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  1. Broad-spectrum fluoroquinolone antibiotics are central in modern health care and are used to treat and prevent a wide range of bacterial infections. The recently discovered qnr genes provide a mechanism of resist...

    Authors: Fredrik Boulund, Anna Johnning, Mariana Buongermino Pereira, DG Joakim Larsson and Erik Kristiansson
    Citation: BMC Genomics 2012 13:695
    Content type: Methodology article Published on:

  2. Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen of grasses Blumeria graminis causes one of the most important diseases of cereal...

    Authors: Carsten Pedersen, Emiel Ver Loren van Themaat, Liam J McGuffin, James C Abbott, Timothy A Burgis, Geraint Barton, Laurence V Bindschedler, Xunli Lu, Takaki Maekawa, Ralf Weßling, Rainer Cramer, Hans Thordal-Christensen, Ralph Panstruga and Pietro D Spanu
    Citation: BMC Genomics 2012 13:694
    Content type: Research article Published on:

  4. The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acet...

    Authors: Muktak Aklujkar, Shelley A Haveman, Raymond DiDonato Jr, Olga Chertkov, Cliff S Han, Miriam L Land, Peter Brown and Derek R Lovley
    Citation: BMC Genomics 2012 13:690
    Content type: Research article Published on:

  5. Batch effect is one type of variability that is not of primary interest but ubiquitous in sizable genomic experiments. To minimize the impact of batch effects, an ideal experiment design should ensure the even...

    Authors: Li Yan, Changxing Ma, Dan Wang, Qiang Hu, Maochun Qin, Jeffrey M Conroy, Lara E Sucheston, Christine B Ambrosone, Candace S Johnson, Jianmin Wang and Song Liu
    Citation: BMC Genomics 2012 13:689
    Content type: Software Published on:

  6. Information about the composition of regulatory regions is of great value for designing experiments to functionally characterize gene expression. The multiplicity of available applications to predict transcrip...

    Authors: Enrique Blanco and Montserrat Corominas
    Citation: BMC Genomics 2012 13:688
    Content type: Software Published on:

  7. Brown planthopper (BPH), Nilaparvata lugens Stål, is one of the most destructive insect pests of rice. The molecular responses of plants to sucking insects resemble responses to pathogen infection. However, the m...

    Authors: Yubing Wang, Huimin Guo, Haichao Li, Hao Zhang and Xuexia Miao
    Citation: BMC Genomics 2012 13:687
    Content type: Research article Published on:

  9. Proteases regulate pathogenesis in apicomplexan parasites but investigations of proteases have been largely confined to the asexual stages of Plasmodium falciparum and Toxoplasma gondii. Thus, little is known abo...

    Authors: Marilyn Katrib, Rowan J Ikin, Fabien Brossier, Michelle Robinson, Iveta Slapetova, Philippa A Sharman, Robert A Walker, Sabina I Belli, Fiona M Tomley and Nicholas C Smith
    Citation: BMC Genomics 2012 13:685
    Content type: Research article Published on:

  11. Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring ...

    Authors: Enrique Ramos, Benjamin T Levinson, Sara Chasnoff, Andrew Hughes, Andrew L Young, Katherine Thornton, Allie Li, Francesco LM Vallania, Michael Province and Todd E Druley
    Citation: BMC Genomics 2012 13:683
    Content type: Methodology article Published on:

  12. The small RNAs (sRNA) are a regulatory class of RNA mainly represented by the 21 and 24-nucleotide size classes. The cellular sRNAs are processed by RNase III family enzyme dicer (Dicer like in plant) from a s...

    Authors: Rishi Aryal, Xiaozeng Yang, Qingyi Yu, Ramanjulu Sunkar, Lei Li and Ray Ming
    Citation: BMC Genomics 2012 13:682
    Content type: Research article Published on:

  13. ChIP-seq provides new opportunities to study allele-specific protein-DNA binding (ASB). However, detecting allelic imbalance from a single ChIP-seq dataset often has low statistical power since only sequence r...

