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  1. The availability of diverse second- and third-generation sequencing technologies enables the rapid determination of the sequences of bacterial genomes. However, identifying the sequencing technology most suita...

    Authors: Mari Miyamoto, Daisuke Motooka, Kazuyoshi Gotoh, Takamasa Imai, Kazutoshi Yoshitake, Naohisa Goto, Tetsuya Iida, Teruo Yasunaga, Toshihiro Horii, Kazuharu Arakawa, Masahiro Kasahara and Shota Nakamura
    Citation: BMC Genomics 2014 15:699
    Content type: Research article Published on:

  2. Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations o...

    Authors: Alessandra Rogato, Hugues Richard, Alexis Sarazin, Björn Voss, Soizic Cheminant Navarro, Raphaël Champeimont, Lionel Navarro, Alessandra Carbone, Wolfgang R Hess and Angela Falciatore
    Citation: BMC Genomics 2014 15:698
    Content type: Research article Published on:

  3. Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role...

    Authors: Sara Lopez-Gomollon, Matthew Beckers, Tina Rathjen, Simon Moxon, Florian Maumus, Irina Mohorianu, Vincent Moulton, Tamas Dalmay and Thomas Mock
    Citation: BMC Genomics 2014 15:697
    Content type: Research article Published on:

  4. The phylum Apicomplexa comprises important unicellular human parasites such as Toxoplasma and Plasmodium. Eimeria is the largest and most diverse genus of apicomplexan parasites and some species of the genus are ...

    Authors: Emanuel Heitlinger, Simone Spork, Richard Lucius and Christoph Dieterich
    Citation: BMC Genomics 2014 15:696
    Content type: Research article Published on:

  5. In plants, microRNAs (miRNAs) regulate gene expression mainly at the post-transcriptional level. Previous studies have demonstrated that miRNA-mediated gene silencing pathways play vital roles in plant develop...

    Authors: Yuanlong Liu, Lun Wang, Dijun Chen, Xiaomeng Wu, Ding Huang, Lingling Chen, Li Li, Xiuxin Deng and Qiang Xu
    Citation: BMC Genomics 2014 15:695
    Content type: Research article Published on:

  6. Uranium (U) is a naturally occurring radionuclide that has been found in the aquatic environment due to anthropogenic activities. Exposure to U may pose risk to aquatic organisms due to its radiological and ch...

    Authors: You Song, Brit Salbu, Hans-Christian Teien, Lene Sørlie Heier, Bjørn Olav Rosseland, Tore Høgåsen and Knut Erik Tollefsen
    Citation: BMC Genomics 2014 15:694
    Content type: Research article Published on:

  7. Previous studies have shown that CpG dinucleotides are enriched in a subset of promoters and the CpG content of promoters is positively correlated with gene expression levels. But the relationship between dive...

    Authors: Huan Yang, Dawei Li and Chao Cheng
    Citation: BMC Genomics 2014 15:693
    Content type: Research article Published on:

  9. Although mitochondrial (mt) gene order is highly conserved among vertebrates, widespread gene rearrangements occur in anurans, especially in neobatrachians. Protein coding genes in the mitogenome experience ad...

    Authors: Yun Xia, Yuchi Zheng, Ikuo Miura, Pamela BY Wong, Robert W Murphy and Xiaomao Zeng
    Citation: BMC Genomics 2014 15:691
    Content type: Research article Published on:

  10. The yolk sac (YS) is an extra-embryonic tissue that surrounds the yolk and absorbs, digests and transports nutrients during incubation of the avian embryo as well as during early term mammalian embryonic devel...

    Authors: Liran Yadgary, Eric A Wong and Zehava Uni
    Citation: BMC Genomics 2014 15:690
    Content type: Research article Published on:

  11. Herbaceous peony (Paeonia lactiflora Pall.) is a traditional flower in China and a wedding attractive flower in worldwide. In its flower colour, yellow is the rarest which is ten times the price of the other colo...

    Authors: Daqiu Zhao, Yao Jiang, Chuanlong Ning, Jiasong Meng, Shasha Lin, Wen Ding and Jun Tao
    Citation: BMC Genomics 2014 15:689
    Content type: Research article Published on:

  12. Variability in protein levels is generated through intricate control of the different gene decoding phases. Presently little is known about the links between the various gene expression stages. Here we investi...

