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  1. Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Entero...

    Authors: Stanford Kwenda, Vladimir Gorshkov, Aadi Moolam Ramesh, Sanushka Naidoo, Enrico Rubagotti, Paul R. J. Birch and Lucy N. Moleleki
    Citation: BMC Genomics 2016 17:47
    Content type: Research article Published on:

  2. Epistasis is one of the central themes in viral evolution due to its importance in drug resistance, immune escape, and interspecies transmission. However, there is a lack of experimental approach to systematic...

    Authors: Nicholas C. Wu, Yushen Du, Shuai Le, Arthur P. Young, Tian-Hao Zhang, Yuanyuan Wang, Jian Zhou, Janice M. Yoshizawa, Ling Dong, Xinmin Li, Ting-Ting Wu and Ren Sun
    Citation: BMC Genomics 2016 17:46
    Content type: Methodology Article Published on:

  3. Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from mult...

    Authors: Jeanneth Mosquera-Rendón, Ana M. Rada-Bravo, Sonia Cárdenas-Brito, Mauricio Corredor, Eliana Restrepo-Pineda and Alfonso Benítez-Páez
    Citation: BMC Genomics 2016 17:45
    Content type: Research article Published on:

  4. Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the g...

    Authors: Antony T. Vincent, Mélanie V. Trudel, Luca Freschi, Vandan Nagar, Cynthia Gagné-Thivierge, Roger C. Levesque and Steve J. Charette
    Citation: BMC Genomics 2016 17:44
    Content type: Research article Published on:

  5. Auxin plays a critical role in inducing adventitious rooting in many plants. Indole-3-butyric acid (IBA) is the most widely employed auxin for adventitious rooting. However, the molecular mechanisms by which a...

    Authors: Shi-Weng Li, Rui-Fang Shi, Yan Leng and Yuan Zhou
    Citation: BMC Genomics 2016 17:43
    Content type: Research article Published on:

  6. The filamentous actinomycete Microbispora ATCC-PTA-5024 produces the lantibiotic NAI-107, which is an antibiotic peptide effective against multidrug-resistant Gram-positive bacteria. In actinomycetes, antibiotic ...

    Authors: Giuseppe Gallo, Giovanni Renzone, Emilia Palazzotto, Paolo Monciardini, Simona Arena, Teresa Faddetta, Anna Giardina, Rosa Alduina, Tilmann Weber, Fabio Sangiorgi, Alessandro Russo, Giovanni Spinelli, Margherita Sosio, Andrea Scaloni and Anna Maria Puglia
    Citation: BMC Genomics 2016 17:42
    Content type: Research article Published on:

  7. Discovering the location of gene duplications and multiple gene duplication episodes is a fundamental issue in evolutionary molecular biology. The problem introduced by Guigó et al. in 1996 is to map gene dupl...

    Authors: Jarosław Paszek and Paweł Górecki
    Citation: BMC Genomics 2016 17(Suppl 1):15
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  8. In cell differentiation, a less specialized cell differentiates into a more specialized one, even though all cells in one organism have (almost) the same genome. Epigenetic factors such as histone modification...

    Authors: Nishanth Ulhas Nair, Laura Hunter, Mingfu Shao, Paulina Grnarova, Yu Lin, Philipp Bucher and Bernard M. E. Moret
    Citation: BMC Genomics 2016 17(Suppl 1):14
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  9. Anguilla japonica (Japanese eel) is currently one of the most important research subjects in eastern Asia aquaculture. Enigmatic life cycle of the organism makes study of artificial reproduction extremely limited...

    Authors: Yu-Chen Liu, Sheng-Da Hsu, Chih-Hung Chou, Wei-Yun Huang, Yu-Hung Chen, Chia-Yu Liu, Guan-Jay Lyu, Shao-Zhen Huang, Sergey Aganezov, Max A. Alekseyev, Chung-Der Hsiao and Hsien-Da Huang
    Citation: BMC Genomics 2016 17(Suppl 1):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  10. Recent studies have revealed that large numbers of non-coding RNAs are transcribed in humans, but only a few of them have been identified with their functions. Identification of the interaction target RNAs of ...

