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  1. The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of ...

    Authors: Richard Guyon, Michaelle Rakotomanga, Naoual Azzouzi, Jean Pierre Coutanceau, Celine Bonillo, Helena D’Cotta, Elodie Pepey, Lucile Soler, Marguerite Rodier-Goud, Angelique D’Hont, Matthew A Conte, Nikkie EM van Bers, David J Penman, Christophe Hitte, Richard PMA Crooijmans, Thomas D Kocher…
    Citation: BMC Genomics 2012 13:222
    Content type: Research article Published on:

  2. Carotenoids are isoprenoid pigments, essential for photosynthesis and photoprotection in plants. The enzyme phytoene synthase (PSY) plays an essential role in mediating condensation of two geranylgeranyl dipho...

    Authors: Bianca Dibari, Florent Murat, Audrey Chosson, Véronique Gautier, Charles Poncet, Philippe Lecomte, Ingrid Mercier, Hélène Bergès, Caroline Pont, Antonio Blanco and Jérôme Salse
    Citation: BMC Genomics 2012 13:221
    Content type: Research article Published on:

  3. The classical view on eukaryotic gene expression proposes the scheme of a forward flow for which fluctuations in mRNA levels upon a stimulus contribute to determine variations in mRNA availability for translat...

    Authors: Toma Tebaldi, Angela Re, Gabriella Viero, Ilaria Pegoretti, Andrea Passerini, Enrico Blanzieri and Alessandro Quattrone
    Citation: BMC Genomics 2012 13:220
    Content type: Research article Published on:

  4. Single nucleotide polymorphisms (SNPs) provide essential tools for the advancement of research in plant genomics, and the development of SNP resources for many species has been accelerated by the capabilities ...

    Authors: Melanie L Hand, Noel Oi Cogan and John W Forster
    Citation: BMC Genomics 2012 13:219
    Content type: Research article Published on:

  5. In animals, microRNAs (miRNA) are important genetic regulators. Animal miRNAs appear to have expanded in conjunction with an escalation in complexity during early bilaterian evolution. Their small size and hig...

    Authors: José Afonso Guerra-Assunção and Anton J Enright
    Citation: BMC Genomics 2012 13:218
    Content type: Research article Published on:

  6. Genotyping assays often require substantial amounts of DNA. To overcome the problem of limiting amounts of available DNA, Whole Genome Amplification (WGA) methods have been developed. The multiple displacement...

    Authors: Tao Han, Ching-Wei Chang, Joshua C Kwekel, Ying Chen, Yun Ge, Francisco Martinez-Murillo, Donna Roscoe, Živana Težak, Reena Philip, Karen Bijwaard and James C Fuscoe
    Citation: BMC Genomics 2012 13:217
    Content type: Research article Published on:

  7. The TERT gene encodes the catalytic subunit of the telomerase complex and is responsible for maintaining telomere length. Vertebrate telomerase has been studied in eutherian mammals, fish, and the chicken, but le...

    Authors: Radmila Hrdličková, Jiří Nehyba, Shu Ly Lim, Frank Grützner and Henry R Bose Jr
    Citation: BMC Genomics 2012 13:216
    Content type: Research article Published on:

  8. The cellular proteome and metabolome are underlying dynamic regulation allowing rapid adaptation to changes in the environment. System-wide analysis of these dynamics will provide novel insights into mechanism...

    Authors: Guido Mastrobuoni, Susann Irgang, Matthias Pietzke, Heike E Aßmus, Markus Wenzel, Waltraud X Schulze and Stefan Kempa
    Citation: BMC Genomics 2012 13:215
    Content type: Research article Published on:

  9. Post-transcriptional control of gene expression is mostly conducted by specific elements in untranslated regions (UTRs) of mRNAs, in collaboration with specific binding proteins and RNAs. In several well chara...

