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  1. 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:

  2. 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:

  3. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  23. 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:

  25. GDSL esterases/lipases are a newly discovered subclass of lipolytic enzymes that are very important and attractive research subjects because of their multifunctional properties, such as broad substrate specifi...

    Authors: Hanna Chepyshko, Chia-Ping Lai, Li-Ming Huang, Jyung-Hurng Liu and Jei-Fu Shaw
    Citation: BMC Genomics 2012 13:309
    Content type: Research article Published on:

  27. Cysteine peptidases in the two-spotted spider mite Tetranychus urticae are involved in essential physiological processes, including proteolytic digestion. Cystatins and thyropins are inhibitors of cysteine peptid...

    Authors: María Estrella Santamaría, Pedro Hernández-Crespo, Félix Ortego, Vojislava Grbic, Miodrag Grbic, Isabel Diaz and Manuel Martinez
    Citation: BMC Genomics 2012 13:307
    Content type: Research article Published on:

  28. A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. We used microarray techniques to determine microRNA (miRNA) ...

    Authors: Shumao Lin, Hongmei Li, Heping Mu, Wen Luo, Ying Li, Xinzheng Jia, Sibing Wang, Xiaolu Jia, Qinghua Nie, Yugu Li and Xiquan Zhang
    Citation: BMC Genomics 2012 13:306
    Content type: Research article Published on:

  29. Though genomic-level data are becoming widely available, many of the metazoan species sequenced are laboratory systems whose natural history is not well documented. In contrast, the wide array of species with ...

    Authors: Mark P Peterson, Danielle J Whittaker, Shruthi Ambreth, Suhas Sureshchandra, Aaron Buechlein, Ram Podicheti, Jeong-Hyeon Choi, Zhao Lai, Keithanne Mockatis, John Colbourne, Haixu Tang and Ellen D Ketterson
    Citation: BMC Genomics 2012 13:305
    Content type: Research article Published on:

  30. mRNA expression data from next generation sequencing platforms is obtained in the form of counts per gene or exon. Counts have classically been assumed to follow a Poisson distribution in which the variance is...

    Authors: Ann L Oberg, Brian M Bot, Diane E Grill, Gregory A Poland and Terry M Therneau
    Citation: BMC Genomics 2012 13:304
    Content type: Research article Published on:

  32. Modern allotetraploid cotton contains an “A” and “D” genome from an ancestral polyploidy event that occurred approximately 1–2 million years ago. Diploid A- and D-genome species can be compared to the A- and D...

    Authors: Lex E Flagel, Jonathan F Wendel and Joshua A Udall
    Citation: BMC Genomics 2012 13:302
    Content type: Research article Published on:

  34. DNA methylation plays important biological roles in plants and animals. To examine the rice genomic methylation landscape and assess its functional significance, we generated single-base resolution DNA methylo...

    Authors: Xin Li, Jingde Zhu, Fengyi Hu, Song Ge, Mingzhi Ye, Hui Xiang, Guojie Zhang, Xiaoming Zheng, Hongyu Zhang, Shilai Zhang, Qiong Li, Ruibang Luo, Chang Yu, Jian Yu, Jingfeng Sun, Xiaoyu Zou…
    Citation: BMC Genomics 2012 13:300
    Content type: Research article Published on:

  36. Both bone morphogenetic proteins (BMPs) and histone deacetylases (HDACs) have previously been established to play a role in the development of the three major cell types of the central nervous system: neurons,...

    Authors: Catharina Scholl, Kathrin Weiβmüller, Pavlo Holenya, Maya Shaked-Rabi, Kerry L Tucker and Stefan Wölfl
    Citation: BMC Genomics 2012 13:298
    Content type: Research article Published on:

  37. Membrane trafficking involves the complex regulation of proteins and lipids intracellular localization and is required for metabolic uptake, cell growth and development. Different trafficking pathways passing ...

    Authors: Johan-Owen De Craene, Raymond Ripp, Odile Lecompte, Julie D Thompson, Olivier Poch and Sylvie Friant
    Citation: BMC Genomics 2012 13:297
    Content type: Research article Published on:

  38. Measuring gene transcription using real-time reverse transcription polymerase chain reaction (RT-qPCR) technology is a mainstay of molecular biology. Technologies now exist to measure the abundance of many tra...

