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  1. De novo mutations arising in the germline are a source of genetic variation and their discovery broadens our understanding of genetic disorders and evolutionary patterns. Although the number of de novo single nuc...

    Authors: Marije J. Steensma, Y. L. Lee, A. C. Bouwman, C. Pita Barros, M. F.L. Derks, M. C.A.M. Bink, B. Harlizius, A. E. Huisman, R. P.M.A. Crooijmans, M. A.M. Groenen, H. A. Mulder and C. M. Rochus
    Citation: BMC Genomics 2023 24:208
  2. Monocytes -key regulators of the innate immune response- are actively involved in the pathogenesis of systemic lupus erythematosus (SLE). We sought to identify novel compounds that might serve as monocyte-dire...

    Authors: Dimitrios Nikolakis, Panagiotis Garantziotis, George Sentis, Antonis Fanouriakis, George Bertsias, Eleni Frangou, Dionysis Nikolopoulos, Aggelos Banos and Dimitrios T Boumpas
    Citation: BMC Genomics 2023 24:207
  3. Inherited retinal diseases (IRD) are genetically heterogeneous disorders that cause the dysfunction or loss of photoreceptor cells and ultimately lead to blindness. To date, next-generation sequencing procedur...

    Authors: Karla Alejandra Ruiz-Ceja, Dalila Capasso, Michele Pinelli, Eugenio Del Prete, Diego Carrella, Diego di Bernardo and Sandro Banfi
    Citation: BMC Genomics 2023 24:206
  4. RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming – to allow analysis of a broader range of transcripts – remains challenging.

    Authors: Charlotte Gustafsson, Julia Hauenstein, Nicolai Frengen, Aleksandra Krstic, Sidinh Luc and Robert Månsson
    Citation: BMC Genomics 2023 24:205
  5. Jute is considered one of the most important crops for fiber production and multipurpose usages. Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is a crucial enzyme involved in lignin biosynthesis in plants. The pot...

    Authors: Mohamed Ali Kahie, Yongjun Wang, Pingping Fang, Jianmin Qi, Rongjie Lei, Jiantang Xu, Lihui Lin, Liwu Zhang, Jisen Zhang and Aifen Tao
    Citation: BMC Genomics 2023 24:204
  6. The freshwater leech Whitmania pigra (W. pigra) Whitman (Annelida phylum) is a model organism for neurodevelopmental studies. However, molecular biology research on its embryonic development is still scarce. Here...

    Authors: Jiali Liu, Jinxin Liu, Mingyue Li, Lisi Zhou, Weijun Kong, Hailin Zhang, Panpan Jin, Fuhua Lu, Gufa Lin and Linchun Shi
    Citation: BMC Genomics 2023 24:203
  7. High throughput sequencing has enabled the interrogation of the transcriptomic landscape of glucagon-secreting alpha cells, insulin-secreting beta cells, and somatostatin-secreting delta cells. These approache...

    Authors: Alex M. Mawla, Talitha van der Meulen and Mark O. Huising
    Citation: BMC Genomics 2023 24:202
  8. Nucleosome remodeling factors regulate the occupancy and positioning of nucleosomes genome-wide through ATP-driven DNA translocation. While many nucleosomes are consistently well-positioned, some nucleosomes a...

    Authors: David C. Klein, Kris Troy, Sarah A. Tripplehorn and Sarah J. Hainer
    Citation: BMC Genomics 2023 24:201
  9. The auxin indole-3-acetic acid (IAA) is a vital phytohormone that influences plant growth and development. Our previous work showed that IAA content decreased during flower development in the medicinally impor...

    Authors: Can Si, Danqi Zeng, Jaime A. Teixeira da Silva, Shengxiang Qiu, Jun Duan, Song Bai and Chunmei He
    Citation: BMC Genomics 2023 24:199
  10. As a diverse and abundant class of endogenous RNAs, circular RNAs (circRNAs) participate in various biological processes including cell proliferation and apoptosis. Nevertheless, few researchers have investiga...

    Authors: Jiale Yun, Xiaoyu Huang, Chang Liu, Mingyue Shi, Wenxia Li, Jin Niu, Chunbo Cai, Yang Yang, Pengfei Gao, Xiaohong Guo, Bugao Li, Chang Lu and Guoqing Cao
    Citation: BMC Genomics 2023 24:196
  11. In plants, RNA silencing is an important conserved mechanism to regulate gene expression and combat against abiotic and biotic stresses. Dicer-like (DCL) and Argonaute (AGO) proteins and RNA-dependent RNA poly...

