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  1. RNA viruses mutate at extremely high rates, forming an intra-host viral population of closely related variants, which allows them to evade the host’s immune system and makes them particularly dangerous. Viral ...

    Authors: Andrew Melnyk, Sergey Knyazev, Fredrik Vannberg, Leonid Bunimovich, Pavel Skums and Alex Zelikovsky

    Citation: BMC Genomics 2020 21(Suppl 5):582

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 5

  2. Comparative genomics methods enable the reconstruction of bacterial regulatory networks using available experimental data. In spite of their potential for accelerating research into the composition and evoluti...

    Authors: Sefa Kılıç, Miquel Sánchez-Osuna, Antonio Collado-Padilla, Jordi Barbé and Ivan Erill

    Citation: BMC Genomics 2020 21(Suppl 5):466

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 5

  3. One possible approach how to economically facilitate gene expression profiling is to use the L1000 platform which measures the expression of ∼1,000 landmark genes and uses a computational method to infer the e...

    Authors: Vladimír Kunc and Jiří Kléma

    Citation: BMC Genomics 2020 21(Suppl 5):454

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 5

  4. Codon usage is an important determinant of gene expression levels that can help us understand codon biology, evolution and mRNA translation of species. The majority of previous codon usage studies have focused...

    Authors: Zenan Shen, Zhimeng Gan, Fa Zhang, Xinyao Yi, Jinzhi Zhang and Xiaohua Wan

    Citation: BMC Genomics 2020 21(Suppl 5):234

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 5

  5. High throughput single-cell transcriptomic technology produces massive high-dimensional data, enabling high-resolution cell type definition and identification. To uncover the expressional patterns beneath the ...

    Authors: Yixin Chen, Sijie Chen and Xuegong Zhang

    Citation: BMC Genomics 2020 21(Suppl 5):222

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 5

  6. In marine invertebrate life cycles, which often consist of planktonic larval and benthonic adult stages, settlement of the free-swimming larva to the sea floor in response to environmental cues is a key life c...

    Authors: Xitan Hou, Zhenkui Qin, Maokai Wei, Zhong Fu, Ruonan Liu, Li Lu, Shumiao Bai, Yubin Ma and Zhifeng Zhang

    Citation: BMC Genomics 2020 21:892

    Content type: Research article

    Published on:

  7. Porcine epidemic diarrhea virus (PEDV) is a causative agent of serious viral enteric disease in suckling pigs. Such diseases cause considerable economic losses in the global swine industry. Enhancing our knowl...

    Authors: Zhengzheng Hu, Yuchen Li, Heng Du, Junxiao Ren, Xianrui Zheng, Kejian Wei and Jianfeng Liu

    Citation: BMC Genomics 2020 21:891

    Content type: Research article

    Published on:

  8. There are challenges in generating mRNA-Seq data from whole-blood derived RNA as globin gene and rRNA are frequent contaminants. Given the abundance of erythrocytes in whole blood, globin genes comprise some 8...

    Authors: Jin Sung Jang, Brianna Berg, Eileen Holicky, Bruce Eckloff, Mark Mutawe, Minerva M. Carrasquillo, Nilüfer Ertekin-Taner and Julie M. Cuninngham

    Citation: BMC Genomics 2020 21:890

    Content type: Methodology article

    Published on:

  9. Voice disorders are a worldwide problem impacting human health, particularly for occupational voice users. Avoidance of surface dehydration is commonly prescribed as a protective factor against the development...

    Authors: Taylor W. Bailey, Andrea Pires dos Santos, Naila Cannes do Nascimento, Shaojun Xie, Jyothi Thimmapuram, M. Preeti Sivasankar and Abigail Cox

    Citation: BMC Genomics 2020 21:888

    Content type: Research article

    Published on:

  10. Brassica nigra (BB), also called black mustard, is grown as a condiment crop in India. B. nigra represents the B genome of U’s triangle and is one of the progenitor species of B. juncea (AABB), an important oilse...

