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  1. Innate immunity is essential in defending against invading pathogens in invertebrates. The cotton bollworm, Helicoverpa armigera (Hübner) is one of the most destructive lepidopteran pests, which causes enormous e...

    Authors: Guang-Hua Xiong, Long-Sheng Xing, Zhe Lin, Tusar T Saha, Chengshu Wang, Haobo Jiang and Zhen Zou
    Citation: BMC Genomics 2015 16:321
    Content type: Research article Published on:

  2. Cryptosporidium hominis is a dominant species for human cryptosporidiosis. Within the species, IbA10G2 is the most virulent subtype responsible for all C. hominis–associated outbreaks in Europe...

    Authors: Yaqiong Guo, Kevin Tang, Lori A Rowe, Na Li, Dawn M Roellig, Kristine Knipe, Michael Frace, Chunfu Yang, Yaoyu Feng and Lihua Xiao
    Citation: BMC Genomics 2015 16:320
    Content type: Research article Published on:

  3. Eucalyptus species and interspecific hybrids exhibit valuable growth and wood properties that make them a highly desirable commodity. However, these trees are challenged by a wide array of biot...

    Authors: Ronishree Mangwanda, Alexander A Myburg and Sanushka Naidoo
    Citation: BMC Genomics 2015 16:319
    Content type: Research article Published on:

  4. HLA genotyping by next generation sequencing (NGS) requires three basic steps, PCR, NGS, and allele assignment. Compared to the conventional methods, such as PCR-sequence specific oligonucleotide primers (SSOP...

    Authors: Yuki Ozaki, Shingo Suzuki, Koichi Kashiwase, Atsuko Shigenari, Yuko Okudaira, Sayaka Ito, Anri Masuya, Fumihiro Azuma, Toshio Yabe, Satoko Morishima, Shigeki Mitsunaga, Masahiro Satake, Masao Ota, Yasuo Morishima, Jerzy K Kulski, Katsuyuki Saito…
    Citation: BMC Genomics 2015 16:318
    Content type: Methodology article Published on:

  5. In low-copy-number plasmids, the partitioning loci (par) act to ensure proper plasmid segregation and copy number maintenance in the daughter cells. In many bacterial species, par gene homologues are encoded on t...

    Authors: Haijuan Li, Angel Angelov, Vu Thuy Trang Pham, Benedikt Leis and Wolfgang Liebl
    Citation: BMC Genomics 2015 16:317
    Content type: Research article Published on:

  6. Cattle populations are characterized by regular outburst of genetic defects as a result of the extensive use of elite sires. The causative genes and mutations can nowadays be rapidly identified by means of gen...

    Authors: Arnaud Sartelet, Wanbo Li, Eric Pailhoux, Christophe Richard, Nico Tamma, Latifa Karim, Corinne Fasquelle, Tom Druet, Wouter Coppieters, Michel Georges and Carole Charlier
    Citation: BMC Genomics 2015 16:316
    Content type: Research article Published on:

  7. The toxicity of manufactured fumed silica nanoparticles (NPs) remains poorly investigated compared to that of crystalline silica NPs, which have been associated with lung diseases after inhalation. Amorphous s...

    Authors: Cédric Pisani, Jean-Charles Gaillard, Virginie Nouvel, Michaël Odorico, Jean Armengaud and Odette Prat
    Citation: BMC Genomics 2015 16:315
    Content type: Research article Published on:

  8. Soybean cyst nematode (SCN) is the most economically devastating pathogen of soybean. Two resistance loci, Rhg1 and Rhg4 primarily contribute resistance to SCN race 3 in soybean. Peking and PI 88788 are the two m...

    Authors: Zi Shi, Shiming Liu, James Noe, Prakash Arelli, Khalid Meksem and Zenglu Li
    Citation: BMC Genomics 2015 16:314
    Content type: Research article Published on:

  9. Phylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across th...

    Authors: Anukriti Sharma, Naseer Sangwan, Vivek Negi, Puneet Kohli, Jitendra Paul Khurana, Desiraju Lakshmi Narsimha Rao and Rup Lal
    Citation: BMC Genomics 2015 16:313
    Content type: Research article Published on:

  10. Cattle breeding populations are susceptible to the propagation of recessive diseases. Individual sires generate tens of thousands of progeny via artificial insemination. The frequency of deleterious alleles carri...

