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  1. Drug resistance in Mycobacterium tuberculosis (MTB) is one of the major challenges in tuberculosis (TB) treatment. However, known mutations cannot explain all of the cases of resistance and little research has fo...

    Authors: Xi Zeng, Jamie Sui-Lam Kwok, Kevin Yi Yang, Kenneth Siu-Sing Leung, Mai Shi, Zhiyuan Yang, Wing-Cheong Yam and Stephen Kwok-Wing Tsui
    Citation: BMC Genomics 2018 19:365
    Content type: Research article Published on:

  2. The black yeast Hortaea werneckii (Dothideomycetes, Ascomycota) is one of the most extremely halotolerant fungi, capable of growth at NaCl concentrations close to saturation. Although dothideomycetous fungi are t...

    Authors: Cene Gostinčar, Jason E. Stajich, Jerneja Zupančič, Polona Zalar and Nina Gunde-Cimerman
    Citation: BMC Genomics 2018 19:364
    Content type: Research article Published on:

  3. The factors determining sex in teleosts are diverse. Great efforts have been made to characterize the underlying genetic network in various species. However, only seven master sex-determining genes have been i...

    Authors: Wenjing Tao, Jinlin Chen, Dejie Tan, Jing Yang, Lina Sun, Jing Wei, Matthew A. Conte, Thomas D. Kocher and Deshou Wang
    Citation: BMC Genomics 2018 19:363
    Content type: Research article Published on:

  4. A gene regulatory network (GRN) comprises many weak links that are often regulated by microRNAs. Since miRNAs rarely repress their target genes by more than 30%, doubts have been expressed about the biological...

    Authors: Fuqiang Ma, Pei Lin, Qingjian Chen, Xuemei Lu, Yong E. Zhang and Chung-I Wu
    Citation: BMC Genomics 2018 19:362
    Content type: Research article Published on:

  5. Acoustic or hydrodynamic shearing, sonication and enzymatic digestion are used to fragment DNA. However, these methods have several disadvantages, such as DNA damage, difficulties in fragmentation control, irr...

    Authors: Daria Krefft, Aliaksei Papkov, Maciej Prusinowski, Agnieszka Zylicz-Stachula and Piotr M. Skowron
    Citation: BMC Genomics 2018 19:361
    Content type: Methodology article Published on:

  6. Tan sheep is an indigenous Chinese breed well known for its beautiful curly fleece. One prominent breed characteristic of this sheep breed is that the degree of curliness differs markedly between lambs and adu...

    Authors: Yufang Liu, Jibin Zhang, Qiao Xu, Xiaolong Kang, Kejun Wang, Keliang Wu and Meiying Fang
    Citation: BMC Genomics 2018 19:360
    Content type: Research article Published on:

  7. In somatic cells, homologous recombination (HR) is a rare event caused by eventual DNA double-strand breaks (DSBs). In contrast, germ cells show high frequency of HR caused by programmed DSBs. Microsatellites ...

    Authors: Jianbo Zheng, Heng Li, Qi Zhang, Lei Sun, Xiangfang Liu and Chen Luo
    Citation: BMC Genomics 2018 19:359
    Content type: Research article Published on:

  8. Leaf blight caused by Calonectria spp. is one of the most destructive diseases to affect Eucalyptus nurseries and plantations. These pathogens mainly attack Eucalyptus, a tree with a diversity of secondary metabo...

    Authors: Xiaozhen Ye, Zhenhui Zhong, Hongyi Liu, Lianyu Lin, Mengmeng Guo, Wenshuo Guo, Zonghua Wang, Qinghua Zhang, Lizhen Feng, Guodong Lu, Feiping Zhang and Quanzhu Chen
    Citation: BMC Genomics 2018 19:358
    Content type: Research article Published on:

  9. Aspergillus fumigatus has to cope with a combination of several stress types while colonizing the human body. A functional interplay between these different stress responses can increase the chances of survival f...

    Authors: Vivien Kurucz, Thomas Krüger, Károly Antal, Anna-Maria Dietl, Hubertus Haas, István Pócsi, Olaf Kniemeyer and Tamás Emri
    Citation: BMC Genomics 2018 19:357
    Content type: Research article Published on:

  10. Cryptosporidium baileyi is the most common Cryptosporidium species in birds. However, effective prevention measures and treatment for C. baileyi infection were still not available. Long non-coding RNAs (lncRNAs) ...

    Authors: Guan-Jing Ren, Xian-Cheng Fan, Ting-Li Liu, Sha-Sha Wang and Guang-Hui Zhao
    Citation: BMC Genomics 2018 19:356
    Content type: Research article Published on:

  11. Evolution occurred exclusively under the full spectrum of sunlight. Conscription of narrow regions of the solar spectrum by specific photoreceptors suggests a common strategy for regulation of genetic pathways...

