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  2. Presently, there is no comprehensive analysis of the transcription regulation network in hematopoiesis. Comparison of networks arising from gene co-expression across species can facilitate an understanding of ...

    Authors: Shouguo Gao, Zhijie Wu, Xingmin Feng, Sachiko Kajigaya, Xujing Wang and Neal S. Young
    Citation: BMC Genomics 2020 21(Suppl 11):849
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  3. Single-cell sequencing enables us to better understand genetic diseases, such as cancer or autoimmune disorders, which are often affected by changes in rare cells. Currently, no existing software is aimed at i...

    Authors: Adam Cornish, Shrabasti Roychoudhury, Krishna Sarma, Suravi Pramanik, Kishor Bhakat, Andrew Dudley, Nitish K. Mishra and Chittibabu Guda
    Citation: BMC Genomics 2020 21(Suppl 11):830
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  4. Long-read RNA-Seq techniques can generate reads that encompass a large proportion or the entire mRNA/cDNA molecules, so they are expected to address inherited limitations of short-read RNA-Seq techniques that ...

    Authors: Qian Liu, Yu Hu, Andres Stucky, Li Fang, Jiang F. Zhong and Kai Wang
    Citation: BMC Genomics 2020 21(Suppl 11):793
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  5. Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is ...

    Authors: Johannes Balkenhol, Kristin V. Kaltdorf, Elmina Mammadova-Bach, Attila Braun, Bernhard Nieswandt, Marcus Dittrich and Thomas Dandekar
    Citation: BMC Genomics 2020 21:897
    Content type: Research article Published on:

  6. Third-generation single molecule sequencing technologies can sequence long reads, which is advancing the frontiers of genomics research. However, their high error rates prohibit accurate and efficient downstre...

    Authors: Haowen Zhang, Chirag Jain and Srinivas Aluru
    Citation: BMC Genomics 2020 21(Suppl 6):889
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  7. Microbe-microbe and host-microbe interactions in a microbiome play a vital role in both health and disease. However, the structure of the microbial community and the colonization patterns are highly complex to...

    Authors: Musfiqur Sazal, Kalai Mathee, Daniel Ruiz-Perez, Trevor Cickovski and Giri Narasimhan
    Citation: BMC Genomics 2020 21(Suppl 6):663
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  8. Next-generation sequencing (NGS) enables unbiased detection of pathogens by mapping the sequencing reads of a patient sample to the known reference sequence of bacteria and viruses. However, for a new pathogen...

    Authors: Chi-Ming Leung, Dinghua Li, Yan Xin, Wai-Chun Law, Yifan Zhang, Hing-Fung Ting, Ruibang Luo and Tak-Wah Lam
    Citation: BMC Genomics 2020 21(Suppl 6):500
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  9. Analysis of heterogeneous populations such as viral quasispecies is one of the most challenging bioinformatics problems. Although machine learning models are becoming to be widely employed for analysis of sequ...

    Authors: Sunitha Basodi, Pelin Icer Baykal, Alex Zelikovsky, Pavel Skums and Yi Pan
    Citation: BMC Genomics 2020 21(Suppl 6):405
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

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

    Authors: Zhe Zhang, Lei Liu, Melis Kucukoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi and Bo Zheng
    Citation: BMC Genomics 2020 21:895
    Content type: Correction Published on:

    The original article was published in BMC Genomics 2020 21:709

  12. Researchers discover LncRNA–miRNA regulatory paradigms modulate gene expression patterns and drive major cellular processes. Identification of lncRNA-miRNA interactions (LMIs) is critical to reveal the mechani...

    Authors: Chengshuai Zhao, Yang Qiu, Shuang Zhou, Shichao Liu, Wen Zhang and Yanqing Niu
    Citation: BMC Genomics 2020 21(Suppl 13):867
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  13. RNA binding proteins (RBPs) play a vital role in post-transcriptional processes in all eukaryotes, such as splicing regulation, mRNA transport, and modulation of mRNA translation and decay. The identification ...

    Authors: Lei Deng, Youzhi Liu, Yechuan Shi, Wenhao Zhang, Chun Yang and Hui Liu
    Citation: BMC Genomics 2020 21(Suppl 13):866
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  14. Many transcripts have been generated due to the development of sequencing technologies, and lncRNA is an important type of transcript. Predicting lncRNAs from transcripts is a challenging and important task. T...

    Authors: Yanzhen Xu, Xiaohan Zhao, Shuai Liu and Wen Zhang
    Citation: BMC Genomics 2020 21(Suppl 13):865
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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, Joo-Hwan Kim and SeonJoo Park
    Citation: BMC Genomics 2020 21:855
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:97

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BMC Genomics

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