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  1. Chromatin accessibility profiling assays such as ATAC-seq and DNase1-seq offer the opportunity to rapidly characterize the regulatory state of the genome at a single nucleotide resolution. Optimization of mole...

    Authors: Thomas J. F. Pranzatelli, Drew G. Michael and John A. Chiorini
    Citation: BMC Genomics 2018 19:563
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Genomics 2019 20:44

  3. In order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial anaerobes from chicken caecum.

    Authors: Matej Medvecky, Darina Cejkova, Ondrej Polansky, Daniela Karasova, Tereza Kubasova, Alois Cizek and Ivan Rychlik
    Citation: BMC Genomics 2018 19:561
    Content type: Research article Published on:

  4. Barley is relatively sensitive to Aluminum (Al) toxicity among cereal crops, but shows a wide genotypic difference in Al tolerance. The well-known Al-tolerant mechanism in barley is related to Al exclusion med...

    Authors: Liyuan Wu, Jiahua Yu, Qiufang Shen, Lu Huang, Dezhi Wu and Guoping Zhang
    Citation: BMC Genomics 2018 19:560
    Content type: Short report Published on:

  5. After the publication of this work [1], a mistake was noticed in the Eq. 1. Given an m  ×  n expression matrix with m genes and samples of n tissues, the correct definition of the Gini index for gene i is:

    Authors: Jitao David Zhang, Klas Hatje, Gregor Sturm, Clemens Broger, Martin Ebeling, Martine Burtin, Fabiola Terzi, Silvia Ines Pomposiello and Laura Badi
    Citation: BMC Genomics 2018 19:558
    Content type: Correction Published on:

    The original article was published in BMC Genomics 2017 18:277

  6. Colletotrichum is a fungal genus in Ascomycota that contain many plant pathogens. Among all Colletotrichum genomes that have been sequenced, C. fructicola contains the largest number of candidate virulence factor...

    Authors: Xiaofei Liang, Shengping Shang, Qiuyue Dong, Bo Wang, Rong Zhang, Mark L. Gleason and Guangyu Sun
    Citation: BMC Genomics 2018 19:557
    Content type: Research article Published on:

  7. Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from ...

    Authors: Ivan Rodrigo Wolf, Alexandre Rossi Paschoal, Cecilia Quiroga, Douglas Silva Domingues, Rogério Fernandes de Souza, Lucienne Garcia Pretto-Giordano and Laurival Antonio Vilas-Boas
    Citation: BMC Genomics 2018 19:556
    Content type: Research article Published on:

  8. Mycobacterium tuberculosis infection in humans is often associated with extended period of latency. To adapt to the hostile hypoxic environment inside a macrophage, M. tuberculosis cells undergo several physiolog...

    Authors: Tungadri Bose, Chandrani Das, Anirban Dutta, Vishnuvardhan Mahamkali, Sudipta Sadhu and Sharmila S. Mande
    Citation: BMC Genomics 2018 19:555
    Content type: Research article Published on:

  9. Flower morphology, a phenomenon regulated by a complex network, is one of the vital ornamental features in Nelumbo nucifera. Stamen petaloid is very prevalent in lotus flowers. However, the mechanism underlying t...

    Authors: Zhongyuan Lin, Rebecca Njeri Damaris, Tao Shi, Juanjuan Li and Pingfang Yang
    Citation: BMC Genomics 2018 19:554
    Content type: Research article Published on:

  10. Plant-parasitic nematodes cause severe damage to a wide range of crop and forest species worldwide. The migratory endoparasitic nematode, Bursaphelenchus xylophilus, (pinewood nematode) is a quarantine pathogen t...

    Authors: Margarida Espada, Sebastian Eves-van den Akker, Tom Maier, Paramasivan Vijayapalani, Thomas Baum, Manuel Mota and John T. Jones
    Citation: BMC Genomics 2018 19:553
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2018 19:603

  12. Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify ...

