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  1. Polyploidization is an important mechanism in plant evolution. By analyzing the leaf transcriptomes taken from the allotetraploid Nicotiana tabacum (tobacco) and parental genome donors, N. sylvesteris (S-Genome) ...

    Authors: Aureliano Bombarely, Kieron D Edwards, Juan Sanchez-Tamburrino and Lukas A Mueller
    Citation: BMC Genomics 2012 13:406
    Content type: Research article Published on:

  2. Streptococcus pyogenes (GAS) harbors several superantigens (SAgs) in the prophage region of its genome, although speG and smez are not located in this region. The diversity of SAgs is thought to arise during hori...

    Authors: Kayo Okumura, Yumi Shimomura, Somay Yamagata Murayama, Junji Yagi, Kimiko Ubukata, Teruo Kirikae and Tohru Miyoshi-Akiyama
    Citation: BMC Genomics 2012 13:404
    Content type: Research article Published on:

  3. Cowpea, Vigna unguiculata L. Walp., is one of the most important food and forage legumes in the semi-arid tropics. While most domesticated forms of cowpea are susceptible to the root parasitic weed Striga gesneri...

    Authors: Kan Huang, Karolina E Mellor, Shom N Paul, Mark J Lawson, Aaron J Mackey and Michael P Timko
    Citation: BMC Genomics 2012 13:402
    Content type: Research article Published on:

  4. In the last few years several studies have shown that Transposable Elements (TEs) in the human genome are significantly associated with Transcription Factor Binding Sites (TFBSs) and that in several cases thei...

    Authors: Alessandro Testori, Livia Caizzi, Santina Cutrupi, Olivier Friard, Michele De Bortoli, Davide Cora' and Michele Caselle
    Citation: BMC Genomics 2012 13:400
    Content type: Research article Published on:

  5. The pathogenesis of natural scrapie and other prion diseases is still poorly understood. Determining the variations in the transcriptome in the early phases of the disease might clarify some of the molecular m...

    Authors: Hicham Filali, Inmaculada Martin-Burriel, Frank Harders, Luis Varona, Carmen Serrano, Cristina Acín, Juan J Badiola, Alex Bossers and Rosa Bolea
    Citation: BMC Genomics 2012 13:399
    Content type: Research article Published on:

  6. The ovine Major Histocompatibility Complex (MHC) harbors genes involved in overall resistance/susceptibility of the host to infectious diseases. Compared to human and mouse, the ovine MHC is interrupted by a l...

    Authors: Gang Li, Ka Liu, Shasha Jiao, Haibo Liu, Hugh T Blair, Peng Zhang, Xiaoran Cui, Pingping Tan, Jianfeng Gao and Runlin Z Ma
    Citation: BMC Genomics 2012 13:398
    Content type: Research article Published on:

  7. Seedlessness is an important agronomic trait for citrus, and male sterility (MS) is one main cause of seedless citrus fruit. However, the molecular mechanism of citrus seedlessness remained not well explored.

    Authors: Wen-Ming Qiu, An-Dan Zhu, Yao Wang, Li-Jun Chai, Xiao-Xia Ge, Xiu-Xin Deng and Wen-Wu Guo
    Citation: BMC Genomics 2012 13:397
    Content type: Research article Published on:

  8. Drug susceptible clinical isolates of Candida albicans frequently become highly tolerant to drugs during chemotherapy, with dreadful consequences to patient health. We used RNA sequencing (RNA-seq) to analyze the...

    Authors: Sanjiveeni Dhamgaye, Maria Bernard, Gaelle Lelandais, Odile Sismeiro, Sophie Lemoine, Jean-Yves Coppée, Stéphane Le Crom, Rajendra Prasad and Frédéric Devaux
    Citation: BMC Genomics 2012 13:396
    Content type: Research article Published on:

  10. Genomic imprinting is an epigenetic phenomenon resulting in parent-of-origin specific monoallelic gene expression. It is postulated to have evolved in placental mammals to modulate intrauterine resource alloca...

    Authors: Radhika Das, Nathan Anderson, MaryEllen I Koran, Jennifer R Weidman, Tarjei S Mikkelsen, Michael Kamal, Susan K Murphy, Kerstin Linblad-Toh, John M Greally and Randy L Jirtle
    Citation: BMC Genomics 2012 13:394
    Content type: Research article Published on:

  11. Nephronophthisis (NPHP) as a cause of cystic kidney disease is the most common genetic cause of progressive renal failure in children and young adults. NPHP is characterized by abnormal and/or loss of function...

