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  1. WRKY proteins belong to the WRKY-GCM1 superfamily of zinc finger transcription factors that have been subject to a large plant-specific diversification. For the cereal crop barley (Hordeum vulgare), three differe...

    Authors: Elke Mangelsen, Joachim Kilian, Kenneth W Berendzen, Üner H Kolukisaoglu, Klaus Harter, Christer Jansson and Dierk Wanke
    Citation: BMC Genomics 2008 9:194
  2. Although microbiota play a critical role in the normal development and function of host immune systems, the underlying mechanisms, especially those involved in the large intestine (LI), remain unknown. In the ...

    Authors: Kaori Munakata, Masahiro Yamamoto, Naoko Anjiki, Mitsue Nishiyama, Sachiko Imamura, Seiichi Iizuka, Kiyoe Takashima, Atsushi Ishige, Kyoji Hioki, Yasuyuki Ohnishi and Kenji Watanabe
    Citation: BMC Genomics 2008 9:192
  3. Alternative splicing expands transcriptome diversity and plays an important role in regulation of gene expression. Previous studies focus on the regulation of a single cassette exon, but recent experiments ind...

    Authors: Tao Peng, Chenghai Xue, Jianning Bi, Tingting Li, Xiaowo Wang, Xuegong Zhang and Yanda Li
    Citation: BMC Genomics 2008 9:191
  4. Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulenc...

    Authors: Sarinna Tumapa, Matthew TG Holden, Mongkol Vesaratchavest, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Wirongrong Chierakul, Edward J Feil, Bart J Currie, Nicholas PJ Day, William C Nierman and Sharon J Peacock
    Citation: BMC Genomics 2008 9:190
  5. UnTranslated Regions (UTRs) of mRNAs contain regulatory elements for various aspects of mRNA metabolism, such as mRNA localization, translation, and mRNA stability. Several RNA stem-loop structures in UTRs hav...

    Authors: Mugdha Khaladkar, Jianghui Liu, Dongrong Wen, Jason TL Wang and Bin Tian
    Citation: BMC Genomics 2008 9:189
  6. The extent of linkage disequilibrium (LD) within a population determines the number of markers that will be required for successful association mapping and marker-assisted selection. Most studies on LD in catt...

    Authors: Mehar S Khatkar, Frank W Nicholas, Andrew R Collins, Kyall R Zenger, Julie AL Cavanagh, Wes Barris, Robert D Schnabel, Jeremy F Taylor and Herman W Raadsma
    Citation: BMC Genomics 2008 9:187
  7. The use of new, deep sequencing technologies has greatly accelerated microRNA discovery. We have applied this approach to the identification of chicken microRNAs and to the comparison of microRNAs in chicken e...

    Authors: Joan Burnside, Ming Ouyang, Amy Anderson, Erin Bernberg, Cheng Lu, Blake C Meyers, Pamela J Green, Milos Markis, Grace Isaacs, Emily Huang and Robin W Morgan
    Citation: BMC Genomics 2008 9:185
  8. Gene ortholog identification is now a major objective for mining the increasing amount of sequence data generated by complete or partial genome sequencing projects. Comparative and functional genomics urgently...

    Authors: Matthieu G Conte, Sylvain Gaillard, Gaetan Droc and Christophe Perin
    Citation: BMC Genomics 2008 9:183
  9. Plant circadian systems regulate various biological processes in harmony with daily environmental changes. In Arabidopsis thaliana, the underlying clock mechanism is comprised of multiple integrated transcription...

    Authors: Shigeru Hanano, Ralf Stracke, Marc Jakoby, Thomas Merkle, Malgorzata A Domagalska, Bernd Weisshaar and Seth J Davis
    Citation: BMC Genomics 2008 9:182
  10. In bacterial pathogens, both cell surface-exposed outer membrane proteins and proteins secreted into the extracellular environment play crucial roles in host-pathogen interaction and pathogenesis. Considerable...

    Authors: Wasna Viratyosin, Supawadee Ingsriswang, Eakasit Pacharawongsakda and Prasit Palittapongarnpim
    Citation: BMC Genomics 2008 9:181
  11. Infectious salmon anemia virus (ISAV) causes a multisystemic disease responsible for severe losses in salmon aquaculture. Better understanding of factors that explain variations in resistance between individua...

