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  1. Citrobacter species are Gram-negative opportunistic pathogens commonly reported in nosocomial-acquired infections. This study characterised four Citrobacter species that were isolated from surface water in the No...

    Authors: Lee-Hendra Chenhaka, Deidré A.B. Van Wyk, Charlotte Mienie, Cornelius C. Bezuidenhout and Kgaugelo E. Lekota
    Citation: BMC Genomics 2023 24:755
  2. Bergenia purpurascens is an important medicinal, edible and ornamental plant. It generally grows in high-altitude areas with complex climates. There have been no reports about how B. purpurascens survives under c...

    Authors: Xuebin Zhang, Fang Yu, Xin Lyu, Jingyu Chen, Hongyan Zeng, Nuomei Xu, Yufeng Wu and Qiankun Zhu
    Citation: BMC Genomics 2023 24:754
  3. Enterococcus faecalis is the most commonly isolated enterococcal species in clinical infection. This bacterium is notorious for its ability to share genetic content within and outside of its species. With this in...

    Authors: Baylie R. Hochstedler-Kramer, Adriana Ene, Catherine Putonti and Alan J. Wolfe
    Citation: BMC Genomics 2023 24:752
  4. High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck’s tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasan...

    Authors: Xuejuan Li, Xiaoyang Wang, Xiaoping Yu, Chao Yang, Liliang Lin and Yuan Huang
    Citation: BMC Genomics 2023 24:751
  5. Improving the egg production of goose is a crucial goal of breeding, because genetics is the key factor affecting egg production. Thus, we sequenced the genomes of 55 Chinese indigenous geese from six breeds, ...

    Authors: Hongchang Zhao, Guobo Sun, Xiaohui Mu, Xiaoming Li, Jun Wang, Mengli Zhao, Gansheng Zhang, Rongchao Ji, Chao Chen, Guangliang Gao and Jian Wang
    Citation: BMC Genomics 2023 24:750
  6. Chiloschista (Orchidaceae, Aeridinae) is an epiphytic leafless orchid that is mainly distributed in tropical or subtropical forest canopies. This rare and threatened orchid lacks molecular resources for phylogene...

    Authors: Ding-Kun Liu, Cheng-Yuan Zhou, Xiong-De Tu, Zhuang Zhao, Jin-Liao Chen, Xu-Yong Gao, Shao-Wei Xu, Meng-Yao Zeng, Liang Ma, Sagheer Ahmad, Ming-He Li, Siren Lan and Zhong-Jian Liu
    Citation: BMC Genomics 2023 24:749
  7. Infection by beet cyst nematodes (BCN, Heterodera schachtii) causes a serious disease of sugar beet, and climatic change is expected to improve the conditions for BCN infection. Yield and yield stability under ad...

    Authors: Katharina Sielemann, Boas Pucker, Elena Orsini, Abdelnaser Elashry, Lukas Schulte, Prisca Viehöver, Andreas E. Müller, Axel Schechert, Bernd Weisshaar and Daniela Holtgräwe
    Citation: BMC Genomics 2023 24:748
  8. Traumatic brain injury (TBI) is a central nervous system disease caused by external trauma, which has complex pathological and physiological mechanisms. The aim of this study was to explore the correlation bet...

    Authors: Liyan Yan, Xiaonan Han, Mingkang Zhang, Yikun Fu, Fei Yang, Qian Li and Tian Cheng
    Citation: BMC Genomics 2023 24:747
  9. Glioblastoma multiforme (GBM) is the most common and lethal primary brain tumor with a poor prognosis. The C-C motif chemokine ligand 2 (CCL2) has shown abnormal expression associated with progression of multi...

    Authors: Longfei Deng, Jie Ren, Benqin Li, Yinggang Wang, Nianfen Jiang, Yi Wang and Hongjuan Cui
    Citation: BMC Genomics 2023 24:746
  10. Root-knot nematode Meloidogyne graminicola has emerged as a major threat in rice agroecosystems owing to climate change-induced changes in cultivation practices. Synthetic nematicides are continually being withdr...

    Authors: Tushar K. Dutta, Voodikala S. Akhil, Manoranjan Dash, Artha Kundu, Victor Phani and Anil Sirohi
    Citation: BMC Genomics 2023 24:745
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. In this study, we explored the characteristics and causes of freckle formation. We collected 15 normal and freckled eggs each for eggshell index testing and hypothesized that the structure and function of the ...

    Authors: Guochao Duan, Wei Liu, Haixia Han, Dapeng Li, Qiuxia Lei, Yan Zhou, Jie Liu, Jie Wang, Yuanjun Du, Dingguo Cao, Fu Chen and Fuwei Li
    Citation: BMC Genomics 2023 24:738
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. Two-component systems (TCSs) assume a pivotal function in Mycobacterium tuberculosis (M.tuberculosis) growth. However, the exact regulatory mechanism of this system needs to be elucidated, and only a few studies ...

    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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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

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