    Authors: Jun Yasuda, Fumiki Katsuoka, Inaho Danjoh, Yosuke Kawai, Kaname Kojima, Masao Nagasaki, Sakae Saito, Yumi Yamaguchi-Kabata, Shu Tadaka, Ikuko N. Motoike, Kazuki Kumada, Mika Sakurai-Yageta, Osamu Tanabe, Nobuo Fuse, Gen Tamiya, Koichiro Higasa…
    Citation: BMC Genomics 2018 19:551
    Content type: Research article Published on:

  13. Cinnamomum camphora has been cultivated as an economically important tree for its medicinal and aromatic properties. Selective breeding has produced Cinnamomum plants for special uses, including spice strains wit...

    Authors: Caihui Chen, Yongjie Zheng, Yongda Zhong, Yangfang Wu, Zhiting Li, Li-An Xu and Meng Xu
    Citation: BMC Genomics 2018 19:550
    Content type: Research article Published on:

  14. In flowering plants, the male gametophyte (pollen) is one of the most vulnerable cells to temperature stress. In Arabidopsis thaliana, a pollen-specific Cyclic Nucleotide-Gated cation Channel 16 (cngc16), is requ...

    Authors: Maryam Rahmati Ishka, Elizabeth Brown, Chrystle Weigand, Richard L. Tillett, Karen A. Schlauch, Gad Miller and Jeffrey F. Harper
    Citation: BMC Genomics 2018 19:549
    Content type: Research article Published on:

  15. The flower of the safflower (Carthamus tinctorius L.) has been widely used in traditional Chinese medicine for the ability to improve cerebral blood flow. Flavonoids are the primary bioactive components in safflo...

    Authors: Jiang Chen, Xiaohui Tang, Chaoxiang Ren, Bin Wei, Yiyun Wu, Qinghua Wu and Jin Pei
    Citation: BMC Genomics 2018 19:548
    Content type: Research article Published on:

  16. Since the proposal of Brachypodium distachyon as a model for the grasses, over 500 Bdi-miRNAs have been annotated in miRBase making Brachypodium second in number only to rice. Other monocots, such as switchgrass,...

    Authors: Karl R. Franke, Skye A. Schmidt, Sunhee Park, Dong-Hoon Jeong, Monica Accerbi and Pamela J. Green
    Citation: BMC Genomics 2018 19:547
    Content type: Research article Published on:

  18. Lung cancer is a major cause of cancer-related mortality worldwide, and around two-thirds of patients have metastasis at diagnosis. Thus, detecting lung cancer at an early stage could reduce mortality. Aberran...

    Authors: Yuhong Dou, Yong Zhu, Junmei Ai, Hankui Chen, Helu Liu, Jeffrey A. Borgia, Xiao Li, Fan Yang, Bin Jiang, Jun Wang and Youping Deng
    Citation: BMC Genomics 2018 19:545
    Content type: Research article Published on:

  19. The peach fruit moth, Carposina sasakii Matsumura (Lepidoptera: Carposinidae), poses a serious threat to a variety of fruits and causes significant economic loss owing to difficulties in its prevention and contro...

    Authors: Zhiqiang Tian, Lina Sun, Yanyan Li, Linfa Quan, Huaijiang Zhang, Wentao Yan, Qiang Yue and Guisheng Qiu
    Citation: BMC Genomics 2018 19:544
    Content type: Research article Published on:

  21. Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding...

    Authors: De-Long Guan, Li-Bin Ma, Muhammad Salabat Khan, Xiu-Xiu Zhang, Sheng-Quan Xu and Juan-Ying Xie
    Citation: BMC Genomics 2018 19:542
    Content type: Research article Published on:

  22. Thraustochytrids are unicellular fungal-like marine protists with ubiquitous existence in marine environments. They are well-known for their ability to produce high-valued omega-3 polyunsaturated fatty acids (...

