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  1. Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the ...

    Authors: Brenda Pardo, Abby Spangler, Lukas M. Weber, Stephanie C. Page, Stephanie C. Hicks, Andrew E. Jaffe, Keri Martinowich, Kristen R. Maynard and Leonardo Collado-Torres
    Citation: BMC Genomics 2022 23:434
  2. Shotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep insights from the raw reads heavily depends on the availability of fas...

    Authors: Felix Van der Jeugt, Rien Maertens, Aranka Steyaert, Pieter Verschaffelt, Caroline De Tender, Peter Dawyndt and Bart Mesuere
    Citation: BMC Genomics 2022 23:433
  3. The collection of circRNAs mostly focused on their sequence composition such as protein/miRNA binding motif, and/or regulatory elements such as internal ribosome entry site. However, less attention was paid to...

    Authors: Ya-Chi Lin, Yun-Chin Wang, Yueh-Chun Lee, Hui-Hsuan Lin, Kai-Li Chang, Yu-Chieh Tai and Kuei-Yang Hsiao
    Citation: BMC Genomics 2022 22(Suppl 5):921

    This article is part of a Supplement: Volume 22 Supplement 5

  4. The R2R3-MYB transcription factor is one of the largest gene families in plants and involved in the regulation of plant development, hormone signal transduction, biotic and abiotic stresses. Tobacco is one of ...

    Authors: Jiahan Yang, Binghui Zhang, Gang Gu, Jiazheng Yuan, Shaojun Shen, Liao Jin, Zhiqiang Lin, Jianfeng Lin and Xiaofang Xie
    Citation: BMC Genomics 2022 23:432
  5. Radiation proctitis (RP) is the most common complication of radiotherapy for pelvic tumor. Currently there is a lack of effective clinical treatment and its underlying mechanism is poorly understood. In this s...

    Authors: Qingzhi Zeng, Jingyang Cheng, Haiyong Wu, Wenfeng Liang and Yanmei Cui
    Citation: BMC Genomics 2022 23:431
  6. Seizures are a common symptom in glioma patients, and they can cause brain dysfunction. However, the mechanism by which glioma-related epilepsy (GRE) causes alterations in brain networks remains elusive.

    Authors: Zhi-Bin Wang, Jian Qu, Pan Xie, Zhi-Quan Yang, Chen-Xue Mao, Ying Zhang, Zheng-Wen He, Zhuan-Yi Yang, Xiao-Yuan Mao and Zhao-Qian Liu
    Citation: BMC Genomics 2022 23:430
  7. Merino sheep are the most famous fine wool sheep in the world. They have high wool production and excellent wool quality and have attracted worldwide attention. The fleece of the Merino sheep is composed predo...

    Authors: Junmin He, Bingru Zhao, Xixia Huang, Xuefeng Fu, Guifen Liu, Yuezhen Tian, Cuiling Wu, Jingyi Mao, Jing Liu, Shuangbao Gun and Kechuan Tian
    Citation: BMC Genomics 2022 23:428
  8. The expected increase of sustainable energy demand has shifted the attention towards bioenergy crops. Due to their know tolerance against abiotic stress and relatively low nutritional requirements, they have b...

    Authors: Danilo Fabrizio Santoro, Angelo Sicilia, Giorgio Testa, Salvatore Luciano Cosentino and Angela Roberta Lo Piero
    Citation: BMC Genomics 2022 23:427
  9. An optimal starting point for relating genome function to organismal biology is a high-quality nuclear genome assembly, and long-read sequencing is revolutionizing the production of this genomic resource in in...

    Authors: Igor Filipović, Gordana Rašić, James Hereward, Maria Gharuka, Gregor J. Devine, Michael J. Furlong and Kayvan Etebari
    Citation: BMC Genomics 2022 23:426
  10. Long non-coding RNA (lncRNA) plays crucial role in osteogenic differentiation of bone marrow mesenchymal stem cells (BMMSCs), involving in regulation of competing endogenous RNA (ceRNA) mechanisms and conducti...

    Authors: Jialin Liu, Yuan Yao, Jinyong Huang, Hao Sun, Yixuan Pu, Mengting Tian, Meijie Zheng, Huiyu He and Zheng Li
    Citation: BMC Genomics 2022 23:425
  11. Feed efficiency (FE) related traits play a key role in the economy and sustainability of beef cattle production systems. The accurate knowledge of the physiologic background for FE-related traits can help the ...

