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  1. In the past few decades, non-coding RNAs (ncRNAs) have emerged as important regulators of gene expression in eukaryotes. Most studies of ncRNAs in plants have focused on the identification of silencing microRN...

    Authors: Ge Qu, Katarzyna Kruszka, Patrycja Plewka, Shu-Yi Yang, Tzyy-Jen Chiou, Artur Jarmolowski, Zofia Szweykowska-Kulinska, Manuel Echeverria and Wojciech M. Karlowski
    Citation: BMC Genomics 2015 16:1009
    Content type: Research article Published on:

  2. Baculoviruses are insect-associated viruses carrying large, circular double-stranded-DNA genomes with significant biotechnological applications such as biological pest control, recombinant protein production, ...

    Authors: Gloria Patricia Barrera, Mariano Nicolás Belaich, Manuel Alfonso Patarroyo, Laura Fernanda Villamizar and Pablo Daniel Ghiringhelli
    Citation: BMC Genomics 2015 16:1008
    Content type: Research article Published on:

  3. Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation...

    Authors: Juan C. Castro, J. Dylan Maddox, Marianela Cobos, David Requena, Mirko Zimic, Aureliano Bombarely, Sixto A. Imán, Luis A. Cerdeira and Andersson E. Medina
    Citation: BMC Genomics 2015 16:997
    Content type: Research article Published on:

  5. With the availability of rapidly increasing number of genome and transcriptome sequences, lineage-specific genes (LSGs) can be identified and characterized. Like other conserved functional genes, LSGs play imp...

    Authors: Yuantao Xu, Guizhi Wu, Baohai Hao, Lingling Chen, Xiuxin Deng and Qiang Xu
    Citation: BMC Genomics 2015 16:995
    Content type: Research article Published on:

  6. More than 80 % of all terrestrial plant species establish an arbuscular mycorrhiza (AM) symbiosis with Glomeromycota fungi. This plant-microbe interaction primarily improves phosphate uptake, but also supports ni...

    Authors: Natalija Hohnjec, Lisa F. Czaja-Hasse, Claudia Hogekamp and Helge Küster
    Citation: BMC Genomics 2015 16:994
    Content type: Research article Published on:

  7. Allele specific gene expression (ASE), with the paternal allele more expressed than the maternal allele or vice versa, appears to be a common phenomenon in humans and mice. In other species the extent of ASE i...

    Authors: Amanda J. Chamberlain, Christy J. Vander Jagt, Benjamin J. Hayes, Majid Khansefid, Leah C. Marett, Catriona A. Millen, Thuy T. T. Nguyen and Michael E. Goddard
    Citation: BMC Genomics 2015 16:993
    Content type: Research article Published on:

  8. The skin is the outermost layer of the human body and one of the key sites for host-microbe interactions. Both environmental and host genetic factors influence microbial communities in distinct anatomical nich...

    Authors: Jiyeon Si, Sunghee Lee, Jin Mo Park, Joohon Sung and GwangPyo Ko
    Citation: BMC Genomics 2015 16:992
    Content type: Research article Published on:

  9. Lysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To bette...

    Authors: Irene de Bruijn, Xu Cheng, Victor de Jager, Ruth Gómez Expósito, Jeramie Watrous, Nrupali Patel, Joeke Postma, Pieter C. Dorrestein, Donald Kobayashi and Jos M. Raaijmakers
    Citation: BMC Genomics 2015 16:991
    Content type: Research article Published on:

  10. We used RNA sequencing to analyze transcript profiles of ten autopsy brain regions from ten subjects. RNA sequencing techniques were designed to detect both coding and non-coding RNA, splice isoform compositio...

    Authors: Amy Webb, Audrey C. Papp, Amanda Curtis, Leslie C. Newman, Maciej Pietrzak, Michal Seweryn, Samuel K. Handelman, Grzegorz A. Rempala, Daqing Wang, Erica Graziosa, Rachel F. Tyndale, Caryn Lerman, John R. Kelsoe, Deborah C. Mash and Wolfgang Sadee
    Citation: BMC Genomics 2015 16:990
    Content type: Research article Published on:

  12. The capacity of marine species to survive chronic heat stress underpins their ability to survive warming oceans as a result of climate change. In this study RNA-Seq and 2-DE proteomics were employed to deciphe...