    Authors: Hubert Pausch, Hermann Schwarzenbacher, Johann Burgstaller, Krzysztof Flisikowski, Christine Wurmser, Sandra Jansen, Simone Jung, Angelika Schnieke, Thomas Wittek and Ruedi Fries
    Citation: BMC Genomics 2015 16:312
    Content type: Research article Published on:

  11. Marek’s disease (MD) is a highly contagious, lymphomatous disease of chickens induced by a herpesvirus, Marek’s disease virus (MDV) that is the cause of major annual losses to the poultry industry. MD pathogen...

    Authors: Apratim Mitra, Juan Luo, Yanghua He, Yulan Gu, Huanmin Zhang, Keji Zhao, Kairong Cui and Jiuzhou Song
    Citation: BMC Genomics 2015 16:311
    Content type: Research article Published on:

  12. Little is known about invertebrate responses to DNA viruses. Here, we infect a commercially important pest moth species Plodia interpunctella with its naturally infecting DNA virus. We sequenced, assembled and an...

    Authors: Seanna J McTaggart, Tidbury Hannah, Stephen Bridgett, Jennie S Garbutt, Gaganjot Kaur and Mike Boots
    Citation: BMC Genomics 2015 16:310
    Content type: Research article Published on:

  13. Many leukemias result from chromosomal rearrangements. The t(8;21) chromosomal translocation produces AML1-ETO, an oncogenic fusion protein that compromises the function of AML1, a transcription factor critica...

    Authors: Daniel J Trombly, Troy W Whitfield, Srivatsan Padmanabhan, Jonathan AR Gordon, Jane B Lian, Andre J van Wijnen, Sayyed K Zaidi, Janet L Stein and Gary S Stein
    Citation: BMC Genomics 2015 16:309
    Content type: Research article Published on:

  14. Snails belong to the molluscan class Gastropoda, which inhabit land, freshwater and marine environments. Several land snail species, including Theba pisana, are crop pests of major concern, causing extensive dama...

    Authors: Kevin J Adamson, Tianfang Wang, Min Zhao, Francesca Bell, Anna V Kuballa, Kenneth B Storey and Scott F Cummins
    Citation: BMC Genomics 2015 16:308
    Content type: Research article Published on:

  16. Plastid genomes, also known as plastomes, are shaped by the selective forces acting on the fundamental cellular functions they code for and thus they are expected to preserve signatures of the adaptive path un...

    Authors: Shiliang Hu, Gaurav Sablok, Bo Wang, Dong Qu, Enrico Barbaro, Roberto Viola, Mingai Li and Claudio Varotto
    Citation: BMC Genomics 2015 16:306
    Content type: Research article Published on:

  17. Environmental temperature has serious implications in life cycle of aquatic ectotherms. Understanding the molecular mechanisms of temperature acclimation and adaptation of marine organisms is of the uttermost ...

    Authors: Teshome Tilahun Bizuayehu, Steinar D Johansen, Velmurugu Puvanendran, Hilde Toften and Igor Babiak
    Citation: BMC Genomics 2015 16:305
    Content type: Research article Published on:

  18. The genotype information carried by Genome-wide association studies (GWAS) seems to have the potential to explain more of the ‘missing heritability’ of complex human phenotypes, given improved statistical appr...

    Authors: Luiz F Goulart, Francesco Bettella, Ida E Sønderby, Andrew J Schork, Wesley K Thompson, Morten Mattingsdal, Vidar M Steen, Verena Zuber, Yunpeng Wang, Anders M Dale, Ole A Andreassen and Srdjan Djurovic
    Citation: BMC Genomics 2015 16:304
    Content type: Research article Published on:

  19. Citrus represents a crop of global importance both in economic impact and significance to nutrition. Citrus production worldwide is threatened by the disease Huanglongbing (HLB), caused by the phloem-limited p...