    Authors: Stefan E Seemann, Susan M Sunkin, Michael J Hawrylycz, Walter L Ruzzo and Jan Gorodkin
    Citation: BMC Genomics 2012 13:214
    Content type: Research article Published on:

  10. Intramuscular fat (IMF) is one of the important factors influencing meat quality, however, for chickens, the molecular regulatory mechanisms underlying this trait have not yet been determined. In this study, a...

    Authors: Huan-Xian Cui, Ran-Ran Liu, Gui-Ping Zhao, Mai-Qing Zheng, Ji-Lan Chen and Jie Wen
    Citation: BMC Genomics 2012 13:213
    Content type: Research article Published on:

  11. The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of synt...

    Authors: Rocio Canals, Xiao-Qin Xia, Catrina Fronick, Sandra W Clifton, Brian MM Ahmer, Helene L Andrews-Polymenis, Steffen Porwollik and Michael McClelland
    Citation: BMC Genomics 2012 13:212
    Content type: Research article Published on:

  12. Insects detect environmental chemicals via a large and rapidly evolving family of chemosensory receptor proteins. Although our understanding of the molecular genetic basis for Drosophila chemoreception has inc...

    Authors: Natalie Howlett, Katherine L Dauber, Aditi Shukla, Brian Morton, John I Glendinning, Elyssa Brent, Caroline Gleason, Fahmida Islam, Denisse Izquierdo, Sweta Sanghavi, Anika Afroz, Aanam Aslam, Marissa Barbaro, Rebekah Blutstein, Margarita Borovka, Brianna Desire…
    Citation: BMC Genomics 2012 13:211
    Content type: Research article Published on:

  13. Microbial degradation of plant cell walls and its conversion to sugars and other byproducts is a key step in the carbon cycle on Earth. In order to process heterogeneous plant-derived biomass, specialized anae...

    Authors: Bareket Dassa, Ilya Borovok, Raphael Lamed, Bernard Henrissat, Pedro Coutinho, Christopher L Hemme, Yue Huang, Jizhong Zhou and Edward A Bayer
    Citation: BMC Genomics 2012 13:210
    Content type: Research article Published on:

  14. The biphasic life cycle with pelagic larva and benthic adult stages is widely observed in the animal kingdom, including the Porifera (sponges), which are the earliest branching metazoans. The demosponge, Amphimed...

    Authors: Cecilia Conaco, Pierre Neveu, Hongjun Zhou, Mary Luz Arcila, Sandie M Degnan, Bernard M Degnan and Kenneth S Kosik
    Citation: BMC Genomics 2012 13:209
    Content type: Research article Published on:

  16. Human Malaria is transmitted by mosquitoes of the genus Anopheles. Transmission is a complex phenomenon involving biological and environmental factors of humans, parasites and mosquitoes. Among more than 500 anop...

    Authors: Jesús Martínez-Barnetche, Rosa E Gómez-Barreto, Marbella Ovilla-Muñoz, Juan Téllez-Sosa, David E García López, Rhoel R Dinglasan, Ceereena Ubaida Mohien, Robert M MacCallum, Seth N Redmond, John G Gibbons, Antonis Rokas, Carlos A Machado, Febe E Cazares-Raga, Lilia González-Cerón, Salvador Hernández-Martínez and Mario H Rodríguez López
    Citation: BMC Genomics 2012 13:207
    Content type: Research article Published on:

  18. Cardiomyopathy syndrome (CMS) is a severe disease of Atlantic salmon (Salmo salar L.) associated with significant economic losses in the aquaculture industry. CMS is diagnosed with a severe inflammation and degra...

    Authors: Gerrit Timmerhaus, Aleksei Krasnov, Harald Takle, Sergey Afanasyev, Pål Nilsen, Marit Rode and Sven Martin Jørgensen
    Citation: BMC Genomics 2012 13:205
    Content type: Research article Published on:

  19. Bronchopulmonary dysplasia is a chronic lung disease of premature neonates characterized by arrested pulmonary alveolar development. There is increasing evidence that microRNAs (miRNAs) regulate translation of...