    Authors: Goro Terai, Junichi Iwakiri, Tomoshi Kameda, Michiaki Hamada and Kiyoshi Asai
    Citation: BMC Genomics 2016 17(Suppl 1):12
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  11. The advent of next-generation RNA sequencing (RNA-seq) has greatly advanced transcriptomic studies, including system-wide identification and quantification of mRNA isoforms under various biological conditions....

    Authors: Yuting Ye and Jingyi Jessica Li
    Citation: BMC Genomics 2016 17(Suppl 1):11
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

    The Erratum to this article has been published in BMC Genomics 2016 17:296

  12. The dynamics of epigenomic marks in their relevant chromatin states regulate distinct gene expression patterns, biological functions and phenotypic variations in biological processes. The availability of high-...

    Authors: Wei Vivian Li, Zahra S. Razaee and Jingyi Jessica Li
    Citation: BMC Genomics 2016 17(Suppl 1):S10
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  13. Protein S-sulfenylation is a type of post-translational modification (PTM) involving the covalent binding of a hydroxyl group to the thiol of a cysteine amino acid. Recent evidence has shown the importance of S-s...

    Authors: Van-Minh Bui, Shun-Long Weng, Cheng-Tsung Lu, Tzu-Hao Chang, Julia Tzu-Ya Weng and Tzong-Yi Lee
    Citation: BMC Genomics 2016 17(Suppl 1):9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  14. Recent studies of eukaryotes including human and Neandertal, mice, and butterflies have highlighted the major role that interspecific introgression has played in adaptive trait evolution. A common question ari...

    Authors: Hussein A. Hejase and Kevin J. Liu
    Citation: BMC Genomics 2016 17(Suppl 1):S8
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

    The Erratum to this article has been published in BMC Genomics 2016 17:292

  15. microRNAs (miRNAs) play an essential role in the post-transcriptional gene regulation in plants and animals. They regulate a wide range of biological processes by targeting messenger RNAs (mRNAs). Evidence sug...

    Authors: S. M. Masud Karim, Lin Liu, Thuc Duy Le and Jiuyong Li
    Citation: BMC Genomics 2016 17(Suppl 1):7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  16. Despite the enormous medical impact of cancers and intensive study of their biology, detailed characterization of tumor growth and development remains elusive. This difficulty occurs in large part because of e...

    Authors: Theodore Roman, Lu Xie and Russell Schwartz
    Citation: BMC Genomics 2016 17(Suppl 1):6
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  17. RNA-editing is an important post-transcriptional RNA sequence modification performed by two catalytic enzymes, "ADAR"(A-to-I) and "APOBEC"(C-to-U). By utilizing high-throughput sequencing technologies, the bio...

    Authors: Min-su Kim, Benjamin Hur and Sun Kim
    Citation: BMC Genomics 2016 17(Suppl 1):5
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  18. The identification of inversions of DNA segments shorter than read length (e.g., 100 bp), defined as micro-inversions (MIs), remains challenging for next-generation sequencing reads. It is acknowledged that MI...

    Authors: Feifei He, Yang Li, Yu-Hang Tang, Jian Ma and Huaiqiu Zhu
    Citation: BMC Genomics 2016 17(Suppl 1):4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  19. Replication study is a commonly used verification method to filter out false positives in genome-wide association studies (GWAS). If an association can be confirmed in a replication study, it will have a high ...

    Authors: Wei Jiang and Weichuan Yu
    Citation: BMC Genomics 2016 17(Suppl 1):3
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

    The Erratum to this article has been published in BMC Genomics 2017 18:73

  20. RNA-sequencing (RNA-Seq) has become a popular tool for transcriptome profiling in mammals. However, accurate estimation of allele-specific expression (ASE) based on alignments of reads to the reference genome ...

    Authors: Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yosuke Kawai and Masao Nagasaki
    Citation: BMC Genomics 2016 17(Suppl 1):2
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  21. The inference of genome rearrangement operations requires complete genome assemblies as input data, since a rearrangement can involve an arbitrarily large proportion of one or more chromosomes. Most genome seq...

    Authors: Chunfang Zheng and David Sankoff
    Citation: BMC Genomics 2016 17(Suppl 1):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  22. Several in vitro studies document the function of the transcriptional regulator TrmBL1 of Pyrococcus furiosus. These data indicate that the protein can act as repressor or activator and is mainly involved in tran...

