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  1. The central metabolic pathway of glycolysis converts glucose to pyruvate, with the net production of 2 ATP and 2 NADH per glucose molecule. Each of the ten reactions in this pathway is typically catalyzed by m...

    Authors: Soumya A Vemuganti, Fernando Pardo-Manuel de Villena and Deborah A O'Brien
    Citation: BMC Genomics 2010 11:285
    Content type: Research article Published on:

  2. CCCH type zinc finger proteins are RNA binding proteins with regulatory functions at all stages of mRNA metabolism. The best-characterized member, tritetraproline (TTP), binds to AU rich elements in 3' UTRs of...

    Authors: Susanne Kramer, Nicola C Kimblin and Mark Carrington
    Citation: BMC Genomics 2010 11:283
    Content type: Research article Published on:

  3. RNA-Seq exploits the rapid generation of gigabases of sequence data by Massively Parallel Nucleotide Sequencing, allowing for the mapping and digital quantification of whole transcriptomes. Whilst previous com...

    Authors: James R Bradford, Yvonne Hey, Tim Yates, Yaoyong Li, Stuart D Pepper and Crispin J Miller
    Citation: BMC Genomics 2010 11:282
    Content type: Research article Published on:

  4. Post-transcriptional regulation in eukaryotes can be operated through microRNA (miRNAs) mediated gene silencing. MiRNAs are small (18-25 nucleotides) non-coding RNAs that play crucial role in regulation of gen...

    Authors: Fabrice Legeai, Guillaume Rizk, Thomas Walsh, Owain Edwards, Karl Gordon, Dominique Lavenier, Nathalie Leterme, Agnès Méreau, Jacques Nicolas, Denis Tagu and Stéphanie Jaubert-Possamai
    Citation: BMC Genomics 2010 11:281
    Content type: Research article Published on:

  5. In tropical countries, losses caused by bovine tick Rhipicephalus (Boophilus) microplus infestation have a tremendous economic impact on cattle production systems. Genetic variation between Bos taurus and Bos ind...

    Authors: Marco Antonio Machado, Ana Luisa S Azevedo, Roberto L Teodoro, Maria A Pires, Maria Gabriela CD Peixoto, Célio de Freitas, Márcia Cristina A Prata, John Furlong, Marcos Vinicius GB da Silva, Simone EF Guimarães, Luciana CA Regitano, Luiz L Coutinho, Gustavo Gasparin and Rui S Verneque
    Citation: BMC Genomics 2010 11:280
    Content type: Research article Published on:

  6. Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This ...

    Authors: Jong S Leong, Stuart G Jantzen, Kristian R von Schalburg, Glenn A Cooper, Amber M Messmer, Nancy Y Liao, Sarah Munro, Richard Moore, Robert A Holt, Steven JM Jones, William S Davidson and Ben F Koop
    Citation: BMC Genomics 2010 11:279
    Content type: Research article Published on:

  7. Large collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-norma...

    Authors: Bo-Young Lee, Aimee E Howe, Matthew A Conte, Helena D'Cotta, Elodie Pepey, Jean-Francois Baroiller, Federica di Palma, Karen L Carleton and Thomas D Kocher
    Citation: BMC Genomics 2010 11:278
    Content type: Research article Published on:

  10. While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studyin...

    Authors: Soroush Sharbati, Marc R Friedländer, Jutta Sharbati, Lena Hoeke, Wei Chen, Andreas Keller, Peer F Stähler, Nikolaus Rajewsky and Ralf Einspanier
    Citation: BMC Genomics 2010 11:275
    Content type: Research article Published on:

  11. High-throughput microarray experiments now permit researchers to screen thousands of genes simultaneously and determine the different expression levels of genes in normal or cancerous tissues. In this paper, w...

    Authors: Austin H Chen, Yin-Wu Tsau and Ching-Heng Lin
    Citation: BMC Genomics 2010 11:274
    Content type: Methodology article Published on:

  12. The use of gene expression profiling for the classification of human cancer tumors has been widely investigated. Previous studies were successful in distinguishing several tumor types in binary problems. As th...

