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  1. 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
  2. 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
  3. 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
  4. 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

  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. Auxin/induced-3-acetic acid (Aux/IAA) is an important plant hormone that affects plant growth and resistance to abiotic stresses. Drought stress is a vital factor in reducing plant biomass yield and production...

    Authors: Jinqing Zhang, Shuxia Li, Xueqin Gao, Yaling Liu and BingZhe Fu
    Citation: BMC Genomics 2024 25:382
  22. Klebsiella pneumoniae is a Gram-negative Enterobacteriaceae that is classified by the World Health Organisation (WHO) as a Priority One ESKAPE pathogen. South and Southeast Asian countries are regions where both ...

    Authors: Souradeep Das, Anish K. Pandey, Denise E Morris, Rebecca Anderson, Victor Lim, Chong Chun Wie, Ivan Kok Seng Yap, Ahmed Ghazi Alattraqchi, Hafis Simin, Ramle Abdullah, Chew Chieng Yeo, Stuart C. Clarke and David W. Cleary
    Citation: BMC Genomics 2024 25:381
  23. Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers...

    Authors: Hadil A. Alkathiry, Samia Q. Alghamdi, Amit Sinha, Gabriele Margos, Alexandr A. Stekolnikov, Abdulaziz N. Alagaili, Alistair C. Darby, Benjamin L. Makepeace and Jing Jing Khoo
    Citation: BMC Genomics 2024 25:380
  24. Tumor cells exhibit a heightened susceptibility to lysosomal-dependent cell death (LCD) compared to normal cells. However, the role of LCD-related genes (LCD-RGs) in Osteosarcoma (OS) remains unelucidated. Thi...

    Authors: Yueshu Wu, Jun Yang, Gang Xu, Xiaolin Chen and Xiaochen Qu
    Citation: BMC Genomics 2024 25:379
  25. Mycobacterium avium complex (MAC), including Mycobacterium intracellulare is a member of slow-growing mycobacteria and contributes to a substantial proportion of nontuberculous mycobacterial lung disease in human...

    Authors: Hyun-Eui Park, Kyu-Min Kim, Jeong-Ih Shin, Jeong-Gyu Choi, Won-Jun An, Minh Phuong Trinh, Kyeong-Min Kang, Jung-Wan Yoo, Jung-Hyun Byun, Myung Hwan Jung, Kon-Ho Lee, Hyung-Lyun Kang, Seung Cheol Baik, Woo-Kon Lee and Min-Kyoung Shin
    Citation: BMC Genomics 2024 25:376
  26. Approximately 95% of samples analyzed in univariate genome-wide association studies (GWAS) are of European ancestry. This bias toward European ancestry populations in association screening also exists for othe...

    Authors: Lucie Troubat, Deniz Fettahoglu, Léo Henches, Hugues Aschard and Hanna Julienne
    Citation: BMC Genomics 2024 25:375
  27. Fatty liver hemorrhagic syndrome (FLHS) in the modern poultry industry is primarily caused by nutrition. Despite encouraging progress on FLHS, the mechanism through which nutrition influences susceptibility to...

    Authors: Yong Cui, Meng Ru, Yujie Wang, Linjian Weng, Ramlat Ali Haji, Haiping Liang, Qingjie Zeng, Qing Wei, Xianhua Xie, Chao Yin and Jianzhen Huang
    Citation: BMC Genomics 2024 25:374
  28. The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary su...

    Authors: Kui Ding, Qinzeng Xu, Liyuan Zhao, Yixuan Li, Zhong Li, Wenge Shi, Qianhui Zeng, Xianyan Wang and Xuelei Zhang
    Citation: BMC Genomics 2024 25:373
  29. Alternative polyadenylation (APA), alternative splicing (AS), and long non-coding RNAs (lncRNAs) play regulatory roles in post-transcriptional processes in plants. However, little is known about their involvem...

    Authors: Nanbo Jiao, Jieru Xu, Yue Wang, Dunxi Li, Feifei Chen, Yu Chen and Jinhui Chen
    Citation: BMC Genomics 2024 25:372
  30. X-chromosome inactivation (XCI) is an epigenetic process that occurs during early development in mammalian females by randomly silencing one of two copies of the X chromosome in each cell. The preferential ina...

    Authors: Numrah Fadra, Laura E Schultz-Rogers, Pritha Chanana, Margot A Cousin, Erica L Macke, Alejandro Ferrer, Filippo Pinto e Vairo, Rory J Olson, Gavin R Oliver, Lindsay A Mulvihill, Garrett Jenkinson and Eric W Klee
    Citation: BMC Genomics 2024 25:371
  31. Quinoa (Chenopodium quinoa Willd.) is valued for its nutritional richness. However, pre-harvest sprouting poses a significant threat to yield and grain quality. This study aims to enhance our understanding of pre...

    Authors: Xiaoxue Zhao, Shiyu Wang, Fenggen Guo and Pan Xia
    Citation: BMC Genomics 2024 25:370
  32. Pigeon circovirus infections in pigeons (Columba livia domestica) have been reported worldwide. Pigeons should be PiCV-free when utilized as qualified experimental animals. However, pigeons can be freely purchase...