    Authors: Yingying Wei, Xia Li, Qian-fei Wang and Hongkai Ji
    Citation: BMC Genomics 2012 13:681
    Content type: Methodology article Published on:

  14. Root length and its architecture govern the adaptability of plants to various stress conditions, including drought stress. Genetic variations in root growth, length, and architecture are genotypes dependent. I...

    Authors: Alok Ranjan, Neha Pandey, Deepika Lakhwani, Neeraj Kumar Dubey, Uday V Pathre and Samir V Sawant
    Citation: BMC Genomics 2012 13:680
    Content type: Research article Published on:

  15. The increasing number of infections caused by strains of Klebsiella pneumoniae that are resistant to multiple antibiotics has developed into a major medical problem worldwide. The development of next-generation s...

    Authors: Joo-Hyun Seo, Jay Sung-Joong Hong, Donghyuk Kim, Byung-Kwan Cho, Tzu-Wen Huang, Shih-Feng Tsai, Bernhard O Palsson and Pep Charusanti
    Citation: BMC Genomics 2012 13:679
    Content type: Research article Published on:

  16. Anaplasma phagocytophilum is an intracellular organism in the Order Rickettsiales that infects diverse animal species and is causing an emerging disease in humans, dogs and horses. Different strains have very dif...

    Authors: Basima Al-Khedery, Anna M Lundgren, Snorre Stuen, Erik G Granquist, Ulrike G Munderloh, Curtis M Nelson, A Rick Alleman, Suman M Mahan and Anthony F Barbet
    Citation: BMC Genomics 2012 13:678
    Content type: Research article Published on:

  17. HIV-associated dementia (HAD) is the most common dementia type in young adults less than 40 years of age. Although the neurotoxins, oxidative/metabolic stress and impaired activity of neurotrophic factors are ...

    Authors: Li Zhou, Gulietta M Pupo, Priyanka Gupta, Bing Liu, Sieu L Tran, Raany Rahme, Bin Wang, Rejane Rua, Helen Rizos, Adam Carroll, Murray J Cairns and Nitin K Saksena
    Citation: BMC Genomics 2012 13:677
    Content type: Research article Published on:

  18. We applied a new weighted pairwise shared genomic segment (pSGS) analysis for susceptibility gene localization to high-density genomewide SNP data in three extended high-risk breast cancer pedigrees.

    Authors: Zheng Cai, Alun Thomas, Craig Teerlink, James M Farnham, Lisa A Cannon-Albright and Nicola J Camp
    Citation: BMC Genomics 2012 13:676
    Content type: Research article Published on:

  19. Unlike maternal inheritance of mitochondria in sexual reproduction, somatic hybrids follow no obvious pattern. The introgressed segment orf138 from the mitochondrial genome of radish (Raphanus sativus) to its cou...

    Authors: Juan Wang, Jinjin Jiang, Xiaoming Li, Aimin Li, Yongtai Zhang, Rongzhan Guan and Youping Wang
    Citation: BMC Genomics 2012 13:675
    Content type: Research article Published on:

  20. For decades the tobacco plant has served as a model organism in plant biology to answer fundamental biological questions in the areas of plant development, physiology, and genetics. Due to the lack of sufficie...

    Authors: Florian Martin, Lucien Bovet, Audrey Cordier, Mario Stanke, Irfan Gunduz, Manuel C Peitsch and Nikolai V Ivanov
    Citation: BMC Genomics 2012 13:674
    Content type: Research article Published on:

  21. Douglas-fir (Pseudotsuga menziesii) extends over a wide range of contrasting environmental conditions, reflecting substantial local adaptation. For this reason, it is an interesting model species to study plant a...

    Authors: Thomas Müller, Ingo Ensminger and Karl J Schmid
    Citation: BMC Genomics 2012 13:673
    Content type: Research article Published on:

  22. Japanese gentians (Gentiana triflora and Gentiana scabra) are amongst the most popular floricultural plants in Japan. However, genomic resources for Japanese gentians have not yet been developed, mainly because o...