    Authors: William R Belknap, Kent F McCue, Leslie A Harden, William H Vensel, Michael G Bausher and Ed Stover
    Citation: BMC Genomics 2015 16:303
    Content type: Research article Published on:

  22. Several post-translational histone modifications are mainly found in gene promoters and are associated with the promoter activity. It has been hypothesized that histone modifications regulate the transcription...

    Authors: Susanne Bornelöv, Jan Komorowski and Claes Wadelius
    Citation: BMC Genomics 2015 16:300
    Content type: Research article Published on:

  23. While the gargantuan multi-nation effort of sequencing T. aestivum gets close to completion, the annotation process for the vast number of wheat genes and proteins is in its infancy. Previous experimental studies...

    Authors: Dan Tulpan, Serge Leger, Alain Tchagang and Youlian Pan
    Citation: BMC Genomics 2015 16:299
    Content type: Research article Published on:

  24. Camellia taliensis is one of the most important wild relatives of cultivated tea tree, C. sinensis. The species extensively occupies mountainous habitats representing a wide-range abiotic toler...

    Authors: Hai-Bin Zhang, En-Hua Xia, Hui Huang, Jian-Jun Jiang, Ben-Ying Liu and Li-Zhi Gao
    Citation: BMC Genomics 2015 16:298
    Content type: Research article Published on:

  25. Trypanosomatid parasites possess a single mitochondrion which is classically involved in the energetic metabolism of the cell, but also, in a much more original way, through its single and complex DNA (termed ...

    Authors: Diane-Ethna Mbang-Benet, Yvon Sterkers, Lucien Crobu, Amélie Sarrazin, Patrick Bastien and Michel Pagès
    Citation: BMC Genomics 2015 16:297
    Content type: Research article Published on:

  26. Propionibacterium freudenreichii (PF) is an actinobacterium used in cheese technology and for its probiotic properties. PF is also extremely adaptable to several ecological niches and can grow ...

    Authors: Valentin Loux, Mahendra Mariadassou, Sintia Almeida, Hélène Chiapello, Amal Hammani, Julien Buratti, Annie Gendrault, Valérie Barbe, Jean-Marc Aury, Stéphanie-Marie Deutsch, Sandrine Parayre, Marie-Noëlle Madec, Victoria Chuat, Gwenaël Jan, Pierre Peterlongo, Vasco Azevedo…
    Citation: BMC Genomics 2015 16:296
    Content type: Research article Published on:

  27. As sex determines mammalian development, understanding the nature and developmental dynamics of the sexually dimorphic transcriptome is important. To explore this, we generated 76 genome-wide RNA-seq profiles ...

    Authors: Robert Lowe, Carolina Gemma, Vardhman K Rakyan and Michelle L Holland
    Citation: BMC Genomics 2015 16:295
    Content type: Research article Published on:

  28. Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by t...

    Authors: Rafael David Rosengarten, Balaji Santhanam, Danny Fuller, Mariko Katoh-Kurasawa, William F Loomis, Blaz Zupan and Gad Shaulsky
    Citation: BMC Genomics 2015 16:294
    Content type: Research article Published on:

  29. Synonymous codons are used differentially in organisms from the three domains of life, a phenomenon referred to as codon usage bias. In addition, codon pair bias, particularly in the 3’ codon context, has also...

    Authors: Marcelo Baeza, Jennifer Alcaíno, Salvador Barahona, Dionisia Sepúlveda and Víctor Cifuentes
    Citation: BMC Genomics 2015 16:293
    Content type: Research article Published on:

  31. In mammalian meiotic prophase, homologous chromosome recognition is aided by formation and repair of programmed DNA double-strand breaks (DSBs). Subsequently, stable associations form through homologous chromo...

    Authors: Federica Federici, Eskeatnaf Mulugeta, Sam Schoenmakers, Evelyne Wassenaar, Jos W Hoogerbrugge, Godfried W van der Heijden, Wiggert A van Cappellen, Johan A Slotman, Wilfred FJ van IJcken, Joop SE Laven, J Anton Grootegoed and Willy M Baarends
    Citation: BMC Genomics 2015 16:291
    Content type: Research article Published on:

  32. Barley, globally the fourth most important cereal, provides food and beverages for humans and feed for animal husbandry. Maximizing grain yield under varying climate conditions largely depends on the optimal t...