    Authors: Yongqiang Li, Enze Ma, Kai Yang, Bo Zhao, Yisong Li and Ping Wan
    Citation: BMC Genomics 2023 24:195
  12. Maize has many kernel colors, from white to dark black. However, research on the color and nutritional quality of the different varieties is limited. The color of the maize grain is an important characteristic...

    Authors: Yufeng Jiang, Li Yang, Hexia Xie, Lanqiu Qin, Lingqiang Wang, Xiaodong Xie, Haiyu Zhou, Xianjie Tan, Jinguo Zhou and Weidong Cheng
    Citation: BMC Genomics 2023 24:194
  13. Aparapotamon, a freshwater crab genus endemic to China, includes 13 species. The distribution of Aparapotamon spans the first and second tiers of China's terrain ladder, showing great altitudinal differences. To ...

    Authors: Yu-Tong Ji, Xiao-Juan Zhou, Qian Yang, Yuan-Biao Lu, Jun Wang and Jie-Xin Zou
    Citation: BMC Genomics 2023 24:193
  14. Genetic correlations between complex traits suggest that pleiotropic variants contribute to trait variation. Genome-wide association studies (GWAS) aim to uncover the genetic underpinnings of traits. Multivari...

    Authors: A. Nosková, A. Mehrotra, N. K. Kadri, A. Lloret-Villas, S. Neuenschwander, A. Hofer and H. Pausch
    Citation: BMC Genomics 2023 24:192
  15. Starch hydrolysates are energy sources for plant growth and development, regulate osmotic pressure and transmit signals in response to both biological and abiotic stresses. The α-amylase (AMY) and the β-amylas...

    Authors: Taiyi Yang, Hengrui Li, Liangwu Li, Wanling Wei, Yuanhang Huang, Faqian Xiong and Maogui Wei
    Citation: BMC Genomics 2023 24:190
  16. Authors: Shelly A. Wanamaker, Kaitlyn R. Mitchell, Rhonda Elliott Thompson, Benoit Eudeline, Brent Vadopalas, Emma B. Timmins-Schiffman and Steven B. Roberts
    Citation: BMC Genomics 2023 24:188

    The original article was published in BMC Genomics 2020 21:723

  17. Understanding the evolutionary forces related to climate changes that have been shaped genetic variation within species has long been a fundamental pursuit in biology. In this study, we generated whole-genome ...

    Authors: Rugang Tian, Hojjat Asadollahpour Nanaie, Xiao Wang, Baolige Dalai, Meng Zhao, Fenf Wang, Hui Li, Ding Yang, Hao Zhang, Yuan Li, Tingyue Wang, Tu Luan and Jianghong Wu
    Citation: BMC Genomics 2023 24:186
  18. Rice is one of the most important cereals consumed worldwide. Two major abiotic factors affecting rice plants in different growth stages are flooding stress and cold stress. These abiotic stresses can take pla...

    Authors: Ranjita Thapa, Rodante E. Tabien, Charles D. Johnson and Endang M. Septiningsih
    Citation: BMC Genomics 2023 24:185
  19. In-depth knowledge of the cellular and molecular composition of dental pulp (DP) and the crosstalk between DP cells that drive tissue homeostasis are not well understood. To address these questions, we perform...

    Authors: Natnicha Jiravejchakul, Gabriela L. Abe, Martin Loza, Soyoung Park, Ponpan Matangkasombut, Jun-Ichi Sasaki, Satoshi Imazato, Diego Diez and Daron M. Standley
    Citation: BMC Genomics 2023 24:184
  20. Red-tail catfish (Hemibagrus wyckioides) is an important commercially farmed catfish in southern China. Males of red-tail catfish grow faster than females, suggesting that all-male catfish will produce more signi...

    Authors: Wen-Yu Wei, Yi Gong, Xin-Fen Guo, Min Liu, Yu-Lin Zhou, Zhi Li, Li Zhou, Zhong-Wei Wang and Jian-Fang Gui
    Citation: BMC Genomics 2023 24:183
  21. Agaricus bisporus is the most widely cultivated edible mushroom in the world with a only around three hundred years known history of cultivation. Therefore, it represents an ideal organism not only to investigate...