    Authors: Takashi Nakatsuka, Eri Yamada, Misa Saito, Takashi Hikage, Yuka Ushiku and Masahiro Nishihara
    Citation: BMC Genomics 2012 13:672
    Content type: Research article Published on:

  23. Maternal RNAs play a critical role in early development. Variation in the diversity and levels of maternally derived gene transcripts may be central to the origin of phenotypic novelty -- a longstanding proble...

    Authors: Kevin M Preuss, Jacqueline A Lopez, John K Colbourne and Michael J Wade
    Citation: BMC Genomics 2012 13:671
    Content type: Research article Published on:

  24. Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environm...

    Authors: Laura Hobley, Thomas R Lerner, Laura E Williams, Carey Lambert, Rob Till, David S Milner, Sarah M Basford, Michael J Capeness, Andrew K Fenton, Robert J Atterbury, Maximilian ATS Harris and R Elizabeth Sockett
    Citation: BMC Genomics 2012 13:670
    Content type: Research article Published on:

  25. The Order Rickettsiales includes important tick-borne pathogens, from Rickettsia rickettsii, which causes Rocky Mountain spotted fever, to Anaplasma marginale, the most prevalent vector-borne pathogen of cattle. ...

    Authors: Sebastián Aguilar Pierlé, Michael J Dark, Dani Dahmen, Guy H Palmer and Kelly A Brayton
    Citation: BMC Genomics 2012 13:669
    Content type: Research article Published on:

  26. White mold, caused by Sclerotinia sclerotiorum, is one of the most important diseases of pea (Pisum sativum L.), however, little is known about the genetics and biochemistry of this interaction. Identification of...

    Authors: Xiaofeng Zhuang, Kevin E McPhee, Tristan E Coram, Tobin L Peever and Martin I Chilvers
    Citation: BMC Genomics 2012 13:668
    Content type: Research article Published on:

  28. When using Illumina high throughput short read data, sometimes the genotype inferred from the positive strand and negative strand are significantly different, with one homozygous and the other heterozygous. Th...

    Authors: Yan Guo, Jiang Li, Chung-I Li, Jirong Long, David C Samuels and Yu Shyr
    Citation: BMC Genomics 2012 13:666
    Content type: Research article Published on:

  29. The present study coupled expression profiling with chromatin immunoprecipitation sequencing (ChIP-seq) to examine peroxisome proliferator-activated receptor-β/δ (PPARβ/δ)-dependent regulation of gene expressi...

    Authors: Combiz Khozoie, Michael G Borland, Bokai Zhu, Songjoon Baek, Sam John, Gordon L Hager, Yatrik M Shah, Frank J Gonzalez and Jeffrey M Peters
    Citation: BMC Genomics 2012 13:665
    Content type: Research article Published on:

  30. The cellular response to DNA damage is immediate and highly coordinated in order to maintain genome integrity and proper cell division. During the DNA damage response (DDR), the sensor kinases Tel1 and Mec1 in Sa...

    Authors: Hannah C Cheung, F Anthony San Lucas, Stephanie Hicks, Kyle Chang, Alison A Bertuch and Albert Ribes-Zamora
    Citation: BMC Genomics 2012 13:664
    Content type: Research article Published on:

  31. Phyto-remedies for diabetic control are popular among patients with Type II Diabetes mellitus (DM), in addition to other diabetic control measures. A number of plant species are known to possess diabetic contr...

    Authors: Ramasamy S Annadurai, Vasanthan Jayakumar, Raja C Mugasimangalam, Mohan AVSK Katta, Sanchita Anand, Sreeja Gopinathan, Santosh Prasad Sarma, Sunjay Jude Fernandes, Nandita Mullapudi, S Murugesan and Sudha Narayana Rao
    Citation: BMC Genomics 2012 13:663
    Content type: Research article Published on:

  32. DNA damage response (DDR) plays pivotal roles in maintaining genome integrity and stability. An effective DDR requires the involvement of hundreds of genes that compose a complicated network. Because DDR is hi...