    Authors: Wensheng Zhang, Kelly Robbins, Yupeng Wang, Keith Bertrand and Romdhane Rekaya
    Citation: BMC Genomics 2010 11:273
    Content type: Methodology article Published on:

  13. Shigella flexneri inhibits apoptosis in infected epithelial cells. In order to understand the pro-survival effects induced by the bacteria, we utilized apoptosis-specific microarrays to analyze the changes in euk...

    Authors: Christina S Faherty, D Scott Merrell, Cristina Semino-Mora, Andre Dubois, Aishwarya V Ramaswamy and Anthony T Maurelli
    Citation: BMC Genomics 2010 11:272
    Content type: Research article Published on:

  14. Genome-wide analysis of sequence divergence among species offers profound insights into the evolutionary processes that shape lineages. When full-genome sequencing is not feasible for a broad comparative study...

    Authors: Suzy CP Renn, Heather E Machado, Albyn Jones, Kosha Soneji, Rob J Kulathinal and Hans A Hofmann
    Citation: BMC Genomics 2010 11:271
    Content type: Methodology article Published on:

  15. Surprisingly little is known about the organization and distribution of tRNA genes and tRNA-related sequences on a genome-wide scale. While tRNA gene complements are usually reported in passing as part of geno...

    Authors: Clara Bermudez-Santana, Camille Stephan-Otto Attolini, Toralf Kirsten, Jan Engelhardt, Sonja J Prohaska, Stephan Steigele and Peter F Stadler
    Citation: BMC Genomics 2010 11:270
    Content type: Research article Published on:

  16. Genetic maps constitute the basis of breeding programs for many agricultural organisms. The creation of these maps is dependent on marker discovery. Melon, among other crops, is still lagging in genomic resour...

    Authors: Ron Ophir, Ravit Eshed, Rotem Harel-Beja, Galil Tzuri, Vitaly Portnoy, Yoseph Burger, Shai Uliel, Nurit Katzir and Amir Sherman
    Citation: BMC Genomics 2010 11:269
    Content type: Research article Published on:

  17. Glycyrrhiza uralensis is one of the most popular medicinal plants in the world and is also widely used in the flavoring of food and tobacco. Due to limited genomic and transcriptomic data, the biosynthetic pathwa...

    Authors: Ying Li, Hong-Mei Luo, Chao Sun, Jing-Yuan Song, Yong-Zhen Sun, Qiong Wu, Ning Wang, Hui Yao, André Steinmetz and Shi-Lin Chen
    Citation: BMC Genomics 2010 11:268
    Content type: Research article Published on:

  18. To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP) da...

    Authors: Toshio Yamamoto, Hideki Nagasaki, Jun-ichi Yonemaru, Kaworu Ebana, Maiko Nakajima, Taeko Shibaya and Masahiro Yano
    Citation: BMC Genomics 2010 11:267
    Content type: Research article Published on:

  19. The disease caused by Haemonchus contortus, a blood-feeding nematode of small ruminants, is of major economic importance worldwide. The infective third-stage larva (L3) of this gastric nematode is enclosed in a c...

    Authors: Cinzia Cantacessi, Bronwyn E Campbell, Neil D Young, Aaron R Jex, Ross S Hall, Paul JA Presidente, Jodi L Zawadzki, Weiwei Zhong, Boanerges Aleman-Meza, Alex Loukas, Paul W Sternberg and Robin B Gasser
    Citation: BMC Genomics 2010 11:266
    Content type: Research article Published on:

  20. Epithelial and especially mucosal immunity represents the first line of defence against the plethora of potential pathogens trying to invade via the gastrointestinal tract. The salivary glands of the fruit fly...

    Authors: Ahmed Abdelsadik and Thomas Roeder
    Citation: BMC Genomics 2010 11:265
    Content type: Research article Published on:

  21. Myxococcus xanthus is a Gram negative bacterium that can differentiate into metabolically quiescent, environmentally resistant spores. Little is known about the mechanisms involved in differentiation in part beca...

    Authors: Frank-Dietrich Müller, Anke Treuner-Lange, Johann Heider, Stuart M Huntley and Penelope I Higgs
    Citation: BMC Genomics 2010 11:264
    Content type: Research article Published on:

  22. The major toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) appear to result from dysregulation of mRNA levels mediated by the aryl hydrocarbon receptor (AHR). Dioxin-like chemicals alter expression of ...