    Authors: Andreas Maurer, Vera Draba, Yong Jiang, Florian Schnaithmann, Rajiv Sharma, Erika Schumann, Benjamin Kilian, Jochen Christoph Reif and Klaus Pillen
    Citation: BMC Genomics 2015 16:290
    Content type: Research article Published on:

  33. Astaxanthin is a potent antioxidant with increasing biotechnological interest. In Xanthophyllomyces dendrorhous, a natural source of this pigment, carotenogenesis is a complex process regulated through several me...

    Authors: Pilar Martinez-Moya, Karsten Niehaus, Jennifer Alcaíno, Marcelo Baeza and Víctor Cifuentes
    Citation: BMC Genomics 2015 16:289
    Content type: Research article Published on:

  34. Resistance inducers have been used in annual crops as an alternative for disease control. Wood perennial fruit trees, such as those of the citrus species, are candidates for treatment with resistance inducers,...

    Authors: Danila Souza Oliveira Coqueiro, Alessandra Alves de Souza, Marco Aurélio Takita, Carolina Munari Rodrigues, Luciano Takeshi Kishi and Marcos Antonio Machado
    Citation: BMC Genomics 2015 16:288
    Content type: Research article Published on:

  35. DNA methylation directs the epigenetic silencing of selected regions of DNA, including the regulation of pseudogenes, and is widespread throughout the genome. Pseudogenes are decayed copies of duplicated genes...

    Authors: Aaron P Davis, Abby D Benninghoff, Aaron J Thomas, Benjamin R Sessions and Kenneth L White
    Citation: BMC Genomics 2015 16:287
    Content type: Research article Published on:

  36. Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural varia...

    Authors: Adam C English, William J Salerno, Oliver A Hampton, Claudia Gonzaga-Jauregui, Shruthi Ambreth, Deborah I Ritter, Christine R Beck, Caleb F Davis, Mahmoud Dahdouli, Singer Ma, Andrew Carroll, Narayanan Veeraraghavan, Jeremy Bruestle, Becky Drees, Alex Hastie, Ernest T Lam…
    Citation: BMC Genomics 2015 16:286
    Content type: Research article Published on:

  37. MicroRNAs (miRNA) are small endogenous non-coding RNA involved in the post-transcriptional regulation of specific mRNA targets. The first whole goat genome sequence became available in 2013, with few annotatio...

    Authors: Lenha Mobuchon, Sylvain Marthey, Mekki Boussaha, Sandrine Le Guillou, Christine Leroux and Fabienne Le Provost
    Citation: BMC Genomics 2015 16:285
    Content type: Research article Published on:

  38. In the honeybee Apis mellifera, the bacterial gut community is consistently colonized by eight distinct phylotypes of bacteria. Managed bee colonies are of considerable economic interest and it is therefore impor...

    Authors: Kirsten M Ellegaard, Daniel Tamarit, Emelie Javelind, Tobias C Olofsson, Siv GE Andersson and Alejandra Vásquez
    Citation: BMC Genomics 2015 16:284
    Content type: Research article Published on:

  39. In recent years, the use of genomic information in livestock species for genetic improvement, association studies and many other fields has become routine. In order to accommodate different market requirements...

    Authors: Ezequiel L Nicolazzi, Andrea Caprera, Nelson Nazzicari, Paolo Cozzi, Francesco Strozzi, Cindy Lawley, Ali Pirani, Chandrasen Soans, Fiona Brew, Hossein Jorjani, Gary Evans, Barry Simpson, Gwenola Tosser-Klopp, Rudiger Brauning, John L Williams and Alessandra Stella
    Citation: BMC Genomics 2015 16:283
    Content type: Software Published on:

  40. The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including antimicrobial resistance genes...

    Authors: Theresa Mikalsen, Torunn Pedersen, Rob Willems, Teresa M Coque, Guido Werner, Ewa Sadowy, Willem van Schaik, Lars Bogø Jensen, Arnfinn Sundsfjord and Kristin Hegstad
    Citation: BMC Genomics 2015 16:282
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2015 16:689

  41. One of the most important evolutionary processes in plants is polyploidization. The combination of two or more genomes in one organism often initially leads to changes in gene expression and extensive genomic ...

