or intellectual disability (ID) is a very large group of early onset disorders that affects 1–2% of children worldwide, which have diverse genetic causes that should be identified. Ge...

    Authors: Heqian Ma, Lina Zhu, Xiao Yang, Meng Ao, Shunxiang Zhang, Meizhen Guo, Xuelin Dai, Xiuwei Ma and Xiaoying Zhang
    Citation: BMC Genomics 2024 25:391
  39. Medicinal plants are rich sources for treating various diseases due their bioactive secondary metabolites. Fenugreek (Trigonella foenum-graecum) is one of the medicinal plants traditionally used in human nutritio...

    Authors: Sara Lamei Javan, Arman Beyraghdar Kashkooli, AbdolAli Shojaeiyan and Sina Majidian
    Citation: BMC Genomics 2024 25:390
  40. The genus Sulfitobacter, a member of the family Roseobacteraceae, is widely distributed in the ocean and is believed to play crucial roles in the global sulfur cycle. However, gene clusters associated with sulfur...

    Authors: Xiaokun Xu, Mengdan He, Qingjie Xue, Xiuzhen Li and Ang Liu
    Citation: BMC Genomics 2024 25:389
  41. Myxozoa is a class of cnidarian parasites that encompasses over 2,400 species. Phylogenetic relationships among myxozoans remain highly debated, owing to both a lack of informative morphological characters and...

    Authors: Tatiana Orli Milkewitz Sandberg, Dayana Yahalomi, Noam Bracha, Michal Haddas-Sasson, Tal Pupko, Stephen D. Atkinson, Jerri L. Bartholomew, Jin Yong Zhang and Dorothée Huchon
    Citation: BMC Genomics 2024 25:388
  42. Drug-resistant tuberculosis (TB) is a major threat to global public health. Whole-genome sequencing (WGS) is a useful tool for species identification and drug resistance prediction, and many clinical laborator...

    Authors: Doyoung Kim, Jeong-Ih Shin, In Young Yoo, Sungjin Jo, Jiyon Chu, Woo Young Cho, Seung-Hun Shin, Yeun-Jun Chung, Yeon-Joon Park and Seung-Hyun Jung
    Citation: BMC Genomics 2024 25:387
  43. The growth and development of organism were dependent on the effect of genetic, environment, and their interaction. In recent decades, lots of candidate additive genetic markers and genes had been detected by ...

    Authors: Xinrui Liu, Mingxiu Wang, Jie Qin, Yaxin Liu, Shikai Wang, Shiyu Wu, Ming Zhang, Jincheng Zhong and Jiabo Wang
    Citation: BMC Genomics 2024 25:386
  44. The C2H2 zinc finger protein family plays important roles in plants. However, precisely how C2H2s function in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear.

    Authors: Xiaojuan Zhou, Ting Gao, Yimeng Zhang, Mian Han, Yuexin Shen, Yu Su, Xiaolong Feng, Qi Wu, Genlou Sun and Yiling Wang
    Citation: BMC Genomics 2024 25:385
  45. Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but ...

    Authors: Shuilian He, Bin Xu, Siyun Chen, Gengyun Li, Jie Zhang, Junqiang Xu, Hang Wu, Xuejiao Li and Zhengan Yang
    Citation: BMC Genomics 2024 25:384
  46. The Asian yellow pond turtle (Mauremys mutica) is an important commercial freshwater aquaculture species in China. This species is a highly sexually dimorphic species, with males growing at a faster rate than fem...

    Authors: Xiaoli Liu, Haoyang Xu, Mingwei Peng, Chenyao Zhou, Chengqing Wei, Xiaoyou Hong, Wei Li, Chen Chen, Liqin Ji and Xinping Zhu
    Citation: BMC Genomics 2024 25:383

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