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  1. Chinese indigenous pigs in Yunnan exhibit considerable phenotypic diversity, but their population structure and the biological interpretation of signatures of artificial selection require further investigation...

    Authors: Xueyan Feng, Shuqi Diao, Yuqiang Liu, Zhiting Xu, Guangzhen Li, Ye Ma, Zhanqin Su, Xiaohong Liu, Jiaqi Li and Zhe Zhang
    Citation: BMC Genomics 2023 24:743
  2. DNA methylation, instrumental in numerous life processes, underscores the paramount importance of its accurate prediction. Recent studies suggest that deep learning, due to its capacity to extract profound ins...

    Authors: Linlin Zhuo, Rui Wang, Xiangzheng Fu and Xiaojun Yao
    Citation: BMC Genomics 2023 24:742
  3. Xanthomonas translucens pv. graminis (Xtg) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly of draf...

    Authors: Florian Goettelmann, Ralf Koebnik, Veronica Roman-Reyna, Bruno Studer and Roland Kölliker
    Citation: BMC Genomics 2023 24:741
  4. Genetic diversity is crucial for the success of plant breeding programs and core collections are important resources to capture this diversity. Many core collections have already been constructed by gene banks...

    Authors: T. Koorevaar, J. H. Willemsen, R. G. F. Visser, P. Arens and C. Maliepaard
    Citation: BMC Genomics 2023 24:740
  5. Prunus cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources for P. ...

    Authors: Lijuan Feng, Guopeng Zhao, Mengmeng An, Chuanzeng Wang and Yanlei Yin
    Citation: BMC Genomics 2023 24:739
  6. Single-cell chromatin accessibility has emerged as a powerful means of understanding the epigenetic landscape of diverse tissues and cell types, but profiling cells from many independent specimens is challengi...

    Authors: Gregory T. Booth, Riza M. Daza, Sanjay R. Srivatsan, José L. McFaline-Figueroa, Rula Green Gladden, Andrew C. Mullen, Scott N. Furlan, Jay Shendure and Cole Trapnell
    Citation: BMC Genomics 2023 24:737
  7. Transcription factors regulate gene expression by binding to transcription factor binding sites (TFBSs). Most models for predicting TFBSs are based on position weight matrices (PWMs), which require a specific ...

    Authors: Sebastian Proft, Janna Leiz, Udo Heinemann, Dominik Seelow, Kai M. Schmidt-Ott and Maria Rutkiewicz
    Citation: BMC Genomics 2023 24:736
  8. The frass of several herbivorous insect species has been utilised as natural medicines in Asia; however, the metabolite makeup and pharmaceutical activities of insect frass have yet to be investigated. Oligoph...

    Authors: Miho Nakano, Takuma Sakamoto, Yoshikazu Kitano, Hidemasa Bono, Richard J. Simpson and Hiroko Tabunoki
    Citation: BMC Genomics 2023 24:735
  9. Actinomyces strains are commonly found as part of the normal microflora on human tissue surfaces, including the oropharynx, gastrointestinal tract, and female genital tract. Understanding the diversity and charac...

    Authors: Xuechen Tian, Wee Fei Aaron Teo, Wei Yee Wee, Yixin Yang, Halah Ahmed, Nicholas S. Jakubovics, Siew Woh Choo and Geok Yuan Annie Tan
    Citation: BMC Genomics 2023 24:734
  10. Eurasian pigs have undergone lineage admixture throughout history. It has been confirmed that the genes of indigenous pig breeds in China have been introduced into Western commercial pigs, providing genetic ma...

    Authors: Chenxi Liu, Ruihua Huang, Guosheng Su, Liming Hou, Wuduo Zhou, Qian Liu, Zijian Qiu, Qingbo Zhao and Pinghua Li
    Citation: BMC Genomics 2023 24:733
  11. Single synonymous codon mutations typically have only minor or no effects on gene function. Here, we estimate the effects on cell growth of ~ 200 single synonymous codon mutations in an operonic context by mut...