    Authors: Xian Pan, Bingkun Lei, Nan Zhou, Biwei Feng, Wei Yao, Xin Zhao, Yao Yu and Hong Lu
    Citation: BMC Genomics 2012 13:662
    Content type: Research article Published on:

  33. Numerous single nucleotide polymorphisms (SNPs) associated with complex diseases have been identified by genome-wide association studies (GWAS) and expression quantitative trait loci (eQTLs) studies. However, ...

    Authors: Chenxing Liu, Fuquan Zhang, Tingting Li, Ming Lu, Lifang Wang, Weihua Yue and Dai Zhang
    Citation: BMC Genomics 2012 13:661
    Content type: Database Published on:

  34. Downy mildew, caused by Plasmopara viticola, is one of the most severe diseases of grapevine and is commonly controlled by fungicide treatments. The beneficial microorganism Trichoderma harzianum T39 (T39) can in...

    Authors: Michele Perazzolli, Marco Moretto, Paolo Fontana, Alberto Ferrarini, Riccardo Velasco, Claudio Moser, Massimo Delledonne and Ilaria Pertot
    Citation: BMC Genomics 2012 13:660
    Content type: Research article Published on:

  35. Mitochondria are organelles found in nearly all eukaryotic cells that play a crucial role in cellular survival and function. Mitochondrial function is under the control of nuclear and mitochondrial genomes. Wh...

    Authors: Patricia Jumbo-Lucioni, Su Bu, Susan T Harbison, Juanita C Slaughter, Trudy FC Mackay, Douglas R Moellering and Maria De Luca
    Citation: BMC Genomics 2012 13:659
    Content type: Research article Published on:

  36. Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species of Xanthomonas. For example, thi...

    Authors: Isabelle Pieretti, Monique Royer, Valérie Barbe, Sébastien Carrere, Ralf Koebnik, Arnaud Couloux, Armelle Darrasse, Jérôme Gouzy, Marie-Agnès Jacques, Emmanuelle Lauber, Charles Manceau, Sophie Mangenot, Stéphane Poussier, Béatrice Segurens, Boris Szurek, Valérie Verdier…
    Citation: BMC Genomics 2012 13:658
    Content type: Research article Published on:

  37. To study the role of microRNA (miRNA) in the regulation of Chinese hamster ovary (CHO) cell growth, qPCR, microarray and quantitative LC-MS/MS analysis were utilised for simultaneous expression profiling of mi...

    Authors: Colin Clarke, Michael Henry, Padraig Doolan, Shane Kelly, Sinead Aherne, Noelia Sanchez, Paul Kelly, Paula Kinsella, Laura Breen, Stephen F Madden, Lin Zhang, Mark Leonard, Martin Clynes, Paula Meleady and Niall Barron
    Citation: BMC Genomics 2012 13:656
    Content type: Research article Published on:

  38. MicroRNAs are small non-coding RNAs that regulate gene expression at the post-transcriptional level. While they have been implicated in various diseases, the profile changes in allergen inhalation challenge ar...

    Authors: Masatsugu Yamamoto, Amrit Singh, Jian Ruan, Gail M Gauvreau, Paul M O'Byrne, Christopher R Carlsten, J Mark FitzGerald, Louis-Philippe Boulet and Scott J Tebbutt
    Citation: BMC Genomics 2012 13:655
    Content type: Research article Published on:

  40. The genus Nelumbo Adans. comprises two living species, N. nucifera Gaertan. (Asian lotus) and N. lutea Pers. (American lotus). A genetic linkage map is an essential resource for plant genetic studies and crop imp...

    Authors: Mei Yang, Yanni Han, Robert VanBuren, Ray Ming, Liming Xu, Yuepeng Han and Yanling Liu
    Citation: BMC Genomics 2012 13:653
    Content type: Research article Published on:

  41. Elucidating the genomic basis of adaptation and speciation is a major challenge in natural systems with large quantities of environmental and phenotypic data, mostly because of the scarcity of genomic resource...