    Authors: Ronald B. Walter, Mikki Boswell, Jordan Chang, William T. Boswell, Yuan Lu, Kaela Navarro, Sean M. Walter, Dylan J. Walter, Raquel Salinas and Markita Savage
    Citation: BMC Genomics 2018 19:355
    Content type: Research article Published on:

  12. Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake’s mitogenome. Here, we analyzed the com...

    Authors: Lifu Qian, Hui Wang, Jie Yan, Tao Pan, Shanqun Jiang, Dingqi Rao and Baowei Zhang
    Citation: BMC Genomics 2018 19:354
    Content type: Research article Published on:

  13. Brucellosis is a bacterial zoonotic disease. Annually in the world more than 500,000 new cases of brucellosis in humans are registered. In this study, we propose an evolutionary model of the historical distrib...

    Authors: Sergey V. Pisarenko, Dmitry A. Kovalev, Anna S. Volynkina, Dmitry G. Ponomarenko, Diana V. Rusanova, Nina V. Zharinova, Anna A. Khachaturova, Lyudmila E. Tokareva, Irina G. Khvoynova and Alexander N. Kulichenko
    Citation: BMC Genomics 2018 19:353
    Content type: Research article Published on:

  16. Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochond...

    Authors: Matthew T. Oetjens, Axel Martin, Krishna R. Veeramah and Jeffrey M. Kidd
    Citation: BMC Genomics 2018 19:350
    Content type: Research article Published on:

  17. Cell-type-specific genes exhibit heterogeneity in genomic contexts and may be subject to different epigenetic regulations through different gene transcriptional processes depending on the cell type involved. T...

    Authors: Mayumi Oda, Shunichi Wakabayashi, N. Ari Wijetunga, Shinsuke Yuasa, Hirokazu Enomoto, Ruri Kaneda, Sung Han Yoon, Nishant Mittal, Qiang Jing, Masako Suzuki, John M. Greally, Keiichi Fukuda and Shinji Makino
    Citation: BMC Genomics 2018 19:349
    Content type: Research article Published on:

  18. Cotton is a major fiber and oil crop worldwide. Cotton production, however, is often threatened by abiotic environmental stresses. GRAS family proteins are among the most abundant transcription factors in plan...

    Authors: Bin Zhang, J. Liu, Zhao E. Yang, Er Y. Chen, Chao J. Zhang, Xue Y. Zhang and Fu G. Li
    Citation: BMC Genomics 2018 19:348
    Content type: Research article Published on:

  19. Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions ...

    Authors: Erica S. Nielsen, Romina Henriques, Robert J. Toonen, Ingrid S. S. Knapp, Baocheng Guo and Sophie von der Heyden
    Citation: BMC Genomics 2018 19:347
    Content type: Research article Published on:

  20. The BES1 gene family, an important class of plant-specific transcription factors, play key roles in the BR signal pathway in plants, regulating various development processes. Until now, there has been no comprehe...

    Authors: Xiaoming Song, Xiao Ma, Chunjin Li, Jingjing Hu, Qihang Yang, Tong Wang, Li Wang, Jinpeng Wang, Di Guo, Weina Ge, Zhenyi Wang, Miaomiao Li, Qiumei Wang, Tianzeng Ren, Shuyan Feng, Lixia Wang…
    Citation: BMC Genomics 2018 19:346
    Content type: Research article Published on:

  21. Identification of mutations from next-generation sequencing data typically requires a balance between sensitivity and accuracy. This is particularly true of DNA insertions and deletions (indels), that can impa...

    Authors: Adam B. Burkholder, Scott A. Lujan, Christopher A. Lavender, Sara A. Grimm, Thomas A. Kunkel and David C. Fargo
    Citation: BMC Genomics 2018 19:345
    Content type: Methodology article Published on:

  22. Caponization results in reduced androgen levels, which leads to abdominal fat accumulation in capons. In this study, we sought to understand the molecular mechanisms behind this fat accumulation.

    Authors: Xiaoyan Cui, Huanxian Cui, Lu Liu, Guiping Zhao, Ranran Liu, Qinghe Li, Maiqing Zheng and Jie Wen
    Citation: BMC Genomics 2018 19:344
    Content type: Research article Published on:

  23. Euryale ferox Salisb., an annual aquatic plant, is the only species in the genus Euryale in the Nymphaeaceae. Seeds of E. ferox are a nutritious food and also used in traditional Chinese medicine (Qian Shi in Man...

