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  1. RNA secondary structure plays a scaffolding role for RNA tertiary conformation. Accurate secondary structure prediction can not only identify double-stranded helices and single stranded-loops but also help pro...

    Authors: Pooya Shareghi, Yingfeng Wang, Russell Malmberg and Liming Cai
    Citation: BMC Genomics 2012 13(Suppl 3):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  2. Multi-objective optimization (MOO) involves optimization problems with multiple objectives. Generally, theose objectives is used to estimate very different aspects of the solutions, and these aspects are often...

    Authors: Junwan Liu, Zhoujun Li, Xiaohua Hu, Yiming Chen and Feifei Liu
    Citation: BMC Genomics 2012 13(Suppl 3):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  3. Computational approaches to generate hypotheses from biomedical literature have been studied intensively in recent years. Nevertheless, it still remains a challenge to automatically discover novel, cross-silo ...

    Authors: Jayasimha Reddy Katukuri, Ying Xie, Vijay V Raghavan and Ashish Gupta
    Citation: BMC Genomics 2012 13(Suppl 3):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  4. One of the many unique features of biological databases is that the mere existence of a ground data item is not always a precondition for a query response. It may be argued that from a biologist's standpoint, ...

    Authors: Hasan M Jamil
    Citation: BMC Genomics 2012 13(Suppl 3):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  5. MiRNA are about 22nt long small noncoding RNAs that post transcriptionally regulate gene expression in animals, plants and protozoa. Confident identification of MiRNA-Target Interactions (MTI) is vital to unde...

    Authors: Jiandong Ding, Danqing Li, Uwe Ohler, Jihong Guan and Shuigeng Zhou
    Citation: BMC Genomics 2012 13(Suppl 3):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  6. In the biomedical domain, there are immense data and tremendous increase of genomics and biomedical relevant publications. The wealth of information has led to an increasing amount of interest in and need for ...

    Authors: Yan Chen, Xiaoshi Yin, Zhoujun Li, Xiaohua Hu and Jimmy Xiangji Huang
    Citation: BMC Genomics 2012 13(Suppl 3):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  7. Phenylalanine ammonia lyase (PAL) is a key enzyme of the phenylpropanoid pathway that catalyzes the deamination of phenylalanine to trans-cinnamic acid, a precursor for the lignin and flavonoid biosynthetic pa...

    Authors: Ujwal R Bagal, James H Leebens-Mack, W Walter Lorenz and Jeffrey FD Dean
    Citation: BMC Genomics 2012 13(Suppl 3):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  8. The activity of the yeast activator protein 1 (Yap1p) increases under stress conditions, which leads to enhanced transcription of a number of genes encoding protective enzymes or other proteins. To obtain a gl...

    Authors: He Jun, Thomas Kieselbach and Leif J Jönsson
    Citation: BMC Genomics 2012 13:230
    Content type: Research article Published on:

  9. The subtelomeres of many protozoa are highly enriched in genes with roles in niche adaptation. T. cruzi trypomastigotes express surface proteins from Trans-Sialidase (TS) and Dispersed Gene Family-1 (DGF-1) super...

    Authors: Roberto R Moraes Barros, Marjorie M Marini, Cristiane Regina Antônio, Danielle R Cortez, Andrea M Miyake, Fábio M Lima, Jeronimo C Ruiz, Daniella C Bartholomeu, Miguel A Chiurillo, José Luis Ramirez and José Franco da Silveira
    Citation: BMC Genomics 2012 13:229
    Content type: Research article Published on:

  10. Staphylococcus epidermidis is a commensal bacterium but can colonize the hospital environment due to its ability to form biofilms favouring adhesion to host tissues, medical devices and increasing resistance to a...

    Authors: Diana Gutiérrez, Beatriz Martínez, Ana Rodríguez and Pilar García
    Citation: BMC Genomics 2012 13:228
    Content type: Research article Published on:

  11. Recent studies have shown that plant genomes have potentially undergone rampant horizontal gene transfer (HGT). In plant parasitic systems HGT appears to be facilitated by the intimate physical association bet...

    Authors: Zhenxiang Xi, Robert K Bradley, Kenneth J Wurdack, KM Wong, M Sugumaran, Kirsten Bomblies, Joshua S Rest and Charles C Davis
    Citation: BMC Genomics 2012 13:227
    Content type: Research article Published on:

  12. The sex chromosomes of Silene latifolia are heteromorphic as in mammals, with females being homogametic (XX) and males heterogametic (XY). While recombination occurs along the entire X chromosome in females, reco...

    Authors: Nicolas Blavet, Hana Blavet, Radim Čegan, Niklaus Zemp, Jana Zdanska, Bohuslav Janoušek, Roman Hobza and Alex Widmer
    Citation: BMC Genomics 2012 13:226
    Content type: Research article Published on:

  15. Genomic analysis of bacteriophages infecting the Burkholderia cepacia complex (BCC) is an important preliminary step in the development of a phage therapy protocol for these opportunistic pathogens. The objective...

    Authors: Karlene H Lynch, Paul Stothard and Jonathan J Dennis
    Citation: BMC Genomics 2012 13:223
    Content type: Research article Published on:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  31. 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:

  33. 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:

  34. 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:

  35. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:

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