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  1. The publication of the first draft chicken sequence assembly became available in 2004 and was updated in 2006. However, this does not constitute a definitive and complete sequence of the chicken genome, since ...

    Authors: Marine Douaud, Katia Fève, Marie Gerus, Valérie Fillon, Suzanne Bardes, David Gourichon, Deborah A Dawson, Olivier Hanotte, Terry Burke, Florence Vignoles, Mireille Morisson, Michèle Tixier-Boichard, Alain Vignal and Frédérique Pitel
    Citation: BMC Genomics 2008 9:129
    Content type: Research article Published on:

  2. In the past years, several studies begun to unravel the structure, dynamical properties, and evolution of transcriptional regulatory networks. However, even those comparative studies that focus on a group of c...

    Authors: Abel D González Pérez, Evelyn González González, Vladimir Espinosa Angarica, Ana Tereza R Vasconcelos and Julio Collado-Vides
    Citation: BMC Genomics 2008 9:128
    Content type: Research article Published on:

  3. The Hedgehog (Hh) signaling pathway plays important roles in human and animal development as well as in carcinogenesis. Hh molecules have been found in both protostomes and deuterostomes, but curiously the nem...

    Authors: Thomas R Bürglin
    Citation: BMC Genomics 2008 9:127
    Content type: Research article Published on:

  4. Lepeophtheirus salmonis is an ectoparasitic copepod feeding on skin, mucus and blood from salmonid hosts. Initial analysis of EST sequences from pre adult and adult stages of L. salmonis revealed a large proporti...

    Authors: Christiane Eichner, Petter Frost, Bjarte Dysvik, Inge Jonassen, Bjørn Kristiansen and Frank Nilsen
    Citation: BMC Genomics 2008 9:126
    Content type: Research article Published on:

  5. The processes of gene transcription, translation, as well as the reactions taking place between gene products, are subject to stochastic fluctuations. These stochastic events are being increasingly examined as...

    Authors: Alessandra Riva, Anne-Sophie Carpentier, Frédérique Barloy-Hubler, Angélique Chéron and Alain Hénaut
    Citation: BMC Genomics 2008 9:125
    Content type: Research article Published on:

  6. The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expresse...

    Authors: Paola Pedotti, Peter AC 't Hoen, Erno Vreugdenhil, Geert J Schenk, Rolf HAM Vossen, Yavuz Ariyurek, Mattias de Hollander, Rowan Kuiper, Gertjan JB van Ommen, Johan T den Dunnen, Judith M Boer and Renée X de Menezes
    Citation: BMC Genomics 2008 9:124
    Content type: Research article Published on:

  7. Transcriptomic approaches are relevant for studying virus-host cell dialogues to better understand the physiopathology of infection and the immune response at the cellular level. Pseudorabies virus (PrV), a po...

    Authors: Laurence Flori, Claire Rogel-Gaillard, Marielle Cochet, Gaetan Lemonnier, Karine Hugot, Patrick Chardon, Stéphane Robin and François Lefèvre
    Citation: BMC Genomics 2008 9:123
    Content type: Research article Published on:

  8. Exceptionally, a single nucleotide sequence can be translated in vivo in two different frames to yield distinct proteins. In the case of the G-protein alpha subunit XL-alpha-s transcript, a frameshifted open read...

    Authors: Sebastien Ribrioux, Adrian Brüngger, Birgit Baumgarten, Klaus Seuwen and Markus R John
    Citation: BMC Genomics 2008 9:122
    Content type: Research article Published on:

  9. Hexaploid wheat is one of the most important cereal crops for human nutrition. Molecular understanding of the biology of the developing grain will assist the improvement of yield and quality traits for differe...

    Authors: Yongfang Wan, Rebecca L Poole, Alison K Huttly, Claudia Toscano-Underwood, Kevin Feeney, Sue Welham, Mike J Gooding, Clare Mills, Keith J Edwards, Peter R Shewry and Rowan AC Mitchell
    Citation: BMC Genomics 2008 9:121
    Content type: Research article Published on:

  10. Hepcidin/LEAP-1 is an iron regulatory hormone originally identified as an antimicrobial peptide. As part of a systematic analysis of the evolution of host defense peptides in primates, we have sequenced the or...