    Authors: Sven Martin Jørgensen, Sergey Afanasyev and Aleksei Krasnov
    Citation: BMC Genomics 2008 9:179
  12. The mouse has more than 30 Major histocompatibility complex (Mhc) class Ib genes, most of which exist in the H2 region of chromosome 17 in distinct gene clusters. Although recent progress in Mhc research has reve...

    Authors: Masato Ohtsuka, Hidetoshi Inoko, Jerzy K Kulski and Shinichi Yoshimura
    Citation: BMC Genomics 2008 9:178
  13. Since its discovery more than 100 years ago, potato (Solanum tuberosum) tuber cold-induced sweetening (CIS) has been extensively investigated. Several carbohydrate-associated genes would seem to be involved in th...

    Authors: Paolo Bagnaresi, Anna Moschella, Ottavio Beretta, Federico Vitulli, Paolo Ranalli and Pierdomenico Perata
    Citation: BMC Genomics 2008 9:176
  14. Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps be...

    Authors: Giulia Soldà, Mikita Suyama, Paride Pelucchi, Silvia Boi, Alessandro Guffanti, Ermanno Rizzi, Peer Bork, Maria Luisa Tenchini and Francesca D Ciccarelli
    Citation: BMC Genomics 2008 9:174
  15. Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How rele...

    Authors: André LJ Ferraz, Ana Ojeda, Manel López-Béjar, Lana T Fernandes, Anna Castelló, Josep M Folch and Miguel Pérez-Enciso
    Citation: BMC Genomics 2008 9:173
  16. Accumulating evidence suggests an important role for the enzyme poly(ADP-ribose) polymerase-1 (PARP-1) as an integral part of the gene expression regulatory machinery during development and in response to spec...

    Authors: Luis Saenz, Juan J Lozano, Rut Valdor, Alberto Baroja-Mazo, Pablo Ramirez, Pascual Parrilla, Pedro Aparicio, Lauro Sumoy and José Yélamos
    Citation: BMC Genomics 2008 9:171
  17. The large sensitivity, high reproducibility and essentially unlimited dynamic range of real-time PCR to measure gene expression in complex samples provides the opportunity for powerful multivariate and multiwa...

    Authors: Anders Ståhlberg, Karin Elbing, José Manuel Andrade-Garda, Björn Sjögreen, Amin Forootan and Mikael Kubista
    Citation: BMC Genomics 2008 9:170
  18. Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pa...

    Authors: Chaitanya R Sanna, Wen-Hsiung Li and Liqing Zhang
    Citation: BMC Genomics 2008 9:169
  19. Comparative genomics is a powerful means of establishing inter-specific relationships between gene function/location and allows insight into genomic rearrangements, conservation and evolutionary phylogeny. The...

    Authors: Darren K Griffin, Lindsay B Robertson, Helen G Tempest, Alain Vignal, Valérie Fillon, Richard PMA Crooijmans, Martien AM Groenen, Svetlana Deryusheva, Elena Gaginskaya, Wilfrid Carré, David Waddington, Richard Talbot, Martin Völker, Julio S Masabanda and Dave W Burt
    Citation: BMC Genomics 2008 9:168
  20. Small RNAs (sRNAs) are widespread among bacteria and have diverse regulatory roles. Most of these sRNAs have been discovered by a combination of computational and experimental methods. In Pseudomonas aeruginosa, ...

    Authors: Nicolas González, Stephan Heeb, Claudio Valverde, Elisabeth Kay, Cornelia Reimmann, Thomas Junier and Dieter Haas
    Citation: BMC Genomics 2008 9:167
  21. Neuronal tissue has limited potential to self-renew or repair after neurological diseases. Cellular therapies using stem cells are promising approaches for the treatment of neurological diseases. However, the ...

    Authors: Tatiana Tondreau, Marielle Dejeneffe, Nathalie Meuleman, Basile Stamatopoulos, Alain Delforge, Philippe Martiat, Dominique Bron and Laurence Lagneaux
    Citation: BMC Genomics 2008 9:166
  22. Pseudogenes are an integral component of the human genome. Little attention, however, has so far been paid to the phenomenon that some pseudogenes are transcriptionally active. Recently, we demonstrated that t...