    Authors: John K McCooke, Rudi Appels, Roberto A Barrero, Alice Ding, Justyna E Ozimek-Kulik, Mathew I Bellgard, Grant Morahan and Jacqueline K Phillips
    Citation: BMC Genomics 2012 13:393
    Content type: Research article Published on:

  13. The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding pro...

    Authors: Muhammad L Aslam, John WM Bastiaansen, Martin G Elferink, Hendrik-Jan Megens, Richard PMA Crooijmans, Le Ann Blomberg, Robert C Fleischer, Curtis P Van Tassell, Tad S Sonstegard, Steven G Schroeder, Martien AM Groenen and Julie A Long
    Citation: BMC Genomics 2012 13:391
    Content type: Research article Published on:

  14. Small nucleolar RNAs are a highly conserved group of small RNAs found in eukaryotic cells. Genes encoding these RNAs are diversely located throughout the genome. They are functionally conserved, performing pos...

    Authors: Devinder Kaur, Abhishek Kumar Gupta, Vandana Kumari, Rahul Sharma, Alok Bhattacharya and Sudha Bhattacharya
    Citation: BMC Genomics 2012 13:390
    Content type: Research article Published on:

  16. In post-genomic era, the study of transcriptional regulation is pivotal to decode genetic information. Transcription factors (TFs) are central proteins for transcriptional regulation, and interactions between ...

    Authors: Guangyong Zheng, Qi Liu, Guohui Ding, Chaochun Wei and Yixue Li
    Citation: BMC Genomics 2012 13:388
    Content type: Research article Published on:

  17. Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut producti...

    Authors: Patricia M Guimarães, Ana CM Brasileiro, Carolina V Morgante, Andressa CQ Martins, Georgios Pappas, Orzenil B Silva Jr, Roberto Togawa, Soraya CM Leal-Bertioli, Ana CG Araujo, Marcio C Moretzsohn and David J Bertioli
    Citation: BMC Genomics 2012 13:387
    Content type: Research article Published on:

  19. Escherichia coli strains lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS), which is the major bacterial component involved in glucose transport and its phosphorylation, accumulate hig...

    Authors: César Aguilar, Adelfo Escalante, Noemí Flores, Ramón de Anda, Fernando Riveros-McKay, Guillermo Gosset, Enrique Morett and Francisco Bolívar
    Citation: BMC Genomics 2012 13:385
    Content type: Research article Published on:

  20. The class of small non-coding RNA molecules (sRNA) regulates gene expression by different mechanisms and enables bacteria to mount a physiological response due to adaptation to the environment or infection. Ov...

    Authors: Jordan Pischimarov, Carsten Kuenne, André Billion, Jüergen Hemberger, Franz Cemič, Trinad Chakraborty and Torsten Hain
    Citation: BMC Genomics 2012 13:384
    Content type: Database Published on:

  21. microRNAs (miRNAs) have been shown to regulate the expression of a large number of genes and play key roles in many biological processes. Several previous studies have quantified the inhibitory effect of a miR...

    Authors: Paul Geeleher, Stephanie R Huang, Eric R Gamazon, Aaron Golden and Cathal Seoighe
    Citation: BMC Genomics 2012 13:383
    Content type: Research article Published on:

  22. The fungus Marssonina brunnea is a causal pathogen of Marssonina leaf spot that devastates poplar plantations by defoliating susceptible trees before normal fall leaf drop.

    Authors: Sheng Zhu, You-Zhi Cao, Cong Jiang, Bi-Yue Tan, Zhong Wang, Sisi Feng, Liang Zhang, Xiao-Hua Su, Brona Brejova, Tomas Vinar, Meng Xu, Ming-Xiu Wang, Shou-Gong Zhang, Min-Ren Huang, Rongling Wu and Yan Zhou
    Citation: BMC Genomics 2012 13:382
    Content type: Research article Published on:

  23. Plants contain significant quantities of small RNAs (sRNAs) derived from various sRNA biogenesis pathways. Many of these sRNAs play regulatory roles in plants. Previous analysis revealed that numerous sRNAs in...

    Authors: Yuanji Zhang, B Elizabeth Wiggins, Christina Lawrence, Jay Petrick, Sergey Ivashuta and Greg Heck
    Citation: BMC Genomics 2012 13:381
    Content type: Research article Published on:

  24. Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening starvation condition...

    Authors: Benjamin M Nitsche, Thomas R Jørgensen, Michiel Akeroyd, Vera Meyer and Arthur FJ Ram
    Citation: BMC Genomics 2012 13:380
    Content type: Research article Published on:

  25. Blood-born miRNA signatures have recently been reported for various tumor diseases. Here, we compared the miRNA signature in Wilms tumor patients prior and after preoperative chemotherapy according to SIOP pro...