    Authors: Priyanka Bajaj, Munmun Bhasin and Raghavan Varadarajan
    Citation: BMC Genomics 2023 24:732
  12. There has been a gradual increase in the occurrence of cardiovascular and cerebrovascular ischemic diseases, particularly as comorbidities. Yet, the mechanisms underlying these diseases remain unclear. Ferropt...

    Authors: Wei Liao, Yuehui Wen, Chuan Zeng, Shaochun Yang, Yanyu Duan, Chunming He and Ziyou Liu
    Citation: BMC Genomics 2023 24:731
  13. Venom phospholipase D (PLDs), dermonecrotic toxins like, are the major molecules in the crude venom of scorpions, which are mainly responsible for lethality and dermonecrotic lesions during scorpion envenoming...

    Authors: Masoumeh Baradaran and Fatemeh Salabi
    Citation: BMC Genomics 2023 24:730
  14. The epididymis is a highly regionalized tubular organ possesses vectorial functions of sperm concentration, maturation, transport, and storage. The epididymis-expressed genes and proteins are characterized by ...

    Authors: Shaoming Fang, Zhechen Li, Shuo Pang, Yating Gan, Xiaoning Ding and Hui peng
    Citation: BMC Genomics 2023 24:729
  15. Collective cell migration underlies many essential processes, including sculpting organs during embryogenesis, wound healing in the adult, and metastasis of cancer cells. At mid-oogenesis, Drosophila border cells...

    Authors: Emily Burghardt, Jessica Rakijas, Antariksh Tyagi, Pralay Majumder, Bradley J.S.C. Olson and Jocelyn A. McDonald
    Citation: BMC Genomics 2023 24:728
  16. While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmente...

    Authors: Sophie A. Simon, Katharina Schmidt, Lea Griesdorn, André R. Soares, Till L. V. Bornemann and Alexander J. Probst
    Citation: BMC Genomics 2023 24:727
  17. Pre-exposing plants to abiotic stresses can induce stress memory, which is crucial for adapting to subsequent stress exposure. Although numerous genes involved in salt stress response have been identified, the...

    Authors: Zhiying Zhu, Yan Dai, Guangrun Yu, Xin Zhang, Qi Chen, Xiaobing Kou, Eid M. Mehareb, Ghulam Raza, Baohong Zhang, Baohua Wang, Kai Wang and Jinlei Han
    Citation: BMC Genomics 2023 24:726
  18. In recent single-cell -omics studies, both the differential activity of transcription factors regulating cell fate determination and differential genome activation have been tested for utility as descriptors o...

    Authors: Sami Kilpinen, Heidi Heliölä and Kaia Achim
    Citation: BMC Genomics 2023 24:725
  19. MicroRNA (miRNA) which can act as post-transcriptional regulators of mRNAs via base-pairing with complementary sequences within mRNAs is involved in processes of the complex interaction between immune system a...

    Authors: Cheng Liu, Chun Yu, Guoxin Song, Xingchen Fan, Shuang Peng, Shiyu Zhang, Xin Zhou, Cheng zhang, Xiangnan Geng, Tongshan Wang, Wenfang Cheng and Wei Zhu
    Citation: BMC Genomics 2023 24:724
  20. Patinopecten yessoensis, a large and old molluscan group, has been one of the most important aquaculture shellfish in Asian countries because of its high economic value. However, the aquaculture of the species ha...

    Authors: Yiying Wang, Junxia Mao, Zhiyue Fan, Yunna Hang, AnQi Tang, Ying Tian, Xubo Wang, Zhenlin Hao, Bing Han, Jun Ding and Yaqing Chang
    Citation: BMC Genomics 2023 24:723
  21. Cell type-specific differential gene expression analyses based on single-cell transcriptome datasets are sensitive to the presence of cell-free mRNA in the droplets containing single cells. This so-called ambi...

