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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  14. 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:

  15. 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:

  16. 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:

  17. As a polycistronic transcriptional unit of one or more adjacent genes, operons play a key role in regulation and function in prokaryotic biology, and a better understanding of how they are constituted and cont...

    Authors: Emma Laing, Khushwant Sidhu and Simon J Hubbard
    Citation: BMC Genomics 2008 9:79
    Content type: Research article Published on:

  18. Thyroid hormones (TH) induce gene expression programs that orchestrate amphibian metamorphosis. In contrast to anurans, many salamanders do not undergo metamorphosis in nature. However, they can be induced to ...

    Authors: Robert B Page, Stephen R Voss, Amy K Samuels, Jeramiah J Smith, Srikrishna Putta and Christopher K Beachy
    Citation: BMC Genomics 2008 9:78
    Content type: Research article Published on:

  19. Earlier we have shown that the mobile phone radiation (radiofrequency modulated electromagnetic fields; RF-EMF) alters protein expression in human endothelial cell line. This does not mean that similar respons...

    Authors: Anu Karinen, Sirpa Heinävaara, Reetta Nylund and Dariusz Leszczynski
    Citation: BMC Genomics 2008 9:77
    Content type: Research article Published on:

  20. Cholesterol homeostasis and xenobiotic metabolism are complex biological processes, which are difficult to study with traditional methods. Deciphering complex regulation and response of these two processes to ...

    Authors: Tadeja Režen, Peter Juvan, Klementina Fon Tacer, Drago Kuzman, Adrian Roth, Denis Pompon, Lawrence P Aggerbeck, Urs A Meyer and Damjana Rozman
    Citation: BMC Genomics 2008 9:76
    Content type: Methodology article Published on:

  21. The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.

    Authors: Ramy K Aziz, Daniela Bartels, Aaron A Best, Matthew DeJongh, Terrence Disz, Robert A Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth M Glass, Michael Kubal, Folker Meyer, Gary J Olsen, Robert Olson, Andrei L Osterman, Ross A Overbeek, Leslie K McNeil…
    Citation: BMC Genomics 2008 9:75
    Content type: Database Published on:

  23. Retinal degeneration is a main cause of blindness in humans. Neuroprotective therapies may be used to rescue retinal cells and preserve vision. Hypoxic preconditioning stabilizes the transcription factor HIF-1...

    Authors: Markus Thiersch, Wolfgang Raffelsberger, Rico Frigg, Marijana Samardzija, Andreas Wenzel, Olivier Poch and Christian Grimm
    Citation: BMC Genomics 2008 9:73
    Content type: Research article Published on:

  24. Glycolipid transfer protein is the prototypical and founding member of the new GLTP superfamily distinguished by a novel conformational fold and glycolipid binding motif. The present investigation provides the...

    Authors: Xianqiong Zou, Taeowan Chung, Xin Lin, Margarita L Malakhova, Helen M Pike and Rhoderick E Brown
    Citation: BMC Genomics 2008 9:72
    Content type: Research article Published on:

  25. Microarray analysis provides a powerful approach to identify gene expression alterations following transplantation. In patients the heterogeneity of graft specimens, co-morbidity, co-medications and the challe...

    Authors: Bayram Edemir, Sunil M Kurian, Martin Eisenacher, Detlef Lang, Carsten Müller-Tidow, Gert Gabriëls, Daniel R Salomon and Eberhard Schlatter
    Citation: BMC Genomics 2008 9:71
    Content type: Research article Published on:

  26. With the sequence of the Plasmodium falciparum genome and several global mRNA and protein life cycle expression profiling projects now completed, elucidating the underlying networks of transcriptional control imp...

    Authors: Jason A Young, Jeffery R Johnson, Chris Benner, S Frank Yan, Kaisheng Chen, Karine G Le Roch, Yingyao Zhou and Elizabeth A Winzeler
    Citation: BMC Genomics 2008 9:70
    Content type: Research article Published on:

  27. The head and neck/oral squamous cell carcinoma (HNOSCC) is a diverse group of cancers, which develop from many different anatomic sites and are associated with different risk factors and genetic characteristic...

    Authors: Hui Ye, Tianwei Yu, Stephane Temam, Barry L Ziober, Jianguang Wang, Joel L Schwartz, Li Mao, David T Wong and Xiaofeng Zhou
    Citation: BMC Genomics 2008 9:69
    Content type: Research article Published on:

  28. Most of the biological processes rely on the formation of protein complexes. Investigation of protein-protein interactions (PPI) is therefore essential for understanding of cellular functions. It is advantageo...