    Authors: Jana Schmitt, Christina Backes, Nasenien Nourkami-Tutdibi, Petra Leidinger, Stephanie Deutscher, Markus Beier, Manfred Gessler, Norbert Graf, Hans-Peter Lenhof, Andreas Keller and Eckart Meese
    Citation: BMC Genomics 2012 13:379
    Content type: Research article Published on:

  26. High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a la...

    Authors: Simon M Lank, Brittney A Golbach, Hannah M Creager, Roger W Wiseman, Derin B Keskin, Ellis L Reinherz, Vladimir Brusic and David H O’Connor
    Citation: BMC Genomics 2012 13:378
    Content type: Methodology article Published on:

  27. Although a number of intestinal inflammatory conditions pertain to the ileum, whole-genome gene expression analyses in animal models of ileal inflammation are lacking to date. Therefore, we aimed to identify a...

    Authors: Leela Rani Avula, Dries Knapen, Roeland Buckinx, Lucia Vergauwen, Dirk Adriaensen, Luc Van Nassauw and Jean-Pierre Timmermans
    Citation: BMC Genomics 2012 13:377
    Content type: Research article Published on:

  28. Btau_4.0 and UMD3.1 are two distinct cattle reference genome assemblies. In our previous study using the low density BovineSNP50 array, we reported a copy number variation (CNV) analysis on Btau_4.0 with 521 a...

    Authors: Yali Hou, Derek M Bickhart, Miranda L Hvinden, Congjun Li, Jiuzhou Song, Didier A Boichard, Sébastien Fritz, André Eggen, Sue DeNise, George R Wiggans, Tad S Sonstegard, Curtis P Van Tassell and George E Liu
    Citation: BMC Genomics 2012 13:376
    Content type: Research article Published on:

  29. Pacific Biosciences technology provides a fundamentally new data type that provides the potential to overcome some limitations of current next generation sequencing platforms by providing significantly longer ...

    Authors: Mauricio O Carneiro, Carsten Russ, Michael G Ross, Stacey B Gabriel, Chad Nusbaum and Mark A DePristo
    Citation: BMC Genomics 2012 13:375
    Content type: Research article Published on:

  30. Fusarium wilt, caused by the fungal pathogen Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), is considered the most lethal disease of Cavendish bananas in the world. The disease can be managed in the...

    Authors: Chun-yu Li, Gui-ming Deng, Jing Yang, Altus Viljoen, Yan Jin, Rui-bin Kuang, Cun-wu Zuo, Zhi-cheng Lv, Qiao-song Yang, Ou Sheng, Yue-rong Wei, Chun-hua Hu, Tao Dong and Gan-jun Yi
    Citation: BMC Genomics 2012 13:374
    Content type: Research article Published on:

  31. Oenococcus oeni, a member of the lactic acid bacteria, is one of a limited number of microorganisms that not only survive, but actively proliferate in wine. It is also unusual as, unlike the majority of bacteria ...

    Authors: Anthony R Borneman, Jane M McCarthy, Paul J Chambers and Eveline J Bartowsky
    Citation: BMC Genomics 2012 13:373
    Content type: Research article Published on:

  33. MicroRNAs (miRNAs) are a class of endogenous, small, non-coding RNAs that regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in high plants. However, the di...

    Authors: Zhihong Gao, Ting Shi, Xiaoyan Luo, Zhen Zhang, Weibing Zhuang and Liangju Wang
    Citation: BMC Genomics 2012 13:371
    Content type: Research article Published on:

  34. The domestic pig is an important livestock species and there is strong interest in the factors that affect the development of viable embryos and offspring in this species. A limited understanding of the molecu...

    Authors: Stephen Tsoi, Chi Zhou, Jason R Grant, J Alexander Pasternak, John Dobrinsky, Philippe Rigault, Julie Nieminen, Marc-André Sirard, Claude Robert, George R Foxcroft and Michael K Dyck
    Citation: BMC Genomics 2012 13:370
    Content type: Research article Published on:

  35. Fusarium head blight (FHB) caused by Fusarium species like F. graminearum is a devastating disease of wheat (Triticum aestivum) worldwide. Mycotoxins such as deoxynivalenol produced by the fungus affect plant and...

    Authors: Sven Gottwald, Birgit Samans, Stefanie Lück and Wolfgang Friedt
    Citation: BMC Genomics 2012 13:369
    Content type: Research article Published on:

  36. Soybean (Glycine max (L. Merr.)) resistance to any population of Heterodera glycines (I.), or Fusarium virguliforme (Akoi, O’Donnell, Homma & Lattanzi) required a functional allele at Rhg1/Rfs2. H. glycines, the ...