    Authors: Xian Liu, Zhen He, Yulai Yin, Xu Xu, Weiwen Wu and Liangjun Li
    Citation: BMC Genomics 2018 19:343
    Content type: Research article Published on:

  24. Valine-glutamine (VQ) motif containing proteins play important roles in abiotic and biotic stress responses in plants. However, little is known about the origin and evolution as well as comprehensive expressio...

    Authors: Shu-Ye Jiang, Mayalagu Sevugan and Srinivasan Ramachandran
    Citation: BMC Genomics 2018 19:342
    Content type: Research article Published on:

  25. Although sleep deprivation is associated with neurobehavioral impairment that may underlie significant risks to performance and safety, there is no reliable biomarker test to detect dangerous levels of impairm...

    Authors: Hilary A. Uyhelji, Doris M. Kupfer, Vicky L. White, Melinda L. Jackson, Hans P. A. Van Dongen and Dennis M. Burian
    Citation: BMC Genomics 2018 19:341
    Content type: Research article Published on:

  26. Circular RNAs (circRNAs) are a novel class of endogenous, non-coding RNAs that form covalently closed continuous loops and that are both highly conserved and abundant in the mammalian brain. A role for circRNA...

    Authors: Shobana Sekar, Lori Cuyugan, Jonathan Adkins, Philipp Geiger and Winnie S. Liang
    Citation: BMC Genomics 2018 19:340
    Content type: Research article Published on:

  27. The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment ...

    Authors: J. Auvinet, P. Graça, L. Belkadi, L. Petit, E. Bonnivard, A. Dettaï, W. H Detrich III, C. Ozouf-Costaz and D. Higuet
    Citation: BMC Genomics 2018 19:339
    Content type: Research article Published on:

  28. Emerging evidence indicates that Circular RNAs (circRNAs) exert post-transcriptional regulation of gene expression. A subclass of circRNA was found enriched with miRNA target sites. This evidence suggests that...

    Authors: Yu-Chen Liu, Hsiao-Chin Hong, Chi-Dung Yang, Wei-Hsiang Lee, Hsin-Tzu Huang and Hsien-Da Huang
    Citation: BMC Genomics 2018 19(Suppl 2):171
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  29. Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. ...

    Authors: Wen Chen, Xuan Zhang, Jing Li, Shulan Huang, Shuanglin Xiang, Xiang Hu and Changning Liu
    Citation: BMC Genomics 2018 19(Suppl 2):112
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  30. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citr...

    Authors: Li Liu, Shuchao Ren, Junqiang Guo, Qingyi Wang, Xiaotuo Zhang, Peiran Liao, Shipeng Li, Ramanjulu Sunkar and Yun Zheng
    Citation: BMC Genomics 2018 19(Suppl 2):111
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  31. Inference of haplotypes, or the sequence of alleles along the same chromosomes, is a fundamental problem in genetics and is a key component for many analyses including admixture mapping, identifying regions of...

    Authors: Dan He, Subrata Saha, Richard Finkers and Laxmi Parida
    Citation: BMC Genomics 2018 19(Suppl 2):110
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  32. Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in ...

    Authors: Chih-Hung Chou, Hsi-Yuan Huang, Wei-Chih Huang, Sheng-Da Hsu, Chung-Der Hsiao, Chia-Yu Liu, Yu-Hung Chen, Yu-Chen Liu, Wei-Yun Huang, Meng-Lin Lee, Yi-Chang Chen and Hsien-Da Huang
    Citation: BMC Genomics 2018 19(Suppl 2):103
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  33. Several methods have been developed for the accurate reconstruction of gene trees. Some of them use reconciliation with a species tree to correct, a posteriori, errors in gene trees inferred from multiple sequenc...

    Authors: Emmanuel Noutahi and Nadia El-Mabrouk
    Citation: BMC Genomics 2018 19(Suppl 2):102
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  34. We developed a classifier using RNA sequencing data that identifies the usual interstitial pneumonia (UIP) pattern for the diagnosis of idiopathic pulmonary fibrosis. We addressed significant challenges, inclu...

    Authors: Yoonha Choi, Tiffany Ting Liu, Daniel G. Pankratz, Thomas V. Colby, Neil M. Barth, David A. Lynch, P. Sean Walsh, Ganesh Raghu, Giulia C. Kennedy and Jing Huang
    Citation: BMC Genomics 2018 19(Suppl 2):101
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  35. The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions.

    Authors: Chunfang Zheng, Yuji Jeong, Madisyn Gabrielle Turcotte and David Sankoff
    Citation: BMC Genomics 2018 19(Suppl 2):100
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  36. Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by curre...

    Authors: Yoann Anselmetti, Wandrille Duchemin, Eric Tannier, Cedric Chauve and Sèverine Bérard
    Citation: BMC Genomics 2018 19(Suppl 2):96
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  37. Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Sta...