    Authors: Ana Tamarkin-Ben-Harush, Edna Schechtman and Rivka Dikstein
    Citation: BMC Genomics 2014 15:688
    Content type: Research article Published on:

  13. Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression arra...

    Authors: Marina Panova, Tomas Johansson, Björn Canbäck, Johan Bentzer, Magnus Alm Rosenblad, Kerstin Johannesson, Anders Tunlid and Carl André
    Citation: BMC Genomics 2014 15:687
    Content type: Research article Published on:

  14. Hypoxia is a critical aspect of the glioma microenvironment and has been associated with poor prognosis and resistance to various therapies. However, the mechanisms responsible for hypoxic survival of glioma c...

    Authors: Rahul Agrawal, Priyatama Pandey, Prerana Jha, Vivek Dwivedi, Chitra Sarkar and Ritu Kulshreshtha
    Citation: BMC Genomics 2014 15:686
    Content type: Research article Published on:

  15. Sequences up to several megabases in length have been found to be present in individual genomes but absent in the human reference genome. These sequences may be common in populations, and their absence in the ...

    Authors: Yu Liu, Mehmet Koyutürk, Sean Maxwell, Min Xiang, Martina Veigl, Richard S Cooper, Bamidele O Tayo, Li Li, Thomas LaFramboise, Zhenghe Wang, Xiaofeng Zhu and Mark R Chance
    Citation: BMC Genomics 2014 15:685
    Content type: Research article Published on:

  16. Prokaryotes have relatively small genomes, densely-packed with protein-encoding sequences. RNA sequencing has, however, revealed surprisingly complex transcriptomes and here we report the transcripts present i...

    Authors: Dominik Jäger, Konrad U Förstner, Cynthia M Sharma, Thomas J Santangelo and John N Reeve
    Citation: BMC Genomics 2014 15:684
    Content type: Research article Published on:

  17. Milk production is an economically important sector of global agriculture. Much attention has been paid to the identification of quantitative trait loci (QTL) associated with milk, fat, and protein yield and t...

    Authors: Lingyang Xu, John B Cole, Derek M Bickhart, Yali Hou, Jiuzhou Song, Paul M VanRaden, Tad S Sonstegard, Curtis P Van Tassell and George E Liu
    Citation: BMC Genomics 2014 15:683
    Content type: Research article Published on:

  18. Bats are a major source of new and emerging viral diseases. Despite the fact that bats carry and shed highly pathogenic viruses including Ebola, Nipah and SARS, they rarely display clinical symptoms of infecti...

    Authors: Christopher Cowled, Cameron R Stewart, Vladimir A Likic, Marc R Friedländer, Mary Tachedjian, Kristie A Jenkins, Mark L Tizard, Pauline Cottee, Glenn A Marsh, Peng Zhou, Michelle L Baker, Andrew G Bean and Lin-fa Wang
    Citation: BMC Genomics 2014 15:682
    Content type: Research article Published on:

  19. High density stress, also known as intraspecies competition, causes significant yield losses in a wide variety of crop plants. At the same time, increases in density tolerance through selective breeding and th...

    Authors: Maksym Misyura, David Guevara, Sanjeena Subedi, Darryl Hudson, Paul D McNicholas, Joseph Colasanti and Steven J Rothstein
    Citation: BMC Genomics 2014 15:681
    Content type: Research article Published on:

  20. Mapping expression quantitative trait loci (eQTL) of targeted genes represents a powerful and widely adopted approach to identify putative regulatory variants. Linking regulation differences to specific genes ...

    Authors: Yan Wang, Yingpeng Han, Weili Teng, Xue Zhao, Yongguang Li, Lin Wu, Dongmei Li and Wenbin Li
    Citation: BMC Genomics 2014 15:680
    Content type: Research article Published on:

  21. A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including the gastrointestinal tracts (GIT) of humans and other animals and may contribute sig...

    Authors: Guillaume Borrel, Nicolas Parisot, Hugh MB Harris, Eric Peyretaillade, Nadia Gaci, William Tottey, Olivier Bardot, Kasie Raymann, Simonetta Gribaldo, Pierre Peyret, Paul W O’Toole and Jean-François Brugère
    Citation: BMC Genomics 2014 15:679
    Content type: Research article Published on:

  22. Babesia bovis is an apicomplexan parasite that causes babesiosis in infected cattle. Genomes of pathogens contain promising information that can facilitate the development of methods for controlling infections. A...