    Authors: Armin P Piehler, Marit Hellum, Jürgen J Wenzel, Ellen Kaminski, Kari Bente Foss Haug, Peter Kierulf and Wolfgang E Kaminski
    Citation: BMC Genomics 2008 9:165
  23. Genes continuously duplicate and the duplicated copies remain in the genome or get deleted. The DAL5 subfamily of transmembrane transporter genes has eight known members in S. cerevisiae. All are putative anion:c...

    Authors: Linda Hellborg, Megan Woolfit, Mattias Arthursson-Hellborg and Jure Piškur
    Citation: BMC Genomics 2008 9:164
  24. Aspergillus nidulans is a member of a diverse group of filamentous fungi, sharing many of the properties of its close relatives with significance in the fields of medicine, agriculture and industry. Furthermore,

    Authors: Helga David, İlknur Ş Özçelik, Gerald Hofmann and Jens Nielsen
    Citation: BMC Genomics 2008 9:163
  25. Oct4 is a POU-domain transcriptional factor which is essential for maintaining pluripotency in several mammalian species. The mouse, human, and bovine Oct4 orthologs display a high conservation of nucleotide sequ...

    Authors: Sergey P Medvedev, Alexander I Shevchenko, Eugene A Elisaphenko, Tatyana B Nesterova, Neil Brockdorff and Suren M Zakian
    Citation: BMC Genomics 2008 9:162
  26. Small RNAs regulate a number of developmental processes in plants and animals. However, the role of small RNAs in legume-rhizobial symbiosis is largely unexplored. Symbiosis between legumes (e.g. soybean) and ...

    Authors: Senthil Subramanian, Yan Fu, Ramanjulu Sunkar, W Brad Barbazuk, Jian-Kang Zhu and Oliver Yu
    Citation: BMC Genomics 2008 9:160
  27. Several recent studies indicate that alternative splicing in Arabidopsis and other plants is a common mechanism for post-transcriptional modulation of gene expression. However, few analyses have been done so f...

    Authors: Stefanie Schindler, Karol Szafranski, Michael Hiller, Gul Shad Ali, Saiprasad G Palusa, Rolf Backofen, Matthias Platzer and Anireddy SN Reddy
    Citation: BMC Genomics 2008 9:159
  28. The interactions between pathogens and hosts lead to a massive upregulation of antimicrobial host effector molecules. Among these, the 65 kDa guanylate binding proteins (GBPs) are interesting candidates as int...

    Authors: Alexandra Kresse, Carolin Konermann, Daniel Degrandi, Cornelia Beuter-Gunia, Jan Wuerthner, Klaus Pfeffer and Sandra Beer
    Citation: BMC Genomics 2008 9:158
  29. Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena. Although recent studies suggest the possible existence of yet undi...

    Authors: Hideya Kawaji, Mari Nakamura, Yukari Takahashi, Albin Sandelin, Shintaro Katayama, Shiro Fukuda, Carsten O Daub, Chikatoshi Kai, Jun Kawai, Jun Yasuda, Piero Carninci and Yoshihide Hayashizaki
    Citation: BMC Genomics 2008 9:157
  30. The reduced folate carrier (RFC1) is an integral membrane protein and facilitative anion exchanger that mediates delivery of 5-methyltetrahydrofolate into mammalian cells. Adequate maternal-fetal transport of fol...

    Authors: Janee Gelineau-van Waes, Joyce R Maddox, Lynette M Smith, Michael van Waes, Justin Wilberding, James D Eudy, Linda K Bauer and Richard H Finnell
    Citation: BMC Genomics 2008 9:156
  31. Transcriptional control of embryonic stem (ES) cell pluripotency has been a subject of intense study. Transcriptional regulators including Oct4 (Oct3/4 index), Sox2 and Nanog are fundamental for maintaining th...