    Authors: Zhiquan Song, Jason E. Stajich, Yunxuan Xie, Xianhua Liu, Yaodong He, Jinfeng Chen, Glenn R. Hicks and Guangyi Wang
    Citation: BMC Genomics 2018 19:541
    Content type: Research article Published on:

  23. S. latifolia is a model organism for the study of sex chromosome evolution in plants. Its sex chromosomes include large regions in which recombination became gradually suppressed. The regions tend to expand over ...

    Authors: José Luis Rodríguez Lorenzo, Roman Hobza and Boris Vyskot
    Citation: BMC Genomics 2018 19:540
    Content type: Research article Published on:

  24. Spermatogenesis, which is the complex and highly regulated process of producing haploid spermatozoa, involves testis-specific transcripts. Recent studies have discovered that long noncoding RNAs (lncRNAs) are ...

    Authors: Seong Hyeon Hong, Jun Tae Kwon, Jihye Kim, Juri Jeong, Jaehwan Kim, Seonhee Lee and Chunghee Cho
    Citation: BMC Genomics 2018 19:539
    Content type: Research article Published on:

  25. Esophageal squamous cell carcinomas (ESCC) is the fourth most lethal cancer in China. Previous studies reveal several highly conserved mutational processes in ESCC. However, it remains unclear what are the tru...

    Authors: Jintao Guo, Jiankun Huang, Ying Zhou, Yulin Zhou, Liying Yu, Huili Li, Lingyun Hou, Liuwei Zhu, Dandan Ge, Yuanyuan Zeng, Bayasi Guleng and Qiyuan Li
    Citation: BMC Genomics 2018 19:538
    Content type: Research article Published on:

  27. Alternative polyadenylation (APA) results in messenger RNA molecules with different 3′ untranslated regions (3’ UTRs), affecting the molecules’ stability, localization, and translation. APA is pervasive and im...

    Authors: Zhuyi Xue, René L. Warren, Ewan A. Gibb, Daniel MacMillan, Johnathan Wong, Readman Chiu, S. Austin Hammond, Chen Yang, Ka Ming Nip, Catherine A. Ennis, Abigail Hahn, Sheila Reynolds and Inanc Birol
    Citation: BMC Genomics 2018 19:536
    Content type: Research article Published on:

  28. The Zika virus (ZIKV) can cause microcephaly and congenital abnormalities in the foetus. Recent studies have provided insights into the evolution of ZIKV from the current and previous outbreaks, but the types ...

    Authors: Hyeji Lee, Mai Phuong Nguyen, Yunhee Choi and Yong-Hak Kim
    Citation: BMC Genomics 2018 19:535
    Content type: Methodology article Published on:

  29. Aspergillus fumigatus is the main causative agent of aspergillosis. Infections rarely occur in immunocompetent individuals, indicating efficient clearance of conidia by pulmonary defense mechanisms. Other aspergi...

    Authors: Natalia Escobar, Ivan D. Valdes, Esther M. Keizer, Soledad R. Ordonez, Robin A. Ohm, Han A. B. Wösten and Hans de Cock
    Citation: BMC Genomics 2018 19:534
    Content type: Research article Published on:

  30. Genomic methods can provide extraordinary tools to explore the genetic background of wild species and domestic breeds, optimize breeding practices, monitor and limit the spread of recessive diseases, and disco...

    Authors: Romolo Caniglia, Elena Fabbri, Pavel Hulva, Barbora Černá Bolfíková, Milena Jindřichová, Astrid Vik Stronen, Ihor Dykyy, Alessio Camatta, Paolo Carnier, Ettore Randi and Marco Galaverni
    Citation: BMC Genomics 2018 19:533
    Content type: Research article Published on:

  31. Nitrogen (N) is a key macronutrient essential for plant growth, and its availability has a strong influence on crop development. The application of synthetic N fertilizers on crops has increased substantially ...