    Authors: Robert Reichelt, Antonia Gindner, Michael Thomm and Winfried Hausner
    Citation: BMC Genomics 2016 17:40
    Content type: Research article Published on:

  23. RNA sequencing (RNA-seq), a next-generation sequencing technique for transcriptome profiling, is being increasingly used, in part driven by the decreasing cost of sequencing. Nevertheless, the analysis of the ...

    Authors: Shanrong Zhao, Li Xi, Jie Quan, Hualin Xi, Ying Zhang, David von Schack, Michael Vincent and Baohong Zhang
    Citation: BMC Genomics 2016 17:39
    Content type: Software Published on:

  24. Head and neck cancer is morbid with a poor prognosis that has not significantly improved in the past several decades. The purpose of this study was to identify biological pathways underlying progressive head a...

    Authors: Sophia Bornstein, Mark Schmidt, Gabrielle Choonoo, Trevor Levin, Joe Gray, Charles R. Thomas Jr., Melissa Wong and Shannon McWeeney
    Citation: BMC Genomics 2016 17:38
    Content type: Research article Published on:

  25. Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, ...

    Authors: Yingjia Shen, Domitille Chalopin, Tzintzuni Garcia, Mikki Boswell, William Boswell, Sergey A. Shiryev, Richa Agarwala, Jean-Nicolas Volff, John H. Postlethwait, Manfred Schartl, Patrick Minx, Wesley C. Warren and Ronald B. Walter
    Citation: BMC Genomics 2016 17:37
    Content type: Research article Published on:

  26. Fruit ripening is a complex developmental process that depends on a coordinated regulation of numerous genes, including ripening-related transcription factors (TFs), fruit-related microRNAs, DNA methylation an...

    Authors: Shan Li, Ka Li, Zheng Ju, Dongyan Cao, Daqi Fu, Hongliang Zhu, Benzhong Zhu and Yunbo Luo
    Citation: BMC Genomics 2016 17:36
    Content type: Research article Published on:

  27. It is well known that in the rhizosphere soluble Fe sources available for plants are mainly represented by a mixture of complexes between the micronutrient and organic ligands such as carboxylates and phytosid...

    Authors: Anita Zamboni, Laura Zanin, Nicola Tomasi, Linda Avesani, Roberto Pinton, Zeno Varanini and Stefano Cesco
    Citation: BMC Genomics 2016 17:35
    Content type: Research article Published on:

  28. The microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a ...

    Authors: Ndongo Dia, Laurence Lavie, Ngor Faye, Guy Méténier, Edouard Yeramian, Christophe Duroure, Bhen S. Toguebaye, Roger Frutos, Mbayame N. Niang, Christian P. Vivarès, Choukri Ben Mamoun and Emmanuel Cornillot
    Citation: BMC Genomics 2016 17:34
    Content type: Research article Published on:

  29. A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built...

    Authors: Qijian Song, Jerry Jenkins, Gaofeng Jia, David L. Hyten, Vince Pantalone, Scott A. Jackson, Jeremy Schmutz and Perry B. Cregan
    Citation: BMC Genomics 2016 17:33
    Content type: Research article Published on:

  30. A complete genome sequence and the advent of genome editing open up non-traditional model organisms to mechanistic genetic studies. The mosquito Aedes aegypti is an important vector of infectious diseases such as...

    Authors: Benjamin J. Matthews, Carolyn S. McBride, Matthew DeGennaro, Orion Despo and Leslie B. Vosshall
    Citation: BMC Genomics 2016 17:32
    Content type: Research article Published on:

  31. Sesame is an important high-quality oil seed crop. The sesame genome was de novo sequenced and assembled in 2014 (version 1.0); however, the number of anchored pseudomolecules was higher than the chromosome numbe...

    Authors: Linhai Wang, Qiuju Xia, Yanxin Zhang, Xiaodong Zhu, Xiaofeng Zhu, Donghua Li, Xuemei Ni, Yuan Gao, Haitao Xiang, Xin Wei, Jingyin Yu, Zhiwu Quan and Xiurong Zhang
    Citation: BMC Genomics 2016 17:31
    Content type: Research article Published on:

  32. The limited genetic diversity of elite maize germplasms raises concerns about the potential to breed for new challenges. Initiatives have been formed over the years to identify and utilize useful diversity fro...