    Authors: Ming-Zhe Zhang, Jian-Ping Xu, Philippe Callac, Mei-Yuan Chen, Qi Wu, Mark Wach, Gerardo Mata and Rui-Lin Zhao
    Citation: BMC Genomics 2023 24:182
  22. CircRNAs are involved in the pathogenesis of several central nervous system diseases. However, their functions and mechanisms in spinal cord injury (SCI) are still unclear. Therefore, the purpose of this study...

    Authors: Jian Cao, Chongzhi Pan, Jian Zhang, Qi Chen, Tao Li, Dingwen He and Xigao Cheng
    Citation: BMC Genomics 2023 24:181
  23. The extremely harsh environment of the desert is changing dramatically every moment, and the rapid adaptive stress response in the short term requires enormous energy expenditure to mobilize widespread regulat...

    Authors: Jipeng Cui, Tianhang Qiu, Li Li and Suxia Cui
    Citation: BMC Genomics 2023 24:180
  24. Fusarium crown rot (FCR) is a chronic disease of cereals worldwide. Compared with tetraploid wheat, hexaploid wheat is more resistant to FCR infection. The underlying reasons for the differences are still not ...

    Authors: Ying Chen, Yunpeng Wang, Fangnian Guan, Li Long, Yuqi Wang, Hao Li, Mei Deng, Yazhou Zhang, Zhien Pu, Wei Li, Qiantao Jiang, Jirui Wang, Yuming Wei, Jian Ma, Qiang Xu, Houyang Kang…
    Citation: BMC Genomics 2023 24:178
  25. Geranylgeranyl pyrophosphate synthase (GGPS) is a structural enzyme of the terpene biosynthesis pathway that is involved in regulating plant photosynthesis, growth and development, but this gene family has not...

    Authors: Wenxiang Feng, Teame Gereziher Mehari, Hui Fang, Meijun Ji, Zijian Qu, Mengxue Jia, Dongmei Wang, Allah Ditta, Muhammad K. R. Khan, Yunying Cao, Jianyong Wu and Baohua Wang
    Citation: BMC Genomics 2023 24:176
  26. Lamellibrachia luymesi dominates cold sulfide-hydrocarbon seeps and is known for its ability to consume bacteria for energy. The symbiotic relationship between tubeworms and bacteria with particular adaptations ...

    Authors: Hong Shi, Lingwei Ruan, Zimeng Chen, Yifei Liao, Wenhao Wu, Linmin Liu and Xun Xu
    Citation: BMC Genomics 2023 24:175
  27. Eutrema salsugineum (2n = 14), a halophyte in the family Brassicaceae, is an attractive model to study abiotic stress tolerance in plants. Two versions of E. salsugineum genomes that previously reported were base...

    Authors: Meng Xiao, Guoqian Hao, Xinyi Guo, Landi Feng, Hao Lin, Wenjie Yang, Yanyu Chen, Kexin Zhao, Ling Xiang, Xinyao Jiang, Dong Mei and Quanjun Hu
    Citation: BMC Genomics 2023 24:174
  28. Gymnosporangium asiaticum and G. yamadae can share Juniperus chinensis as the telial host, but the symptoms are completely different. The infection of G. yamadae causes the enlargement of the phloem and cortex of...

    Authors: Chenxi Shao, Siqi Tao and Yingmei Liang
    Citation: BMC Genomics 2023 24:173
  29. Molecular characterization of late-onset Alzheimer’s disease (LOAD), the leading cause of age-related dementia, has revealed transcripts, proteins, and pathway alterations associated with disease. Assessing th...

    Authors: Ravi S. Pandey, Kevin P. Kotredes, Michael Sasner, Gareth R. Howell and Gregory W. Carter
    Citation: BMC Genomics 2023 24:172
  30. Chromatin immunoprecipitation (ChIP) is an antibody-based approach that is frequently utilized in chromatin biology and epigenetics. The challenge in experimental variability by unpredictable nature of usable ...

