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  1. Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a pathogen known to reside in cattle feedlots. This retrospective study examined 181 STEC O157:H7 strains collected over 23 years from a closed-system feed...

    Authors: Margaret D. Weinroth, Michael L. Clawson, Terrance M. Arthur, James E. Wells, Dayna M. Brichta-Harhay, Norval Strachan and James L. Bono
    Citation: BMC Genomics 2022 23:275
    Content type: Research article Published on:

  2. Transcription factors (TFs) play central roles in regulating gene expression. With the rapid growth in the use of high-throughput sequencing methods, there is a need to develop a comprehensive data processing ...

    Authors: Guan-Dong Shang, Zhou-Geng Xu, Mu-Chun Wan, Fu-Xiang Wang and Jia-Wei Wang
    Citation: BMC Genomics 2022 23(Suppl 1):272
    Content type: Software Published on:

    This article is part of a Supplement: Volume 23 Supplement 1

  3. Authors: Yanxian Yang, Yongqiang Yang, Mohamed Abd El-Gawad El-Sayed Ahmed, Mingyang Qin, Ruowen He, Yiping Wu, Xiaoxue Liang, Lan-Lan Zhong, Ping Chen, Baoguo Deng, Reem Mostafa Hassan, Weihong Wen, Lingqing Xu, Xubin Huang, Lin Xu and Guo-Bao Tian
    Citation: BMC Genomics 2022 23:270
    Content type: Correction Published on:

    The original article was published in BMC Genomics 2022 23:20

  4. In biological systems, metabolomics can not only contribute to the discovery of metabolic signatures for disease diagnosis, but is very helpful to illustrate the underlying molecular disease-causing mechanism....

    Authors: Yongtian Wang, Liran Juan, Jiajie Peng, Tao Wang, Tianyi Zang and Yadong Wang
    Citation: BMC Genomics 2022 23(Suppl 1):269
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 1

  5. Of the > 2600 Salmonella serovars, Salmonella enterica serovar I 4,[5],12:i:- (serovar I 4,[5],12:i:-) has emerged as one of the most common causes of human salmonellosis and the most frequent multidrug-resistant...

    Authors: Julian M. Trachsel, Bradley L. Bearson, Brian W. Brunelle and Shawn M. D. Bearson
    Citation: BMC Genomics 2022 23:268
    Content type: Research Published on:

  6. The growth and development of muscle stem cells (MuSCs) are significant events known to affect muscle plasticity, disease, meat production, and meat quality, which involves the types and functions of mRNA and ...

    Authors: Rui-Men Zhang, Yu Pan, Chao-Xia Zou, Qiang An, Juan-Ru Cheng, Peng-Ju Li, Zi-Hua Zheng, Yan Pan, Wan-You Feng, Su-Fang Yang, De-Shun Shi, Ying-Ming Wei and Yan-Fei Deng
    Citation: BMC Genomics 2022 23:267
    Content type: Research Published on:

  9. The plant-specific IQ67-domain (IQD) gene family plays an important role in plant development and stress responses. However, little is known about the IQD family in common wheat (Triticum aestivum L), an agricult...

    Authors: Qinglin Ke, Huifan Sun, Minqiang Tang, Ruihan Luo, Yan Zeng, Mengxing Wang, Yihan Li, Zhimin Li and Licao Cui
    Citation: BMC Genomics 2022 23:264
    Content type: Research Published on:

  10. Wound healing is a representative phenomenon of potato tubers subjected to mechanical injuries. Our previous results found that benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH) promoted the wo...

    Authors: Hong Jiang, Xue Li, Li Ma, Yingyue Ren, Yang Bi and Dov Prusky
    Citation: BMC Genomics 2022 23:263
    Content type: Research Published on:

  11. Cool temperature egg storage prior to incubation is a common practice in the broiler industry; however, prolonged egg storage causes increased embryonic mortality and decreased hatchability and growth in survi...

    Authors: K. Brady, C. C. Talbot Jr, J. A. Long, G. Welch, N. French, D. Nicholson and M. R. Bakst
    Citation: BMC Genomics 2022 23:262
    Content type: Research Published on:

  12. Colorectal cancer (CRC) is the third most common cancer worldwide and is influenced by environmental and genetic factors. Although numerous genetic loci for CRC have been identified, the overall understanding ...

    Authors: Eun Bi Lim, Ho-Suk Oh, Kang Chang Kim, Moon-Ho Kim, Young Jin Kim, Bong Jo Kim, Chu Won Nho and Yoon Shin Cho
    Citation: BMC Genomics 2022 23:261
    Content type: Research Published on:

  13. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform pub...