    Authors: Junya Yamagishi, Hiroyuki Wakaguri, Naoaki Yokoyama, Riu Yamashita, Yutaka Suzuki, Xuenan Xuan and Ikuo Igarashi
    Citation: BMC Genomics 2014 15:678
    Content type: Research article Published on:

  23. Mitochondrial DNA (mtDNA) deletions cause disease and accumulate during aging, yet our understanding of the molecular mechanisms underlying their formation remains rudimentary. Guanine-quadruplex (GQ) DNA stru...

    Authors: Dawei W Dong, Filipe Pereira, Steven P Barrett, Jill E Kolesar, Kajia Cao, Joana Damas, Liliya A Yatsunyk, F Brad Johnson and Brett A Kaufman
    Citation: BMC Genomics 2014 15:677
    Content type: Research article Published on:

  24. The major medicinal alkaloids isolated from Uncaria rhynchophylla (gouteng in chinese) capsules are rhynchophylline (RIN) and isorhynchophylline (IRN). Extracts containing these terpene indole alkaloids (TIAs) ca...

    Authors: Qianqian Guo, Xiaojun Ma, Shugen Wei, Deyou Qiu, Iain W Wilson, Peng Wu, Qi Tang, Lijun Liu, Shoukun Dong and Wei Zu
    Citation: BMC Genomics 2014 15:676
    Content type: Research article Published on:

  25. Gene expression analysis by RNA sequencing is now widely used in a number of applications surveying the whole transcriptomes of cells and tissues. The recent introduction of ribosomal RNA depletion protocols, ...

    Authors: Marc Sultan, Vyacheslav Amstislavskiy, Thomas Risch, Moritz Schuette, Simon Dökel, Meryem Ralser, Daniela Balzereit, Hans Lehrach and Marie-Laure Yaspo
    Citation: BMC Genomics 2014 15:675
    Content type: Research article Published on:

  26. Brown planthopper (BPH, Nilaparvata lugens Stål), is the most destructive phloem-feeding insect pest of rice (Oryza sativa). The BPH-resistance gene BPH15 has been proved to be effective in controlling the pest a...

    Authors: Wentang Lv, Ba Du, Xinxin Shangguan, Yan Zhao, Yufang Pan, Lili Zhu, Yuqing He and Guangcun He
    Citation: BMC Genomics 2014 15:674
    Content type: Research article Published on:

  27. Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers fo...

    Authors: Ikuko N Motoike, Mitsuyo Matsumoto, Inaho Danjoh, Fumiki Katsuoka, Kaname Kojima, Naoki Nariai, Yukuto Sato, Yumi Yamaguchi-Kabata, Shin Ito, Hisaaki Kudo, Ichiko Nishijima, Satoshi Nishikawa, Xiaoqing Pan, Rumiko Saito, Sakae Saito, Tomo Saito…
    Citation: BMC Genomics 2014 15:673
    Content type: Research article Published on:

  28. We have previously proposed transcriptome instability as a genome-wide, pre-mRNA splicing-related characteristic of colorectal cancer. Here, we explore the hypothesis of transcriptome instability being a gener...

    Authors: Anita Sveen, Bjarne Johannessen, Manuel R Teixeira, Ragnhild A Lothe and Rolf I Skotheim
    Citation: BMC Genomics 2014 15:672
    Content type: Research article Published on:

  29. The molecular mechanisms involved in plant tolerance to either drought or cold have been extensively studied in many plant species. However, few studies have focused on their comparisons especially using non-m...

    Authors: Yaqi Wu, Wei Wei, Xinyue Pang, Xuefeng Wang, Huiling Zhang, Bo Dong, Yanping Xing, Xinguo Li and Maoyan Wang
    Citation: BMC Genomics 2014 15:671
    Content type: Research article Published on:

  30. Recent mapping of 5-hydroxymethylcytosine (5hmC) provides a genome-wide view of the distribution of this important chromatin mark. However, the role of 5hmC in specific regulatory regions is not clear, especia...