    Authors: Ludovica Segat, Alessandra Pontillo, Michele Milanese, Alessandro Tossi and Sergio Crovella
    Citation: BMC Genomics 2008 9:120
    Content type: Research article Published on:

  11. The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic require...

    Authors: Rute R da Fonseca, Warren E Johnson, Stephen J O'Brien, Maria João Ramos and Agostinho Antunes
    Citation: BMC Genomics 2008 9:119
    Content type: Research article Published on:

  13. The brown planthopper (BPH), Nilaparvata lugens (Hemiptera, Delphacidae), is a serious insect pests of rice plants. Major means of BPH control are application of agricultural chemicals and cultivation of BPH resi...

    Authors: Hiroaki Noda, Sawako Kawai, Yoko Koizumi, Kageaki Matsui, Qiang Zhang, Shigetoyo Furukawa, Michihiko Shimomura and Kazuei Mita
    Citation: BMC Genomics 2008 9:117
    Content type: Research article Published on:

  15. Arsenic is a carcinogen that is known to induce cell transformation and tumor formation. Although studies have been performed to examine the modulation of signaling molecules caused by arsenic exposure, the mo...

    Authors: Tisha Posey, Tingting Weng, Zhongming Chen, Narendranath R Chintagari, Pengcheng Wang, Nili Jin, Heidi Stricker and Lin Liu
    Citation: BMC Genomics 2008 9:115
    Content type: Research article Published on:

  16. Prion infection results in progressive neurodegeneration of the central nervous system invariably resulting in death. The pathological effects of prion diseases in the brain are morphologically well defined, s...

    Authors: Garrett Sorensen, Sarah Medina, Debra Parchaliuk, Clark Phillipson, Catherine Robertson and Stephanie A Booth
    Citation: BMC Genomics 2008 9:114
    Content type: Research article Published on:

  17. Extensive mapping efforts are currently underway for the establishment of comparative genomics between the model plant, Arabidopsis thaliana and various Brassica species. Most of these studies have deployed RFLP ...

    Authors: Priya Panjabi, Arun Jagannath, Naveen C Bisht, K Lakshmi Padmaja, Sarita Sharma, Vibha Gupta, Akshay K Pradhan and Deepak Pental
    Citation: BMC Genomics 2008 9:113
    Content type: Research article Published on:

  18. It is essential in modern biology to understand how transcriptional regulatory regions are composed of cis-elements, yet we have limited knowledge of, for example, the combinational uses of these elements and the...

    Authors: Katsuhiko Murakami, Tadashi Imanishi, Takashi Gojobori and Kenta Nakai
    Citation: BMC Genomics 2008 9:112
    Content type: Research article Published on:

  19. All jawed-vertebrates have four T cell receptor (TCR) chains: alpha (TRA), beta (TRB), gamma (TRG) and delta (TRD). Marsupials appear unique by having an additional TCR: mu (TRM). The evolutionary origin of TR...

    Authors: Zuly E Parra, Michelle L Baker, Jennifer Hathaway, April M Lopez, Jonathan Trujillo, Alana Sharp and Robert D Miller
    Citation: BMC Genomics 2008 9:111
    Content type: Research article Published on:

  20. The initial stages of development depend on mRNA and proteins accumulated in the oocyte, and during these stages, certain genes are essential for fertilization, first cleavage and embryonic genome activation. ...

    Authors: Sebastien Elis, Florence Batellier, Isabelle Couty, Sandrine Balzergue, Marie-Laure Martin-Magniette, Philippe Monget, Elisabeth Blesbois and Marina S Govoroun
    Citation: BMC Genomics 2008 9:110
    Content type: Research article Published on:

  21. Because the gene expression patterns of nonobese hepatic steatosis in affected patients remain unclear, we sought to explore these patterns using an animal model of nonobese hepatic steatosis.