    Authors: Longhua Guo, James Boocock, Evann E. Hilt, Sukantha Chandrasekaran, Yi Zhang, Chetan Munugala, Laila Sathe, Noah Alexander, Valerie A. Arboleda, Jonathan Flint, Eleazar Eskin, Chongyuan Luo, Shangxin Yang, Omai B. Garner, Yi Yin, Joshua S. Bloom…
    Citation: BMC Genomics 2022 23:260
    Content type: Research Published on:

  15. The characteristics of muscle fibers determine the growth and meat quality of poultry. In this study, we performed a weighted gene co-expression network analysis (WGCNA) on the muscle fiber characteristics and...

    Authors: Yuanfang Li, Pengtao Yuan, Shengxin Fan, Bin Zhai, Wenjiao Jin, Donghua Li, Hong Li, Guirong Sun, Ruili Han, Xiaojun Liu, Yadong Tian, Guoxi Li and Xiangtao Kang
    Citation: BMC Genomics 2022 23:258
    Content type: Research Published on:

  16. Polyandrous social insects such as the honey bee are prime candidates for parental manipulation of gene expression in offspring. Although there is good evidence for parent-of-origin effects in honey bees the e...

    Authors: Owen T. Watson, Gabriele Buchmann, Paul Young, Kitty Lo, Emily J. Remnant, Boris Yagound, Mitch Shambrook, Andrew F. Hill, Benjamin P. Oldroyd and Alyson Ashe
    Citation: BMC Genomics 2022 23:257
    Content type: Research Published on:

  17. Ophiorrhiza pumila (Rubiaceae) is capable of producing camptothecin (CPT), one monoterpene indole alkaloid extensively employed in the treatment of multiple cancers. Transcription factors (TFs) GATA are a group ...

    Authors: Min Shi, Qikai Huang, Yao Wang, Can Wang, Ruiyan Zhu, Siwei Zhang and Guoyin Kai
    Citation: BMC Genomics 2022 23:256
    Content type: Research Published on:

  18. The pro-neural transcription factor ASCL1 is a master regulator of neurogenesis and a key factor necessary for the reprogramming of permissive cell types to neurons. Endogenously, ASCL1 expression is often ass...

    Authors: Laura M. Woods, Fahad R. Ali, Roshna Gomez, Igor Chernukhin, Daniel Marcos, Lydia M. Parkinson, Ahmad N. Abou Tayoun, Jason S. Carroll and Anna Philpott
    Citation: BMC Genomics 2022 23:255
    Content type: Research Published on:

  19. Long noncoding RNAs (lncRNAs) are involved in physiological and pathological processes. However, no studies have been conducted on the relationship between lncRNAs and renal aging.

    Authors: Jie Li, Fanfan Gao, Limin Wei, Lei Chen, Ning Qu, Lu Zeng, Yulong Luo, Xinmei Huang and Hongli Jiang
    Citation: BMC Genomics 2022 23:254
    Content type: Research Published on:

  20. Classification of parasitic bopyrids has traditionally been based on morphological characteristics, but phylogenetic relationships have remained elusive due to limited information provided by morphological dat...

    Authors: Ruiwen Wu, Rongxiu Guo, Qianqian Xi, Gustav Paulay and Jianmei An
    Citation: BMC Genomics 2022 23:253
    Content type: Research Published on:

  21. Cystic fibrosis (CF, MIM# 219,700) is an autosomal recessive disease caused by pathogenic variants within the CFTR gene. It was shown that genetic variants located in cis can affect disease severity or treatment ...

    Authors: Nika V. Petrova, Nataliya Y. Kashirskaya, Tatyana A. Vasilyeva, Natalia V. Balinova, Andrey V. Marakhonov, Elena I. Kondratyeva, Elena K. Zhekaite, Anna Y. Voronkova, Sergey I. Kutsev and Rena A. Zinchenko
    Citation: BMC Genomics 2022 23:252
    Content type: Research Published on:

  22. When plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury. Indica cultivars can usually withstand only mild cold stress in a relat...

    Authors: Zhichi Zeng, Sichen Zhang, Wenyan Li, Baoshan Chen and Wenlan Li
    Citation: BMC Genomics 2022 23:251
    Content type: Research Published on:

  23. With advances in next-generation sequencing technologies, an unprecedented amount of soybean accessions has been sequenced by many individual studies and made available as raw sequencing reads for post-genomic...

    Authors: Hengyou Zhang, He Jiang, Zhenbin Hu, Qijian Song and Yong-qiang Charles An
    Citation: BMC Genomics 2022 23:250
    Content type: Research Published on:

  25. The recent big data revolution in Genomics, coupled with the emergence of Deep Learning as a set of powerful machine learning methods, has shifted the standard practices of machine learning for Genomics. Even ...