    Authors: Gregor Gorjanc, Janez Jenko, Sarah J. Hearne and John M. Hickey
    Citation: BMC Genomics 2016 17:30
    Content type: Research article Published on:

  33. Harmful algal blooms (HABs) caused by the dinoflagellate Cochlodinium polykrikoides lead to severe environmental impacts in oceans worldwide followed by huge economic losses. Algicide agent copper sulfate (CuSO4)...

    Authors: Ruoyu Guo, Hui Wang, Young Sang Suh and Jang-Seu Ki
    Citation: BMC Genomics 2016 17:29
    Content type: Research article Published on:

  34. A generally accepted approach to the analysis of RNA-Seq read count data does not yet exist. We sequenced the mRNA of 726 individuals from the Drosophila Genetic Reference Panel in order to quantify differences i...

    Authors: Yanzhu Lin, Kseniya Golovnina, Zhen-Xia Chen, Hang Noh Lee, Yazmin L. Serrano Negron, Hina Sultana, Brian Oliver and Susan T. Harbison
    Citation: BMC Genomics 2016 17:28
    Content type: Methodology article Published on:

  36. Somatic embryogenesis is a notable illustration of cell totipotency, by which somatic cells undergo dedifferentiation and then differentiate into somatic embryos. Our previous work demonstrated that pretreatme...

    Authors: Xueping Shi, Cuijie Zhang, Qinhong Liu, Zhe Zhang, Bo Zheng and Manzhu Bao
    Citation: BMC Genomics 2016 17:26
    Content type: Research article Published on:

  37. Roberts syndrome (RBS) is a human developmental disorder caused by mutations in the cohesin acetyltransferase ESCO2. We previously reported that mTORC1 signaling was depressed and overall translation was reduc...

    Authors: Baoshan Xu, Madelaine Gogol, Karin Gaudenz and Jennifer L. Gerton
    Citation: BMC Genomics 2016 17:25
    Content type: Research article Published on:

  38. Cytoplasmic male sterility (CMS) provides crucial breeding materials that facilitate hybrid seed production in various crops, and thus plays an important role in the study of hybrid vigor (heterosis), in plant...

    Authors: Xianlong Ding, Jiajia Li, Hao Zhang, Tingting He, Shaohuai Han, Yanwei Li, Shouping Yang and Junyi Gai
    Citation: BMC Genomics 2016 17:24
    Content type: Research article Published on:

  39. Legumes are important to humans by providing food, feed and raw materials for industrial utilizations. Some legumes, such as alfalfa, are potential bioenergy crops due to their high biomass productivity. Globa...

    Authors: Huanzhong Wang, Jung Hyun Yang, Fang Chen, Ivone Torres-Jerez, Yuhong Tang, Mingyi Wang, Qian Du, Xiaofei Cheng, Jiangqi Wen and Richard Dixon
    Citation: BMC Genomics 2016 17:23
    Content type: Research article Published on:

  40. Artificial light at night (ALAN) is a typical feature of urban areas and most organisms living in urban or suburban habitats are exposed to low levels of ALAN. Light is one of the most important environmental ...

    Authors: Ann-Christin Honnen, Paul R. Johnston and Michael T. Monaghan
    Citation: BMC Genomics 2016 17:22
    Content type: Research article Published on:

  41. The species Xanthomonas translucens encompasses a complex of bacterial strains that cause diseases and yield loss on grass species including important cereal crops. Three pathovars, X. translucens pv. undulosa, X...

    Authors: Zhao Peng, Ying Hu, Jingzhong Xie, Neha Potnis, Alina Akhunova, Jeffrey Jones, Zhaohui Liu, Frank F. White and Sanzhen Liu
    Citation: BMC Genomics 2016 17:21
    Content type: Research article Published on:

  42. RNA interference (RNAi) is a powerful platform utilized to target transcription of specific genes and downregulate the protein product. To achieve effective silencing, RNAi is usually applied to cells or tissu...

