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  1. Although the high mobility group A1 (HMGA1) gene is widely overexpressed in diverse cancers and portends a poor prognosis in some tumors, the molecular mechanisms that mediate its role in transformation have rema...

    Authors: Andrew Schuldenfrei, Amy Belton, Jeanne Kowalski, C Conover Talbot Jr, Francescopaolo Di Cello, Weijie Poh, Hua-Ling Tsai, Sandeep N Shah, Tait H Huso, David L Huso and Linda MS Resar
    Citation: BMC Genomics 2011 12:549
    Content type: Research article Published on:

  2. The genetics of transcript-level variation is an exciting field that has recently given rise to many studies. Genetical genomics studies have mainly focused on cell lines, blood cells or adipose tissues, from ...

    Authors: Laurence Liaubet, Valérie Lobjois, Thomas Faraut, Aurélie Tircazes, Francis Benne, Nathalie Iannuccelli, José Pires, Jérome Glénisson, Annie Robic, Pascale Le Roy, Magali SanCristobal and Pierre Cherel
    Citation: BMC Genomics 2011 12:548
    Content type: Research article Published on:

  4. MicroRNAs (miRNAs) are a class of small regulatory RNAs that target sequences in messenger RNAs (mRNAs) to inhibit their protein output. Dissecting the complexities of miRNA function continues to prove challen...

    Authors: Jos B Poell, Rick J van Haastert, Francesco Cerisoli, Anne S Bolijn, Lisette M Timmer, Begoña Diosdado-Calvo, Gerrit A Meijer, Andre AFL van Puijenbroek, Eugene Berezikov, Roel QJ Schaapveld and Edwin Cuppen
    Citation: BMC Genomics 2011 12:546
    Content type: Methodology article Published on:

  5. Corynebacterium variabile is part of the complex microflora on the surface of smear-ripened cheeses and contributes to the development of flavor and textural properties during cheese ripening. Still little is kno...

    Authors: Jasmin Schröder, Irena Maus, Eva Trost and Andreas Tauch
    Citation: BMC Genomics 2011 12:545
    Content type: Research article Published on:

  6. Initiation and elongation of RNA polymerase II (RNAPII) transcription is regulated by both DNA sequence and chromatin signals. Recent breakthroughs make it possible to measure the chromatin state and activity ...

    Authors: Yun Chen, Mette Jørgensen, Raivo Kolde, Xiaobei Zhao, Brian Parker, Eivind Valen, Jiayu Wen and Albin Sandelin
    Citation: BMC Genomics 2011 12:544
    Content type: Research article Published on:

  7. Small nucleolar RNAs (snoRNAs) are a large group of non-coding RNAs (ncRNAs) that mainly guide 2'-O-methylation (C/D RNAs) and pseudouridylation (H/ACA RNAs) of ribosomal RNAs. The pattern of rRNA modification...

    Authors: Julia A Makarova and Dmitri A Kramerov
    Citation: BMC Genomics 2011 12:543
    Content type: Correspondence Published on:

  8. Amoebae are phagocytic protists where genetic exchanges might take place between amoeba-resistant bacteria. These amoebal pathogens are able to escape the phagocytic behaviour of their host. They belong to dif...

    Authors: Gregory Gimenez, Claire Bertelli, Claire Moliner, Catherine Robert, Didier Raoult, Pierre-Edouard Fournier and Gilbert Greub
    Citation: BMC Genomics 2011 12:542
    Content type: Research article Published on:

  9. Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains us...

    Authors: Silvia T Rodríguez-Ramilo, Miguel A Toro, Carmen Bouza, Miguel Hermida, Belén G Pardo, Santiago Cabaleiro, Paulino Martínez and Jesús Fernández
    Citation: BMC Genomics 2011 12:541
    Content type: Research article Published on:

  11. Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. The ...

    Authors: Chun Sui, Jie Zhang, Jianhe Wei, Shilin Chen, Ying Li, Jiesen Xu, Yue Jin, Caixiang Xie, Zhihui Gao, Hongjiang Chen, Chengmin Yang, Zheng Zhang and Yanhong Xu
    Citation: BMC Genomics 2011 12:539
    Content type: Research article Published on:

  12. In a context of climate change, phenotypic plasticity provides long-lived species, such as trees, with the means to adapt to environmental variations occurring within a single generation. In eucalyptus plantat...