    Authors: Sébastien Artigaud, Joëlle Richard, Michael AS Thorne, Romain Lavaud, Jonathan Flye-Sainte-Marie, Fred Jean, Lloyd S. Peck, Melody S. Clark and Vianney Pichereau
    Citation: BMC Genomics 2015 16:988
    Content type: Research article Published on:

  13. Understanding the phylogenetic relationships among major lineages of multicellular animals (the Metazoa) is a prerequisite for studying the evolution of complex traits such as nervous systems, muscle tissue, o...

    Authors: Marek L. Borowiec, Ernest K. Lee, Joanna C. Chiu and David C. Plachetzki
    Citation: BMC Genomics 2015 16:987
    Content type: Research article Published on:

  14. The genetic program, as manifested as the cellular phenotype, is in large part dictated by the cell’s protein composition. Since characterisation of the proteome remains technically laborious it is attractive ...

    Authors: Francois-Xavier Dieudonné, Patrick B. F. O’Connor, Pascale Gubler-Jaquier, Haleh Yasrebi, Beatrice Conne, Sergey Nikolaev, Stylianos Antonarakis, Pavel V. Baranov and Joseph Curran
    Citation: BMC Genomics 2015 16:986
    Content type: Research article Published on:

  15. The evolution of insecticide resistance in Spodoptera frugiperda (Lepidoptera: Noctuidae) has resulted in large economic losses and disturbances to the environment and agroecosystems. Resistance to lufenuron, a c...

    Authors: Antonio Rogério Bezerra do Nascimento, Pablo Fresia, Fernando Luis Cônsoli and Celso Omoto
    Citation: BMC Genomics 2015 16:985
    Content type: Research article Published on:

  16. Although extensive studies have investigated radiation-induced injuries in particular gastrointestinal (GI) segments, a systematic comparison among the different segments on the basis of mode, magnitude and me...

    Authors: Junying Zheng, Junru Wang, Mylene Pouliot, Simon Authier, Daohong Zhou, David S. Loose and Martin Hauer-Jensen
    Citation: BMC Genomics 2015 16:984
    Content type: Research article Published on:

  18. Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new qu...

    Authors: Cinthya J. Zepeda-Mendoza, Swagatam Mukhopadhyay, Emily S. Wong, Nathalie Harder, Erik Splinter, Elzo de Wit, Melanie A. Eckersley-Maslin, Thomas Ried, Roland Eils, Karl Rohr, Alea Mills, Wouter de Laat, Paul Flicek, Anirvan M. Sengupta and David L. Spector
    Citation: BMC Genomics 2015 16:982
    Content type: Research article Published on:

  20. The trematode parasite, Schistosoma mansoni, has evolved to switch from oxidative phosphorylation to glycolysis in the presence of glucose immediately after invading the human host. This metabolic switch is depen...

    Authors: Alejandro Cabezas-Cruz, James J. Valdés, Julien Lancelot and Raymond J. Pierce
    Citation: BMC Genomics 2015 16:980
    Content type: Research article Published on:

  21. The liver possesses an ability of compensatory growth after removing three of five lobes in mammals or one of three lobes in zebrafish. The reenter of hepatocytes into the cell cycle is one of the hallmarks fo...

    Authors: Guohui Feng, Yong Long, Jinrong Peng, Qing Li and Zongbin Cui
    Citation: BMC Genomics 2015 16:979
    Content type: Research article Published on:

  22. Transcription start sites (TSSs) with pronounced and phased nucleosome arrays downstream and nucleosome-depleted regions upstream of TSSs are observed in various species.

    Authors: Yoichiro Nakatani, Cecilia C. Mello, Shin-ichi Hashimoto, Atsuko Shimada, Ryohei Nakamura, Tatsuya Tsukahara, Wei Qu, Jun Yoshimura, Yutaka Suzuki, Sumio Sugano, Hiroyuki Takeda, Andrew Fire and Shinichi Morishita
    Citation: BMC Genomics 2015 16:978
    Content type: Research article Published on:

  23. RNA-seq enables gene expression profiling in selected spatiotemporal windows and yields massive sequence information with relatively low cost and time investment, even for non-model species. However, there rem...