    Authors: Ivy D Moffat, Paul C Boutros, Hanbo Chen, Allan B Okey and Raimo Pohjanvirta
    Citation: BMC Genomics 2010 11:263
    Content type: Research article Published on:

  23. American ginseng (Panax quinquefolius L.) is one of the most widely used herbal remedies in the world. Its major bioactive constituents are the triterpene saponins known as ginsenosides. However, little is known ...

    Authors: Chao Sun, Ying Li, Qiong Wu, Hongmei Luo, Yongzhen Sun, Jingyuan Song, Edmund MK Lui and Shilin Chen
    Citation: BMC Genomics 2010 11:262
    Content type: Research article Published on:

  24. Sugarcane (Saccharum spp.) has become an increasingly important crop for its leading role in biofuel production. The high sugar content species S. officinarum is an octoploid without known diploid or tetraploid p...

    Authors: Jianping Wang, Bruce Roe, Simone Macmil, Qingyi Yu, Jan E Murray, Haibao Tang, Cuixia Chen, Fares Najar, Graham Wiley, John Bowers, Marie-Anne Van Sluys, Daniel S Rokhsar, Matthew E Hudson, Stephen P Moose, Andrew H Paterson and Ray Ming
    Citation: BMC Genomics 2010 11:261
    Content type: Research article Published on:

  27. Microbial eukaryotes show large variations in genome structure and content between lineages, indicating extensive flexibility over evolutionary timescales. Here we address the tempo and mode of such changes wi...

    Authors: Katarina Roxström-Lindquist, Jon Jerlström-Hultqvist, Anders Jørgensen, Karin Troell, Staffan G Svärd and Jan O Andersson
    Citation: BMC Genomics 2010 11:258
    Content type: Research article Published on:

  28. Histone modifications play an important role in gene regulation. Acetylation of histone 3 lysine 9 (H3K9ac) is generally associated with transcription initiation and unfolded chromatin, thereby positively infl...

    Authors: Anton Kratz, Erik Arner, Rintaro Saito, Atsutaka Kubosaki, Jun Kawai, Harukazu Suzuki, Piero Carninci, Takahiro Arakawa, Masaru Tomita, Yoshihide Hayashizaki and Carsten O Daub
    Citation: BMC Genomics 2010 11:257
    Content type: Research article Published on:

  29. Pre-clinical models that effectively recapitulate human disease are critical for expanding our knowledge of cancer biology and drug resistance mechanisms. For haematological malignancies, the non-obese diabeti...

    Authors: Amy L Samuels, Violet K Peeva, Rachael A Papa, Marin J Firth, Richard W Francis, Alex H Beesley, Richard B Lock and Ursula R Kees
    Citation: BMC Genomics 2010 11:256
    Content type: Research article Published on:

  30. Many Firmicutes bacteria, including solvent-producing clostridia such as Clostridium acetobutylicum, are able to utilize xylose, an abundant carbon source in nature. Nevertheless, homology searches failed to reco...

    Authors: Yang Gu, Yi Ding, Cong Ren, Zhe Sun, Dmitry A Rodionov, Weiwen Zhang, Sheng Yang, Chen Yang and Weihong Jiang
    Citation: BMC Genomics 2010 11:255
    Content type: Research article Published on:

  31. Tissue plasminogen activator (tPA) is known to have functions beyond fibrinolysis in acute ischemic stroke, such as blood brain barrier disruption. To further delineate tPA functions in the blood, we examined ...

    Authors: Glen C Jickling, Xinhua Zhan, Bradley P Ander, Renée J Turner, Boryana Stamova, Huichun Xu, Yingfang Tian, Dazhi Liu, Ryan R Davis, Paul A Lapchak and Frank R Sharp
    Citation: BMC Genomics 2010 11:254
    Content type: Research article Published on:

  32. Previous studies have shown that acute intake of high-phenol virgin olive oil reduces pro-inflammatory, pro-oxidant and pro-thrombotic markers compared with low phenols virgin olive oil, but it still remains u...