    Authors: Kumar Paritosh, Akshay Kumar Pradhan and Deepak Pental

    Citation: BMC Genomics 2020 21:887

    Content type: Research article

    Published on:

  11. Ophiocordyceps sinensis is an important traditional Chinese medicine for its comprehensive active ingredients, such as cordycepin, cordycepic acid, and Cordyceps polysaccharide. O. sinensis zjut, a special strain...

    Authors: Bo Zhang, Bo Li, Xiao-Hui Men, Zhe-Wen Xu, Hui Wu, Xiang-Tian Qin, Feng Xu, Yi Teng, Shui-Jin Yuan, Li-Qun Jin, Zhi-Qiang Liu and Yu-Guo Zheng

    Citation: BMC Genomics 2020 21:886

    Content type: Research article

    Published on:

  12. The degradation of cellulose and hemicellulose molecules into simpler sugars such as glucose is part of the second generation biofuel production process. Hydrolysis of lignocellulosic substrates is usually per...

    Authors: Aurélie Pirayre, Laurent Duval, Corinne Blugeon, Cyril Firmo, Sandrine Perrin, Etienne Jourdier, Antoine Margeot and Frédérique Bidard

    Citation: BMC Genomics 2020 21:885

    Content type: Research article

    Published on:

  13. Women account for 60% of all stroke deaths and are more often permanently disabled than men, despite their higher observed stroke incidence. Considering the clinical population affected by stroke, an obvious d...

    Authors: Mimmi Rehnström, Simona Denise Frederiksen, Saema Ansar and Lars Edvinsson

    Citation: BMC Genomics 2020 21:883

    Content type: Research article

    Published on:

  14. Whole mitogenomes or short fragments (i.e., 300–700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include ...

    Authors: J. Antonio Baeza

    Citation: BMC Genomics 2020 21:882

    Content type: Methodology article

    Published on:

  15. Bisphenol S (BPS) is a common bisphenol A (BPA) substitute, since BPA is virtually banned worldwide. However, BPS and BPA have both endocrine disrupting properties. Their effects appear mostly in adulthood fol...

    Authors: Axelle Brulport, Daniel Vaiman, Elias Bou-Maroun, Marie-Christine Chagnon and Ludovic Le Corre

    Citation: BMC Genomics 2020 21:881

    Content type: Research article

    Published on:

  16. Late blight disease (LBD) caused by the pathogen Phytophthora infestans (PI), is the most devastating disease limiting potato (Solanum tuberosum) production globally. Currently, this disease pathogen is re-emergi...

    Authors: Chunfang Xiao, Mengling Huang, Jianhua Gao, Zhen Wang, Denghong Zhang, Yuanxue Zhang, Lei Yan, Xiao Yu, Bo Li and Yanfen Shen

    Citation: BMC Genomics 2020 21:880

    Content type: Research article

    Published on:

  17. The RNA interference (RNAi) pathway is a gene regulation mechanism that utilizes small RNA (sRNA) and Argonaute (Ago) proteins to silence target genes. Our previous work identified a functional RNAi pathway in...

    Authors: Hanbang Zhang, Gretchen M. Ehrenkaufer, Neil Hall and Upinder Singh

    Citation: BMC Genomics 2020 21:879

    Content type: Research article

    Published on:

  18. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Chitrita Goswami, Smriti Chawla, Deepshi Thakral, Himanshu Pant, Pramod Verma, Prabhat Singh Malik, Jayadeva, Ritu Gupta, Gaurav Ahuja and Debarka Sengupta

    Citation: BMC Genomics 2020 21:877

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2020 21:744

  19. Planarians reliably regenerate all body parts after injury, including a fully functional head and central nervous system. But until now, the expression dynamics and functional role of miRNAs and other small RN...

    Authors: Zhonghong Cao, David Rosenkranz, Suge Wu, Hongjin Liu, Qiuxiang Pang, Xiufang Zhang, Baohua Liu and Bosheng Zhao

    Citation: BMC Genomics 2020 21:876

    Content type: Research article

    Published on:

  20. The electrosensory ampullary organs (AOs) and mechanosensory neuromasts (NMs) found in sturgeon and some other non-neopterygian fish or amphibians are both originated from lateral line placodes. However, these...