    Authors: Galih Kunarso, Kee-Yew Wong, Lawrence W Stanton and Leonard Lipovich
    Citation: BMC Genomics 2008 9:155
  32. Plants are exposed to attack from a large variety of herbivores. Feeding insects can induce substantial changes of the host plant transcriptome. Arabidopsis thaliana has been established as a relevant system for ...

    Authors: Jürgen Ehlting, Sunita G Chowrira, Nathalie Mattheus, Dana S Aeschliman, Gen-Ichiro Arimura and Jörg Bohlmann
    Citation: BMC Genomics 2008 9:154
  33. In this study, differential gene expression analysis using complementary DNA (cDNA) libraries has been improved. Firstly by the introduction of an accurate method of assigning Expressed Sequence Tags (ESTs) to...

    Authors: John MJ Herbert, Dov Stekel, Sharon Sanderson, Victoria L Heath and Roy Bicknell
    Citation: BMC Genomics 2008 9:153
  34. Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences be...

    Authors: Hirokazu Chiba, Riu Yamashita, Kengo Kinoshita and Kenta Nakai
    Citation: BMC Genomics 2008 9:152
  35. The superfamily of ser ine p roteinase in hibitors (serpins) is involved in numerous fundamental biological processes as inflammation, blood coagulation and apoptosis. Our interest is focused on the SERPINA3 sub-...

    Authors: Patrick Pelissier, Didier Delourme, Agnes Germot, Xavier Blanchet, Samira Becila, Abderrahman Maftah, Hubert Leveziel, Ahmed Ouali and Laure Bremaud
    Citation: BMC Genomics 2008 9:151
  36. Transposable elements (TEs) are major players in evolution. We know that they play an essential role in genome size determination, but we still have an incomplete understanding of the processes involved in the...

    Authors: Rita Rebollo, Emmanuelle Lerat, Liliana Lopez Kleine, Christian Biémont and Cristina Vieira
    Citation: BMC Genomics 2008 9:149
  37. In order to develop a framework for the analysis of sex-biased genes, we present a characterization of microarray data comparing male and female gene expression in 18 day chicken embryos for brain, gonad, and ...

    Authors: Judith E Mank, Lina Hultin-Rosenberg, Matthew T Webster and Hans Ellegren
    Citation: BMC Genomics 2008 9:148
  38. Duplication, followed by fixation or random loss of novel genes, contributes to genome evolution. Particular outcomes of duplication events are possibly associated with pathogenic life histories in fungi. To d...

    Authors: Amy J Powell, Gavin C Conant, Douglas E Brown, Ignazio Carbone and Ralph A Dean
    Citation: BMC Genomics 2008 9:147
  39. The neuronal ceroid lipofuscinoses (NCL) are a group of children's inherited neurodegenerative disorders, characterized by blindness, early dementia and pronounced cortical atrophy. The similar pathological an...

    Authors: Carina von Schantz, Juha Saharinen, Outi Kopra, Jonathan D Cooper, Massimiliano Gentile, Iiris Hovatta, Leena Peltonen and Anu Jalanko
    Citation: BMC Genomics 2008 9:146
  40. A key problem in the sequence-based reconstruction of regulatory networks in bacteria is the lack of specificity in operator predictions. The problem is especially prominent in the identification of transcript...

    Authors: Christof Francke, Robert Kerkhoven, Michiel Wels and Roland J Siezen
    Citation: BMC Genomics 2008 9:145
  41. Dietary non-digestible carbohydrates stimulate the gut microflora and are therefore presumed to improve host resistance to intestinal infections. However, several strictly controlled rat infection studies show...

    Authors: Wendy Rodenburg, Jaap Keijer, Evelien Kramer, Carolien Vink, Roelof van der Meer and Ingeborg MJ Bovee-Oudenhoven
    Citation: BMC Genomics 2008 9:144
  42. The transcription regulator PhoP has been shown to be important for Y. pestis survival in macrophages and under various in vitro stresses. However, the mechanism by which PhoP promotes bacterial intracellular sur...

    Authors: Yingli Li, He Gao, Long Qin, Bei Li, Yanping Han, Zhaobiao Guo, Yajun Song, Junhui Zhai, Zongmin Du, Xiaoyi Wang, Dongsheng Zhou and Ruifu Yang
    Citation: BMC Genomics 2008 9:143

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