    Authors: Nurazhani A. Raof, Deepa Rajamani, Hsun-Chieh Chu, Aniket Gurav, Joel M. Johnson, Frank W. LoGerfo, Manoj Bhasin and Leena Pradhan-Nabzdyk
    Citation: BMC Genomics 2016 17:20
    Content type: Research article Published on:

  43. Penicillium griseofulvum is associated in stored apples with blue mould, the most important postharvest disease of pome fruit. This pathogen can simultaneously produce both detrimental...

    Authors: Houda Banani, Marina Marcet-Houben, Ana-Rosa Ballester, Pamela Abbruscato, Luis González-Candelas, Toni Gabaldón and Davide Spadaro
    Citation: BMC Genomics 2016 17:19
    Content type: Research article Published on:

  44. There are three basic Brassica genomes (A, B, and C) and three parallel sets of subgenomes distinguished in the diploid Brassica (i.e.: B. rapa, ArAr; B. nigra, BniBni; B. oleracea, CoCo) and the derived allotetr...

    Authors: Jun Zou, Dandan Hu, Peifa Liu, Harsh Raman, Zhongsong Liu, Xianjun Liu, Isobel A. P. Parkin, Boulos Chalhoub and Jinling Meng
    Citation: BMC Genomics 2016 17:18
    Content type: Research article Published on:

  45. The yeast Kloeckera apiculata strain 34–9 is an antagonist that shows biological control activity against the postharvest fungal pathogens of citrus. An antifungal compound, 2-phenylethanol (PEA), has been identi...

    Authors: Pu Liu, Kai Chen, Guofeng Li, Xiaoping Yang and Chao-an Long
    Citation: BMC Genomics 2016 17:17
    Content type: Research article Published on:

  46. The limited duration and compromised efficiency of oocyte-mediated reprogramming, which occurs during the early hours following somatic cell nuclear transfer (SCNT), may significantly interfere with epigenetic...

    Authors: Sayyed Morteza Hosseini, Isabelle Dufort, Julie Nieminen, Fariba Moulavi, Hamid Reza Ghanaei, Mahdi Hajian, Farnoosh Jafarpour, Mohsen Forouzanfar, Hamid Gourbai, Abdol Hossein Shahverdi, Mohammad Hossein Nasr-Esfahani and Marc-André Sirard
    Citation: BMC Genomics 2016 17:16
    Content type: Research article Published on:

  47. Fructobacillus spp. in fructose-rich niches belong to the family Leuconostocaceae. They were originally classified as Leuconostoc spp., but were later grouped into a novel genus, Fruct...

    Authors: Akihito Endo, Yasuhiro Tanizawa, Naoto Tanaka, Shintaro Maeno, Himanshu Kumar, Yuh Shiwa, Sanae Okada, Hirofumi Yoshikawa, Leon Dicks, Junichi Nakagawa and Masanori Arita
    Citation: BMC Genomics 2015 16:1117
    Content type: Research article Published on:

  48. Next-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficienc...

    Authors: Lynsey K. Whitacre, Polyana C. Tizioto, JaeWoo Kim, Tad S. Sonstegard, Steven G. Schroeder, Leeson J. Alexander, Juan F. Medrano, Robert D. Schnabel, Jeremy F. Taylor and Jared E. Decker
    Citation: BMC Genomics 2015 16:1114
    Content type: Research article Published on:

  49. Rare variants have gathered increasing attention as a possible alternative source of missing heritability. Since next generation sequencing technology is not yet cost-effective for large-scale genomic studies,...

    Authors: Young Jin Kim, Juyoung Lee, Bong-Jo Kim and Taesung Park
    Citation: BMC Genomics 2015 16:1109
    Content type: Methodology article Published on:

  50. Pseudomonas aeruginosa establishes life-long chronic airway infections in cystic fibrosis (CF) patients. As the disease progresses, P. aeruginosa pathoadaptive variants are distinguish...

    Authors: Irene Bianconi, Julie Jeukens, Luca Freschi, Beatriz Alcalá-Franco, Marcella Facchini, Brian Boyle, Antonio Molinaro, Irena Kukavica-Ibrulj, Burkhard Tümmler, Roger C. Levesque and Alessandra Bragonzi
    Citation: BMC Genomics 2015 16:1105
    Content type: Research article Published on:

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