    Authors: Joanna L Kelley, Courtney N Passow, Martin Plath, Lenin Arias Rodriguez, Muh-Ching Yee and Michael Tobler
    Citation: BMC Genomics 2012 13:652
    Content type: Database Published on:

  42. Grouper (Epinephelus spp) is an economically important fish species worldwide. However, viral pathogens such as nervous necrosis virus (NNV) have been causing severe infections in the fish, resulting in great los...

    Authors: Ming-Wei Lu, Fang-Huar Ngou, Yung-Mei Chao, Yu-Shen Lai, Nai-Yu Chen, Fan-Yao Lee and Pinwen P Chiou
    Citation: BMC Genomics 2012 13:651
    Content type: Research article Published on:

  43. Bananas and plantains (Musa spp.) are among the most important crops in the world due to their nutritional and export value. However, banana production has been devastated by fungal infestations caused by Fusariu...

    Authors: Zhuo Wang, JianBin Zhang, CaiHong Jia, JuHua Liu, YanQiang Li, XiaoMin Yin, BiYu Xu and ZhiQiang Jin
    Citation: BMC Genomics 2012 13:650
    Content type: Research article Published on:

  44. Exome sequencing has transformed human genetic analysis and may do the same for other vertebrate model systems. However, a major challenge is sifting through the large number of sequence variants to identify t...

    Authors: Florencia del Viso, Dipankan Bhattacharya, Yong Kong, Michael J Gilchrist and Mustafa K Khokha
    Citation: BMC Genomics 2012 13:649
    Content type: Methodology article Published on:

  45. Chinese fir (Cunninghamia lanceolata) is an important timber species that accounts for 20–30% of the total commercial timber production in China. However, the available genomic information of Chinese fir is limit...

    Authors: Hua-Hong Huang, Li-Li Xu, Zai-Kang Tong, Er-Pei Lin, Qing-Po Liu, Long-Jun Cheng and Mu-Yuan Zhu
    Citation: BMC Genomics 2012 13:648
    Content type: Research article Published on:

  46. Cryptosporidium parvum is a globally distributed zoonotic parasite and an important opportunistic pathogen in immunocompromised patients. Little is known on the metabolic dynamics of the parasite, and study is ha...

    Authors: Haili Zhang, Fengguang Guo, Huaijun Zhou and Guan Zhu
    Citation: BMC Genomics 2012 13:647
    Content type: Research article Published on:

  47. Penicillium digitatum is a fungal necrotroph causing a common citrus postharvest disease known as green mold. In order to gain insight into the genetic bases of its virulence mechanisms and its high degree of hos...

    Authors: Marina Marcet-Houben, Ana-Rosa Ballester, Beatriz de la Fuente, Eleonora Harries, Jose F Marcos, Luis González-Candelas and Toni Gabaldón
    Citation: BMC Genomics 2012 13:646
    Content type: Research article Published on:

  48. Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant...

    Authors: Gregor D Gilfillan, Timothy Hughes, Ying Sheng, Hanne S Hjorthaug, Tobias Straub, Kristina Gervin, Jennifer R Harris, Dag E Undlien and Robert Lyle
    Citation: BMC Genomics 2012 13:645
    Content type: Methodology article Published on:

  49. Flax (Linum usitatissimum L.) is an important crop for the production of bioproducts derived from its seed and stem fiber. Transposable elements (TEs) are widespread in plant genomes and are a key component of th...

    Authors: Leonardo Galindo González and Michael K Deyholos
    Citation: BMC Genomics 2012 13:644
    Content type: Research article Published on:

  50. We have previously shown that lipophilic components (LPC) of the brown seaweed Ascophyllum nodosum (ANE) improved freezing tolerance in Arabidopsis thaliana. However, the mechanism(s) of this induced freezing str...

    Authors: Prasanth Nair, Saveetha Kandasamy, Junzeng Zhang, Xiuhong Ji, Chris Kirby, Bernhard Benkel, Mark D Hodges, Alan T Critchley, David Hiltz and Balakrishnan Prithiviraj
    Citation: BMC Genomics 2012 13:643
    Content type: Research article Published on:

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BMC Genomics

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