    Authors: Lucio F. M. Mota, Samuel W. B. Santos, Gerardo A. Fernandes Júnior, Tiago Bresolin, Maria E. Z. Mercadante, Josineudson A. V. Silva, Joslaine N. S. G. Cyrillo, Fábio M. Monteiro, Roberto Carvalheiro and Lucia G. Albuquerque
    Citation: BMC Genomics 2022 23:424
  12. MiRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression in organisms ranging from viruses to mammals. There is great relevance in understanding how miRNAs regulate genes involved ...

    Authors: Alison Ricafrente, Krystyna Cwiklinski, Hieu Nguyen, John P. Dalton, Nham Tran and Sheila Donnelly
    Citation: BMC Genomics 2022 23:419
  13. Temperature is involved in the regulation of carotenoid accumulation in many plants. The floral color of sweet osmanthus (Osmanthus fragrans Lour.) which is mainly contributed by carotenoid content, is affected b...

    Authors: Yiguang Wang, Chao Zhang, Bin Xu, Jianxin Fu, Yanxia Du, Qiu Fang, Bin Dong and Hongbo Zhao
    Citation: BMC Genomics 2022 23:418
  14. The SARS-CoV-2 Delta variant was first identified in the U.S. in March 2021 and has rapidly become the predominant lineage across the U.S. due to increased transmissibility, immune evasion and vaccine breakthr...

    Authors: Lauren Brinkac, Sheila Diepold, Shane Mitchell, Stephanie Sarnese, Lee F. Kolakowski, William M. Nelson and Katharine Jennings
    Citation: BMC Genomics 2022 23:417
  15. Frameshift mutations have been considered of significant importance for the molecular evolution of proteins and their coding genes, while frameshift protein sequences encoded in the alternative reading frames ...

    Authors: Xiaolong Wang, Quanjiang Dong, Gang Chen, Jianye Zhang, Yongqiang Liu and Yujia Cai
    Citation: BMC Genomics 2022 23:416
  16. As transcription factors, the TCP genes are considered to be promising targets for crop enhancement for their responses to abiotic stresses. However, information on the systematic characterization and functional ...

    Authors: Mingfang Yang, Guandi He, Qiandong Hou, Yu Fan, Lili Duan, Kuiyin Li, Xiaoliao Wei, Zhilang Qiu, Erjuan Chen and Tengbing He
    Citation: BMC Genomics 2022 23:415
  17. Although genome-wide association studies (GWAS) have successfully located various genetic variants susceptible to Alzheimer’s Disease (AD), it is still unclear how specific variants interact with genes and tis...

    Authors: Brian Lee, Xiaohui Yao and Li Shen
    Citation: BMC Genomics 2022 23(Suppl 4):414

    This article is part of a Supplement: Volume 23 Supplement 4

  18. Despite sexual development being ubiquitous to vertebrates, the molecular mechanisms underpinning this fundamental transition remain largely undocumented in many organisms. We designed a time course experiment...

    Authors: Amin R. Mohamed, Marina Naval-Sanchez, Moira Menzies, Bradley Evans, Harry King, Antonio Reverter and James W. Kijas
    Citation: BMC Genomics 2022 23:413
  19. Among the adaptive capacities of animals, the management of energetic body reserves (BR) through the BR mobilization and accretion processes (BR dynamics, BRD) has become an increasingly valuable attribute for...

    Authors: Tiphaine Macé, Eliel González-García, Didier Foulquié, Fabien Carrière, Julien Pradel, Christian Durand, Sebastien Douls, Charlotte Allain, Sara Parisot and Dominique Hazard
    Citation: BMC Genomics 2022 23:412
  20. Catalases (CATs) break down hydrogen peroxide into water and oxygen to prevent cellular oxidative damage, and play key roles in the development, biotic and abiotic stresses of plants. However, the evolutionary re...

    Authors: Luzhao Pan, Yin Luo, Jin Wang, Xiumin Li, Bingqian Tang, Huiping Yang, Xilin Hou, Feng Liu and Xuexiao Zou
    Citation: BMC Genomics 2022 23:411
  21. Tick-borne relapsing fever (TBRF) is a globally prevalent, yet under-studied vector-borne disease transmitted by soft and hard bodied ticks. While soft TBRF (sTBRF) spirochetes have been described for over a c...