    Authors: Sang-Yoon Shin, Jin Seo Jeong, Jae Yun Lim, Taewook Kim, June Hyun Park, Ju-Kon Kim and Chanseok Shin
    Citation: BMC Genomics 2018 19:532
    Content type: Research article Published on:

  32. RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting materi...

    Authors: Yu Fu, Pei-Hsuan Wu, Timothy Beane, Phillip D. Zamore and Zhiping Weng
    Citation: BMC Genomics 2018 19:531
    Content type: Methodology article Published on:

  33. Infections with the West Nile virus (WNV) can attack neurological tissues in the host and alter gene expression levels therein. Several individual studies have analyzed these changes in the transcriptome based...

    Authors: Robin Kosch, Julien Delarocque, Peter Claus, Stefanie C. Becker and Klaus Jung
    Citation: BMC Genomics 2018 19:530
    Content type: Research article Published on:

  34. Large-scale molecular changes occur during aging and have many downstream consequences on whole-organism function, such as motor function, learning, and memory. The marine mollusk Aplysia californica can be used ...

    Authors: Justin B. Greer, Michael C. Schmale and Lynne A. Fieber
    Citation: BMC Genomics 2018 19:529
    Content type: Research article Published on:

  35. Bacterial genomes have characteristic compositional skews, which are differences in nucleotide frequency between the leading and lagging DNA strands across a segment of a genome. It is thought that these stran...

    Authors: Lena M. Joesch-Cohen, Max Robinson, Neda Jabbari, Christopher G. Lausted and Gustavo Glusman
    Citation: BMC Genomics 2018 19:528
    Content type: Methodology article Published on:

  36. Enterococcus faecalis is widely studied as a common gut commensal and a nosocomial pathogen. In fact, Enterococcus faecalis is ubiquitous in nature, and it has been isolated from various niches, including the gas...

    Authors: Qiuwen He, Qiangchuan Hou, Yanjie Wang, Jing Li, Weicheng Li, Lai-Yu Kwok, Zhihong Sun, Heping Zhang and Zhi Zhong
    Citation: BMC Genomics 2018 19:527
    Content type: Research article Published on:

  37. Anopheles mosquitoes are efficient vectors of human malaria, but it is unknown why they do not transmit viruses as well as Aedes and Culex mosquitoes. The only arbovirus known to be consistently transmitted by An...

    Authors: Guillaume Carissimo, Adrien Pain, Eugeni Belda and Kenneth D. Vernick
    Citation: BMC Genomics 2018 19:526
    Content type: Research article Published on:

  38. Mycoplasma hominis is a human urogenital pathogen involved in gynaecological, neonatal and extra-genital infections. However, no versatile genetic tools are currently available to study the pathogenicity of this ...

    Authors: S. Pereyre, C. Bénard, C. Brès, C. Le Roy, J. P. Mauxion, F. Rideau, P. Sirand-Pugnet, B. Henrich and C. Bébéar
    Citation: BMC Genomics 2018 19:525
    Content type: Methodology article Published on:

  39. Common variants have explained less than the amount of heritability expected for complex diseases, which has led to interest in less-common variants and more powerful approaches to the analysis of whole-genome...

    Authors: John Cologne, Lenora Loo, Yurii B. Shvetsov, Munechika Misumi, Philip Lin, Christopher A. Haiman, Lynne R. Wilkens and Loïc Le Marchand
    Citation: BMC Genomics 2018 19:524
    Content type: Methodology article Published on:

  41. Human Endogenous Retroviruses (HERVs) and Mammalian apparent LTR-retrotransposons (MaLRs) represent the 8% of our genome and are distributed among our 46 chromosomes. These LTR-retrotransposons are thought to ...