    Authors: Xiaobo Li, Shujing Wang, Wei Li, Shasha Wang, Xiao Qin, Ji Wang and Rui Fu
    Citation: BMC Genomics 2024 25:369
  33. The tissue damage caused by transient ischemic injury is an essential component of the pathogenesis of retinal ischemia, which mainly hinges on the degree and duration of interruption of the blood supply and t...

    Authors: Kai-Xiong Qing, Amy C. Y. Lo, Siduo Lu, You Zhou, Dan Yang and Di Yang
    Citation: BMC Genomics 2024 25:367
  34. Large-scale copy number variants (CNVs) are structural alterations in the genome that involve the duplication or deletion of DNA segments, contributing to genetic diversity and playing a crucial role in the ev...

    Authors: Zuzana Holesova, Ondrej Pös, Juraj Gazdarica, Marcel Kucharik, Jaroslav Budis, Michaela Hyblova, Gabriel Minarik and Tomas Szemes
    Citation: BMC Genomics 2024 25:366
  35. Pseudoalteromonas viridis strain BBR56 was isolated from seawater at Dutungan Island, South Sulawesi, Indonesia. Bacterial DNA was isolated using Promega Genomic DNA TM050. DNA purity and quantity were assessed u...

    Authors: Desy Putri Handayani, Alim Isnansetyo and Indah Istiqomah
    Citation: BMC Genomics 2024 25:364
  36. Cold hardiness is fundamental for amphibians to survive during the extremely cold winter on the Qinghai-Tibet plateau. Exploring the gene regulation mechanism of freezing-tolerant Rana kukunoris could help us to ...

    Authors: Tao Zhang, Lun Jia, Zhiyi Niu, Xinying Li, Shengkang Men, Lu Jiang, Miaojun Ma, Huihui Wang, Xiaolong Tang and Qiang Chen
    Citation: BMC Genomics 2024 25:363
  37. Rose is recognized as an important ornamental plant worldwide, and it is also one of the most widely used flowers in gardens. At present, the improvement of rose traits is still difficult and uncertain, and mo...

    Authors: Li Du, Xiaoling Kang, Haoran Guo, Zhongfeng Zhu, Rui Wu, Meijing Yuan and Chuanyu Ding
    Citation: BMC Genomics 2024 25:362
  38. Single-cell sequencing techniques are revolutionizing every field of biology by providing the ability to measure the abundance of biological molecules at a single-cell resolution. Although single-cell sequenci...

    Authors: Lucas Kuijpers, Bastian Hornung, Mirjam C. G. N. van den Hout - van Vroonhoven, Wilfred F. J. van IJcken, Frank Grosveld and Eskeatnaf Mulugeta
    Citation: BMC Genomics 2024 25:361
  39. During mitosis the cell depends on proper attachment and segregation of replicated chromosomes to generate two identical progeny. In cancers defined by overexpression or dysregulation of the MYC oncogene this pro...

    Authors: Sarah A. Streeter, Alexandria G. Williams, James R. Evans, Jing Wang, Alissa D. Guarnaccia, Andrea C. Florian, Rafet Al-Tobasei, Qi Liu, William P. Tansey and April M. Weissmiller
    Citation: BMC Genomics 2024 25:360
  40. Inherited hearing impairment is a remarkably heterogeneous monogenic condition, involving hundreds of genes, most of them with very small (< 1%) epidemiological contributions. The exception is GJB2, the gene enco...

    Authors: María Domínguez-Ruiz, Silvia Murillo-Cuesta, Julio Contreras, Marta Cantero, Gema Garrido, Belén Martín-Bernardo, Elena Gómez-Rosas, Almudena Fernández, Francisco J. del Castillo, Lluís Montoliu, Isabel Varela-Nieto and Ignacio del Castillo
    Citation: BMC Genomics 2024 25:359
  41. Hox gene family is an important transcription factor that regulates cell process, and plays a role in the process of adipocytes differentiation and fat deposition. Previous transcriptome sequencing studies hav...

    Authors: Lixia He, Xue Feng, Chunli Hu, Shuang Liu, Hui Sheng, Bei Cai and Yun Ma
    Citation: BMC Genomics 2024 25:358
  42. Broodiness significantly impacts poultry egg production, particularly notable in specific breeds such as the black-boned Silky, characterized by pronounced broodiness. An understanding of the alterations in ov...

    Authors: Yuting Tan, Yunyan Huang, Chunhui Xu, Xuan Huang, Shibao Li and Zhaozheng Yin
    Citation: BMC Genomics 2024 25:357
  43. Centromeres play a crucial and conserved role in cell division, although their composition and evolutionary history in green algae, the evolutionary ancestors of land plants, remains largely unknown.

    Authors: Bo Wang, Yanyan Jia, Ningxin Dang, Jie Yu, Stephen J. Bush, Shenghan Gao, Wenxi He, Sirui Wang, Hongtao Guo, Xiaofei Yang, Weimin Ma and Kai Ye
    Citation: BMC Genomics 2024 25:356

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