    Authors: Hala Badr Khalil, Mohammad-Reza Ehdaeivand, Yong Xu, André Laroche and Patrick J Gulick
    Citation: BMC Genomics 2015 16:281
    Content type: Research article Published on:

  42. In this study we applied the extreme groups/selective genotyping approach for identifying copy number variations in high and low fertility breeding boars. The fertility indicator was the calculated Direct Boar...

    Authors: Tamas Revay, Anh T Quach, Laurence Maignel, Brian Sullivan and W Allan King
    Citation: BMC Genomics 2015 16:280
    Content type: Research article Published on:

  43. Despite the recent identification of several prognostic gene signatures, the lack of common genes among experimental cohorts has posed a considerable challenge in uncovering the molecular basis underlying hepa...

    Authors: Bu-Yeo Kim, Dong Wook Choi, Seon Rang Woo, Eun-Ran Park, Je-Geun Lee, Su-Hyeon Kim, Imhoi Koo, Sun-Hoo Park, Chul Ju Han, Sang Bum Kim, Young Il Yeom, Suk-Jin Yang, Ami Yu, Jae Won Lee, Ja June Jang, Myung-Haing Cho…
    Citation: BMC Genomics 2015 16:279
    Content type: Research article Published on:

  45. Genes and signalling pathways involved in pluripotency have been studied extensively in mouse and human pre-implantation embryos and embryonic stem (ES) cells. The unsuccessful attempts to generate ES cell lin...

    Authors: Bas Brinkhof, Helena TA van Tol, Marian JA Groot Koerkamp, Frank M Riemers, Sascha G IJzer, Kaveh Mashayekhi, Henk P Haagsman and Bernard AJ Roelen
    Citation: BMC Genomics 2015 16:277
    Content type: Research article Published on:

  47. Changes to mRNA lifetime adjust mRNA concentration, facilitating the adaptation of growth rate to changes in growth conditions. However, the mechanisms regulating mRNA lifetime are poorly understood at the gen...

    Authors: Thomas Esquerré, Annick Moisan, Hélène Chiapello, Liisa Arike, Raivo Vilu, Christine Gaspin, Muriel Cocaign-Bousquet and Laurence Girbal
    Citation: BMC Genomics 2015 16:275
    Content type: Research article Published on:

  48. The pronuclear injection (PI) is the simplest and widely used method to generate transgenic (Tg) mice. Unfortunately, PI-based Tg mice show uncertain transgene expression due to random transgene insertion in t...

    Authors: Masato Ohtsuka, Hiromi Miura, Keiji Mochida, Michiko Hirose, Ayumi Hasegawa, Atsuo Ogura, Ryuta Mizutani, Minoru Kimura, Ayako Isotani, Masahito Ikawa, Masahiro Sato and Channabasavaiah B Gurumurthy
    Citation: BMC Genomics 2015 16:274
    Content type: Methodology article Published on:

  49. The secreted Meloidogyne javanica fatty acid- and retinol-binding (FAR) protein Mj-FAR-1 is involved in nematode development and reproduction in host tomato roots. To gain further insight into the role of Mj-FAR-...

    Authors: Ionit Iberkleid, Noa Sela and Sigal Brown Miyara
    Citation: BMC Genomics 2015 16:272
    Content type: Research article Published on:

  50. Ralstonia solanacearum is a vascular soil-borne plant pathogen with an unusually broad host range. This economically destructive and globally distributed bacterium has thousands of distinct lin...

    Authors: Florent Ailloud, Tiffany Lowe, Gilles Cellier, David Roche, Caitilyn Allen and Philippe Prior
    Citation: BMC Genomics 2015 16:270
    Content type: Research article Published on:

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BMC Genomics

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