    Authors: Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan and Onur Mutlu
    Citation: BMC Genomics 2018 19(Suppl 2):89
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  38. Influenza viruses are undergoing continuous and rapid evolution. The fatal influenza A/H7N9 has drawn attention since the first wave of infections in March 2013, and raised more grave concerns with its increas...

    Authors: Xinrui Zhou, Jie Zheng, Fransiskus Xaverius Ivan, Rui Yin, Shoba Ranganathan, Vincent T. K. Chow and Chee-Keong Kwoh
    Citation: BMC Genomics 2018 19(Suppl 2):88
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  39. Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exom...

    Authors: Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen and Veli Mäkinen
    Citation: BMC Genomics 2018 19(Suppl 2):87
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  40. High throughput sequencing technologies have been an increasingly critical aspect of precision medicine owing to a better identification of disease targets, which contributes to improved health care cost and c...

    Authors: Po-Jung Huang, Chi-Ching Lee, Ling-Ya Chiu, Kuo-Yang Huang, Yuan-Ming Yeh, Chia-Yu Yang, Cheng-Hsun Chiu and Petrus Tang
    Citation: BMC Genomics 2018 19(Suppl 2):86
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  41. Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expres...

    Authors: Chi-Nga Chow, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Han-Qin Zheng, Tzong-Yi Lee, Nai-Yun Wu, Kuan-Chieh Tseng, Ping-Fu Hou and Wen-Chi Chang
    Citation: BMC Genomics 2018 19(Suppl 2):85
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  42. Precise identification of three-dimensional genome organization, especially enhancer-promoter interactions (EPIs), is important to deciphering gene regulation, cell differentiation and disease mechanisms. Curr...

    Authors: Wanwen Zeng, Mengmeng Wu and Rui Jiang
    Citation: BMC Genomics 2018 19(Suppl 2):84
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 2

  43. Acute hepatopancreatic necrosis disease (AHPND) has emerged as a major debilitating disease that causes massive shrimp death resulting in substantial economic losses in shrimp aquaculture. Given that several d...

    Authors: Zhihong Zheng, Jude Juventus Aweya, Fan Wang, Defu Yao, Jingsheng Lun, Shengkang Li, Hongyu Ma and Yueling Zhang
    Citation: BMC Genomics 2018 19:335
    Content type: Research article Published on:

  44. The Jurkat cell line has an extensive history as a model of T cell signaling. But at the turn of the 21st century, some expression irregularities were observed, raising doubts about how closely the cell line p...

    Authors: Louis Gioia, Azeem Siddique, Steven R. Head, Daniel R. Salomon and Andrew I. Su
    Citation: BMC Genomics 2018 19:334
    Content type: Research article Published on:

  45. 337S is a novel bi-pole-photo-thermo-sensitive genic male sterile line in wheat, and sensitive to both long day length/high temperature and short day length/low temperature condition. Although the regulatory f...

    Authors: Longqing Sun, Genlou Sun, Chenxia Shi and Dongfa Sun
    Citation: BMC Genomics 2018 19:333
    Content type: Research article Published on:

  46. Here we present an in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells w...

    Authors: Maura Costello, Mark Fleharty, Justin Abreu, Yossi Farjoun, Steven Ferriera, Laurie Holmes, Brian Granger, Lisa Green, Tom Howd, Tamara Mason, Gina Vicente, Michael Dasilva, Wendy Brodeur, Timothy DeSmet, Sheila Dodge, Niall J. Lennon…
    Citation: BMC Genomics 2018 19:332
    Content type: Research article Published on:

  47. Hi-C sequencing offers novel, cost-effective means to study the spatial conformation of chromosomes. We use data obtained from Hi-C experiments to provide new evidence for the existence of spatial gene clusters. ...

    Authors: Tizian Schulz, Jens Stoye and Daniel Doerr
    Citation: BMC Genomics 2018 19(Suppl 5):308
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 5

  48. Fractionation is the genome-wide process of losing one gene per duplicate pair following whole genome multiplication (doubling, tripling, …). This is important in the evolution of plants over tens of millions ...

    Authors: Yue Zhang, Chunfang Zheng and David Sankoff
    Citation: BMC Genomics 2018 19(Suppl 5):287
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 5

  49. Estimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer, that result in gene trees that differ fr...

    Authors: Michael Nute, Jed Chou, Erin K. Molloy and Tandy Warnow
    Citation: BMC Genomics 2018 19(Suppl 5):286
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 5

    The Correction to this article has been published in BMC Genomics 2020 21:133

  50. Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when missed, the erroneous sequences often appear as unexp...

    Authors: Uyen Mai and Siavash Mirarab
    Citation: BMC Genomics 2018 19(Suppl 5):272
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 5

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