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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  19. 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:

  20. 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:

  22. 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:

  23. A genome-wide set of single nucleotide polymorphisms (SNPs) is a valuable resource in genetic research and breeding and is usually developed by re-sequencing a genome. If a genome sequence is not available, an...

    Authors: Frank M You, Karin R Deal, Jirui Wang, Monica T Britton, Joseph N Fass, Dawei Lin, Abhaya M Dandekar, Charles A Leslie, Mallikarjuna Aradhya, Ming-Cheng Luo and Jan Dvorak
    Citation: BMC Genomics 2012 13:354
    Content type: Research article Published on:

  24. 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:

  25. 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:

  26. Previous work has shown that the hypersaline-adapted archaeon, Halobacterium salinarum NRC-1, is highly resistant to oxidative stress caused by exposure to hydrogen peroxide, UV, and gamma radiation. Dynamic alte...

    Authors: Kriti Sharma, Nicholas Gillum, J Lomax Boyd and Amy Schmid
    Citation: BMC Genomics 2012 13:351
    Content type: Research article Published on:

  27. HacA/Xbp1 is a conserved bZIP transcription factor in eukaryotic cells which regulates gene expression in response to various forms of secretion stress and as part of secretory cell differentiation. In the pre...

    Authors: Neuza DSP Carvalho, Thomas R Jørgensen, Mark Arentshorst, Benjamin M Nitsche, Cees AMJJ van den Hondel, David B Archer and Arthur FJ Ram
    Citation: BMC Genomics 2012 13:350
    Content type: Research article Published on:

  28. Clostridium acetobutylicum has been used to produce butanol in industry. Catabolite control protein A (CcpA), known to mediate carbon catabolite repression (CCR) in low GC gram-positive bacteria, has been identif...

    Authors: Cong Ren, Yang Gu, Yan Wu, Weiwen Zhang, Chen Yang, Sheng Yang and Weihong Jiang
    Citation: BMC Genomics 2012 13:349
    Content type: Research article Published on:

  29. In the postgenome era, a prediction of response to treatment could lead to better dose selection for patients in radiotherapy. To identify a radiosensitive gene signature and elucidate related signaling pathwa...

    Authors: Han Sang Kim, Sang Cheol Kim, Sun Jeong Kim, Chan Hee Park, Hei-Cheul Jeung, Yong Bae Kim, Joong Bae Ahn, Hyun Cheol Chung and Sun Young Rha
    Citation: BMC Genomics 2012 13:348
    Content type: Research article Published on:

  30. Genomic Islands (GIs) have key roles since they modulate the structure and size of bacterial genomes displaying a diverse set of laterally transferred genes. Despite their importance, GIs in marine bacterial g...

    Authors: Beatriz Fernández-Gómez, Antonio Fernàndez-Guerra, Emilio O Casamayor, José M González, Carlos Pedrós-Alió and Silvia G Acinas
    Citation: BMC Genomics 2012 13:347
    Content type: Research article Published on:

  31. Ancestry informative markers (AIMs) are a type of genetic marker that is informative for tracing the ancestral ethnicity of individuals. Application of AIMs has gained substantial attention in population genet...

    Authors: Hsin-Chou Yang, Pei-Li Wang, Chien-Wei Lin, Chien-Hsiun Chen and Chun-Houh Chen
    Citation: BMC Genomics 2012 13:346
    Content type: Research article Published on:

  32. Endodontic infections are a leading cause of oro-facial pain and tooth loss in western countries, and may lead to severe life-threatening infections. These infections are polymicrobial with high bacterial dive...

    Authors: William W L Hsiao, Kevin L Li, Zhenqiu Liu, Cheron Jones, Claire M Fraser-Liggett and Ashraf F Fouad
    Citation: BMC Genomics 2012 13:345
    Content type: Research article Published on:

  33. Lead is a metal with many recognized adverse health side effects, and yet the molecular processes underlying lead toxicity are still poorly understood. Quantifying the injurious effects of lead is also difficu...

    Authors: Bruce S Gillis, Zarema Arbieva and Igor M Gavin
    Citation: BMC Genomics 2012 13:344
    Content type: Research article Published on:

  34. Coupling the control of expression stochasticity (noise) to the ability of expression change (plasticity) can alter gene function and influence adaptation. A number of factors, such as transcription re-initiat...

    Authors: Djordje Bajić and Juan F Poyatos
    Citation: BMC Genomics 2012 13:343
    Content type: Research article Published on:

  35. Somatic Copy Number Alterations (CNAs) in human genomes are present in almost all human cancers. Systematic efforts to characterize such structural variants must effectively distinguish significant consensus e...

    Authors: Xiguo Yuan, Guoqiang Yu, Xuchu Hou, Ie-Ming Shih, Robert Clarke, Junying Zhang, Eric P Hoffman, Roger R Wang, Zhen Zhang and Yue Wang
    Citation: BMC Genomics 2012 13:342
    Content type: Methodology article Published on:

  36. Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion...

    Authors: Michael A Quail, Miriam Smith, Paul Coupland, Thomas D Otto, Simon R Harris, Thomas R Connor, Anna Bertoni, Harold P Swerdlow and Yong Gu
    Citation: BMC Genomics 2012 13:341
    Content type: Research article Published on:

  37. Pre-symptomatic prediction of disease and drug response based on genetic testing is a critical component of personalized medicine. Previous work has demonstrated that the predictive capacity of genetic testing...