    Authors: Jian Wang, Chengcheng Lu, Yifan Zhao, Zhijiao Tang, Jiakun Song and Chunxin Fan

    Citation: BMC Genomics 2020 21:875

    Content type: Research article

    Published on:

  21. Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements inclu...

    Authors: Adam Dawid Urantówka, Aleksandra Kroczak and Paweł Mackiewicz

    Citation: BMC Genomics 2020 21:874

    Content type: Research article

    Published on:

  22. Orang-utans comprise three critically endangered species endemic to the islands of Borneo and Sumatra. Though whole-genome sequencing has recently accelerated our understanding of their evolutionary history, t...

    Authors: Graham L. Banes, Emily D. Fountain, Alyssa Karklus, Hao-Ming Huang, Nian-Hong Jang-Liaw, Daniel L. Burgess, Jennifer Wendt, Cynthia Moehlenkamp and George F. Mayhew

    Citation: BMC Genomics 2020 21:873

    Content type: Research article

    Published on:

  23. Gonad development and differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. However, the mecha...

    Authors: Jun Li, Yinyin Zhou, Zihua Zhou, Chuanxu Lin, Jinkuan Wei, Yanpin Qin, Zhiming Xiang, Haitao Ma, Yang Zhang, Yuehuan Zhang and Ziniu Yu

    Citation: BMC Genomics 2020 21:872

    Content type: Research article

    Published on:

  24. NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family (NPF) members are essential transporters for many substrates in plants, including nitrate, hormones, peptides, and secondary metabolites. Here, we re...

    Authors: Jing Wen, Peng-Feng Li, Feng Ran, Peng-Cheng Guo, Jia-Tian Zhu, Jin Yang, Lan-Lan Zhang, Ping Chen, Jia-Na Li and Hai Du

    Citation: BMC Genomics 2020 21:871

    Content type: Research article

    Published on:

  25. Unlike mammals, zebrafish have a remarkable capacity to regenerate a variety of tissues, including central nervous system tissue. The function of macrophages in tissue regeneration is of great interest, as mac...

    Authors: Ousseini Issaka Salia and Diana M. Mitchell

    Citation: BMC Genomics 2020 21:870

    Content type: Research article

    Published on:

  26. Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations...

    Authors: N. Z. Gebrehiwot, E. M. Strucken, H. Aliloo, K. Marshall and J. P. Gibson

    Citation: BMC Genomics 2020 21:869

    Content type: Research article

    Published on:

  27. Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and ...

    Authors: Weihua Su, Yongjuan Ren, Dongjiao Wang, Long Huang, Xueqin Fu, Hui Ling, Yachun Su, Ning Huang, Hanchen Tang, Liping Xu and Youxiong Que

    Citation: BMC Genomics 2020 21:868

    Content type: Research article

    Published on:

  28. The parasitoid wasp, Trichogramma dendrolimi, can enter diapause at the prepupal stage. Thus, diapause is an efficient preservation method during the mass production of T. dendrolimi. Previous studies on diapause...

    Authors: Xue Zhang, Wenmei Du, Junjie Zhang, Zhen Zou and Changchun Ruan

    Citation: BMC Genomics 2020 21:864

    Content type: Research article

    Published on:

  29. The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of...

    Authors: Daryl M. Gohl, John Garbe, Patrick Grady, Jerry Daniel, Ray H. B. Watson, Benjamin Auch, Andrew Nelson, Sophia Yohe and Kenneth B. Beckman

    Citation: BMC Genomics 2020 21:863

    Content type: Methodology article

    Published on:

  30. Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current hig...

    Authors: Chentao Yang, Yuxuan Zheng, Shangjin Tan, Guanliang Meng, Wei Rao, Caiqing Yang, David G. Bourne, Paul A. O’Brien, Junqiang Xu, Sha Liao, Ao Chen, Xiaowei Chen, Xinrui Jia, Ai-bing Zhang and Shanlin Liu

    Citation: BMC Genomics 2020 21:862

    Content type: Methodology article

    Published on:

  31. As a heavy metal, manganese (Mn) can be toxic to plants. Stylo (Stylosanthes) is an important tropical legume that exhibits tolerance to high levels of Mn. However, little is known about the adaptive responses of...