    Authors: Yuichiro Hara, Kaori Tatsumi, Michio Yoshida, Eriko Kajikawa, Hiroshi Kiyonari and Shigehiro Kuraku
    Citation: BMC Genomics 2015 16:977
    Content type: Research article Published on:

  24. Among the largest and most diverse transcription factor families in plants, basic leucine zipper (bZIP) family participate in regulating various processes, including floral induction and development, stress an...

    Authors: Xueyin Li, Shiqing Gao, Yimiao Tang, Lei Li, Fengjie Zhang, Biane Feng, Zhaofeng Fang, Lingjian Ma and Changping Zhao
    Citation: BMC Genomics 2015 16:976
    Content type: Research article Published on:

  25. The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf sp...

    Authors: Brice Roux, Stéphanie Bolot, Endrick Guy, Nicolas Denancé, Martine Lautier, Marie-Françoise Jardinaud, Marion Fischer-Le Saux, Perrine Portier, Marie-Agnès Jacques, Lionel Gagnevin, Olivier Pruvost, Emmanuelle Lauber, Matthieu Arlat, Sébastien Carrère, Ralf Koebnik and Laurent D. Noël
    Citation: BMC Genomics 2015 16:975
    Content type: Research article Published on:

  26. The European red mite, Panonychus ulmi, is among the most important mite pests in fruit orchards, where it is controlled primarily by acaricide application. However, the species rapidly develops pesticide resista...

    Authors: Sabina Bajda, Wannes Dermauw, Robert Greenhalgh, Ralf Nauen, Luc Tirry, Richard M. Clark and Thomas Van Leeuwen
    Citation: BMC Genomics 2015 16:974
    Content type: Research article Published on:

  27. Controlling sex ratios is essential for the aquaculture industry, especially in those species with sex dimorphism for relevant productive traits, hence the importance of knowing how the sexual phenotype is est...

    Authors: Diego Robledo, Laia Ribas, Rosa Cal, Laura Sánchez, Francesc Piferrer, Paulino Martínez and Ana Viñas
    Citation: BMC Genomics 2015 16:973
    Content type: Research article Published on:

  28. Bacteriophage replication depends on bacterial proteins and inactivation of genes coding for such host factors should interfere with phage infection. To gain further insights into the interactions between S. pneu...

    Authors: Philippe Leprohon, Hélène Gingras, Siham Ouennane, Sylvain Moineau and Marc Ouellette
    Citation: BMC Genomics 2015 16:972
    Content type: Research article Published on:

  29. Gynogenesis is one of unisexual reproduction modes in vertebrates, and produces all-female individuals with identical genetic background. In sexual reproduction vertebrates, the roles of primordial germ cells ...

    Authors: Wei Liu, Shi-Zhu Li, Zhi Li, Yang Wang, Xi-Yin Li, Jian-Xiang Zhong, Xiao-Juan Zhang, Jun Zhang, Li Zhou and Jian-Fang Gui
    Citation: BMC Genomics 2015 16:971
    Content type: Research article Published on:

  30. The FANTOM5 consortium used Cap Analysis of Gene Expression (CAGE) tag sequencing to produce a comprehensive atlas of promoters and enhancers within the human and mouse genomes. We reasoned that the mapping of...

    Authors: Christelle Robert, Ronan Kapetanovic, Dario Beraldi, Mick Watson, Alan L. Archibald and David A. Hume
    Citation: BMC Genomics 2015 16:970
    Content type: Research article Published on:

  31. The genetic architecture of complex traits in farmed animal populations is of interest from a scientific and practical perspective. The use of genetic markers to predict the genetic merit (breeding values) of ...

    Authors: Hsin-Yuan Tsai, Alastair Hamilton, Alan E. Tinch, Derrick R. Guy, Karim Gharbi, Michael J. Stear, Oswald Matika, Steve C. Bishop and Ross D. Houston
    Citation: BMC Genomics 2015 16:969
    Content type: Research article Published on:

  32. Phosphine is a valuable fumigant to control pest populations in stored grains and grain products. However, recent studies indicate a substantial increase in phosphine resistance in stored product pests worldwide.

