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  1. 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
    Content type: Research article Published on:

  2. 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
    Content type: Research article Published on:

  4. 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
    Content type: Research article Published on:

  5. 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
    Content type: Research article Published on:

  6. 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
    Content type: Research article Published on:

  7. 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
    Content type: Research article Published on:

  8. 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
    Content type: Research article Published on:

  9. 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
    Content type: Research article Published on:

  10. 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
    Content type: Research article Published on:

  11. 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
    Content type: Research article Published on:

  12. 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
    Content type: Research article Published on:

  13. 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
    Content type: Research article Published on:

  14. 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
    Content type: Research article Published on:

  15. 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
    Content type: Research article Published on:

  16. 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
    Content type: Research article Published on:

  17. 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
    Content type: Research article Published on:

  18. 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
    Content type: Research article Published on:

  19. 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
    Content type: Research article Published on:

  20. 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
    Content type: Research article Published on:

  21. 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
    Content type: Research article Published on:

  23. 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
    Content type: Research article Published on:

  24. 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
    Content type: Research article Published on:

  25. 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
    Content type: Research article Published on:

  26. 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
    Content type: Research article Published on:

  27. 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
    Content type: Research article Published on:

  28. 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
    Content type: Research article Published on:

  29. 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
    Content type: Research article Published on:

  30. The oomycete Plasmopara viticola (Berk. and Curt.) Berl. and de Toni causes downy mildew in grapevine (Vitis vinifera L.). This pathogen is strictly biotrophic, thus completely dependent on living host cells for ...

    Authors: Marianna Polesani, Filomena Desario, Alberto Ferrarini, Anita Zamboni, Mario Pezzotti, Andreas Kortekamp and Annalisa Polverari
    Citation: BMC Genomics 2008 9:142
    Content type: Research article Published on:

  31. The response of the trout, O. mykiss, head kidney to bacterial lipopolysaccharide (LPS) or active and attenuated infectious hematopoietic necrosis virus (IHNV and attINHV respectively) intraperitoneal challenge, ...

    Authors: Simon MacKenzie, Joan C Balasch, Beatriz Novoa, Laia Ribas, Nerea Roher, Aleksei Krasnov and Antonio Figueras
    Citation: BMC Genomics 2008 9:141
    Content type: Research article Published on:

  33. Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its first generation linkage map has been applied to map QTL for growth traits. To identify genes located in QTL responsible for spec...

    Authors: Chun Ming Wang, Loong Chueng Lo, Felicia Feng, Ping Gong, Jian Li, Ze Yuan Zhu, Grace Lin and Gen Hua Yue
    Citation: BMC Genomics 2008 9:139
    Content type: Research article Published on:

  34. Sequence closure often represents the end-point of a genome project, without a system in place for subsequent improvement and refinement. Building on the genome project of Vibrio fischeri ES114, we used a compara...

    Authors: Mark J Mandel, Eric V Stabb and Edward G Ruby
    Citation: BMC Genomics 2008 9:138
    Content type: Research article Published on:

  37. Identifying consistent changes in cellular function that occur in multiple types of cancer could revolutionize the way cancer is treated. Previous work has produced promising results such as the identification...

    Authors: Leszek A Rybaczyk, Meredith J Bashaw, Dorothy R Pathak and Kun Huang
    Citation: BMC Genomics 2008 9:134
    Content type: Research article Published on:

  39. Simple sequence repeats (SSRs) of GACA/GATA have been implicated with differentiation of sex-chromosomes and speciation. However, the organization of these repeats within genomes and transcriptomes, even in th...

    Authors: Jyoti Srivastava, Sanjay Premi, Sudhir Kumar and Sher Ali
    Citation: BMC Genomics 2008 9:132
    Content type: Research article Published on:

  40. Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular met...

    Authors: Feng Yue, Liying Cui, Claude W dePamphilis, Bernard ME Moret and Jijun Tang
    Citation: BMC Genomics 2008 9(Suppl 1):S25
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  43. Massively parallel pyrosequencing is a high-throughput technology that can sequence hundreds of thousands of DNA/RNA fragments in a single experiment. Combining it with immunoprecipitation-based biochemical as...

    Authors: Xin Wang, Guohua Wang, Changyu Shen, Lang Li, Xinguo Wang, Sean D Mooney, Howard J Edenberg, Jeremy R Sanford and Yunlong Liu
    Citation: BMC Genomics 2008 9(Suppl 1):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  44. Explosive compounds such as TNT and RDX are recalcitrant contaminants often found co-existing in the environment. In order to understand the joint effects of TNT and RDX on earthworms, an important ecological ...

    Authors: Ping Gong, Xin Guan, Laura S Inouye, Youping Deng, Mehdi Pirooznia and Edward J Perkins
    Citation: BMC Genomics 2008 9(Suppl 1):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  45. The budding yeast Saccharomyces cerevisiae is a eukaryotic organism with extensive genetic redundancy. Large-scale gene deletion analysis has shown that over 80% of the ~6200 predicted genes are nonessential and ...

    Authors: Jinghe Mao, Tanwir Habib, Ming Shenwu, Baobin Kang, Wilbur Allen, LaShonda Robertson, Jack Y Yang and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 1):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  46. Several classification and feature selection methods have been studied for the identification of differentially expressed genes in microarray data. Classification methods such as SVM, RBF Neural Nets, MLP Neur...

    Authors: Mehdi Pirooznia, Jack Y Yang, Mary Qu Yang and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 1):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  47. Iron homeostasis is a key metabolism for most organisms. In many bacterial species, coordinate regulation of iron homeostasis depends on the protein product of a Fur gene. Fur also plays roles in virulence, ac...

    Authors: Yunfeng Yang, Daniel P Harris, Feng Luo, Liyou Wu, Andrea B Parsons, Anthony V Palumbo and Jizhong Zhou
    Citation: BMC Genomics 2008 9(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  48. Many protein regions and some entire proteins have no definite tertiary structure, existing instead as dynamic, disorder ensembles under different physiochemical circumstances. Identification of these protein ...

    Authors: Joshua Hecker, Jack Y Yang and Jianlin Cheng
    Citation: BMC Genomics 2008 9(Suppl 1):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  50. Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, compar...

    Authors: Jack Y Yang, Mary Qu Yang, Mengxia Michelle Zhu, Hamid R Arabnia and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 1):I1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

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