    Authors: Marijn Berg, Ilya Petoukhov, Inge van den Ende, Kerstin B. Meyer, Victor Guryev, Judith M. Vonk, Orestes Carpaij, Martin Banchero, Rudi W. Hendriks, Maarten van den Berge and Martijn C. Nawijn
    Citation: BMC Genomics 2023 24:722
  22. The prevalence of obese children in China is increasing, which poses a great challenge to public health. Gut microbes play an important role in human gut health, and changes in gut status are closely related t...

    Authors: Ping Li, Jiyang Jiang, Yifei Li, Yue Lan, Fan Yang, Jiao Wang, Yuxin Xie, Fei Xiong, Jinhui Wu, Hanmin Liu and Zhenxin Fan
    Citation: BMC Genomics 2023 24:721
  23. Numerous factors influence the growth and development of cashmere. Existing research on cashmere has predominantly emphasized a single omics level. Integrating multi-omics analyses can offer a more comprehensi...

    Authors: Yanan Xu, Yu Zhang, Yuting Qin, Ming Gu, Rui Chen, Yinggang Sun, Yanzhi Wu, Qian Li, Yanjun Qiao, Xiaowei Wang, Qiu Zhang, Lingchao Kong, Shuaitong Li and Zeying Wang
    Citation: BMC Genomics 2023 24:720
  24. Adventitious roots (ARs) represent an important organ system for water and nutrient uptake in lotus plants because of degeneration of the principal root. The WUSCHEL-related homeobox (WOX) gene regulates plant de...

    Authors: Liu quan, Liang Shiting, Zhao Chen, Han Yuyan, Zhao Minrong, Li Shuyan and Cheng Libao
    Citation: BMC Genomics 2023 24:719
  25. Two-component systems (TCSs) play a crucial role in the growth of Mycobacterium tuberculosis (M. tuberculosis). However, the precise regulatory mechanism of their contribution remain to be elucidated, and only a ...

    Authors: Yameng Li, Xianglong Kong, Yifan Li, Ningning Tao, Yawei Hou, Tingting Wang, Yingying Li, Qilin Han, Yao Liu and Huaichen Li
    Citation: BMC Genomics 2023 24:718

    The Correction to this article has been published in BMC Genomics 2024 25:38

  26. Cell annotation is a crucial methodological component to interpreting single cell and spatial omics data. These approaches were developed for single cell analysis but are often biased, manually curated and yet...

    Authors: Felipe Segato Dezem, Maycon Marção, Bassem Ben-Cheikh, Nadya Nikulina, Ayodele Omotoso, Destiny Burnett, Priscila Coelho, Judith Hurley, Carmen Gomez, Tien Phan-Everson, Giang Ong, Luciano Martelotto, Zachary R. Lewis, Sophia George, Oliver Braubach, Tathiane M. Malta…
    Citation: BMC Genomics 2023 24:717
  27. The phylogenetic position and classification of Athysanini are poorly defined, as it includes a large group of polyphyletic genera that have historically been assigned to it mainly because they still exhibit t...

    Authors: Muhammad Asghar Hassan, Zhixiang Tan, Rongrong Shen and Jichun Xing
    Citation: BMC Genomics 2023 24:714
  28. Bryozoans are mostly sessile aquatic colonial invertebrates belonging to the clade Lophotrochozoa, which unites many protostome bilaterian phyla such as molluscs, annelids and brachiopods. While Hox and ParaHo...

    Authors: Ahmed J. Saadi, André Luiz de Oliveira, Kevin M. Kocot and Thomas Schwaha
    Citation: BMC Genomics 2023 24:711
  29. Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted ge...

    Authors: Zongling Liu, Zhengjie Zhu, Yuanhe Huang, Song Nong, Minli Jiang, Sangui Yi, Delong Xie and Hongliu Hu
    Citation: BMC Genomics 2023 24:710
  30. As the fetal heart develops, cardiomyocyte proliferation potential decreases while fatty acid oxidative capacity increases in a highly regulated transition known as cardiac maturation. Small noncoding RNAs, su...