    Authors: Alexander R. Kneubehl, Aparna Krishnavajhala, Sebastián Muñoz Leal, Adam J. Replogle, Luke C. Kingry, Sergio E. Bermúdez, Marcelo B. Labruna and Job E. Lopez
    Citation: BMC Genomics 2022 23:410
  22. The yellow catfish, Pelteobagrus fulvidraco, is a commercially important fish species. It is widely distributed in the fresh water areas of China, including rivers, lakes, and reservoirs. Like many other aquacult...

    Authors: Dong Gao, Junrou Huang, Genmei Lin and Jianguo Lu
    Citation: BMC Genomics 2022 23(Suppl 1):409

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

  23. Aggression is an evolutionarily conserved behavior critical for animal survival. In the fish Betta splendens, across different stages of fighting interactions, fighting opponents suffer from various stressors, es...

    Authors: Trieu-Duc Vu, Kenshiro Oshima, Kenya Matsumura, Yuki Iwasaki, Ming-Tzu Chiu, Masato Nikaido and Norihiro Okada
    Citation: BMC Genomics 2022 22(Suppl 5):920

    This article is part of a Supplement: Volume 22 Supplement 5

    The Correction to this article has been published in BMC Genomics 2022 23:464

  24. In mammals, the nutritional status experienced during embryonic development shapes key metabolic pathways and influences the health and phenotype of the future individual, a phenomenon known as nutritional pro...

    Authors: Aurélie Sécula, Hervé Chapuis, Anne Collin, Lisa E. Bluy, Agnès Bonnet, Loys Bodin, Laure Gress, Alexis Cornuez, Xavier Martin, Cécile M. D. Bonnefont and Mireille Morisson
    Citation: BMC Genomics 2022 23:407
  25. Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before seque...

    Authors: Klaudia Chrzastek, Chandana Tennakoon, Dagmara Bialy, Graham Freimanis, John Flannery and Holly Shelton
    Citation: BMC Genomics 2022 23:406
  26. Tardigrades are microscopic animals that are capable of tolerating extreme environments by entering a desiccated state of suspended animation known as anhydrobiosis. While antioxidative stress proteins, antiap...

    Authors: Yuki Yoshida, Tadashi Satoh, Chise Ota, Sae Tanaka, Daiki D. Horikawa, Masaru Tomita, Koichi Kato and Kazuharu Arakawa
    Citation: BMC Genomics 2022 23:405
  27. The autoimmune regulator (Aire) gene is critical for the appropriate establishment of central immune tolerance. As one of the main controllers of promiscuous gene expression in the thymus, Aire promotes the ex...

    Authors: Pedro Paranhos Tanaka, Ernna Hérida Oliveira, Mayara Cristina Vieira-Machado, Max Jordan Duarte, Amanda Freire Assis, Karina Fittipaldi Bombonato-Prado and Geraldo Aleixo Passos
    Citation: BMC Genomics 2022 23:404
  28. Peanut (Arachis hypogaea L.) is a grain legume crop that originated from South America and is now grown around the world. Peanut growth habit affects the variety’s adaptability, planting patterns, mechanized harv...

    Authors: Li Li, Shunli Cui, Phat Dang, Xinlei Yang, Xuejun Wei, Kai Chen, Lifeng Liu and Charles Y. Chen
    Citation: BMC Genomics 2022 23:403
  29. CRISPR-Cas9 screening libraries have arisen as a powerful tool to identify protein-coding (pc) and non-coding genes playing a role along different processes. In particular, the usage of a nuclease active Cas9 ...

    Authors: Carme Arnan, Sebastian Ullrich, Carlos Pulido-Quetglas, Ramil Nurtdinov, Alexandre Esteban, Joan Blanco-Fernandez, Estel Aparicio-Prat, Rory Johnson, Sílvia Pérez-Lluch and Roderic Guigó
    Citation: BMC Genomics 2022 23:402
  30. With a growing number of loci associated with late-onset (sporadic) Alzheimer’s disease (AD), the polygenic contribution to AD is now well established. The development of polygenic risk score approaches have s...