    Authors: Ariel Caride, Jin Sung Jang, Geng-Xian Shi, Sam Lenz, Jian Zhong, Kwan Hyun Kim, Mariet Allen, Keith D. Robertson, Gianrico Farrugia, Tamas Ordog, Nilüfer Ertekin-Taner and Jeong-Heon Lee
    Citation: BMC Genomics 2023 24:171
  31. The flowering biology of wheat plants favours self-pollination which causes obstacles in wheat hybrid breeding. Wheat flowers can be divided into two groups, the first one is characterized by flowering and pol...

    Authors: Magdalena Szeliga, Beata Bakera, Magdalena Święcicka, Mirosław Tyrka and Monika Rakoczy-Trojanowska
    Citation: BMC Genomics 2023 24:170
  32. Spots in pierid butterflies and eyespots in nymphalid butterflies are likely non-homologous wing colour pattern elements, yet they share a few features in common. Both develop black scales that depend on the f...

    Authors: Jocelyn Liang Qi Wee, Suriya Narayanan Murugesan, Christopher W. Wheat and Antónia Monteiro
    Citation: BMC Genomics 2023 24:169
  33. Surface polysaccharides (SPs), such as lipopolysaccharide (O antigen) and capsular polysaccharide (K antigen), play a key role in the pathogenicity of Escherichia coli (E. coli). Gene cluster for polysaccharide a...

    Authors: Ao Dong, Chengzhi Liu, Xiaoting Hua, Yunsong Yu, Yan Guo, Dongshu Wang, Xiankai Liu, Huan Chen, Hengliang Wang and Li Zhu
    Citation: BMC Genomics 2023 24:168
  34. The processes of fertilization and egg activation are vital for early embryogenesis. However, while the mechanisms associated with key events during these processes differ among species and modes of spawning, ...

    Authors: Feng Chen, Yeke Wang, Jun He, Carl Smith, Ge Xue, Yan Zhao, Yanghui Peng, Jia Zhang, Jiarui Liu, Jun Chen and Ping Xie
    Citation: BMC Genomics 2023 24:167
  35. WD40 transcription factors, a large gene family in eukaryotes, are involved in a variety of growth regulation and development pathways. WD40 plays an important role in the formation of MYB-bHLH-WD (MBW) comple...

    Authors: Lin Chen, Yongmei Cui, Youhua Yao, Likun An, Yixiong Bai, Xin Li, Xiaohua Yao and Kunlun Wu
    Citation: BMC Genomics 2023 24:166
  36. The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne outbreak of Salmonella in over a decade. The epidemiological investigation suggested two farms as the likely source of ...

    Authors: Seth Commichaux, Hugh Rand, Kiran Javkar, Erin K. Molloy, James B. Pettengill, Arthur Pightling, Maria Hoffmann, Mihai Pop, Victor Jayeola, Steven Foley and Yan Luo
    Citation: BMC Genomics 2023 24:165
  37. Epithelium-mesenchymal interactions are involved in odontogenic processes. Previous studies have focused on the intracellular signalling regulatory network in tooth development, but the functions of extracellu...

    Authors: Jiawen Chen, Tianyu Sun, Yan You, Binbin Lin, Buling Wu and Jingyi Wu
    Citation: BMC Genomics 2023 24:163
  38. Metabolic detoxification is one of the major mechanisms contributing to the development of resistance in mosquitoes, including the southern house mosquito, Culex quinquefasciatus. The three major detoxification s...

    Authors: Xinyue Huang, Phillip E. Kaufman, Giridhar N. Athrey, Chris Fredregill, Christina Alvarez, Vinaya Shetty and Michel A. Slotman
    Citation: BMC Genomics 2023 24:160
  39. Tomato (Solanum lycopersicum) is both an important agricultural product and an excellent model system for studying plant-pathogen interactions. It is susceptible to bacterial wilt caused by Ralstonia solanacearum

    Authors: Jianlei Shi, Deju Shui, Shiwen Su, Zili Xiong and Wenshan Zai
    Citation: BMC Genomics 2023 24:159
  40. Diet and parasitism can have powerful effects on host gene expression. However, how specific dietary components affect host gene expression that could feed back to affect parasitism is relatively unexplored in...

    Authors: Jonathan J. Giacomini, Lynn S. Adler, Benjamin J. Reading and Rebecca E. Irwin
    Citation: BMC Genomics 2023 24:157

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