    Authors: Jie Dong, William A Carey, Stuart Abel, Christopher Collura, Guoqian Jiang, Sandra Tomaszek, Shari Sutor, Anja C Roden, Yan W Asmann, Y S Prakash and Dennis A Wigle
    Citation: BMC Genomics 2012 13:204
    Content type: Research article Published on:

  20. A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any giv...

    Authors: Laima Antanaviciute, Felicidad Fernández-Fernández, Johannes Jansen, Elisa Banchi, Katherine M Evans, Roberto Viola, Riccardo Velasco, Jim M Dunwell, Michela Troggio and Daniel J Sargent
    Citation: BMC Genomics 2012 13:203
    Content type: Research article Published on:

  22. Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 mil...

    Authors: Yun Jiao, Hui-min Jia, Xiong-wei Li, Ming-liang Chai, Hui-juan Jia, Zhe Chen, Guo-yun Wang, Chun-yan Chai, Eric van de Weg and Zhong-shan Gao
    Citation: BMC Genomics 2012 13:201
    Content type: Research article Published on:

  23. Geobacter lovleyi is a unique member of the Geobacteraceae because strains of this species share the ability to couple tetrachloroethene (PCE) reductive dechlorination to cis-1,2-dichloroethene (cis-DCE) with ene...

    Authors: Darlene D Wagner, Laura A Hug, Janet K Hatt, Melissa R Spitzmiller, Elizabeth Padilla-Crespo, Kirsti M Ritalahti, Elizabeth A Edwards, Konstantinos T Konstantinidis and Frank E Löffler
    Citation: BMC Genomics 2012 13:200
    Content type: Research article Published on:

  24. The human genome contains a large amount of cis-regulatory DNA elements responsible for directing both spatial and temporal gene-expression patterns. Previous studies have shown that based on their mRNA expressio...

    Authors: Himanshu Joshi, Silje H Nord, Arnoldo Frigessi, Anne-Lise Børresen-Dale and Vessela N Kristensen
    Citation: BMC Genomics 2012 13:199
    Content type: Research article Published on:

  25. The serovars Enteritidis and Typhimurium of the Gram-negative bacterium Salmonella enterica are significant causes of human food poisoning. Fowl carrying these bacteria often show no clinical disease, with detect...

    Authors: Tran Thanh-Son, Beaumont Catherine, Salmon Nigel, Fife Mark, Kaiser Pete, Le Bihan-Duval Elisabeth, Vignal Alain, Velge Philippe and Calenge Fanny
    Citation: BMC Genomics 2012 13:198
    Content type: Research article Published on:

  28. Traditional Chinese medicine uses various herbs for the treatment of various diseases for thousands of years and it is now time to assess the characteristics and effectiveness of these medicinal plants based o...

    Authors: Yuan Yuan, Lipu Song, Minhui Li, Guiming Liu, Yanan Chu, Luyu Ma, Yuanyuan Zhou, Xiao Wang, Wei Gao, Shuangshuang Qin, Jun Yu, Xumin Wang and Luqi Huang
    Citation: BMC Genomics 2012 13:195
    Content type: Research article Published on:

  29. Exome sequencing using next-generation sequencing technologies is a cost efficient approach to selectively sequencing coding regions of human genome for detection of disease variants. A significant amount of D...

    Authors: Yan Guo, Jirong Long, Jing He, Chung-I Li, Qiuyin Cai, Xiao-Ou Shu, Wei Zheng and Chun Li
    Citation: BMC Genomics 2012 13:194
    Content type: Methodology article Published on:

  30. The liver is central to most economically important metabolic processes in cattle. However, the changes in expression of genes that drive these processes remain incompletely characterised. RNA-seq is the new g...

    Authors: Matthew McCabe, Sinéad Waters, Dermot Morris, David Kenny, David Lynn and Chris Creevey
    Citation: BMC Genomics 2012 13:193
    Content type: Research article Published on:

  31. In rubber tree, bark is one of important agricultural and biological organs. However, the molecular mechanism involved in the bark formation and development in rubber tree remains largely unknown, which is at ...