    Authors: Emilie Villar, Christophe Klopp, Céline Noirot, Evandro Novaes, Matias Kirst, Christophe Plomion and Jean-Marc Gion
    Citation: BMC Genomics 2011 12:538
    Content type: Research article Published on:

  13. Common carp (Cyprinus carpio), a member of Cyprinidae, is the third most important aquaculture species in the world with an annual global production of 3.4 million metric tons, accounting for nearly 14% of the al...

    Authors: Peng Xu, Jian Wang, Jintu Wang, Runzi Cui, Yan Li, Zixia Zhao, Peifeng Ji, Yan Zhang, Jiongtang Li and Xiaowen Sun
    Citation: BMC Genomics 2011 12:537
    Content type: Research article Published on:

  14. Legionella pneumophila is an intracellular pathogen of environmental protozoa. When humans inhale contaminated aerosols this bacterium may cause a severe pneumonia called Legionnaires' disease. Despite the abunda...

    Authors: Laura Gomez-Valero, Christophe Rusniok, Sophie Jarraud, Benoit Vacherie, Zoé Rouy, Valerie Barbe, Claudine Medigue, Jerome Etienne and Carmen Buchrieser
    Citation: BMC Genomics 2011 12:536
    Content type: Research article Published on:

  15. In the United Kingdom, the thermophilic Campylobacter species C. jejuni and C. coli are the most frequent causes of food-borne gastroenteritis in humans. While campylobacteriosis is usually a relatively mild infe...

    Authors: Aline Metris, Mark Reuter, Duncan JH Gaskin, Jozsef Baranyi and Arnoud HM van Vliet
    Citation: BMC Genomics 2011 12:535
    Content type: Research article Published on:

  16. The canine Gram-negative Helicobacter bizzozeronii is one of seven species in Helicobacter heilmannii sensu lato that are detected in 0.17-2.3% of the gastric biopsies of human patients with gastric symptoms. At ...

    Authors: Thomas Schott, Pradeep K Kondadi, Marja-Liisa Hänninen and Mirko Rossi
    Citation: BMC Genomics 2011 12:534
    Content type: Research article Published on:

  17. Camptotheca acuminata is a Nyssaceae plant, often called the "happy tree", which is indigenous in Southern China. C. acuminata produces the terpenoid indole alkaloid, camptothecin (CPT), which exhibits clinical e...

    Authors: Yongzhen Sun, Hongmei Luo, Ying Li, Chao Sun, Jingyuan Song, Yunyun Niu, Yingjie Zhu, Liang Dong, Aiping Lv, Enzo Tramontano and Shilin Chen
    Citation: BMC Genomics 2011 12:533
    Content type: Research article Published on:

  18. Changes in transcriptional regulation underlie many of the phenotypic differences observed within and between species of bacteria. Lateral genetic transfer (LGT) can significantly impact the transcription fact...

    Authors: Elizabeth Skippington and Mark A Ragan
    Citation: BMC Genomics 2011 12:532
    Content type: Research article Published on:

  19. Functional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genom...

    Authors: Aleksey S Komissarov, Ekaterina V Gavrilova, Sergey Ju Demin, Alexander M Ishov and Olga I Podgornaya
    Citation: BMC Genomics 2011 12:531
    Content type: Research article Published on:

  20. The deep-sea hydrothermal vent mussel Bathymodiolus azoricus harbors thiotrophic and methanotrophic symbiotic bacteria in its gills. While the symbiotic relationship between this hydrothermal mussel and these che...

    Authors: Isabelle Boutet, Raymond Ripp, Odile Lecompte, Carole Dossat, Erwan Corre, Arnaud Tanguy and François H Lallier
    Citation: BMC Genomics 2011 12:530
    Content type: Research article Published on:

  21. The human placenta facilitates the exchange of nutrients, gas and waste between the fetal and maternal circulations. It also protects the fetus from the maternal immune response. Due to its role at the feto-ma...