    Authors: Brenda Oppert, Raul N. C. Guedes, Michael J. Aikins, Lindsey Perkin, Zhaorigetu Chen, Thomas W. Phillips, Kun Yan Zhu, George P. Opit, Kelly Hoon, Yongming Sun, Gavin Meredith, Kelli Bramlett, Natalie Supunpong Hernandez, Brian Sanderson, Madison W. Taylor, Dalia Dhingra…
    Citation: BMC Genomics 2015 16:968
    Content type: Research article Published on:

  33. Gene regulatory relationships can be inferred using matched array comparative genomics and transcriptomics data sets from cancer samples. The way in which copy numbers of genes in cancer samples are often grea...

    Authors: Richard Newton and Lorenz Wernisch
    Citation: BMC Genomics 2015 16:967
    Content type: Research Article Published on:

  34. Daldinia eschscholtzii is a wood-inhabiting fungus that causes wood decay under certain conditions. It has a broad host range and produces a large repertoire of potentially bioactive c...

    Authors: Chai Ling Chan, Su Mei Yew, Yun Fong Ngeow, Shiang Ling Na, Kok Wei Lee, Chee-Choong Hoh, Wai-Yan Yee and Kee Peng Ng
    Citation: BMC Genomics 2015 16:966
    Content type: Research article Published on:

  35. To date, telomere research in fungi has mainly focused on Saccharomyces cerevisiae and Schizosaccharomyces pombe, despite the fact that both yeasts have degenerated telomeric repeats in contrast to the canonical ...

    Authors: Núria Casas-Vila, Marion Scheibe, Anja Freiwald, Dennis Kappei and Falk Butter
    Citation: BMC Genomics 2015 16:965
    Content type: Research article Published on:

  36. Antibacterial biocides and metals can co-select for antibiotic resistance when bacteria harbour resistance or tolerance genes towards both types of compounds. Despite numerous case studies, systematic and quan...

    Authors: Chandan Pal, Johan Bengtsson-Palme, Erik Kristiansson and D. G. Joakim Larsson
    Citation: BMC Genomics 2015 16:964
    Content type: Research article Published on:

  37. Precise quantitative and spatiotemporal control of gene expression is necessary to ensure proper cellular differentiation and the maintenance of homeostasis. The relationship between gene expression and the sp...

    Authors: Nathan Harmston, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić and Boris Lenhard
    Citation: BMC Genomics 2015 16:963
    Content type: Software Published on:

  38. Forward genetic approaches have limited use for agronomic traits that can’t be reliably scored on a single plant basis. Thus, mutants in wheat and other crops are more useful for gene function studies by rever...

    Authors: Gaganjot Sidhu, Amita Mohan, Ping Zheng, Amandeep Kaur Dhaliwal, Dorrie Main and Kulvinder S Gill
    Citation: BMC Genomics 2015 16:962
    Content type: Research article Published on:

  39. HPA axis plays a major role in physiological homeostasis. It is also involved in stress and adaptive response to the environment. In farm animals in general and specifically in pigs, breeding strategies have h...

    Authors: Valérie Sautron, Elena Terenina, Laure Gress, Yannick Lippi, Yvon Billon, Catherine Larzul, Laurence Liaubet, Nathalie Villa-Vialaneix and Pierre Mormède
    Citation: BMC Genomics 2015 16:961
    Content type: Research Article Published on:

  40. Considerable advances have been made in our understanding of the molecular genetics of secondary metabolite biosynthesis. Coupled with increased access to genome sequence data, new insight can be gained into t...

    Authors: Kelley A. Gallagher and Paul R. Jensen
    Citation: BMC Genomics 2015 16:960
    Content type: Research article Published on:

  41. Rice (Oryza sativa) is one of the most important cereal crops, providing food for more than half of the world’s population. However, grain yields are challenged by various abiotic stresses such as drought, fertil...