    Authors: James R Perkins, John M Dawes, Steve B McMahon, David LH Bennett, Christine Orengo and Matthias Kohl
    Citation: BMC Genomics 2012 13:296
    Content type: Software Published on:

  39. Methyl jasmonate (MeJA) has been successfully used as an effective elicitor to enhance production of taxol and other taxanes in cultured Taxus cells. However the mechanism of MeJA-mediated taxane biosynthesis rem...

    Authors: Shu-tao Li, Peng Zhang, Meng Zhang, Chun-hua Fu, Chun-fang Zhao, Yan-shan Dong, An-yuan Guo and Long-jiang Yu
    Citation: BMC Genomics 2012 13:295
    Content type: Research article Published on:

  40. In plants, pollination is a critical step in reproduction. During pollination, constant communication between male pollen and the female stigma is required for pollen adhesion, germination, and tube growth. Th...

    Authors: Xiao Hui Xu, Hao Chen, Ya Lin Sang, Fang Wang, Jun Ping Ma, Xin-Qi Gao and Xian Sheng Zhang
    Citation: BMC Genomics 2012 13:294
    Content type: Research article Published on:

  42. Carnation (Dianthus caryophyllus L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flo...

    Authors: Koji Tanase, Chikako Nishitani, Hideki Hirakawa, Sachiko Isobe, Satoshi Tabata, Akemi Ohmiya and Takashi Onozaki
    Citation: BMC Genomics 2012 13:292
    Content type: Research article Published on:

  43. Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, fun...

    Authors: Susana L Torales, Máximo Rivarola, María F Pomponio, Paula Fernández, Cintia V Acuña, Paula Marchelli, Sergio Gonzalez, María M Azpilicueta, Horacio Esteban Hopp, Leonardo A Gallo, Norma B Paniego and Susana N Marcucci Poltri
    Citation: BMC Genomics 2012 13:291
    Content type: Research article Published on:

  44. MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and...

    Authors: Flávia Thiebaut, Clícia Grativol, Mariana Carnavale-Bottino, Cristian Antonio Rojas, Milos Tanurdzic, Laurent Farinelli, Robert A Martienssen, Adriana Silva Hemerly and Paulo Cavalcanti Gomes Ferreira
    Citation: BMC Genomics 2012 13:290
    Content type: Research article Published on:

  45. Planarians are considered to be among the extant animals close to one of the earliest groups of organisms that acquired a central nervous system (CNS) during evolution. Planarians have a bilobed brain with nin...

    Authors: Osamu Nishimura, Yukako Hirao, Hiroshi Tarui and Kiyokazu Agata
    Citation: BMC Genomics 2012 13:289
    Content type: Research article Published on:

  46. Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Positional cloning and candidate gene s...

    Authors: Heather M Hines, Riccardo Papa, Mayte Ruiz, Alexie Papanicolaou, Charles Wang, H Frederik Nijhout, W Owen McMillan and Robert D Reed
    Citation: BMC Genomics 2012 13:288
    Content type: Research article Published on:

  47. The naid annelids contain a number of species that vary in their ability to regenerate lost body parts, making them excellent candidates for evolution of regeneration studies. However, scant sequence data exis...

    Authors: Kevin G Nyberg, Matthew A Conte, Jamie L Kostyun, Alison Forde and Alexandra E Bely
    Citation: BMC Genomics 2012 13:287
    Content type: Research article Published on:

  48. Drought is one of the main environmental factors limiting tree growth and productivity of plantation forests worldwide. Populus hopeiensis Hu et Chow is one of the most important commercial plantation tree specie...

    Authors: Yuepeng Song, Zeliang Wang, Wenhao Bo, Yuanyuan Ren, Zhiyi Zhang and Deqiang Zhang
    Citation: BMC Genomics 2012 13:286
    Content type: Research article Published on:

  49. We present a comprehensive transcriptome analysis of the fungus Ascosphaera apis, an economically important pathogen of the Western honey bee (Apis mellifera) that causes chalkbrood disease. Our goals were to fur...

    Authors: R Scott Cornman, Anna K Bennett, K Daniel Murray, Jay D Evans, Christine G Elsik and Kate Aronstein
    Citation: BMC Genomics 2012 13:285
    Content type: Research article Published on:

  50. The fish-hunting cone snail, Conus geographus, is the deadliest snail on earth. In the absence of medical intervention, 70% of human stinging cases are fatal. Although, its venom is known to consist of a cocktail...

    Authors: Hao Hu, Pradip K Bandyopadhyay, Baldomero M Olivera and Mark Yandell
    Citation: BMC Genomics 2012 13:284
    Content type: Research article Published on:

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BMC Genomics

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