    Authors: Ali Srour, Ahmed J Afzal, Laureen Blahut-Beatty, Naghmeh Hemmati, Daina H Simmonds, Wenbin Li, Miao Liu, Christopher D Town, Hemlata Sharma, Prakash Arelli and David A Lightfoot
    Citation: BMC Genomics 2012 13:368
    Content type: Research article Published on:

  39. Greying with age in horses is an autosomal dominant trait, associated with loss of hair pigmentation, melanoma and vitiligo-like depigmentation. We recently identified a 4.6 kb duplication in STX17 to be associat...

    Authors: Elisabeth Sundström, Freyja Imsland, Sofia Mikko, Claire Wade, Snaevar Sigurdsson, Gerli Rosengren Pielberg, Anna Golovko, Ino Curik, Monika H Seltenhammer, Johann Sölkner, Kerstin Lindblad-Toh and Leif Andersson
    Citation: BMC Genomics 2012 13:365
    Content type: Research article Published on:

  40. Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought...

    Authors: Bala R Thumma, Navin Sharma and Simon G Southerton
    Citation: BMC Genomics 2012 13:364
    Content type: Research article Published on:

  41. Aquaculture of piscivorous fish is in continual expansion resulting in a global requirement to reduce the dependence on wild caught fish for generation of fishmeal and fish oil. Plant proteins represent a suit...

    Authors: Luca Tacchi, Christopher J Secombes, Ralph Bickerdike, Michael A Adler, Claudia Venegas, Harald Takle and Samuel AM Martin
    Citation: BMC Genomics 2012 13:363
    Content type: Research article Published on:

  42. The scorpion Tityus stigmurus is widely distributed in Northeastern Brazil and known to cause severe human envenoming, inducing pain, hyposthesia, edema, erythema, paresthesia, headaches and vomiting. The present...

    Authors: Diego D Almeida, Katia C Scortecci, Leonardo S Kobashi, Lucymara F Agnez-Lima, Silvia R B Medeiros, Arnóbio A Silva-Junior, Inácio de L M Junqueira-de-Azevedo and Matheus de F Fernandes-Pedrosa
    Citation: BMC Genomics 2012 13:362
    Content type: Research article Published on:

  43. How well does RNA-Seq data perform for quantitative whole gene expression analysis in the absence of a genome? This is one unanswered question facing the rapidly growing number of researchers studying non-mode...

    Authors: Emily A Hornett and Christopher W Wheat
    Citation: BMC Genomics 2012 13:361
    Content type: Research article Published on:

  46. Development and application of transcriptomics-based gene classifiers for ecotoxicological applications lag far behind those of biomedical sciences. Many such classifiers discovered thus far lack vigorous stat...

    Authors: Rong-Lin Wang, David Bencic, Adam Biales, Robert Flick, Jim Lazorchak, Daniel Villeneuve and Gerald T Ankley
    Citation: BMC Genomics 2012 13:358
    Content type: Research article Published on:

  47. MicroRNAs (miRNAs) are a class of small RNA molecules that regulate expression of specific mRNA targets. They can be released from cells, often encapsulated within extracellular vesicles (EVs), and therefore h...

    Authors: Jasenka Guduric-Fuchs, Anna O’Connor, Bailey Camp, Christina L O'Neill, Reinhold J Medina and David A Simpson
    Citation: BMC Genomics 2012 13:357
    Content type: Research article Published on:

  48. The androgen receptor plays a critical role throughout the progression of prostate cancer and is an important drug target for this disease. While chromatin immunoprecipitation coupled with massively parallel s...

    Authors: Zhou Zhu, Manli Shi, Wenyue Hu, Heather Estrella, Jon Engebretsen, Tim Nichols, David Briere, Natilie Hosea, Gerrit Los, Paul A Rejto and Andrea Fanjul
    Citation: BMC Genomics 2012 13:355
    Content type: Research article Published on:

  49. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression and play a critical role in development, homeostasis, and disease. Despite their demonstrated roles in age-associated pathologies, li...

    Authors: Saurabh Gombar, Hwa Jin Jung, Feng Dong, Brent Calder, Gil Atzmon, Nir Barzilai, Xiao-Li Tian, Joris Pothof, Jan HJ Hoeijmakers, Judith Campisi, Jan Vijg and Yousin Suh
    Citation: BMC Genomics 2012 13:353
    Content type: Research article Published on:

  50. Plant mitochondrial genome has unique features such as large size, frequent recombination and incorporation of foreign DNA. Cytoplasmic male sterility (CMS) is caused by rearrangement of the mitochondrial geno...

    Authors: Yoshiyuki Tanaka, Mizue Tsuda, Keita Yasumoto, Hiroshi Yamagishi and Toru Terachi
    Citation: BMC Genomics 2012 13:352
    Content type: Research article Published on:

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BMC Genomics

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