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  1. Mycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis live in swine respiratory tracts. M. flocculare, a commensal bacterium, is genetically closely related to M. hyopneumoniae, the causative a...

    Authors: Franciele Maboni Siqueira, Claudia Elizabeth Thompson, Veridiana Gomes Virginio, Taylor Gonchoroski, Luciano Reolon, Luiz Gonzaga Almeida, Marbella Maria da Fonsêca, Rangel de Souza, Francisco Prosdocimi, Irene Silveira Schrank, Henrique Bunselmeyer Ferreira, Ana Tereza Ribeiro de Vasconcelos and Arnaldo Zaha
    Citation: BMC Genomics 2013 14:175
    Content type: Research article Published on:

  2. Known protein interaction networks have very particular properties. Old proteins tend to have more interactions than new ones. One of the best statistical representatives of this property is the node degree di...

    Authors: Piotr H Pawlowski, Szymon Kaczanowski and Piotr Zielenkiewicz
    Citation: BMC Genomics 2013 14:172
    Content type: Research article Published on:

  4. Cotton is the leading fiber crop worldwide. Gossypium barbadense is an important species of cotton because of its extra-long staple fibers with superior luster and silkiness. However, a systematic analysis and ut...

    Authors: Yuanda Lv, Liang Zhao, Xiaoyang Xu, Lei Wang, Cheng Wang, Tianzhen Zhang and Wangzhen Guo
    Citation: BMC Genomics 2013 14:170
    Content type: Research article Published on:

  5. The pigeon crop is specially adapted to produce milk that is fed to newly hatched young. The process of pigeon milk production begins when the germinal cell layer of the crop rapidly proliferates in response t...

    Authors: Meagan J Gillespie, Tamsyn M Crowley, Volker R Haring, Susanne L Wilson, Jennifer A Harper, Jean S Payne, Diane Green, Paul Monaghan, John A Donald, Kevin R Nicholas and Robert J Moore
    Citation: BMC Genomics 2013 14:169
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2014 15:185

  6. The yeast Metschnikowia fructicola is an antagonist with biological control activity against postharvest diseases of several fruits. We performed a transcriptome analysis, using RNA-Seq technology, to examine the...

    Authors: Vera Hershkovitz, Noa Sela, Leena Taha-Salaime, Jia Liu, Ginat Rafael, Clarita Kessler, Radi Aly, Maggie Levy, Michael Wisniewski and Samir Droby
    Citation: BMC Genomics 2013 14:168
    Content type: Research article Published on:

  7. The lack of genomic resources can present challenges for studies of non-model organisms. Transcriptome sequencing offers an attractive method to gather information about genes and gene expression without the n...

    Authors: Warren R Francis, Lynne M Christianson, Rainer Kiko, Meghan L Powers, Nathan C Shaner and Steven H D Haddock
    Citation: BMC Genomics 2013 14:167
    Content type: Research article Published on:

  8. Despite the importance of wheat as a major staple crop and the negative impact of diseases on its production worldwide, the genetic mechanisms and gene interactions involved in the resistance response in wheat...

    Authors: Dario Cantu, Baoju Yang, Randy Ruan, Kun Li, Virginia Menzo, Daolin Fu, Mawsheng Chern, Pamela C Ronald and Jorge Dubcovsky
    Citation: BMC Genomics 2013 14:166
    Content type: Research article Published on:

  9. Chromosomal rearrangements in the form of deletions, insertions, inversions and translocations are frequently observed in breast cancer genomes, and a subset of these rearrangements may play a crucial role in ...

    Authors: Xiang Jiao, Sean D Hooper, Tatjana Djureinovic, Chatarina Larsson, Fredrik Wärnberg, Christian Tellgren-Roth, Johan Botling and Tobias Sjöblom
    Citation: BMC Genomics 2013 14:165
    Content type: Research article Published on:

  10. Animal models are indispensable to understand the lipid metabolism and lipid metabolic diseases. Over the last decade, the nematode Caenorhabditis elegans has become a popular animal model for exploring the regul...

    Authors: Yuru Zhang, Xiaoju Zou, Yihong Ding, Haizhen Wang, Xiaoyun Wu and Bin Liang
    Citation: BMC Genomics 2013 14:164
    Content type: Research article Published on:

  11. Double strand (ds) DNA breaks are a form of DNA damage that can be generated from both genotoxic exposures and physiologic processes, can disrupt cellular functions and can be lethal if not repaired properly. ...