    Authors: Yidan Jia, Xinyong Li, Qin Liu, Xuan Hu, Jifu Li, Rongshu Dong, Pandao Liu, Guodao Liu, Lijuan Luo and Zhijian Chen

    Citation: BMC Genomics 2020 21:861

    Content type: Research article

    Published on:

  32. Cotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge,

    Authors: Haiyan Zhao, Jianshe Wang, Yunfang Qu, Renhai Peng, Richard Odongo Magwanga, Fang Liu and Jinling Huang

    Citation: BMC Genomics 2020 21:859

    Content type: Research article

    Published on:

  33. Ginkgo (Ginkgo biloba L.) is an excellent landscape species. Its yellow-green leaf mutants are ideal materials for research on pigment synthesis, but the regulatory mechanism of leaf coloration in these ginkgo mu...

    Authors: Yaqiong Wu, Jing Guo, Tongli Wang, Fuliang Cao and Guibin Wang

    Citation: BMC Genomics 2020 21:858

    Content type: Research article

    Published on:

  34. Ammonia is one of the most common toxicological environment factors affecting shrimp health. Although ammonia tolerance in shrimp is closely related to successful industrial production, few genetic studies of ...

    Authors: Digang Zeng, Chunling Yang, Qiangyong Li, Weilin Zhu, Xiuli Chen, Min Peng, Xiaohan Chen, Yong Lin, Huanling Wang, Hong Liu, Jingzhen Liang, Qingyun Liu and Yongzhen Zhao

    Citation: BMC Genomics 2020 21:857

    Content type: Research article

    Published on:

  35. The development and application of CRISPR technologies for the modification of the genome are rapidly expanding. Advances in the field describe new CRISPR components that are strategically engineered to improv...

    Authors: M. Heath Farris, Pamela A. Texter, Agustin A. Mora, Michael V. Wiles, Ellen F. Mac Garrigle, Sybil A. Klaus and Kristine Rosfjord

    Citation: BMC Genomics 2020 21:856

    Content type: Methodology article

    Published on:

  36. The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted.

    Authors: Gurusamy Raman, Kyu Tae Park, JooHwan Kim and SeonJoo Park

    Citation: BMC Genomics 2020 21:855

    Content type: Research article

    Published on:

  37. Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfu...

    Authors: Nicolas Dussex, Federica Alberti, Matti T. Heino, Remi-Andre Olsen, Tom van der Valk, Nils Ryman, Linda Laikre, Hans Ahlgren, Igor V. Askeyev, Oleg V. Askeyev, Dilyara N. Shaymuratova, Arthur O. Askeyev, Doris Döppes, Ronny Friedrich, Susanne Lindauer, Wilfried Rosendahl…

    Citation: BMC Genomics 2020 21:854

    Content type: Research article

    Published on:

  38. Long noncoding RNAs (lncRNAs) have been reported to play critical roles in diverse growth and development processes in plants. However, the systematic identification and characterization of lncRNAs in foxtail ...

    Authors: Zilong Zhao, Dan Liu, Yanjiao Cui, Suying Li, Dan Liang, Daizhen Sun, Jianhe Wang and Zhengli Liu

    Citation: BMC Genomics 2020 21:853

    Content type: Research article

    Published on:

  39. The root growth angle (RGA) typically determines plant rooting depth, which is significant for plant anchorage and abiotic stress tolerance. Several quantitative trait loci (QTLs) for RGA have been identified ...

    Authors: Caixia Zheng, Fei Shen, Yi Wang, Ting Wu, Xuefeng Xu, Xinzhong Zhang and Zhenhai Han

    Citation: BMC Genomics 2020 21:852

    Content type: Research article

    Published on:

  40. Anaerobic ammonium oxidizing bacteria (anammox bacteria) are contributing significantly to the nitrogen cycle and are successfully used in wastewater treatment. Due to the lack of complete genomes in the datab...