    Authors: Ming-Ling Chang, Chau-Ting Yeh, Jeng-Chang Chen, Chau-Chun Huang, Shi-Ming Lin, I-Shyan Sheen, Dar-In Tai, Chia-Ming Chu, Wei-Pin Lin, Ming-Yu Chang, Chun-Kai Liang, Cheng-Tang Chiu and Deng-Yn Lin
    Citation: BMC Genomics 2008 9:109
    Content type: Research article Published on:

  22. Upland cotton (G. hirsutum L.) is the leading fiber crop worldwide. Genetic improvement of fiber quality and yield is facilitated by a variety of genomics tools. An integrated genetic and physical map is needed t...

    Authors: Zhanyou Xu, Russell J Kohel, Guoli Song, Jaemin Cho, Jing Yu, Shuxun Yu, Jeffrey Tomkins and John Z Yu
    Citation: BMC Genomics 2008 9:108
    Content type: Research article Published on:

  23. Cowpea (Vigna unguiculata L. Walp) is an important food and fodder legume of the semiarid tropics and subtropics worldwide, especially in sub-Saharan Africa. High density genetic linkage maps are needed for marke...

    Authors: Sayan Das, Prasanna R Bhat, Chinta Sudhakar, Jeffrey D Ehlers, Steve Wanamaker, Philip A Roberts, Xinping Cui and Timothy J Close
    Citation: BMC Genomics 2008 9:107
    Content type: Research article Published on:

  24. Multi-genome comparative analysis has yielded important insights into the molecular details of gene regulation. We have developed EvoPrinter, a web-accessed genomics tool that provides a single uninterrupted view...

    Authors: Amarendra S Yavatkar, Yong Lin, Jermaine Ross, Yang Fann, Thomas Brody and Ward F Odenwald
    Citation: BMC Genomics 2008 9:106
    Content type: Methodology article Published on:

  25. Microarray technology makes it possible to identify changes in gene expression of an organism, under various conditions. Data mining is thus essential for deducing significant biological information such as th...

    Authors: Philip J Law, Clotilde Claudel-Renard, Fourie Joubert, Abraham I Louw and Dave K Berger
    Citation: BMC Genomics 2008 9:105
    Content type: Database Published on:

  26. The increasing number of sequenced prokaryotic genomes contains a wealth of genomic data that needs to be effectively analysed. A set of statistical tools exists for such analysis, but their strengths and weak...

    Authors: Jon Bohlin, Eystein Skjerve and David W Ussery
    Citation: BMC Genomics 2008 9:104
    Content type: Research article Published on:

  27. Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor quality soils. Approximately 80% of...

    Authors: Michael P Timko, Paul J Rushton, Thomas W Laudeman, Marta T Bokowiec, Edmond Chipumuro, Foo Cheung, Christopher D Town and Xianfeng Chen
    Citation: BMC Genomics 2008 9:103
    Content type: Research article Published on:

  28. Knowledge about the abundance of molecular components is an important prerequisite for building quantitative predictive models of cellular behavior. Proteins are central components of these models, since they ...

    Authors: Yasushi Ishihama, Thorsten Schmidt, Juri Rappsilber, Matthias Mann, F Ulrich Hartl, Michael J Kerner and Dmitrij Frishman
    Citation: BMC Genomics 2008 9:102
    Content type: Research article Published on:

  29. Variability in hypothalamic-pituitary-adrenal (HPA) axis activity has been shown to be influenced by genetic factors and related to great metabolic differences such as obesity. The aim of this study was to inv...

    Authors: Dominique Hazard, Laurence Liaubet, Magali SanCristobal and Pierre Mormède
    Citation: BMC Genomics 2008 9:101
    Content type: Research article Published on:

  30. The capacity of respiring cultures of Saccharomyces cerevisiae to immediately switch to fast alcoholic fermentation upon a transfer to anaerobic sugar-excess conditions is a key characteristic of Saccharomyces ce...