    Authors: Antonio Camargo, Juan Ruano, Juan M Fernandez, Laurence D Parnell, Anabel Jimenez, Monica Santos-Gonzalez, Carmen Marin, Pablo Perez-Martinez, Marino Uceda, Jose Lopez-Miranda and Francisco Perez-Jimenez
    Citation: BMC Genomics 2010 11:253
    Content type: Research article Published on:

  33. The beta-defensin gene cluster (DEFB) at chromosome 8p23.1 is one of the most copy number (CN) variable regions of the human genome. Whereas individual DEFB CNs have been suggested as independent genetic risk ...

    Authors: Stefan Taudien, Marco Groth, Klaus Huse, Andreas Petzold, Karol Szafranski, Jochen Hampe, Philip Rosenstiel, Stefan Schreiber and Matthias Platzer
    Citation: BMC Genomics 2010 11:252
    Content type: Research article Published on:

  34. The ferret (Mustela putorius furo) represents an attractive animal model for the study of respiratory diseases, including influenza. Despite its importance for biomedical research, the number of reagents for mole...

    Authors: Carl E Bruder, Suxia Yao, Francis Larson, Jeremy V Camp, Ronald Tapp, Alexis McBrayer, Nicholas Powers, Willy Valdivia Granda and Colleen B Jonsson
    Citation: BMC Genomics 2010 11:251
    Content type: Research article Published on:

  35. The DUB/USP17 subfamily of deubiquitinating enzymes were originally identified as immediate early genes induced in response to cytokine stimulation in mice (DUB-1, DUB-1A, DUB-2, DUB-2A). Subsequently we have ...

    Authors: James F Burrows, Christopher J Scott and James A Johnston
    Citation: BMC Genomics 2010 11:250
    Content type: Research article Published on:

  36. Digital gene expression (DGE) profiling has become an established tool to study RNA expression. Here, we provide an in-depth analysis of small RNA DGE profiles from two different rat strains (BN-Lx and SHR) fr...

    Authors: Sam EV Linsen, Elzo de Wit, Ewart de Bruijn and Edwin Cuppen
    Citation: BMC Genomics 2010 11:249
    Content type: Research article Published on:

  37. The dinoflagellate Alexandrium minutum typically produces paralytic shellfish poisoning (PSP) toxins, which are known only from cyanobacteria and dinoflagellates. While a PSP toxin gene cluster has recently been ...

    Authors: Ines Yang, Uwe John, Sára Beszteri, Gernot Glöckner, Bernd Krock, Alexander Goesmann and Allan D Cembella
    Citation: BMC Genomics 2010 11:248
    Content type: Research article Published on:

  38. Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea b...

    Authors: Qi-Long Qin, Xi-Ying Zhang, Xu-Min Wang, Gui-Ming Liu, Xiu-Lan Chen, Bin-Bin Xie, Hong-Yue Dang, Bai-Cheng Zhou, Jun Yu and Yu-Zhong Zhang
    Citation: BMC Genomics 2010 11:247
    Content type: Research article Published on:

  39. Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh muta...

    Authors: Qiang Xu, Yuanlong Liu, Andan Zhu, Xiaomeng Wu, Junli Ye, Keqin Yu, Wenwu Guo and Xiuxin Deng
    Citation: BMC Genomics 2010 11:246
    Content type: Research article Published on:

  40. Small untranslated RNAs (sRNAs) are widespread regulators of gene expression in bacteria. This study reports on a comprehensive screen for sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobiu...

    Authors: Jan-Philip Schlüter, Jan Reinkensmeier, Svenja Daschkey, Elena Evguenieva-Hackenberg, Stefan Janssen, Sebastian Jänicke, Jörg D Becker, Robert Giegerich and Anke Becker
    Citation: BMC Genomics 2010 11:245
    Content type: Research article Published on:

  41. DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number.

    Authors: John C Castle, Matthew Biery, Heather Bouzek, Tao Xie, Ronghua Chen, Kira Misura, Stuart Jackson, Christopher D Armour, Jason M Johnson, Carol A Rohl and Christopher K Raymond
    Citation: BMC Genomics 2010 11:244
    Content type: Methodology article Published on:

  42. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and functions as a starter for the production of the traditional Japanese food "natto" made from soybeans. Alt...