    Authors: Cynthia L Innes, Jill E Hesse, Stela S Palii, Beth A Helmink, Abigail J Holub, Barry P Sleckman and Richard S Paules
    Citation: BMC Genomics 2013 14:163
    Content type: Research article Published on:

  12. The ascomycete fungus Ophiostoma ulmi was responsible for the initial pandemic of the massively destructive Dutch elm disease in Europe and North America in early 1910. Dutch elm disease has ravaged the elm tree ...

    Authors: Shima Khoshraftar, Stacy Hung, Sadia Khan, Yunchen Gong, Vibha Tyagi, John Parkinson, Mohini Sain, Alan M Moses and Dinesh Christendat
    Citation: BMC Genomics 2013 14:162
    Content type: Research article Published on:

  13. Statistical analysis of genome-wide microarrays can result in many thousands of identical statistical tests being performed as each probe is tested for an association with a phenotype of interest. If there wer...

    Authors: Sheila J Barton, Sarah R Crozier, Karen A Lillycrop, Keith M Godfrey and Hazel M Inskip
    Citation: BMC Genomics 2013 14:161
    Content type: Methodology article Published on:

  14. The brown planthopper (Nilaparvata lugens) is one of the most serious rice plant pests in Asia. N. lugens causes extensive rice damage by sucking rice phloem sap, which results in stunted plant growth and the tra...

    Authors: Yan-Yuan Bao, Lv-Yu Qu, Dong Zhao, Li-Bo Chen, Hong-Yuan Jin, Liang-Min Xu, Jia-An Cheng and Chuan-Xi Zhang
    Citation: BMC Genomics 2013 14:160
    Content type: Research article Published on:

  15. Pearl millet [Pennisetum glaucum (L.) R. Br.] is a widely cultivated drought- and high-temperature tolerant C4 cereal grown under dryland, rainfed and irrigated conditions in drought-prone regions of the tropics ...

    Authors: Vengaldas Rajaram, Thirunavukkarasu Nepolean, Senapathy Senthilvel, Rajeev K Varshney, Vincent Vadez, Rakesh K Srivastava, Trushar M Shah, Ambawat Supriya, Sushil Kumar, Basava Ramana Kumari, Amindala Bhanuprakash, Mangamoori Lakshmi Narasu, Oscar Riera-Lizarazu and Charles Thomas Hash
    Citation: BMC Genomics 2013 14:159
    Content type: Research article Published on:

  16. Giant viruses in the genus Chlorovirus (family Phycodnaviridae) infect eukaryotic green microalgae. The prototype member of the genus, Paramecium bursaria chlorella virus 1, was sequenced more than 15 years ago, ...

    Authors: Adrien Jeanniard, David D Dunigan, James R Gurnon, Irina V Agarkova, Ming Kang, Jason Vitek, Garry Duncan, O William McClung, Megan Larsen, Jean-Michel Claverie, James L Van Etten and Guillaume Blanc
    Citation: BMC Genomics 2013 14:158
    Content type: Research article Published on:

  17. Ovarian follicular development and hormone secretion are complex and coordinated biological processes which will usually be altered during pregnancy. Ovarian function is tightly regulated by a multitude of gen...

    Authors: Xiao-Dong Zhang, Yun-Hai Zhang, Ying-Hui Ling, Ya Liu, Hong-Guo Cao, Zong-Jun Yin, Jian-Ping Ding and Xiao-Rong Zhang
    Citation: BMC Genomics 2013 14:157
    Content type: Research article Published on:

  18. Sinorhizobium meliloti is a soil-dwelling α-proteobacterium that possesses a large, tripartite genome and engages in a nitrogen fixing symbiosis with its plant hosts. Although much is known about this important m...

    Authors: Jan-Philip Schlüter, Jan Reinkensmeier, Melanie J Barnett, Claus Lang, Elizaveta Krol, Robert Giegerich, Sharon R Long and Anke Becker
    Citation: BMC Genomics 2013 14:156
    Content type: Research article Published on:

  19. The length of cotton fiber is an important agronomic trait characteristic that directly affects the quality of yarn and fabric. The cotton (Gossypium hirsutum L.) fiber mutation, Ligon lintless-2, is controlled b...

