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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. The constant increase in development and spread of bacterial resistance to antibiotics poses a serious threat to human health. New sequencing technologies are now on the horizon that will yield massive increas...

    Authors: Andreas Dötsch, Frank Klawonn, Michael Jarek, Maren Scharfe, Helmut Blöcker and Susanne Häussler
    Citation: BMC Genomics 2010 11:234
    Content type: Research article Published on:

  41. Recently, the discovery of copy number variation (CNV) led researchers to think that there are more variations of genomic DNA than initially believed. Moreover, a certain CNV region has been found to be associ...

    Authors: Joon Seol Bae, Hyun Sub Cheong, Lyoung Hyo Kim, Suk NamGung, Tae Joon Park, Ji-Yong Chun, Jason Yongha Kim, Charisse Flerida A Pasaje, Jin Sol Lee and Hyoung Doo Shin
    Citation: BMC Genomics 2010 11:232
    Content type: Research article Published on:

  42. Chromodomain-containing Gypsy LTR retrotransposons or chromoviruses are widely distributed among eukaryotes and have been found in plants, fungi and vertebrates. The previous comprehensive survey of chromoviru...

    Authors: Olga Novikova, Georgiy Smyshlyaev and Alexander Blinov
    Citation: BMC Genomics 2010 11:231
    Content type: Research article Published on:

  43. Uncovering the molecular mechanisms involved in epileptogenesis is critical to better understand the physiopathology of epilepsies and to help develop new therapeutic strategies for this prevalent and severe n...

    Authors: Oswaldo K Okamoto, Luciana Janjoppi, Felipe M Bonone, Aline P Pansani, Alexandre V da Silva, Fúlvio A Scorza and Esper A Cavalheiro
    Citation: BMC Genomics 2010 11:230
    Content type: Research article Published on:

  45. Perkinsus marinus, a protozoan parasite of the eastern oyster Crassostrea virginica, has devastated natural and farmed oyster populations along the Atlantic and Gulf coasts of the United States. It is classified ...

    Authors: Sandeep J Joseph, José A Fernández-Robledo, Malcolm J Gardner, Najib M El-Sayed, Chih-Horng Kuo, Eric J Schott, Haiming Wang, Jessica C Kissinger and Gerardo R Vasta
    Citation: BMC Genomics 2010 11:228
    Content type: Research article Published on:

  46. The common liver fluke Fasciola hepatica is the agent of a zoonosis with significant economic consequences in livestock production worldwide, and increasing relevance to human health in developing countries. Alth...

    Authors: Martín Cancela, Natalia Ruétalo, Nicolás Dell'Oca, Edileuza da Silva, Pablo Smircich, Gabriel Rinaldi, Leda Roche, Carlos Carmona, Fernando Alvarez-Valín, Arnaldo Zaha and José F Tort
    Citation: BMC Genomics 2010 11:227
    Content type: Research article Published on:

  47. Cytokines such as TNF-alpha and IL-1beta are known for their contribution to inflammatory processes in liver. In contrast, the cytokine IL-17 has not yet been assigned a role in liver diseases. IL-17 can coope...

    Authors: Titus Sparna, Julia Rétey, Kathrin Schmich, Ute Albrecht, Katrin Naumann, Norbert Gretz, Hans-Peter Fischer, Johannes G Bode and Irmgard Merfort
    Citation: BMC Genomics 2010 11:226
    Content type: Research article Published on:

  48. Brugia malayi and B. pahangi are two closely related nematodes that cause filariasis in humans and animals. However, B. pahangi microfilariae are able to develop in and be transmitted by the mosquito, Armigeres s...

    Authors: Michael M Kariuki, Leonard B Hearne and Brenda T Beerntsen
    Citation: BMC Genomics 2010 11:225
    Content type: Research article Published on:

  49. MicroRNA-mediated control of gene expression via translational inhibition has substantial impact on cellular regulatory mechanisms. About 37% of mammalian microRNAs appear to be located within introns of prote...

    Authors: Dominik Lutter, Carsten Marr, Jan Krumsiek, Elmar W Lang and Fabian J Theis
    Citation: BMC Genomics 2010 11:224
    Content type: Research article Published on:

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