    Authors: Yukari Nishito, Yasunori Osana, Tsuyoshi Hachiya, Kris Popendorf, Atsushi Toyoda, Asao Fujiyama, Mitsuhiro Itaya and Yasubumi Sakakibara
    Citation: BMC Genomics 2010 11:243
    Content type: Research article Published on:

  43. While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has...

    Authors: Niranjan Nagarajan, Christopher Cook, MariaPia Di Bonaventura, Hong Ge, Allen Richards, Kimberly A Bishop-Lilly, Robert DeSalle, Timothy D Read and Mihai Pop
    Citation: BMC Genomics 2010 11:242
    Content type: Correspondence Published on:

  44. Prostaglandin E2 (PGE2) is involved in several chronic inflammatory diseases including periodontitis, which causes loss of the gingival tissue and alveolar bone supporting the teeth. We have previously shown that...

    Authors: Tove Båge, Johan Lindberg, Joakim Lundeberg, Thomas Modéer and Tülay Yucel-Lindberg
    Citation: BMC Genomics 2010 11:241
    Content type: Research article Published on:

  45. Due to the high morbidity and mortality of fulminant hepatitis, early diagnosis followed by early effective treatment is the key for prognosis improvement. So far, little is known about the gene expression cha...

    Authors: Feng Chen, Hai-Hong Zhu, Lin-Fu Zhou, Jie Li, Li-Ying Zhao, Shan-Shan Wu, Jing Wang, Wei Liu and Zhi Chen
    Citation: BMC Genomics 2010 11:240
    Content type: Research article Published on:

  46. The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients.

    Authors: Willem van Schaik, Janetta Top, David R Riley, Jos Boekhorst, Joyce EP Vrijenhoek, Claudia ME Schapendonk, Antoni PA Hendrickx, Isaäc J Nijman, Marc JM Bonten, Hervé Tettelin and Rob JL Willems
    Citation: BMC Genomics 2010 11:239
    Content type: Research article Published on:

  47. Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different ...

    Authors: Leandro M Moreira, Nalvo F Almeida Jr, Neha Potnis, Luciano A Digiampietri, Said S Adi, Julio C Bortolossi, Ana C da Silva, Aline M da Silva, Fabrício E de Moraes, Julio C de Oliveira, Robson F de Souza, Agda P Facincani, André L Ferraz, Maria I Ferro, Luiz R Furlan, Daniele F Gimenez…
    Citation: BMC Genomics 2010 11:238
    Content type: Research article Published on:

  48. The thioredoxin and/or glutathione pathways occur in all organisms. They provide electrons for deoxyribonucleotide synthesis, function as antioxidant defenses, in detoxification, Fe/S biogenesis and participat...

    Authors: Lucía Otero, Mariana Bonilla, Anna V Protasio, Cecilia Fernández, Vadim N Gladyshev and Gustavo Salinas
    Citation: BMC Genomics 2010 11:237
    Content type: Research article Published on:

  49. The nematode C. briggsae serves as a useful model organism for comparative analysis of developmental and behavioral processes. The amenability of C. briggsae to genetic manipulations and the availability of its g...

    Authors: Daniel C Koboldt, Julia Staisch, Bavithra Thillainathan, Karen Haines, Scott E Baird, Helen M Chamberlin, Eric S Haag, Raymond D Miller and Bhagwati P Gupta
    Citation: BMC Genomics 2010 11:236
    Content type: Research article Published on:

  50. Plasmodium falciparum, the causative agent of severe human malaria, has evolved to become resistant to previously successful antimalarial chemotherapies, most notably chloroquine and the antifolates. The prevalen...

    Authors: John VW Becker, Linda Mtwisha, Bridget G Crampton, Stoyan Stoychev, Anna C van Brummelen, Shaun Reeksting, Abraham I Louw, Lyn-Marie Birkholtz and Dalu T Mancama
    Citation: BMC Genomics 2010 11:235
    Content type: Research article Published on:

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BMC Genomics

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