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  1. Cellular glucose availability is crucial for the functioning of most biological processes. Our understanding of the glucose regulatory system has been greatly advanced by studying the model organism Saccharomyces...

    Authors: Eva Apweiler, Katrin Sameith, Thanasis Margaritis, Nathalie Brabers, Loes van de Pasch, Linda V Bakker, Dik van Leenen, Frank CP Holstege and Patrick Kemmeren
    Citation: BMC Genomics 2012 13:239
  2. There is considerable interest in developing high-throughput genotyping with single nucleotide polymorphisms (SNPs) for the identification of genes affecting important ecological or economical traits. SNPs are...

    Authors: Mekki Boussaha, René Guyomard, Cédric Cabau, Diane Esquerré and Edwige Quillet
    Citation: BMC Genomics 2012 13:238
  3. Many plant genes have been identified through whole genome and deep transcriptome sequencing and other methods; yet our knowledge on the function of many of these genes remains limited. The integration and ana...

    Authors: Tyler J Wilson, Liming Lai, Yuguang Ban and Steven X Ge
    Citation: BMC Genomics 2012 13:237
  4. Recent advances in genotyping with high-density markers nowadays enable genome-wide genomic analyses in crops. A detailed characterisation of the population structure and linkage disequilibrium (LD) is essenti...

    Authors: Katharina V Alheit, Hans Peter Maurer, Jochen C Reif, Matthew R Tucker, Volker Hahn, Elmar A Weissmann and Tobias Würschum
    Citation: BMC Genomics 2012 13:235
  5. Cowpea [Vigna unguiculata (L.) Walp] exhibits a considerable variation in leaf shape. Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot he...

    Authors: Marti Pottorff, Jeffrey D Ehlers, Christian Fatokun, Philip A Roberts and Timothy J Close
    Citation: BMC Genomics 2012 13:234
  6. Losses of slaughter-weight pigs due to transport stress are both welfare and economic concerns to pork producers. Historically, the HAL-1843 mutation in ryanodine receptor 1 was considered responsible for most...

    Authors: Dan J Nonneman, Tami Brown-Brandl, Shuna A Jones, Ralph T Wiedmann and Gary A Rohrer
    Citation: BMC Genomics 2012 13:233
  7. The morphogenesis of the cerebral cortex depends on the precise control of gene expression during development. Small non-coding RNAs, including microRNAs and other groups of small RNAs, play profound roles in ...

    Authors: Mao-jin Yao, Gang Chen, Ping-ping Zhao, Ming-hua Lu, Jiang Jian, Mo-fang Liu and Xiao-bing Yuan
    Citation: BMC Genomics 2012 13:232
  8. Buckwheat, consisting of two cultivated species Fagopyrum tataricum and F. esculentum, is the richest source of flavonoid rutin. Vegetative tissues of both the Fagopyrum species contain almost similar amount of r...

    Authors: Nidhi Gupta, Pradeep Kumar Naik and Rajinder Singh Chauhan
    Citation: BMC Genomics 2012 13:231
  9. Term clustering, by measuring the string similarities between terms, is known within the natural language processing community to be an effective method for improving the quality of texts and dictionaries. How...

    Authors: Atsuko Yamaguchi, Yasunori Yamamoto, Jin-Dong Kim, Toshihisa Takagi and Akinori Yonezawa
    Citation: BMC Genomics 2012 13(Suppl 3):S8

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

  10. 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

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

  11. 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

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

  12. 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

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

  13. 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

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

  14. 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

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

  15. 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

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

  16. 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

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

  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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

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