    Authors: Boris Novakovic, Ryan K Yuen, Lavinia Gordon, Maria S Penaherrera, Andrew Sharkey, Ashley Moffett, Jeffrey M Craig, Wendy P Robinson and Richard Saffery
    Citation: BMC Genomics 2011 12:529
    Content type: Research article Published on:

  23. Frontotemporal lobar degeneration (FTLD) is a progressive neurodegenerative disorder that can be triggered through genetic or sporadic mechanisms. MicroRNAs (miRNAs) have become a major therapeutic focus as th...

    Authors: Jannet Kocerha, Naomi Kouri, Matt Baker, NiCole Finch, Mariely DeJesus-Hernandez, John Gonzalez, Kumaravel Chidamparam, Keith A Josephs, Bradley F Boeve, Neill R Graff-Radford, Julia Crook, Dennis W Dickson and Rosa Rademakers
    Citation: BMC Genomics 2011 12:527
    Content type: Research article Published on:

  24. The adaptation of pathogenic fungi to the host environment via large-scale genomic changes is a poorly characterized phenomenon. Cryptococcus neoformans is the leading cause of fungal meningoencephalitis in HIV/A...

    Authors: Guanggan Hu, Joyce Wang, Jaehyuk Choi, Won Hee Jung, Iris Liu, Anastasia P Litvintseva, Tihana Bicanic, Rajeev Aurora, Thomas G Mitchell, John R Perfect and James W Kronstad
    Citation: BMC Genomics 2011 12:526
    Content type: Research article Published on:

  25. Soybean is a valuable crop that provides protein and oil. Soybean requires a large amount of nitrogen (N) to accumulate high levels of N in the seed. The yield and protein content of soybean seeds are directly...

    Authors: Qing N Hao, Xin A Zhou, Ai H Sha, Cheng Wang, Rong Zhou and Shui L Chen
    Citation: BMC Genomics 2011 12:525
    Content type: Research article Published on:

  26. Di-(2-ethylhexyl)-phthalate (DEHP) is a commonly used plasticizer in polyvinylchloride (PVC) formulations and a potentially non-genotoxic carcinogen. The aim of this study was to identify genes whose level of ...

    Authors: Yann Landkocz, Pascal Poupin, Franck Atienzar and Paule Vasseur
    Citation: BMC Genomics 2011 12:524
    Content type: Research article Published on:

  27. Streptococcus suis (S. suis) is a major swine pathogen and an emerging zoonotic agent. Serotypes 1, 2, 3, 7, 9, 14 and 1/2 are the most prevalent serotypes of this pathogen. However, almost all studies were carri...

    Authors: Anding Zhang, Ming Yang, Pan Hu, Jiayan Wu, Bo Chen, Yafeng Hua, Jun Yu, Huanchun Chen, Jingfa Xiao and Meilin Jin
    Citation: BMC Genomics 2011 12:523
    Content type: Research article Published on:

  28. Efforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have ...

    Authors: Florian Geay, Serena Ferraresso, Jose L Zambonino-Infante, Luca Bargelloni, Claire Quentel, Marc Vandeputte, Sachi Kaushik, Chantal L Cahu and David Mazurais
    Citation: BMC Genomics 2011 12:522
    Content type: Research article Published on:

  29. Lupinus angustifolius L, also known as narrow-leafed lupin (NLL), is becoming an important grain legume crop that is valuable for sustainable farming and is becoming recognised as a potential human health food. R...

    Authors: Ling-Ling Gao, James K Hane, Lars G Kamphuis, Rhonda Foley, Bu-Jun Shi, Craig A Atkins and Karam B Singh
    Citation: BMC Genomics 2011 12:521
    Content type: Research article Published on:

  30. To investigate the molecular and cellular pathogenesis underlying myocarditis, we used an experimental autoimmune myocarditis (EAM)-induced heart failure rat model that represents T cell mediated postinflammat...

    Authors: Joo Hee Chung, Hee Jung Choi, Soo Young Kim, Kwan Soo Hong, Soo Kee Min, Myung Hee Nam, Chan Wha Kim, Young Ho Koh and Jong Bok Seo
    Citation: BMC Genomics 2011 12:520
    Content type: Research article Published on:

  31. The heterotrophic dinoflagellate Oxyrrhis marina is increasingly studied in experimental, ecological and evolutionary contexts. Its basal phylogenetic position within the dinoflagellates make O. marina useful for...