    Authors: Marine Mommert, Olivier Tabone, Guy Oriol, Elisabeth Cerrato, Audrey Guichard, Magali Naville, Paola Fournier, Jean-Nicolas Volff, Alexandre Pachot, Guillaume Monneret, Fabienne Venet, Karen Brengel-Pesce, Julien Textoris and François Mallet
    Citation: BMC Genomics 2018 19:522
    Content type: Research article Published on:

  42. Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an important economic and m...

    Authors: Ruidong Xiang, Ben J. Hayes, Christy J. Vander Jagt, Iona M. MacLeod, Majid Khansefid, Phil J. Bowman, Zehu Yuan, Claire P. Prowse-Wilkins, Coralie M. Reich, Brett A. Mason, Josie B. Garner, Leah C. Marett, Yizhou Chen, Sunduimijid Bolormaa, Hans D. Daetwyler, Amanda J. Chamberlain…
    Citation: BMC Genomics 2018 19:521
    Content type: Research article Published on:

  43. Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are i...

    Authors: Maarten P. M. Vanhove, Andrew G. Briscoe, Michiel W. P. Jorissen, D. Tim J. Littlewood and Tine Huyse
    Citation: BMC Genomics 2018 19:520
    Content type: Research article Published on:

  44. Streptomyces species produce a vast diversity of secondary metabolites of clinical and biotechnological importance, in particular antibiotics. Recent developments in metabolic engineering, synthetic and systems b...

    Authors: Adam Amara, Eriko Takano and Rainer Breitling
    Citation: BMC Genomics 2018 19:519
    Content type: Research article Published on:

  45. The oriental armyworm, Mythimna separata, is an economically important and common Lepidopteran pest of cereal crops. Chemoreception plays a key role in insect life, such as foraging, oviposition site selection, a...

    Authors: Lixiao Du, Xincheng Zhao, Xiangzhi Liang, Xiwu Gao, Yang Liu and Guirong Wang
    Citation: BMC Genomics 2018 19:518
    Content type: Research article Published on:

  46. Hybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation. Our knowledge regarding the mechanisms of duplicated-gene regulation...

    Authors: Wuhui Li, Junmei Liu, Hui Tan, Lingling Luo, Jialin Cui, Jie Hu, Shi Wang, Qingfeng Liu, Fangzhou Hu, Chenchen Tang, Li Ren, Conghui Yang, Rurong Zhao, Min Tao, Chun Zhang, Qinbo Qin…
    Citation: BMC Genomics 2018 19:517
    Content type: Research article Published on:

  48. Arylamine N-acetyltransferase 1 (NAT1) is a drug metabolizing enzyme that has been associated with cancer cell proliferation in vitro and with survival in vivo. NAT1 expression has been associated with the est...

    Authors: Rodney F. Minchin and Neville J. Butcher
    Citation: BMC Genomics 2018 19:513
    Content type: Research article Published on:

  49. RNA regulation is significantly dependent on its binding protein partner, known as the RNA-binding proteins (RBPs). Unfortunately, the binding preferences for most RBPs are still not well characterized. Interd...

    Authors: Xiaoyong Pan, Peter Rijnbeek, Junchi Yan and Hong-Bin Shen
    Citation: BMC Genomics 2018 19:511
    Content type: Methodology article Published on:

  50. The hemibiotrophic pathogens Moniliophthora perniciosa (witches’ broom disease) and Moniliophthora roreri (frosty pod rot disease) are among the most important pathogens of cacao. Moniliophthora perniciosa has a ...

    Authors: Ceslaine Santos Barbosa, Rute R. da Fonseca, Thiago Mafra Batista, Mariana Araújo Barreto, Caio Suzart Argolo, Mariana Rocha de Carvalho, Daniel Oliveira Jordão do Amaral, Edson Mário de Andrade Silva, Enrique Arévalo-Gardini, Karina Solis Hidalgo, Glória Regina Franco, Carlos Priminho Pirovani, Fabienne Micheli and Karina Peres Gramacho
    Citation: BMC Genomics 2018 19:509
    Content type: Research article Published on:

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BMC Genomics

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