    Authors: Eliška Chalupová, Ondřej Vaculík, Jakub Poláček, Filip Jozefov, Tomáš Majtner and Panagiotis Alexiou
    Citation: BMC Genomics 2022 23:248
    Content type: Software Published on:

  26. Chromatin architecture is critical for gene expression during development. Matrix attachment regions (MARs) control and regulate chromatin dynamics. The position of MARs in the genome determines the expression...

    Authors: Alekhya Rani Chunduri, Resma Rajan, Anugata Lima, Senthilkumar Ramamoorthy and Anitha Mamillapalli
    Citation: BMC Genomics 2022 23:247
    Content type: Research article Published on:

  27. Apple Glomerella leaf spot (GLS) and apple bitter rot (ABR) are two devastating foliar and fruit diseases on apples. The different symptoms of GLS and ABR could be related to different transcriptome patterns. ...

    Authors: Bowen Jiang, Ting Cai, Xiaoying Yang, Yuya Dai, Kaixuan Yu, Pingping Zhang, Pingliang Li, Caixia Wang, Na Liu, Baohua Li and Sen Lian
    Citation: BMC Genomics 2022 23:246
    Content type: Research Published on:

  28. Melanoma is a highly heterogeneous and aggressive cutaneous malignancy. Ferroptosis, a new pathway of cell death depending on the intracellar iron, has been shown to be significantly associated with apoptosis ...

    Authors: Yuxuan Chen, Linlin Guo, Zijie Zhou, Ran An and Jiecong Wang
    Citation: BMC Genomics 2022 23:245
    Content type: Research Published on:

  29. Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in Populus deltoids has not ye...

    Authors: Xiao-jing Wang, Xu-qian Peng, Xiao-chun Shu, Yu-hang Li, Zhong Wang and Wei-bing Zhuang
    Citation: BMC Genomics 2022 23:244
    Content type: Research Published on:

  30. External environmental factors, such as salt, alkali and drought, severely limit the acreage and yield of alfalfa. The mining of tolerance-related genes in alfalfa and improving the stress resistance of this p...

    Authors: Yuying Yuan, Jinqiu Yu, Lingzelai Kong, Wenkai Zhang, Xiangyin Hou and Guowen Cui
    Citation: BMC Genomics 2022 23:243
    Content type: Research Published on:

  31. An important aspect of studying evolution is to understand how new species are formed and their uniqueness is maintained. Hybridization can lead to the formation of new species through reorganization of the ad...

    Authors: Qianhong Gu, Shi Wang, Hui Zhong, Hui Yuan, Junliu Yang, Conghui Yang, Xuexue Huang, Xiaowei Xu, Yude Wang, Zehong Wei, Jing Wang and Shaojun Liu
    Citation: BMC Genomics 2022 23:242
    Content type: Research Published on:

  33. The emerging epitranscriptome plays an essential role in female fertility. As the most prevalent internal mRNA modification, N6-methyladenine (m6A) methylation regulate mRNA fate and translational efficiency. How...

    Authors: Chang Liu, Linshuang Li, Bo Yang, Yiqing Zhao, Xiyuan Dong, Lixia Zhu, Xinling Ren, Bo Huang, Jing Yue, Lei Jin, Hanwang Zhang and Lan Wang
    Citation: BMC Genomics 2022 23:240
    Content type: Research Published on:

  34. Peanut is the most essential oil and food crop globally due to its high oil and protein content. Root-knot nematode infects peanut roots, causing poor development and severely limiting peanut yields worldwide....

    Authors: Ping Xu, Hui Li, Xiaohua Wang, Ge Zhao, Xiaofei Lu, Shengjie Dai, Xiaoyu Cui, Mei Yuan and Zhenning Liu
    Citation: BMC Genomics 2022 23:239
    Content type: Research Published on:

  35. Ribosomal DNAs (rDNAs) are arranged in purely tandem repeats, preventing them from being reliably assembled onto chromosomes during generation of genome assembly. The uncertainty of rDNA genomic structure pres...

    Authors: Qiutao Ding, Runsheng Li, Xiaoliang Ren, Lu-yan Chan, Vincy W. S. Ho, Dongying Xie, Pohao Ye and Zhongying Zhao
    Citation: BMC Genomics 2022 23:238
    Content type: Research article Published on:

  37. Skin pigmentation is a broadly appearing phenomenon of most animals and humans in nature. Here we used a bird model to investigate why melanin spot deposits on the skin.

    Authors: Hehe Liu, Jianmei Wang, Jian Hu, Lei Wang, Zhanbao Guo, Wenlei Fan, Yaxi Xu, Dapeng Liu, Yunsheng Zhang, Ming Xie, Jing Tang, Wei Huang, Qi Zhang, Zhengkui Zhou and Shuisheng Hou
    Citation: BMC Genomics 2022 23:236
    Content type: Research Published on:

  38. Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinfor...