    Authors: Chris D Lowe, Luciane V Mello, Najma Samatar, Laura E Martin, David JS Montagnes and Phillip C Watts
    Citation: BMC Genomics 2011 12:519
    Content type: Research article Published on:

  32. Common genetic variants that regulate gene expression are widely suspected to contribute to the etiology and phenotypic variability of complex diseases. Although high-throughput, microarray-based assays have b...

    Authors: Xiang Xu, Hao Wang, Min Zhu, Yue Sun, Yu Tao, Qin He, Jian Wang, Li Chen and David Saffen
    Citation: BMC Genomics 2011 12:518
    Content type: Methodology article Published on:

  33. Eukaryotic nuclear genomes contain fragments of mitochondrial DNA called NumtS (Nuclear mitochondrial Sequences), whose mode and time of insertion, as well as their functional/structural role within the genome...

    Authors: Domenico Simone, Francesco Maria Calabrese, Martin Lang, Giuseppe Gasparre and Marcella Attimonelli
    Citation: BMC Genomics 2011 12:517
    Content type: Research article Published on:

  34. Cellular function is regulated by the balance of stringently regulated amounts of mRNA. Previous reports revealed that RNA polymerase II (RNAPII), which transcribes mRNA, can be classified into the pausing sta...

    Authors: Jun Odawara, Akihito Harada, Tomohiko Yoshimi, Kazumitsu Maehara, Taro Tachibana, Seiji Okada, Koichi Akashi and Yasuyuki Ohkawa
    Citation: BMC Genomics 2011 12:516
    Content type: Research article Published on:

  36. Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditio...

    Authors: Diana V Dugas, Marcela K Monaco, Andrew Olson, Robert R Klein, Sunita Kumari, Doreen Ware and Patricia E Klein
    Citation: BMC Genomics 2011 12:514
    Content type: Research article Published on:

  37. Wheat is one of the most important cereal crops for human beings, with seeds being the tissue of highly economic value. Various morphogenetic and metabolic processes are exclusively associated with seed matura...

    Authors: Xinglu Yang, Hongliang Xu, Wenhui Li, Le Li, Jinyue Sun, Yaxuan Li, Yueming Yan and Yingkao Hu
    Citation: BMC Genomics 2011 12:513
    Content type: Methodology article Published on:

  38. Several mutations were present in the genome of Streptococcus pneumoniae linezolid-resistant strains but the role of several of these mutations had not been experimentally tested. To analyze the role of these mut...

    Authors: Dewan S Billal, Jie Feng, Philippe Leprohon, Danielle Légaré and Marc Ouellette
    Citation: BMC Genomics 2011 12:512
    Content type: Research article Published on:

  39. The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and speci...

    Authors: Stilianos Arhondakis, Kimon Frousios, Costas S Iliopoulos, Solon P Pissis, German Tischler and Sophia Kossida
    Citation: BMC Genomics 2011 12:511
    Content type: Research article Published on:

  40. RNAi technology by feeding of E. coli containing dsRNA in C. elegans has significantly contributed to further our understanding of many different fields, including genetics, molecular biology, developmental biolo...

    Authors: Mark Elvin, Laurens B Snoek, Martin Frejno, Ulrike Klemstein, Jan E Kammenga and Gino B Poulin
    Citation: BMC Genomics 2011 12:510
    Content type: Methodology article Published on:

  41. Although an adverse early-life environment has been linked to an increased risk of developing the metabolic syndrome, the molecular mechanisms underlying altered disease susceptibility as well as their relevan...

    Authors: Bright Starling Emerald, Keefe Chng, Shinya Masuda, Deborah M Sloboda, Mark H Vickers, Ravi Kambadur and Peter D Gluckman
    Citation: BMC Genomics 2011 12:509
    Content type: Research article Published on:

  42. Classical genetic studies provide strong evidence for heritable contributions to susceptibility to developing dependence on addictive substances. Candidate gene and genome-wide association studies (GWAS) have ...