    Authors: Andrea Fiebitz, Lajos Nyarsik, Bernard Haendler, Yu-Hui Hu, Florian Wagner, Sabine Thamm, Hans Lehrach, Michal Janitz and Dominique Vanhecke
    Citation: BMC Genomics 2008 9:68
    Content type: Methodology article Published on:

  29. The promoters of housekeeping genes are well-bound by RNA polymerase II (RNAP) in different tissues. Although the promoters of these genes are known to contain CpG islands, the specific DNA sequences that are ...

    Authors: Julian M Rozenberg, Andrey Shlyakhtenko, Kimberly Glass, Vikas Rishi, Maxim V Myakishev, Peter C FitzGerald and Charles Vinson
    Citation: BMC Genomics 2008 9:67
    Content type: Research article Published on:

  30. Feline immunodeficiency virus (FIV) naturally infects multiple species of cat and is related to human immunodeficiency virus in humans. FIV infection causes AIDS-like disease and mortality in the domestic cat (Fe...

    Authors: Jill Pecon-Slattery, Carrie L McCracken, Jennifer L Troyer, Sue VandeWoude, Melody Roelke, Kerry Sondgeroth, Christiaan Winterbach, Hanlie Winterbach and Stephen J O'Brien
    Citation: BMC Genomics 2008 9:66
    Content type: Research article Published on:

  31. The human X chromosome has a biased gene content. One group of genes that is over-represented on the human X are those expressed in the brain, explaining the large number of sex-linked mental retardation (MRX)...

    Authors: Margaret L Delbridge, Daniel A McMillan, Ruth J Doherty, Janine E Deakin and Jennifer A Marshall Graves
    Citation: BMC Genomics 2008 9:65
    Content type: Research article Published on:

  32. The highest rates of cervical cancer are found in developing countries. Frontline monitoring has reduced these rates in developed countries and present day screening programs primarily identify precancerous le...

    Authors: Ashleen Shadeo, Raj Chari, Kim M Lonergan, Andrea Pusic, Dianne Miller, Tom Ehlen, Dirk Van Niekerk, Jasenka Matisic, Rebecca Richards-Kortum, Michele Follen, Martial Guillaud, Wan L Lam and Calum MacAulay
    Citation: BMC Genomics 2008 9:64
    Content type: Research article Published on:

  33. Tetraspanins are small membrane proteins that belong to a superfamily encompassing 33 members in human and mouse. These proteins act as organizers of membrane-signalling complexes. So far only two tetraspanin ...

    Authors: Karine Lambou, Didier Tharreau, Annegret Kohler, Catherine Sirven, Mélanie Marguerettaz, Crystel Barbisan, Adrienne C Sexton, Ellen M Kellner, Francis Martin, Barbara J Howlett, Marc J Orbach and Marc-Henri Lebrun
    Citation: BMC Genomics 2008 9:63
    Content type: Research article Published on:

  34. Toll-like receptors (TLRs) perform a vital role in disease resistance through their recognition of pathogen associated molecular patterns (PAMPs). Recent advances in genomics allow comparison of TLR genes with...

    Authors: Nicholas D Temperley, Sofia Berlin, Ian R Paton, Darren K Griffin and David W Burt
    Citation: BMC Genomics 2008 9:62
    Content type: Research article Published on:

  35. Upstream open reading frames (uORFs) are elements found in the 5'-region of an mRNA transcript, capable of regulating protein production of the largest, or major ORF (mORF), and impacting organismal developmen...

    Authors: Celine A Hayden and Giovanni Bosco
    Citation: BMC Genomics 2008 9:61
    Content type: Research article Published on:

  36. The development of microarray technology has greatly enhanced our ability to evaluate gene expression. In theory, the expression of all genes in a given organism can be monitored simultaneously. Sequencing of ...

    Authors: Xianyao Li, Hsin-I Chiang, James Zhu, Scot E Dowd and Huaijun Zhou
    Citation: BMC Genomics 2008 9:60
    Content type: Research article Published on:

  37. DNA methylation based techniques are important tools in both clinical diagnostics and therapeutics. But most of these methods only analyze a few CpG sites in a target region. Indeed, difference of site-specifi...

    Authors: Dingdong Zhang, Yan Wang, Yunfei Bai, Qinyu Ge, Yingjuan Qiao, Junfeng Luo, Chao Jia and Zuhong Lu
    Citation: BMC Genomics 2008 9:59
    Content type: Methodology article Published on:

  38. Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of dis...