    Authors: Adar Aharon-Yariv, Yaxu Wang, Abdalla Ahmed and Paul Delgado-Olguín
    Citation: BMC Genomics 2023 24:709
  31. Forsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear and chloroplast genomes of F. suspensa have been published, its complete mitochondrial genome sequence has yet t...

    Authors: Yun Song, Xiaorong Du, Aoxuan Li, Amei Fan, Longjiao He, Zhe Sun, Yanbing Niu and Yonggang Qiao
    Citation: BMC Genomics 2023 24:708
  32. Basic leucine zipper (bZIP) protein is a plant-specific transcription factor involved in various biological processes, including light signaling, seed maturation, flower development, cell elongation, seed accumul...

    Authors: Xiaozong Wu, Changhe Cheng, Rui Ma, Jianbo Xu, Congcong Ma, Yutao Zhu and Yanyan Ren
    Citation: BMC Genomics 2023 24:705
  33. Eggshell speckle phenotype is an important trait in poultry production because they affect eggshell quality. However, the genetic architecture of speckled eggshells remains unclear. In this study, we determine...

    Authors: Xue Cheng, Xinghua Li, Mengyuan Yang, Chuanwei Zheng, Haiying Li, Lujiang Qu and Zhonghua Ning
    Citation: BMC Genomics 2023 24:704
  34. The Aconitum genus is a crucial member of the Ranunculaceae family. There are 350 Aconitum species worldwide, with about 170 species found in China. These species are known for their various pharmacological effec...

    Authors: Meihua Yang, Jiahao Liu, Wanqing Yang, Zhen Li, Yonglin Hai, Baozhong Duan, Haizhu Zhang, Xiaoli Yang and Conglong Xia
    Citation: BMC Genomics 2023 24:703
  35. Animals typically have either compound eyes, or camera-type eyes, both of which have evolved repeatedly in the animal kingdom. Both eye types include two important kinds of cells: photoreceptor cells, which ca...

    Authors: Shubham Rathore, Aaron Stahl, Joshua B. Benoit and Elke K. Buschbeck
    Citation: BMC Genomics 2023 24:702
  36. Aplasia cutis congenita (ACC) is a rare genetic disorder characterized by the localized or widespread absence of skin in humans and animals. Individuals with ACC may experience developmental abnormalities in t...

    Authors: Fuchen Zhou, Shenghui Wang, Haojun Qin, Haiyu Zeng, Jian Ye, Jie Yang, Gengyuan Cai, Zhenfang Wu and Zebin Zhang
    Citation: BMC Genomics 2023 24:701
  37. Avian pathogenic Escherichia coli (APEC) are the causative agents of colibacillosis in chickens, a disease which has significant economic impact on the poultry industry. Large plasmids detected in APEC are known ...

    Authors: Haley Sanderson, Madeline C. McCarthy, Chinenye R. Nnajide, Jessica Sparrow, Joseph E. Rubin, Jo-Anne R. Dillon and Aaron P. White
    Citation: BMC Genomics 2023 24:698
  38. Isabel Island is a Mexican volcanic island primarily composed of basaltic stones. It features a maar known as Laguna Fragatas, which is classified as a meromictic thalassohaline lake. The constant deposition o...

    Authors: Luis Mario Hernández-Soto, Francisco Martínez-Abarca, Hugo Ramírez-Saad, Marcos López-Pérez and José Félix Aguirre-Garrido
    Citation: BMC Genomics 2023 24:696
  39. Reference genomes provide a foundational framework for evolutionary investigations, ecological analysis, and conservation science, yet uncertainties in the assembly of reference genomes are difficult to assess...

    Authors: Trevor T. Bringloe and Geneviève J. Parent
    Citation: BMC Genomics 2023 24:693

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