    Authors: Dejun Li, Zhi Deng, Bi Qin, Xianghong Liu and Zhonghua Men
    Citation: BMC Genomics 2012 13:192
    Content type: Research article Published on:

  32. The assimilation of nitrogen in bacteria is achieved through only a few metabolic conversions between alpha-ketoglutarate, glutamate and glutamine. The enzymes that catalyze these conversions are glutamine syn...

    Authors: Tom Groot Kormelink, Eric Koenders, Yanick Hagemeijer, Lex Overmars, Roland J Siezen, Willem M de Vos and Christof Francke
    Citation: BMC Genomics 2012 13:191
    Content type: Research article Published on:

  33. The growing use of imaging procedures in medicine has raised concerns about exposure to low-dose ionising radiation (LDIR). While the disastrous effects of high dose ionising radiation (HDIR) is well documente...

    Authors: Monika Ray, Reem Yunis, Xiucui Chen and David M Rocke
    Citation: BMC Genomics 2012 13:190
    Content type: Research article Published on:

  34. SYT-SSX is the oncogene associated with synovial sarcoma (SS), a stem cell disease. SYT-SSX is thought to be responsible for sarcoma initiation and development. It interacts with components of Polycomb and SWI...

    Authors: Christina B Garcia, Christian M Shaffer and Josiane E Eid
    Citation: BMC Genomics 2012 13:189
    Content type: Research article Published on:

  35. Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10–11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nu...

    Authors: Jacob Abel and Jan Mrázek
    Citation: BMC Genomics 2012 13:188
    Content type: Research article Published on:

  36. L-ascorbic acid (AsA; vitamin C) is essential for all living plants where it functions as the main hydrosoluble antioxidant. It has diverse roles in the regulation of plant cell growth and expansion, photosynt...

    Authors: Viviana Lima-Silva, Abel Rosado, Vitor Amorim-Silva, Antonio Muñoz-Mérida, Clara Pons, Aureliano Bombarely, Oswaldo Trelles, Rafael Fernández-Muñoz, Antonio Granell, Victoriano Valpuesta and Miguel Ángel Botella
    Citation: BMC Genomics 2012 13:187
    Content type: Research article Published on:

  37. Microarrays are a powerful tool for transcriptome analysis. Best results are obtained using high-quality RNA samples for preparation and hybridization. Issues with RNA integrity can lead to low data quality an...

    Authors: Mario Fasold and Hans Binder
    Citation: BMC Genomics 2012 13:186
    Content type: Research article Published on:

  38. High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorph...

    Authors: Kevin Stoffel, Hans van Leeuwen, Alexander Kozik, David Caldwell, Hamid Ashrafi, Xinping Cui, Xiaoping Tan, Theresa Hill, Sebastian Reyes-Chin-Wo, Maria-Jose Truco, Richard W Michelmore and Allen Van Deynze
    Citation: BMC Genomics 2012 13:185
    Content type: Methodology article Published on:

  39. Brugia malayi is a nematode parasite that causes lymphatic filariasis, a disfiguring and disabiling tropical disease. Although a first draft genome sequence was released in 2007, very little is understood about t...

    Authors: Ben-Wen Li, Zhengyuan Wang, Amy C Rush, Makedonka Mitreva and Gary J Weil
    Citation: BMC Genomics 2012 13:184
    Content type: Research article Published on:

  40. The female-specific W chromosomes and male-specific Y chromosomes have proven difficult to assemble with whole-genome shotgun methods, creating a demand for new approaches to identify sequence contigs specific...

    Authors: Nancy Chen, Daniel W Bellott, David C Page and Andrew G Clark
    Citation: BMC Genomics 2012 13:183
    Content type: Methodology article Published on:

  41. The NF-κB family plays a prominent role in the innate immune response, cell cycle activation or cell apoptosis. Upon stimulation by pathogen-associated patterns, such as viral RNA a kinase cascade is activated...