    Authors: Marina Naoumkina, Doug J Hinchliffe, Rickie B Turley, John M Bland and David D Fang
    Citation: BMC Genomics 2013 14:155
    Content type: Research article Published on:

  20. Deep sequencing of viruses isolated from infected hosts is an efficient way to measure population-genetic variation and can reveal patterns of dispersal and natural selection. In this study, we mined existing ...

    Authors: Robert Scott Cornman, Humberto Boncristiani, Benjamin Dainat, Yanping Chen, Dennis vanEngelsdorp, Daniel Weaver and Jay D Evans
    Citation: BMC Genomics 2013 14:154
    Content type: Research article Published on:

  21. Biological nitrogen fixation in root nodules is a process of great importance to crops of soybean [Glycine max (L.) Merr.], as it may provide the bulk of the plant’s needs for nitrogen. Legume nodulation involves...

    Authors: Gesiele Almeida Barros de Carvalho, Jesiane Stefânia Silva Batista, Francismar Corrêa Marcelino-Guimarães, Leandro Costa do Nascimento and Mariangela Hungria
    Citation: BMC Genomics 2013 14:153
    Content type: Research article Published on:

  22. In an intercross between the SWR/J and BALB/c mouse strains, the pulmonary adenoma progression 1 (Papg1) locus on chromosome 4 modulates lung tumor size, one of several measures of lung tumor progression. This lo...

    Authors: Alice Dassano, Sara Noci, Federica Galbiati, Francesca Colombo, Gaia Trincucci, Angela Pettinicchio, Tommaso A Dragani and Giacomo Manenti
    Citation: BMC Genomics 2013 14:152
    Content type: Research article Published on:

  23. In China, consumers often prefer indigenous broiler chickens over commercial breeds, as they have characteristic meat qualities requested within traditional culinary customs. However, the growth-rate of these ...

    Authors: Zheya Sheng, Mats E Pettersson, Xiaoxiang Hu, Chenglong Luo, Hao Qu, Dingming Shu, Xia Shen, Örjan Carlborg and Ning Li
    Citation: BMC Genomics 2013 14:151
    Content type: Research article Published on:

  24. An enduring question surrounding sex chromosome evolution is whether effective hemizygosity in the heterogametic sex leads inevitably to dosage compensation of sex-linked genes, and whether this compensation h...

    Authors: Nathaniel K Jue, Michael B Murphy, Seth D Kasowitz, Sohaib M Qureshi, Craig J Obergfell, Sahar Elsisi, Robert J Foley, Rachel J O’Neill and Michael J O’Neill
    Citation: BMC Genomics 2013 14:150
    Content type: Research article Published on:

  25. Trypanosoma vivax is the earliest branching African trypanosome. This crucial phylogenetic position makes T. vivax a fascinating model to tackle fundamental questions concerning the origin and evolution of severa...

    Authors: Gonzalo Greif, Miguel Ponce de Leon, Guillermo Lamolle, Matías Rodriguez, Dolores Piñeyro, Lucinda M Tavares-Marques, Armando Reyna-Bello, Carlos Robello and Fernando Alvarez-Valin
    Citation: BMC Genomics 2013 14:149
    Content type: Research article Published on:

  26. In contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model to study both domestication and relevance of Asian genes in the pig. Besid...

    Authors: Anna Esteve-Codina, Yogesh Paudel, Luca Ferretti, Emanuele Raineri, Hendrik-Jan Megens, Luis Silió, María C Rodríguez, Martein AM Groenen, Sebastian E Ramos-Onsins and Miguel Pérez-Enciso
    Citation: BMC Genomics 2013 14:148
    Content type: Research article Published on:

  27. The meninges (arachnoid and pial membranes) and associated vasculature (MAV) and choroid plexus are important in maintaining cerebrospinal fluid (CSF) generation and flow. MAV vasculature was previously observ...

    Authors: John F Bowyer, Tucker A Patterson, Upasana T Saini, Joseph P Hanig, Monzy Thomas, Luísa Camacho, Nysia I George and James J Chen
    Citation: BMC Genomics 2013 14:147
    Content type: Research article Published on:

  29. Mycobacterial interspersed repetitive units (MIRUs) are minisatellites within the Mycobacterium tuberculosis (Mtb) genome. Copy number variation (CNV) in MIRU loci is used for epidemiological typing, making the r...