    Authors: Federica Palma, Iolanda Mangone, Anna Janowicz, Alexandra Moura, Alexandra Chiaverini, Marina Torresi, Giuliano Garofolo, Alexis Criscuolo, Sylvain Brisse, Adriano Di Pasquale, Cesare Cammà and Nicolas Radomski
    Citation: BMC Genomics 2022 23:235
    Content type: Research Published on:

  40. Abscisic acid (ABA) is a phytohormone that plays important roles in the regulation of plant growth, seed germination, and stress responses. The pyrabactin resistance 1-like (PYR/PYL) protein, an ABA receptor, ...

    Authors: Guoming Wang, Kaijie Qi, Xin Gao, Lei Guo, Peng Cao, Qionghou Li, Xin Qiao, Chao Gu and Shaoling Zhang
    Citation: BMC Genomics 2022 23:233
    Content type: Research Published on:

  41. The application of RNA-seq technology has become more extensive and the number of analysis procedures available has increased over the past years. Selecting an appropriate workflow has become an important issu...

    Authors: Xu Liu, Jialu Zhao, Liting Xue, Tian Zhao, Wei Ding, Yuying Han and Haihong Ye
    Citation: BMC Genomics 2022 23:232
    Content type: Research Published on:

  42. The cryptochromes (CRY) are specific blue light receptors of plants and animals, which play crucial roles in physiological processes of plant growth, development, and stress tolerance.

    Authors: Chaochen Huang, Pengbo Li, Junfeng Cao, Zishou Zheng, Jinquan Huang, Xiufang Zhang, Xiaoxia Shangguan, Lingjian Wang and Zhiwen Chen
    Citation: BMC Genomics 2022 23:231
    Content type: Research Published on:

  44. The soil-dwelling nematode Caenorhabditis elegans serves as a model system to study innate immunity against microbial pathogens. C. elegans have been collected from around the world, where they, presumably, adapt...

    Authors: Patrick Lansdon, Maci Carlson and Brian D. Ackley
    Citation: BMC Genomics 2022 23:229
    Content type: Research Published on:

  45. The tall wheatgrass species Thinopyrum elongatum carries a strong fusarium head blight (FHB) resistance locus located on the long arm of chromosome 7 (7EL) as well as resistance to leaf and stem rusts, all diseas...

    Authors: David Konkin, Ya-Chih Hsueh, Morgan Kirzinger, Marie Kubaláková, Aparna Haldar, Margaret Balcerzak, Fangpu Han, George Fedak, Jaroslav Doležel, Andrew Sharpe and Thérèse Ouellet
    Citation: BMC Genomics 2022 23:228
    Content type: Research Published on:

  46. Genetic variants have been found to influence red blood cell (RBC) susceptibility to hemolytic stress and affect transfusion outcomes and the severity of blood diseases. Males have a higher susceptibility to h...

    Authors: Fang Fang, Kelsey Hazegh, Alan E. Mast, Darrell J. Triulzi, Bryan R. Spencer, Mark T. Gladwin, Michael P. Busch, Tamir Kanias and Grier P. Page
    Citation: BMC Genomics 2022 23:227
    Content type: Research Published on:

  47. BEC-producing Clostridium perfringens is a causative agent of foodborne gastroenteritis. It was first reported in 2014, and since then, several isolates have been identified in Japan and the United Kingdom. The n...

    Authors: Kengo Ueda, Kazuki Kawahara, Narumi Kimoto, Yusuke Yamaguchi, Kazuhiro Yamada, Hiroya Oki, Takuya Yoshida, Shigeaki Matsuda, Yuki Matsumoto, Daisuke Motooka, Kentaro Kawatsu, Tetsuya Iida, Shota Nakamura, Tadayasu Ohkubo and Shinya Yonogi
    Citation: BMC Genomics 2022 23:226
    Content type: Research Published on:

  48. The ability of animals and their microbiomes to adapt to starvation and then restore homeostasis after refeeding is fundamental to their continued survival and symbiosis. The intestine is the primary site of n...

    Authors: Jayanth Jawahar, Alexander W. McCumber, Colin R. Lickwar, Caroline R. Amoroso, Sol Gomez de la Torre Canny, Sandi Wong, Margaret Morash, James H. Thierer, Steven A. Farber, Brendan J. M. Bohannan, Karen Guillemin and John F. Rawls
    Citation: BMC Genomics 2022 23:225
    Content type: Research Published on:

  49. Understanding how evolutionary forces relating to climate have shaped the patterns of genetic variation within and between species is a fundamental pursuit in biology. Iranian indigenous chickens have evolved ...

    Authors: Hojjat Asadollahpour Nanaei, Hamed Kharrati-Koopaee and Ali Esmailizadeh
    Citation: BMC Genomics 2022 23:224
    Content type: Research Published on:

    The Correction to this article has been published in BMC Genomics 2022 23:395

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