    Authors: Inchan Choi, Rinho Kim, Hee-Woong Lim, Klaus H Kaestner and Kyoung-Jae Won
    Citation: BMC Genomics 2014 15:670
    Content type: Research article Published on:

  31. Emerging studies demonstrate that single nucleotide polymorphisms (SNPs) resided in the microRNA recognition element seed sites (MRESSs) in 3′UTR of mRNAs are putative biomarkers for human diseases and cancers...

    Authors: Di Wu, Gang Yang, Lifang Zhang, Jiwei Xue, Zhining Wen and Menglong Li
    Citation: BMC Genomics 2014 15:669
    Content type: Research article Published on:

  32. Kaposi’s sarcoma associated herpes virus (KSHV) is associated with tumors of endothelial and lymphoid origin. During latent infection, KSHV expresses miR-K12-11, an ortholog of the human tumor gene hsa-miR-155...

    Authors: Yajie Yang, Isaac W Boss, Lauren M McIntyre and Rolf Renne
    Citation: BMC Genomics 2014 15:668
    Content type: Research article Published on:

  33. Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of thre...

    Authors: Nathan L Bachmann, Tamieka A Fraser, Claire Bertelli, Martina Jelocnik, Amber Gillett, Oliver Funnell, Cheyne Flanagan, Garry S A Myers, Peter Timms and Adam Polkinghorne
    Citation: BMC Genomics 2014 15:667
    Content type: Research article Published on:

  34. Despite numerous studies suggesting that amphibians are highly sensitive to cumulative anthropogenic stresses, the role pollutants play in the decline of amphibian populations remains unclear. Amongst the most...

    Authors: Christophe Regnault, Isabelle AM Worms, Christine Oger-Desfeux, Christelle MelodeLima, Sylvie Veyrenc, Marie-Laure Bayle, Bruno Combourieu, Aurélie Bonin, Julien Renaud, Muriel Raveton and Stéphane Reynaud
    Citation: BMC Genomics 2014 15:666
    Content type: Research article Published on:

  35. Most of the proteins contained in royal jelly (RJ) are secreted from the hypopharyngeal glands (HG) of young bees. Although generic protein composition of RJ has been investigated, little is known about how ag...

    Authors: Ting Ji, Zhenguo Liu, Jie Shen, Fang Shen, Qin Liang, Liming Wu, Guohong Chen and Miguel Corona
    Citation: BMC Genomics 2014 15:665
    Content type: Research article Published on:

  36. Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by tec...

    Authors: Yukuto Sato, Kaname Kojima, Naoki Nariai, Yumi Yamaguchi-Kabata, Yosuke Kawai, Mamoru Takahashi, Takahiro Mimori and Masao Nagasaki
    Citation: BMC Genomics 2014 15:664
    Content type: Software Published on:

  38. Glucocorticoids (GCs) cause apoptosis in malignant cells of lymphoid lineage by transcriptionally regulating a plethora of genes. As a result, GCs are included in almost all treatment protocols for lymphoid ma...

    Authors: Daniel Bindreither, Simone Ecker, Barbara Gschirr, Anita Kofler, Reinhard Kofler and Johannes Rainer
    Citation: BMC Genomics 2014 15:662
    Content type: Research article Published on:

  39. With advances in next generation sequencing technologies and genomic capture techniques, exome sequencing has become a cost-effective approach for mutation detection in genetic diseases. However, computational...

    Authors: Pubudu Saneth Samarakoon, Hanne Sørmo Sorte, Bjørn Evert Kristiansen, Tove Skodje, Ying Sheng, Geir E Tjønnfjord, Barbro Stadheim, Asbjørg Stray-Pedersen, Olaug Kristin Rødningen and Robert Lyle
    Citation: BMC Genomics 2014 15:661
    Content type: Research article Published on:

  40. Metarhizium anisopliae is an important fungal biocontrol agent of insect pests of agricultural crops. Genomics can aid the successful commercialization of biopesticides by identification of key genes differentiat...

    Authors: Julie A Pattemore, James K Hane, Angela H Williams, Bree AL Wilson, Ben J Stodart and Gavin J Ash
    Citation: BMC Genomics 2014 15:660
    Content type: Research article Published on:

  41. Microgravity facilitates the opportunistic infections by augmenting the pathogenic virulence and suppressing the host resistance. Hence the extraterrestrial infections may activate potentially novel bionetwork...