    Authors: Marta Iwanaszko, Allan R Brasier and Marek Kimmel
    Citation: BMC Genomics 2012 13:182
    Content type: Research article Published on:

  42. The gilthead sea bream (Sparus aurata L.) occurs around the Mediterranean and along Eastern Atlantic coasts from Great Britain to Senegal. It is tolerant of a wide range of temperatures and salinities and is ofte...

    Authors: Daniel Garcia de la serrana, Alicia Estévez, Karl Andree and Ian A Johnston
    Citation: BMC Genomics 2012 13:181
    Content type: Research article Published on:

  43. Under-dimensioned hearts causing functional problems are associated with higher mortality rates in intensive Atlantic salmon aquaculture. Previous studies have indicated that tetradecylthioacetic acid (TTA) in...

    Authors: Fabian Grammes, Kjell-Arne Rørvik, Magny S Thomassen, Rolf K Berge and Harald Takle
    Citation: BMC Genomics 2012 13:180
    Content type: Research article Published on:

  44. The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. ...

    Authors: Tim Kahlke, Alexander Goesmann, Erik Hjerde, Nils Peder Willassen and Peik Haugen
    Citation: BMC Genomics 2012 13:179
    Content type: Research article Published on:

  45. Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic m...

    Authors: Mikkel Schubert, Aurelien Ginolhac, Stinus Lindgreen, John F Thompson, Khaled AS AL-Rasheid, Eske Willerslev, Anders Krogh and Ludovic Orlando
    Citation: BMC Genomics 2012 13:178
    Content type: Methodology article Published on:

  46. Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and ext...

    Authors: Aurelien Ginolhac, Julia Vilstrup, Jesper Stenderup, Morten Rasmussen, Mathias Stiller, Beth Shapiro, Grant Zazula, Duane Froese, Kathleen E Steinmann, John F Thompson, Khaled AS AL-Rasheid, Thomas MP Gilbert, Eske Willerslev and Ludovic Orlando
    Citation: BMC Genomics 2012 13:177
    Content type: Methodology article Published on:

  47. Papaya is a major fruit crop in tropical and subtropical regions worldwide. It is trioecious with three sex forms: male, female, and hermaphrodite. Sex determination is controlled by a pair of nascent sex chro...

    Authors: Jong-Kuk Na, Jianping Wang, Jan E Murray, Andrea R Gschwend, Wenli Zhang, Qingyi Yu, Rafael Navajas‒ Pérez, F Alex Feltus, Cuixia Chen, Zdenek Kubat, Paul H Moore, Jiming Jiang, Andrew H Paterson and Ray Ming
    Citation: BMC Genomics 2012 13:176
    Content type: Research article Published on:

  48. The glycosylation process, catalyzed by ubiquitous glycosyltransferase (GT) family enzymes, is a prevalent modification of plant secondary metabolites that regulates various functions such as hormone homeostas...

    Authors: Vitthal T Barvkar, Varsha C Pardeshi, Sandip M Kale, Narendra Y Kadoo and Vidya S Gupta
    Citation: BMC Genomics 2012 13:175
    Content type: Research article Published on:

  49. At present five evolutionary hypotheses have been proposed to explain the great variability of the genomic GC content among and within genomes: the mutational bias, the biased gene conversion, the DNA breakpoi...

    Authors: Luisa Berná, Ankita Chaurasia, Claudia Angelini, Concetta Federico, Salvatore Saccone and Giuseppe D'Onofrio
    Citation: BMC Genomics 2012 13:174
    Content type: Research article Published on:

  50. The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious dev...

    Authors: Maria A Nilsson, Axel Janke, Elizabeth P Murchison, Zemin Ning and Björn M Hallström
    Citation: BMC Genomics 2012 13:172
    Content type: Research article Published on:

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BMC Genomics

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