    Authors: Mark N Ragheb, Christopher B Ford, Michael R Chase, Philana Ling Lin, JoAnne L Flynn and Sarah M Fortune
    Citation: BMC Genomics 2013 14:145
    Content type: Research article Published on:

  31. Macrosatellite repeats (MSRs), usually spanning hundreds of kilobases of genomic DNA, comprise a significant proportion of the human genome. Because of their highly polymorphic nature, MSRs represent an extrem...

    Authors: Mireille Schaap, Richard JLF Lemmers, Roel Maassen, Patrick J van der Vliet, Lennart F Hoogerheide, Herman K van Dijk, Nalan Baştürk, Peter de Knijff and Silvère M van der Maarel
    Citation: BMC Genomics 2013 14:143
    Content type: Research article Published on:

  32. Tandem repeats are ubiquitous and abundant in higher eukaryotic genomes and constitute, along with transposable elements, much of DNA underlying centromeres and other heterochromatic domains. In maize, centrom...

    Authors: Anupma Sharma, Thomas K Wolfgruber and Gernot G Presting
    Citation: BMC Genomics 2013 14:142
    Content type: Research article Published on:

  33. Proteogenomic mapping is an approach that uses mass spectrometry data from proteins to directly map protein-coding genes and could aid in locating translational regions in the human genome. In concert with the...

    Authors: Jainab Khatun, Yanbao Yu, John A Wrobel, Brian A Risk, Harsha P Gunawardena, Ashley Secrest, Wendy J Spitzer, Ling Xie, Li Wang, Xian Chen and Morgan C Giddings
    Citation: BMC Genomics 2013 14:141
    Content type: Research article Published on:

  34. MicroRNAs (miRNAs) are 20–21 nucleotide RNA molecules that suppress the transcription of target genes and may also inhibit translation. Despite the thousands of miRNAs identified and validated in numerous plan...

    Authors: Daiqing Huang, Chushin Koh, J Allan Feurtado, Edward WT Tsang and Adrian J Cutler
    Citation: BMC Genomics 2013 14:140
    Content type: Research article Published on:

  35. A subset of breast cancer cells displays increased ability to self-renew and reproduce breast cancer heterogeneity. The characterization of these so-called putative breast tumor-initiating cells (BT-ICs) may o...

    Authors: Maria Ouzounova, Tri Vuong, Pierre-Benoit Ancey, Mylène Ferrand, Geoffroy Durand, Florence Le-Calvez Kelm, Carlo Croce, Chantal Matar, Zdenko Herceg and Hector Hernandez-Vargas
    Citation: BMC Genomics 2013 14:139
    Content type: Research article Published on:

  36. In fungi, environmental pH is an important signal for development, and successful host colonization depends on homeostasis. Surprisingly, little is known regarding the role of pH in fungal-fungal interactions....

    Authors: Naomi Trushina, Michal Levin, Prasun K Mukherjee and Benjamin A Horwitz
    Citation: BMC Genomics 2013 14:138
    Content type: Research article Published on:

  37. Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior variet...

    Authors: Glenn T Howe, Jianbin Yu, Brian Knaus, Richard Cronn, Scott Kolpak, Peter Dolan, W Walter Lorenz and Jeffrey FD Dean
    Citation: BMC Genomics 2013 14:137
    Content type: Research article Published on:

  38. Genome-wide association studies (GWAS) identify regions of the genome that are associated with particular traits, but do not typically identify specific causative genetic elements. For example, while a large n...

    Authors: Jay Pendse, Prasanna V Ramachandran, Jianbo Na, Narisu Narisu, Jill L Fink, Ross L Cagan, Francis S Collins and Thomas J Baranski
    Citation: BMC Genomics 2013 14:136
    Content type: Research article Published on:

  39. Genomic resources within the phylum Arthropoda are largely limited to the true insects but are beginning to include unexplored subphyla, such as the Crustacea and Chelicerata. Investigations of these understud...

    Authors: Amanda K Gibson, Zach Smith, Clay Fuqua, Keith Clay and John K Colbourne
    Citation: BMC Genomics 2013 14:135
    Content type: Research article Published on:

  40. There is growing recognition that horizontal DNA transfer, a process known to be common in prokaryotes, is also a significant source of genomic variation in eukaryotes. Horizontal transfer of transposable elem...