    Authors: Michael Vacher, Vincent Doré, Tenielle Porter, Lidija Milicic, Victor L. Villemagne, Pierrick Bourgeat, Sam C. Burnham, Timothy Cox, Colin L. Masters, Christopher C. Rowe, Jurgen Fripp, James D. Doecke and Simon M. Laws
    Citation: BMC Genomics 2022 23:401
  31. Berberine (BBR) is an isoquinoline alkaloid found in the Berberis species. It was found to have protected effects in cardiovascular diseases. Here, we investigated the effect the regulatory function of long no...

    Authors: Ye-Chen Han, Hong-Zhi Xie, Bo Lu, Ruo-Lan Xiang, Jing-Yi Li, Hao Qian and Shu-Yang Zhang
    Citation: BMC Genomics 2022 23:400
  32. Gene regulation is critical for proper cellular function. Next-generation sequencing technology has revealed the presence of regulatory networks that regulate gene expression and essential cellular functions. ...

    Authors: Collin B. Merrill, Austin B. Montgomery, Miguel A. Pabon, Andrey A. Shabalin, Aylin R. Rodan and Adrian Rothenfluh
    Citation: BMC Genomics 2022 23:399
  33. Sucrose non-fermenting 1 (SNF1)-associated protein kinase 2 (SnRK2) proteins belong to a relatively small family of plant-specific serine/threonine (Ser/Thr) protein kinases. SnRK2s participate in the abscisic...

    Authors: Zhu Xiao-lin, Wang Bao-qiang and Wei Xiao-hong
    Citation: BMC Genomics 2022 23:397
  34. Since the first description of lumpy skin disease virus (LSDV) in Africa in the 1920’s, it has brazenly spread beyond Africa into the Middle East, Europe and most recently Asia. In 2017 the first atypical LSDV...

    Authors: Alena Krotova, Olga Byadovskaya, Irina Shumilova, Antoinette van Schalkwyk and Alexander Sprygin
    Citation: BMC Genomics 2022 23:396
  35. The rate of protein accretion and growth affect amino acid requirements in young animals. Differences in amino acid metabolism contribute to individual variations in growth rate. This study aimed at determinin...

    Authors: Shahram Niknafs, Marina R. S. Fortes, Sungbo Cho, John L. Black and Eugeni Roura
    Citation: BMC Genomics 2022 23:393
  36. Transcriptome sequencing is an effective tool to reveal the essential genes and pathways underlying countless biotic and abiotic stress adaptation mechanisms. Although severely challenged by diverse environmen...

    Authors: Grace Afumwaa Boamah, Zekun Huang, Yawei Shen, Yisha Lu, Zhixuan Wang, Ying Su, Changan Xu, Xuan Luo, Caihuan Ke and Weiwei You
    Citation: BMC Genomics 2022 23:392
  37. Grain yield is a complex trait that results from interaction between underlying phenotypic traits and climatic, edaphic, and biotic variables. In rice, main culm panicle node number (MCPNN; the node number on ...

    Authors: Darlene L. Sanchez, Stanley Omar PB. Samonte, Jasper Benedict B. Alpuerto, Peyton A. Croaker, Karina Y. Morales, Yubin Yang, Lloyd T. Wilson, Rodante E. Tabien, Zongbu Yan, Michael J. Thomson and Endang M. Septiningsih
    Citation: BMC Genomics 2022 23:390
  38. Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human h...

    Authors: Dili Lai, Yue Fan, Guoxing Xue, Ailing He, Hao Yang, Chunlin He, Yijing Li, Jingjun Ruan, Jun Yan and Jianping Cheng
    Citation: BMC Genomics 2022 23:389
  39. Spodoptera litura is an important polyphagous pest that causes significant damage to the agricultural sector. We performed RNA-seq of 15 S. litura individuals from larval (fifth and sixth instar larvae), chrysali...

    Authors: Ruixiang Tang, Fangyuan Liu, Yue Lan, Jiao Wang, Lei Wang, Jing Li, Xu Liu, Zhenxin Fan, Tao Guo and Bisong Yue
    Citation: BMC Genomics 2022 23:388
  40. Beef cuts in different regions of the carcass have different meat quality due to their distinct physiological function. The objective of this study was to characterize the region-specific expression difference...

    Authors: Tianliu Zhang, Tianzhen Wang, Qunhao Niu, Xu Zheng, Haipeng Li, Xue Gao, Yan Chen, Huijiang Gao, Lupei Zhang, George E. Liu, Junya Li and Lingyang Xu
    Citation: BMC Genomics 2022 23:387

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