    Authors: Joost van den Brink, Pascale Daran-Lapujade, Jack T Pronk and Johannes H de Winde
    Citation: BMC Genomics 2008 9:100
    Content type: Research article Published on:

  31. Chemotherapy (CT) resistance in ovarian cancer (OC) is broad and encompasses diverse unrelated drugs, suggesting more than one mechanism of resistance. To better understand the molecular mechanisms controlling...

    Authors: Sylvain L'Espérance, Magdalena Bachvarova, Bernard Tetu, Anne-Marie Mes-Masson and Dimcho Bachvarov
    Citation: BMC Genomics 2008 9:99
    Content type: Research article Published on:

  32. With the popularity of DNA microarray technology, multiple groups of researchers have studied the gene expression of similar biological conditions. Different methods have been developed to integrate the result...

    Authors: Xiangrong Kong, Valeria Mas and Kellie J Archer
    Citation: BMC Genomics 2008 9:98
    Content type: Research article Published on:

  33. Scleractinian corals are the foundation of reef ecosystems in tropical marine environments. Their great success is due to interactions with endosymbiotic dinoflagellates (Symbiodinium spp.), with which they are o...

    Authors: Jodi A Schwarz, Peter B Brokstein, Christian Voolstra, Astrid Y Terry, David J Miller, Alina M Szmant, Mary Alice Coffroth and Mónica Medina
    Citation: BMC Genomics 2008 9:97
    Content type: Research article Published on:

  34. The cichlid fishes in general, and the exceptionally diverse East African haplochromine cichlids in particular, are famous examples of adaptive radiation and explosive speciation. Here we report the collection...

    Authors: Walter Salzburger, Susan CP Renn, Dirk Steinke, Ingo Braasch, Hans A Hofmann and Axel Meyer
    Citation: BMC Genomics 2008 9:96
    Content type: Research article Published on:

  35. The laboratory rat (Rattus norvegicus) is an important model for human disease, and is extensively used for studying complex traits for example in the physiological and pharmacological fields. To facilitate genet...

    Authors: Isaäc J Nijman, Sylvia Kuipers, Mark Verheul, Victor Guryev and Edwin Cuppen
    Citation: BMC Genomics 2008 9:95
    Content type: Methodology article Published on:

  36. The amplification of bacterial RNA is required if complex host-pathogen interactions are to be studied where the recovery of bacterial RNA is limited. Here, using a whole genome Mycobacterium tuberculosis microar...

    Authors: Simon J Waddell, Ken Laing, Claire Senner and Philip D Butcher
    Citation: BMC Genomics 2008 9:94
    Content type: Methodology article Published on:

  37. Gene conversion causes a non-reciprocal transfer of genetic information between similar sequences. Gene conversion can both homogenize genes and recruit point mutations thereby shaping the evolution of multige...

    Authors: Shuqing Xu, Terry Clark, Hongkun Zheng, Søren Vang, Ruiqiang Li, Gane Ka-Shu Wong, Jun Wang and Xiaoguang Zheng
    Citation: BMC Genomics 2008 9:93
    Content type: Research article Published on:

  38. Diversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for un...

    Authors: Sandra Moshonov, Rofa Elfakess, Michal Golan-Mashiach, Hadar Sinvani and Rivka Dikstein
    Citation: BMC Genomics 2008 9:92
    Content type: Research article Published on:

  39. Large-scale gene expression analysis of post-mortem brain tissue offers unique opportunities for investigating genetic mechanisms of psychiatric and neurodegenerative disorders. On the other hand microarray da...

    Authors: Tatiana Popova, Detlev Mennerich, Andreas Weith and Karsten Quast
    Citation: BMC Genomics 2008 9:91
    Content type: Research article Published on:

  40. Cynomolgus macaques (Macaca fascicularis) are widely used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as rhesus macaques (M. mulatta). We isolated 85,...