    Authors: Clement Gilbert, Paul Waters, Cedric Feschotte and Sarah Schaack
    Citation: BMC Genomics 2013 14:134
    Content type: Research article Published on:

  41. Transcriptome analysis in combination with pathway-focused bioassays is suggested to be a helpful approach for gaining deeper insights into the complex mechanisms of action of herbal multicomponent preparation...

    Authors: Angela Klein, Oliver A Wrulich, Marcel Jenny, Peter Gruber, Kathrin Becker, Dietmar Fuchs, Johanna M Gostner and Florian Ãœberall
    Citation: BMC Genomics 2013 14:133
    Content type: Research article Published on:

  42. One of the major open challenges in next generation sequencing (NGS) is the accurate identification of structural variants such as insertions and deletions (indels). Current methods for indel calling assign sc...

    Authors: Dominik Grimm, Jörg Hagmann, Daniel Koenig, Detlef Weigel and Karsten Borgwardt
    Citation: BMC Genomics 2013 14:132
    Content type: Methodology article Published on:

  43. Copy number variations (CNVs) are widespread in the human or animal genome and are a significant source of genetic variation, which has been demonstrated to play an important role in phenotypic diversity. Adva...

    Authors: Li Jiang, Jicai Jiang, Jie Yang, Xuan Liu, Jiying Wang, Haifei Wang, Xiangdong Ding, Jianfeng Liu and Qin Zhang
    Citation: BMC Genomics 2013 14:131
    Content type: Research article Published on:

  44. As well known, both natural and synthetic steroidal compounds are powerful endocrine disrupting compounds (EDCs) which can cause reproductive toxicity and affect cellular development in mammals and thus are ge...

    Authors: Zhi-Zhen Li, Xiao-Fei Li, Wei Yang, Xiang Dong, Jie Yu, Shu-Liang Zhu, Man Li, Li Xie and Wang-Yu Tong
    Citation: BMC Genomics 2013 14:130
    Content type: Research article Published on:

  45. Understanding the genetic basis of diseases is key to the development of better diagnoses and treatments. Unfortunately, only a small fraction of the existing data linking genes to phenotypes is available thro...

    Authors: Elodie Portales-Casamar, Carolyn Ch’ng, Frances Lui, Nicolas St-Georges, Anton Zoubarev, Artemis Y Lai, Mark Lee, Cathy Kwok, Willie Kwok, Luchia Tseng and Paul Pavlidis
    Citation: BMC Genomics 2013 14:129
    Content type: Database Published on:

  46. The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the...

    Authors: Nuno Sepúlveda, Susana G Campino, Samuel A Assefa, Colin J Sutherland, Arnab Pain and Taane G Clark
    Citation: BMC Genomics 2013 14:128
    Content type: Methodology article Published on:

  47. Genetic susceptibility to colonic inflammation is poorly defined at the gene level. Although Genome Wide Association studies (GWAS) have identified loci in the human genome which confer susceptibility to Infla...

    Authors: Scott E Levison, Paul Fisher, Jenny Hankinson, Leo Zeef, Steve Eyre, William E Ollier, John T McLaughlin, Andy Brass, Richard K Grencis and Joanne L Pennock
    Citation: BMC Genomics 2013 14:127
    Content type: Research article Published on:

  48. Staphylococcus aureus is a widely distributed human pathogen capable of infecting almost every ecological niche of the host. As a result, it is responsible for causing many different diseases. S. aureus has a vas...

    Authors: Jose Antonio Ibarra, Ernesto Pérez-Rueda, Ronan K Carroll and Lindsey N Shaw
    Citation: BMC Genomics 2013 14:126
    Content type: Research article Published on:

  49. Ramie fiber, extracted from vegetative organ stem bast, is one of the most important natural fibers. Understanding the molecular mechanisms of the vegetative growth of the ramie and the formation and developme...

    Authors: Touming Liu, Siyuan Zhu, Qingming Tang, Ping Chen, Yongting Yu and Shouwei Tang
    Citation: BMC Genomics 2013 14:125
    Content type: Research article Published on:

  50. Copy number variations (CNVs) represent a significant source of genomic structural variation. Their length ranges from approximately one hundred to millions of base pair. Genome-wide screenings have clarified ...

    Authors: Francesco Cicconardi, Giovanni Chillemi, Anna Tramontano, Cinzia Marchitelli, Alessio Valentini, Paolo Ajmone-Marsan and Alessandro Nardone
    Citation: BMC Genomics 2013 14:124
    Content type: Research article Published on:

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BMC Genomics

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