    Authors: Jonathan M Dreyfuss, Daniel Levner, James E Galagan, George M Church and Marco F Ramoni
    Citation: BMC Genomics 2012 13:340
    Content type: Research article Published on:

  38. The uneven distribution of recombination across the length of chromosomes results in inaccurate estimates of genetic to physical distances. In wheat (Triticum aestivum L.) chromosome 3B, it has been estimated tha...

    Authors: Ajay Kumar, Filippo M Bassi, Etienne Paux, Omar Al-Azzam, Monika Michalak de Jimenez, Anne M Denton, Yong Q Gu, Eric Huttner, Andrzej Kilian, Sachin Kumar, Aakash Goyal, Muhammad J Iqbal, Vijay K Tiwari, Munevver Dogramaci, Harindra S Balyan, Harcharan S Dhaliwal…
    Citation: BMC Genomics 2012 13:339
    Content type: Research article Published on:

  40. Streptomyces hygroscopicus 5008 has been used for the production of the antifungal validamycin/jinggangmycin for more than 40 years. A high yield of validamycin is achieved by culturing the strain at 37°C, rather...

    Authors: Hang Wu, Shuang Qu, Chenyang Lu, Huajun Zheng, Xiufen Zhou, Linquan Bai and Zixin Deng
    Citation: BMC Genomics 2012 13:337
    Content type: Research article Published on:

  41. Clostridium thermocellum is a candidate consolidated bioprocessing biocatalyst, which is a microorganism that expresses enzymes for both cellulose hydrolysis and its fermentation to produce fuels such as lignocel...

    Authors: Shihui Yang, Richard J Giannone, Lezlee Dice, Zamin K Yang, Nancy L Engle, Timothy J Tschaplinski, Robert L Hettich and Steven D Brown
    Citation: BMC Genomics 2012 13:336
    Content type: Research article Published on:

  42. Epidemiological studies have suggested that the encounter with commensal microorganisms during the neonatal period is essential for normal development of the host immune system. Basic research involving gnotob...

    Authors: Masahiro Yamamoto, Rui Yamaguchi, Kaori Munakata, Kiyoe Takashima, Mitsue Nishiyama, Kyoji Hioki, Yasuyuki Ohnishi, Masao Nagasaki, Seiya Imoto, Satoru Miyano, Atsushi Ishige and Kenji Watanabe
    Citation: BMC Genomics 2012 13:335
    Content type: Research article Published on:

  43. Changes in energy metabolism of the cells are common to many kinds of tumors and are considered a hallmark of cancer. Gas chromatography followed by time-of-flight mass spectrometry (GC-TOFMS) is a well-suited...

    Authors: Jan Budczies, Carsten Denkert, Berit M Müller, Scarlet F Brockmöller, Frederick Klauschen, Balazs Györffy, Manfred Dietel, Christiane Richter-Ehrenstein, Ulrike Marten, Reza M Salek, Julian L Griffin, Mika Hilvo, Matej Orešič, Gert Wohlgemuth and Oliver Fiehn
    Citation: BMC Genomics 2012 13:334
    Content type: Research article Published on:

  45. MicroRNAs (miRNAs) are nucleic acid regulators of many human mRNAs, and are associated with many tumorigenic processes. miRNA expression levels have been used in profiling studies, but some evidence suggests t...

    Authors: Elena Fountzilas, Andrew D Kelly, Antonio R Perez-Atayde, Jeffrey Goldsmith, Panagiotis A Konstantinopoulos, Nancy Francoeur, Mick Correll, Renee Rubio, Lan Hu, Mark C Gebhardt, John Quackenbush and Dimitrios Spentzos
    Citation: BMC Genomics 2012 13:332
    Content type: Research article Published on:

  46. Haemophilus parasuis, the causative agent of Glässer’s disease, is prevalent in swine herds and clinical signs associated with this disease are meningitis, polyserositis, polyarthritis, and bacterial pneumonia. S...

    Authors: Emilie S Zehr, Louisa B Tabatabai and Darrell O Bayles
    Citation: BMC Genomics 2012 13:331
    Content type: Research article Published on:

  47. Enterotoxigenic Escherichia coli (ETEC) is one of the most important pathogenic bacteria causing severe diarrhoea in human and pigs. In ETEC strains, the fimbrial types F4 and F18 are commonly found differently c...

    Authors: Chuanli Zhou, Zhengzhu Liu, Jicai Jiang, Ying Yu and Qin Zhang
    Citation: BMC Genomics 2012 13:330
    Content type: Research article Published on:

  48. MicroRNAs (miRNAs) are a class of non-coding small RNAs involved in post-transcriptional regulation of gene expression critical for plant growth and development, stress responses and other diverse biological p...

    Authors: Guru Jagadeeswaran, Padma Nimmakayala, Yun Zheng, Kanchana Gowdu, Umesh K Reddy and Ramanjulu Sunkar
    Citation: BMC Genomics 2012 13:329
    Content type: Research article Published on:

  50. The Dehalococcoides are strictly anaerobic bacteria that gain metabolic energy via the oxidation of H2 coupled to the reduction of halogenated organic compounds. Dehalococcoides spp. grow best in mixed microbial ...

    Authors: Laura A Hug, Robert G Beiko, Annette R Rowe, Ruth E Richardson and Elizabeth A Edwards
    Citation: BMC Genomics 2012 13:327
    Content type: Research article Published on:

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BMC Genomics

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