    Authors: Naoki Osada, Katsuyuki Hashimoto, Yosuke Kameoka, Makoto Hirata, Reiko Tanuma, Yasuhiro Uno, Itsuro Inoue, Munetomo Hida, Yutaka Suzuki, Sumio Sugano, Keiji Terao, Jun Kusuda and Ichiro Takahashi
    Citation: BMC Genomics 2008 9:90
    Content type: Research article Published on:

  41. The Sperm-coating protein/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) domain is found across phyla and is a major structural feature of insect allergens, mammalian sperm proteins and parasitic nematode secreted molecules. Prot...

    Authors: Iain W Chalmers, Andrew J McArdle, Richard MR Coulson, Marissa A Wagner, Ralf Schmid, Hirohisa Hirai and Karl F Hoffmann
    Citation: BMC Genomics 2008 9:89
    Content type: Research article Published on:

  42. The master regulator p53 tumor-suppressor protein through coordination of several downstream target genes and upstream transcription factors controls many pathways important for tumor suppression. While it has...

    Authors: Amit U Sinha, Vivek Kaimal, Jing Chen and Anil G Jegga
    Citation: BMC Genomics 2008 9:88
    Content type: Research article Published on:

  43. Low oxygen availability has been shown previously to stimulate M. tuberculosis to establish non-replicative persistence in vitro. The two component sensor/regulator dosRS is a major mediator in the transcriptiona...

    Authors: Yi Zhang, Kim A Hatch, Lorenz Wernisch and Joanna Bacon
    Citation: BMC Genomics 2008 9:87
    Content type: Research article Published on:

  44. Plant non-specific lipid transfer proteins (nsLTPs) are encoded by multigene families and possess physiological functions that remain unclear. Our objective was to characterize the complete nsLtp gene family in r...

    Authors: Freddy Boutrot, Nathalie Chantret and Marie-Françoise Gautier
    Citation: BMC Genomics 2008 9:86
    Content type: Research article Published on:

  45. Pathogens such as fungi, bacteria and especially viruses, are highly variable even within an individual host, intensifying the difficulty of distinguishing and accurately quantifying numerous allelic variants ...

    Authors: Baptiste Monsion, Hervé Duborjal and Stéphane Blanc
    Citation: BMC Genomics 2008 9:85
    Content type: Methodology article Published on:

  46. DNA microarrays provide a powerful method for global analysis of gene expression. The application of this technology to specific cell types and tissues, however, is typically limited by small amounts of availa...

    Authors: Joseph D Watson, Shenglong Wang, Stephen E Von Stetina, W Clay Spencer, Shawn Levy, Phillip J Dexheimer, Nurith Kurn, Joe Don Heath and David M Miller III
    Citation: BMC Genomics 2008 9:84
    Content type: Methodology article Published on:

  48. Myostatin (MSTN) is a member of the transforming growth factor-β superfamily that negatively regulates growth of skeletal muscle tissue. The gene encoding for the MSTN peptide is a consolidate candidate for th...

    Authors: Christian De Santis, Brad S Evans, Carolyn Smith-Keune and Dean R Jerry
    Citation: BMC Genomics 2008 9:82
    Content type: Research article Published on:

  49. In humans and mice ("γδ low species") less than 5% of the peripheral blood T lymphocytes are gamma/delta T cells, whereas in chicken and artiodactyls ("γδ high species") gamma/delta T cells represent about hal...

    Authors: Giovanna Vaccarelli, Maria C Miccoli, Rachele Antonacci, Graziano Pesole and Salvatrice Ciccarese
    Citation: BMC Genomics 2008 9:81
    Content type: Research article Published on:

  50. Microsatellite (SSR) and single nucleotide polymorphism (SNP) markers are widely used in plant breeding and genomic research. Thus, methods to improve the speed and efficiency of SSR and SNP genotyping are hig...

    Authors: Matthew J Hayden, Thao M Nguyen, Amanda Waterman and Kenneth J Chalmers
    Citation: BMC Genomics 2008 9:80
    Content type: Methodology article Published on:

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BMC Genomics

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