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  1. 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:

  2. 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:

  4. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  34. 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:

  35. Structural variations such as copy number variants (CNV) influence the expression of different phenotypic traits. Algorithms to identify CNVs through SNP-array platforms are available. The ability to evaluate ...

    Authors: Gaëlle Marenne, Francisco X Real, Nathaniel Rothman, Benjamin Rodríguez-Santiago, Luis Pérez-Jurado, Manolis Kogevinas, Montse García-Closas, Debra T Silverman, Stephen J Chanock, Emmanuelle Génin and Núria Malats
    Citation: BMC Genomics 2012 13:326
    Content type: Methodology article Published on:

  36. Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms...

    Authors: Yijun Ding, Minjun Chen, Zhichao Liu, Don Ding, Yanbin Ye, Min Zhang, Reagan Kelly, Li Guo, Zhenqiang Su, Stephen C Harris, Feng Qian, Weigong Ge, Hong Fang, Xiaowei Xu and Weida Tong
    Citation: BMC Genomics 2012 13:325
    Content type: Software Published on:

  38. Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in...

    Authors: Robert E Drew, Matthew L Settles, Erin J Churchill, Shayna M Williams, Soniya Balli and Barrie D Robison
    Citation: BMC Genomics 2012 13:323
    Content type: Research article Published on:

  39. Expression profiling has been proposed as a means for screening non-model organisms in their natural environments to identify genes potentially important in adaptive diversification. Tag profiling using high t...

    Authors: Claudia Voelckel, Nicole Gruenheit, Patrick Biggs, Oliver Deusch and Peter Lockhart
    Citation: BMC Genomics 2012 13:322
    Content type: Research article Published on:

  40. Pectins are diverse and very complex biomolecules and their structure depends on the plant species and tissue. It was previously shown that derivatives of pectic polymers and oligosaccharides from pectins have...

    Authors: Isabelle Benoit, Pedro M Coutinho, Henk A Schols, Jan P Gerlach, Bernard Henrissat and Ronald P de Vries
    Citation: BMC Genomics 2012 13:321
    Content type: Research article Published on:

  41. Dysregulation of microRNA (miRNA) expression has been implicated in molecular genetic events leading to the progression and development of atherosclerosis. We hypothesized that miRNA expression profiles differ...

    Authors: Genesio M Karere, Jeremy P Glenn, John L VandeBerg and Laura A Cox
    Citation: BMC Genomics 2012 13:320
    Content type: Research article Published on:

  42. Zebrafish (Danio rerio) is a prominent vertebrate model of human development and pathogenic disease and has recently been utilized to study teleost immune responses to infectious agents threatening the aquacultur...

    Authors: Dahai Yang, Qin Liu, Minjun Yang, Haizhen Wu, Qiyao Wang, Jingfan Xiao and Yuanxing Zhang
    Citation: BMC Genomics 2012 13:319
    Content type: Research article Published on:

  43. In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting t...

    Authors: Huaan Yang, Ye Tao, Zequn Zheng, Chengdao Li, Mark W Sweetingham and John G Howieson
    Citation: BMC Genomics 2012 13:318
    Content type: Methodology article Published on:

  44. Redox homeostasis is essential to sustain metabolism and growth. We recently reported that yeast cells meet a gradual increase in imposed NADPH demand by progressively increasing flux through the pentose phosp...

    Authors: Magalie Celton, Isabelle Sanchez, Anne Goelzer, Vincent Fromion, Carole Camarasa and Sylvie Dequin
    Citation: BMC Genomics 2012 13:317
    Content type: Research article Published on:

  45. Sesame (Sesamum indicum L.) is one of the most important oil crops; however, a lack of useful molecular markers hinders current genetic research. We performed transcriptome sequencing of samples from different se...

    Authors: Haiyang Zhang, Libin Wei, Hongmei Miao, Tide Zhang and Cuiying Wang
    Citation: BMC Genomics 2012 13:316
    Content type: Research article Published on:

  46. The X and Y sex chromosomes are conspicuous features of placental mammal genomes. Mammalian sex chromosomes arose from an ordinary pair of autosomes after the proto-Y acquired a male-determining gene and degen...

    Authors: Jaroslav Mácha, Radka Teichmanová, Amy K Sater, Dan E Wells, Tereza Tlapáková, Lyle B Zimmerman and Vladimír Krylov
    Citation: BMC Genomics 2012 13:315
    Content type: Research article Published on:

  47. Verticillium dahliae (Vd) and Verticillium albo-atrum (Va) are cosmopolitan soil fungi causing very disruptive vascular diseases on a wide range of crop plants. To date, no sexual stage has been identified in eit...

    Authors: Stefan G Amyotte, Xiaoping Tan, Kayla Pennerman, Maria del Mar Jimenez-Gasco, Steven J Klosterman, Li-Jun Ma, Katherine F Dobinson and Paola Veronese
    Citation: BMC Genomics 2012 13:314
    Content type: Research article Published on:

  48. The degradation of plant materials by enzymes is an industry of increasing importance. For sustainable production of second generation biofuels and other products of industrial biotechnology, efficient degrada...

    Authors: Mikael R Andersen, Malene Giese, Ronald P de Vries and Jens Nielsen
    Citation: BMC Genomics 2012 13:313
    Content type: Research article Published on:

  50. Stx bacteriophages are responsible for driving the dissemination of Stx toxin genes (stx) across their bacterial host range. Lysogens carrying Stx phages can cause severe, life-threatening disease and Stx toxin i...

    Authors: Darren L Smith, David J Rooks, Paul CM Fogg, Alistair C Darby, Nick R Thomson, Alan J McCarthy and Heather E Allison
    Citation: BMC Genomics 2012 13:311
    Content type: Research article Published on:

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BMC Genomics

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