    Authors: Chang Ding and Lorenz Adrian

    Citation: BMC Genomics 2020 21:851

    Content type: Research article

    Published on:

  41. Dioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants. However, this mechanism is ...

    Authors: Ning Li, Ziwei Meng, Minjie Tao, Yueyuan Wang, Yulan Zhang, Shufen Li, Wujun Gao and Chuanliang Deng

    Citation: BMC Genomics 2020 21:850

    Content type: Research article

    Published on:

  42. Distichiasis, an ocular disorder in which aberrant cilia (eyelashes) grow from the opening of the Meibomian glands of the eyelid, has been reported in Friesian horses. These misplaced cilia can cause discomfor...

    Authors: E. A. Hisey, H. Hermans, Z. T. Lounsberry, F. Avila, R. A. Grahn, K. E. Knickelbein, S. A. Duward-Akhurst, M. E. McCue, T.S. Kalbfleisch, M. E. Lassaline, W. Back and R. R. Bellone

    Citation: BMC Genomics 2020 21:848

    Content type: Research article

    Published on:

  43. Listeria (L.) monocytogenes strains show a high diversity regarding stress tolerance and virulence potential. Genome studies have mainly focused on specific sequence types (STs) predominantly associated with eith...

    Authors: Eva Wagner, Andreas Zaiser, Rebekka Leitner, Narciso M. Quijada, Nadja Pracser, Ariane Pietzka, Werner Ruppitsch, Stephan Schmitz-Esser, Martin Wagner and Kathrin Rychli

    Citation: BMC Genomics 2020 21:847

    Content type: Research article

    Published on:

  44. Loss of genetic variation negatively impacts breeding efforts and food security. Genebanks house over 7 million accessions representing vast allelic diversity that is a resource for sustainable breeding. Disco...

    Authors: Anna Hawliczek, Leszek Bolibok, Katarzyna Tofil, Ewa Borzęcka, Joanna Jankowicz-Cieślak, Piotr Gawroński, Adam Kral, Bradley J. Till and Hanna Bolibok-Brągoszewska

    Citation: BMC Genomics 2020 21:845

    Content type: Research article

    Published on:

  45. After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial...

    Authors: Tatiana R. Feuerborn, Eleftheria Palkopoulou, Tom van der Valk, Johanna von Seth, Arielle R. Munters, Patrícia Pečnerová, Marianne Dehasque, Irene Ureña, Erik Ersmark, Vendela Kempe Lagerholm, Maja Krzewińska, Ricardo Rodríguez-Varela, Anders Götherström, Love Dalén and David Díez-del-Molino

    Citation: BMC Genomics 2020 21:844

    Content type: Methodology article

    Published on:

  46. Post-traumatic osteoarthritis (PTOA) is a common and significant problem in equine athletes. It is a disease of the entire joint, with the synovium thought to be a key player in disease onset and progression d...

    Authors: Annette M. McCoy, Ann M. Kemper, Mary K. Boyce, Murray P. Brown and Troy N. Trumble

    Citation: BMC Genomics 2020 21:843

    Content type: Research article

    Published on:

  47. Core promoter controls transcription initiation. However, little is known for core promoter diversity in the human genome and its relationship with diseases. We hypothesized that as a functional important comp...

    Authors: Hemant Gupta, Khyati Chandratre, Siddharth Sinha, Teng Huang, Xiaobing Wu, Jian Cui, Michael Q. Zhang and San Ming Wang

    Citation: BMC Genomics 2020 21:842

    Content type: Research article

    Published on:

  48. Diversity of the CRISPR locus of Mycobacterium tuberculosis complex has been studied since 1997 for molecular epidemiology purposes. By targeting solely the 43 spacers present in the two first sequenced genomes (...

    Authors: Guislaine Refrégier, Christophe Sola and Christophe Guyeux

    Citation: BMC Genomics 2020 21:841

    Content type: Research article

    Published on:

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