    Authors: Magali Lescot, Pietro Piffanelli, Ana Y Ciampi, Manuel Ruiz, Guillaume Blanc, Jim Leebens-Mack, Felipe R da Silva, Candice MR Santos, Angélique D'Hont, Olivier Garsmeur, Alberto D Vilarinhos, Hiroyuki Kanamori, Takashi Matsumoto, Catherine M Ronning, Foo Cheung, Brian J Haas…
    Citation: BMC Genomics 2008 9:58
    Content type: Research article Published on:

  39. The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems ...

    Authors: Steven G Ralph, Hye Jung E Chun, Dawn Cooper, Robert Kirkpatrick, Natalia Kolosova, Lee Gunter, Gerald A Tuskan, Carl J Douglas, Robert A Holt, Steven JM Jones, Marco A Marra and Jörg Bohlmann
    Citation: BMC Genomics 2008 9:57
    Content type: Research article Published on:

  40. A small "sigma-like" protein, AfsS, pleiotropically regulates antibiotic biosynthesis in Streptomyces coelicolor. Overexpression of afsS in S. coelicolor and certain related species causes antibiotic stimulatory ...

    Authors: Wei Lian, Karthik P Jayapal, Salim Charaniya, Sarika Mehra, Frank Glod, Yun-Seung Kyung, David H Sherman and Wei-Shou Hu
    Citation: BMC Genomics 2008 9:56
    Content type: Research article Published on:

  42. Glioblastoma multiforme (GBM) is the most common primary intracranial tumor and despite recent advances in treatment regimens, prognosis for affected patients remains poor. Active cell migration and invasion o...

    Authors: Tim Demuth, Jessica L Rennert, Dominique B Hoelzinger, Linsey B Reavie, Mitsutoshi Nakada, Christian Beaudry, Satoko Nakada, Eric M Anderson, Amanda N Henrichs, Wendy S McDonough, David Holz, Anna Joy, Richard Lin, Kuang H Pan, Chih J Lih, Stan N Cohen…
    Citation: BMC Genomics 2008 9:54
    Content type: Research article Published on:

  43. Microarray based comparative genomic hybridisation (CGH) experiments have been used to study numerous biological problems including understanding genome plasticity in pathogenic bacteria. Typically such experi...

    Authors: Ben Carter, Guanghui Wu, Martin J Woodward and Muna F Anjum
    Citation: BMC Genomics 2008 9:53
    Content type: Methodology article Published on:

  44. MicroRNAs (miRNAs) are a novel class of gene expression regulators implicated in cancer biology. Neuroblastoma (NB) is an embryonal tumour consisting of neural crest-derived undifferentiated cells and is chara...

    Authors: Elena A Afanasyeva, Agnes Hotz-Wagenblatt, Karl-Heinz Glatting and Frank Westermann
    Citation: BMC Genomics 2008 9:52
    Content type: Research article Published on:

  46. Prader-Willi syndrome (PWS) is a neurobehavioral disorder characterized by neonatal hypotonia, childhood obesity, dysmorphic features, hypogonadism, mental retardation, and behavioral problems. Although PWS is...

    Authors: Yong-hui Jiang, Kekio Wauki, Qian Liu, Jan Bressler, Yanzhen Pan, Catherine D Kashork, Lisa G Shaffer and Arthur L Beaudet
    Citation: BMC Genomics 2008 9:50
    Content type: Research article Published on:

  47. Synonymous sites are freer to vary because of redundancy in genetic code. Messenger RNA secondary structure restricts this freedom, as revealed by previous findings in mitochondrial genes that mutations at thi...

    Authors: Neeraja M Krishnan, Hervé Seligmann and Basuthkar J Rao
    Citation: BMC Genomics 2008 9:48
    Content type: Research article Published on:

  48. Frankia sp. strains, the nitrogen-fixing facultative endosymbionts of actinorhizal plants, have long been proposed to secrete hydrolytic enzymes such as cellulases, pectinases, and proteases that may contribute t...

    Authors: Juliana E Mastronunzio, Louis S Tisa, Philippe Normand and David R Benson
    Citation: BMC Genomics 2008 9:47
    Content type: Research article Published on:

  49. Gene expression profiling has become a tool of choice to study pathological or developmental questions but in most cases the material is scarce and requires sample amplification. Two main procedures have been ...

    Authors: Séverine A Degrelle, Christelle Hennequet-Antier, Hélène Chiapello, Karine Piot-Kaminski, Francois Piumi, Stéphane Robin, Jean-Paul Renard and Isabelle Hue
    Citation: BMC Genomics 2008 9:46
    Content type: Research article Published on:

  50. Little is known about the genome sequences of Euphausiacea (krill) although these crustaceans are abundant components of the pelagic ecosystems in all oceans and used for aquaculture and pharmaceutical industr...

    Authors: Cristiano De Pittà, Cristiano Bertolucci, Gabriella M Mazzotta, Filippo Bernante, Giorgia Rizzo, Barbara De Nardi, Alberto Pallavicini, Gerolamo Lanfranchi and Rodolfo Costa
    Citation: BMC Genomics 2008 9:45
    Content type: Research article Published on:

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BMC Genomics

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