    Authors: Jun Yang, Xiaorong Chen, Changlan Zhu, Xiaosong Peng, Xiaopeng He, Junru Fu, Linjuan Ouyang, Jianmin Bian, Lifang Hu, Xiaotang Sun, Jie Xu and Haohua He
    Citation: BMC Genomics 2015 16:959
    Content type: Research article Published on:

  42. Dagginess (faecal soiling of the perineum region) and host nematode parasite resistance are important animal welfare traits in New Zealand sheep. Genomic prediction (GP) estimates the genetic merit, as a molec...

    Authors: Natalie K. Pickering, Benoit Auvray, Ken G. Dodds and John C. McEwan
    Citation: BMC Genomics 2015 16:958
    Content type: Research article Published on:

  43. It is generally accepted that gene duplication followed by functional divergence is one of the main sources of metabolic diversity. In this regard, there is an increasing interest in the development of methods...

    Authors: Augusto Cesar Poot-Hernandez, Katya Rodriguez-Vazquez and Ernesto Perez-Rueda
    Citation: BMC Genomics 2015 16:957
    Content type: Research article Published on:

  44. Rice false smut caused by Ustilaginoidea virens has recently become one of the most devastating rice diseases worldwide. Breeding and deployment of resistant varieties is considered as the most effective strategy...

    Authors: Yanqing Han, Kang Zhang, Jun Yang, Nan Zhang, Anfei Fang, Yong Zhang, Yongfeng Liu, Zhiyi Chen, Tom Hsiang and Wenxian Sun
    Citation: BMC Genomics 2015 16:955
    Content type: Research article Published on:

  45. Dormant Mycobacterium tuberculosis bacilli are believed to play an important role in latent tuberculosis infection. Previously, we have demonstrated that cultivation of M. tuberculosis in K+-deficient medium resu...

    Authors: Dmitriy V. Ignatov, Elena G. Salina, Mikhail V. Fursov, Timofey A. Skvortsov, Tatyana L. Azhikina and Arseny S. Kaprelyants
    Citation: BMC Genomics 2015 16:954
    Content type: Research article Published on:

  46. Coxiella burnetii is the causative agent of the zoonotic disease Q fever. As it is an intracellular pathogen, infection by C. burnetii requires adaptation to its eukaryotic host and in...

    Authors: Runa Kuley, Ruth Bossers-deVries, Hilde E. Smith, Mari A. Smits, Hendrik I. J. Roest and Alex Bossers
    Citation: BMC Genomics 2015 16:953
    Content type: Research article Published on:

  47. The plant phytohormone auxin controls many aspects of plant growth and development, which largely depends on its uneven distribution in plant tissues. Transmembrane proteins of the PIN family are auxin efflux ...

    Authors: Yongqin Wang, Chenglin Chai, Babu Valliyodan, Christine Maupin, Brad Annen and Henry T. Nguyen
    Citation: BMC Genomics 2015 16:951
    Content type: Research article Published on:

  48. Limited information is available on aluminum (Al)-toxicity-responsive proteins in woody plant roots. Seedlings of ‘Xuegan’ (Citrus sinensis) and ‘Sour pummelo’ (Citrus grandis) were treated for 18 weeks with nutr...

    Authors: Huan-Xin Jiang, Lin-Tong Yang, Yi-Ping Qi, Yi-Bin Lu, Zeng-Rong Huang and Li-Song Chen
    Citation: BMC Genomics 2015 16:949
    Content type: Research article Published on:

  49. Shiga toxin (Stx)-producing E. coli (STEC) are responsible for foodborne outbreaks that can result in severe human disease. During an outbreak, differential disease outcomes are observed after infection with the ...

    Authors: Lisa M. Russo, Nourtan F. Abdeltawab, Alison D. O’Brien, Malak Kotb and Angela R. Melton-Celsa
    Citation: BMC Genomics 2015 16:947
    Content type: Research article Published on:

  50. MicroRNAs (miRNAs) have functions in diverse biological processes such as growth, signal transduction, disease resistance, and stress responses in plants. Thermotherapy is an effective approach for elimination...

    Authors: Juan Liu, XueJiao Zhang, FangPeng Zhang, Ni Hong, GuoPing Wang, Aiming Wang and LiPing Wang
    Citation: BMC Genomics 2015 16:945
    Content type: Research article Published on:

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BMC Genomics

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