    Authors: Nabarun Chakraborty, Aarti Gautam, Seid Muhie, Stacy-Ann Miller, Marti Jett and Rasha Hammamieh
    Citation: BMC Genomics 2014 15:659
    Content type: Research article Published on:

  42. Cilia are microtubule-based organelles protruding from almost all mammalian cells which, when dysfunctional, result in genetic disorders called “ciliopathies”. High-throughput studies have revealed that cilia ...

    Authors: Roberto Amato, Manuela Morleo, Laura Giaquinto, Diego di Bernardo and Brunella Franco
    Citation: BMC Genomics 2014 15:658
    Content type: Research article Published on:

  43. Autogenous cis-regulators of ribosomal protein synthesis play a critical role in maintaining the stoichiometry of ribosome components. Structured portions within an mRNA transcript typically interact with specifi...

    Authors: Betty L Slinger, Kaila Deiorio-Haggar, Jon S Anthony, Molly M Gilligan and Michelle M Meyer
    Citation: BMC Genomics 2014 15:657
    Content type: Research article Published on:

  44. Inflammation triggered by infection or injury is tightly controlled by glucocorticoid hormones which signal via a dedicated transcription factor, the Glucocorticoid Receptor (GR), to regulate hundreds of genes...

    Authors: Yurii Chinenov, Maddalena Coppo, Rebecca Gupte, Maria A Sacta and Inez Rogatsky
    Citation: BMC Genomics 2014 15:656
    Content type: Research article Published on:

  45. Teleosts are characterized by a remarkable breadth of sexual mechanisms including various forms of hermaphroditism. Sparidae is a fish family exhibiting gonochorism or hermaphroditism even in closely related s...

    Authors: Tereza Manousaki, Alexandros Tsakogiannis, Jacques Lagnel, Elena Sarropoulou, Jenny Z Xiang, Nikos Papandroulakis, Constantinos C Mylonas and Costas S Tsigenopoulos
    Citation: BMC Genomics 2014 15:655
    Content type: Research article Published on:

  46. Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remar...

    Authors: Bas E Dutilh, Cristiane C Thompson, Ana CP Vicente, Michel A Marin, Clarence Lee, Genivaldo GZ Silva, Robert Schmieder, Bruno GN Andrade, Luciane Chimetto, Daniel Cuevas, Daniel R Garza, Iruka N Okeke, Aaron Oladipo Aboderin, Jessica Spangler, Tristen Ross, Elizabeth A Dinsdale…
    Citation: BMC Genomics 2014 15:654
    Content type: Research article Published on:

  47. Age-related physiological, biochemical and functional changes in mammalian skeletal muscle have been shown to begin at the mid-point of the lifespan. However, the underlying changes in DNA methylation that occ...

    Authors: Long Jin, Zhi Jiang, Yudong Xia, Ping’er Lou, Lei Chen, Hongmei Wang, Lu Bai, Yanmei Xie, Yihui Liu, Wei Li, Bangsheng Zhong, Junfang Shen, An’an Jiang, Li Zhu, Jinyong Wang, Xuewei Li…
    Citation: BMC Genomics 2014 15:653
    Content type: Research article Published on:

  48. The major Gram-positive coccoid pathogens cause similar invasive diseases and show high rates of antimicrobial resistance. Uncharacterised proteins shared by these organisms may be involved in virulence or be ...

    Authors: Antonio J Martín-Galiano, José Yuste, María I Cercenado and Adela G de la Campa
    Citation: BMC Genomics 2014 15:652
    Content type: Research article Published on:

  49. The ATP-binding cassette (ABC) transporter superfamily is one of the largest transporter gene families and is observed in all animal taxa. Although a large set of transcriptomic data was recently assembled for...

    Authors: Chang-Bum Jeong, Bo-Mi Kim, Jae-Seong Lee and Jae-Sung Rhee
    Citation: BMC Genomics 2014 15:651
    Content type: Research article Published on:

  50. Chemical senses are one of the foremost means by which organisms make sense of their environment, among them the olfactory and gustatory sense of vertebrates and arthropods. Both senses use large repertoires o...

    Authors: Adnan S Syed and Sigrun I Korsching
    Citation: BMC Genomics 2014 15:650
    Content type: Research article Published on:

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BMC Genomics

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