    Authors: Chuan-Yun Li, Wei-Zhen Zhou, Ping-Wu Zhang, Catherine Johnson, Liping Wei and George R Uhl
    Citation: BMC Genomics 2011 12:508
    Content type: Research article Published on:

  43. The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pac...

    Authors: M Aleksi Kallio, Jarno T Tuimala, Taavi Hupponen, Petri Klemelä, Massimiliano Gentile, Ilari Scheinin, Mikko Koski, Janne Käki and Eija I Korpelainen
    Citation: BMC Genomics 2011 12:507
    Content type: Software Published on:

  44. Several studies have shown that genomes can be studied via a multifractal formalism. Recently, we used a multifractal approach to study the genetic information content of the Caenorhabditis elegans genome. Here w...

    Authors: Pedro A Moreno, Patricia E Vélez, Ember Martínez, Luis E Garreta, Néstor Díaz, Siler Amador, Irene Tischer, José M Gutiérrez, Ashwinikumar K Naik, Fabián Tobar and Felipe García
    Citation: BMC Genomics 2011 12:506
    Content type: Research article Published on:

  45. Approximately half of all human genes use alternative transcription start sites (TSSs) to control mRNA levels and broaden the transcriptional output in healthy tissues. Aberrant expression patterns promoting c...

    Authors: Kasper Thorsen, Troels Schepeler, Bodil Øster, Mads H Rasmussen, Søren Vang, Kai Wang, Kristian Q Hansen, Philippe Lamy, Jakob Skou Pedersen, Asger Eller, Francisco Mansilla, Kirsti Laurila, Carsten Wiuf, Søren Laurberg, Lars Dyrskjøt, Torben F Ørntoft…
    Citation: BMC Genomics 2011 12:505
    Content type: Research article Published on:

  46. Gene variants within regulatory regions are thought to be major contributors of the variation of complex traits/diseases. Genome wide association studies (GWAS), have identified scores of genetic variants that...

    Authors: Kris Richardson, Chao-Qiang Lai, Laurence D Parnell, Yu-Chi Lee and Jose M Ordovas
    Citation: BMC Genomics 2011 12:504
    Content type: Research article Published on:

  47. Albugo candida is a biotrophic oomycete that parasitizes various species of Brassicaceae, causing a disease (white blister rust) with remarkable convergence in behaviour to unrelated rusts of basidiomycete fungi.

    Authors: Matthew G Links, Eric Holub, Rays HY Jiang, Andrew G Sharpe, Dwayne Hegedus, Elena Beynon, Dean Sillito, Wayne E Clarke, Shihomi Uzuhashi and Mohammad H Borhan
    Citation: BMC Genomics 2011 12:503
    Content type: Research article Published on:

  48. Small molecule ligands often have multiple effects on the transcriptional program of a cell: they trigger a receptor specific response and additional, indirect responses ("side effects"). Distinguishing those ...

    Authors: Jacob J Michaelson, Saskia Trump, Susanne Rudzok, Carolin Gräbsch, Danielle J Madureira, Franziska Dautel, Juliane Mai, Sabine Attinger, Kristin Schirmer, Martin von Bergen, Irina Lehmann and Andreas Beyer
    Citation: BMC Genomics 2011 12:502
    Content type: Research article Published on:

  49. Marek's disease (MD) is a lymphoproliferative disease in chickens caused by Marek's disease virus (MDV) and characterized by T cell lymphoma and infiltration of lymphoid cells into various organs such as liver...

    Authors: Ying Yu, Juan Luo, Apratim Mitra, Shuang Chang, Fei Tian, Huanmin Zhang, Ping Yuan, Huaijun Zhou and Jiuzhou Song
    Citation: BMC Genomics 2011 12:501
    Content type: Research article Published on:

  50. Downy mildew in sunflowers (Helianthus annuus L.) is caused by the oomycete Plasmopara halstedii (Farl.) Berlese et de Toni. Despite efforts by the international community to breed mildew-resistant varieties, dow...

    Authors: Falah As-sadi, Sébastien Carrere, Quentin Gascuel, Thibaut Hourlier, David Rengel, Marie-Christine Le Paslier, Amandine Bordat, Marie-Claude Boniface, Dominique Brunel, Jérôme Gouzy, Laurence Godiard and Patrick Vincourt
    Citation: BMC Genomics 2011 12:498
    Content type: Research article Published on:

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BMC Genomics

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