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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. Genes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. They have been known to play important roles in RNA processing as RNA-binding proteins...

    Authors: Dong Wang, Yinghui Guo, Changai Wu, Guodong Yang, Yingying Li and Chengchao Zheng
    Citation: BMC Genomics 2008 9:44
  27. The Arc two-component system is a global regulator controlling many genes involved in aerobic/anaerobic respiration and fermentative metabolism in Escherichia coli. Shewanella oneidensis MR-1 contains a gene enco...

    Authors: Haichun Gao, Xiaohu Wang, Zamin K Yang, Timothy Palzkill and Jizhong Zhou
    Citation: BMC Genomics 2008 9:42
  28. Accurate analyses of comprehensive genome-wide SNP genotyping and gene expression data sets is challenging for many researchers. In fact, obtaining an integrated view of both large scale SNP genotyping and gen...

    Authors: Mathijs A Sanders, Roel GW Verhaak, Wendy MC Geertsma-Kleinekoort, Saman Abbas, Sebastiaan Horsman, Peter J van der Spek, Bob Löwenberg and Peter JM Valk
    Citation: BMC Genomics 2008 9:41
  29. Photorhabdus luminescens and Yersinia enterocolitica are both enteric bacteria which are associated with insects. P. luminescens lives in symbiosis with soil nematodes and is highly pathogenic towards insects but...

    Authors: Ralf Heermann and Thilo M Fuchs
    Citation: BMC Genomics 2008 9:40
  30. The tunicate Ciona intestinalis (Enterogona, Ascidiacea), a major model system for evolutionary and developmental genetics of chordates, harbours two cryptic species. To assess the degree of intra- and inter-spec...

    Authors: Luigi Caputi, Marco Borra, Nikos Andreakis, Elio Biffali and Paolo Sordino
    Citation: BMC Genomics 2008 9:39
  31. To strengthen research and differential diagnostics of mitochondrial disorders, we constructed and validated an oligonucleotide microarray (h-MitoArray) allowing expression analysis of 1632 human genes involve...

    Authors: Alena Čížková, Viktor Stránecký, Robert Ivánek, Hana Hartmannová, Lenka Nosková, Lenka Piherová, Markéta Tesařová, Hana Hansíková, Tomáš Honzík, Jiří Zeman, Petr Divina, Andrea Potocká, Jan Paul, Wolfgang Sperl, Johannes A Mayr, Sara Seneca…
    Citation: BMC Genomics 2008 9:38
  32. Whirling disease, caused by the pathogen Myxobolus cerebralis, afflicts several salmonid species. Rainbow trout are particularly susceptible and may suffer high mortality rates. The disease is persistent and spre...

    Authors: Melinda R Baerwald, Amy B Welsh, Ronald P Hedrick and Bernie May
    Citation: BMC Genomics 2008 9:37
  33. A reanalysis of the sequences reported by Hoegg et al has highlighted the presence of a putative HoxC1a gene in Astatotilapia burtoni. We discuss the evolutionary history of the HoxC1a gene in the teleost fish li...

    Authors: Morgane Thomas-Chollier and Valérie Ledent
    Citation: BMC Genomics 2008 9:35
  34. The Saccharomyces cerevisiae MYO1 gene encodes the myosin II heavy chain (Myo1p), a protein required for normal cytokinesis in budding yeast. Myo1p deficiency in yeast (myo1Δ) causes a cell separation defect char...

    Authors: José F Rodríguez-Quiñones, Rafael A Irizarry, Nitza L Díaz-Blanco, Félix E Rivera-Molina, Diana Gómez-Garzón and José R Rodríguez-Medina
    Citation: BMC Genomics 2008 9:34
  35. Mitochondrial genomes (mtDNA) of numerous sponges have been sequenced as part of an ongoing effort to resolve the class-level phylogeny of the Porifera, as well as to place the various lower metazoan groups on...

    Authors: Rafael D Rosengarten, Erik A Sperling, Maria A Moreno, Sally P Leys and Stephen L Dellaporta
    Citation: BMC Genomics 2008 9:33
  36. Minor groove binding drugs (MGBDs) interact with DNA in a sequence-specific manner and can cause changes in gene expression at the level of transcription. They serve as valuable models for protein interactions...

    Authors: Todd T Eckdahl, Adam D Brown, Steven N Hart, Kelly J Malloy, Martha Shott, Gloria Yiu, Laura L Mays Hoopes and Laurie J Heyer
    Citation: BMC Genomics 2008 9:32
  37. Simple sequence repeats (SSRs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The eukaryotic model organism Neurospora crassa is an excellent system to study evolu...

    Authors: Tae-Sung Kim, James G Booth, Hugh G Gauch Jr, Qi Sun, Jongsun Park, Yong-Hwan Lee and Kwangwon Lee
    Citation: BMC Genomics 2008 9:31
  38. Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling whole genome shotgun sequences. Screening of a BAC library using molecular markers is ...

    Authors: Xiaolei Wu, Guohua Zhong, Seth D Findley, Perry Cregan, Gary Stacey and Henry T Nguyen
    Citation: BMC Genomics 2008 9:28
  39. The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations...

    Authors: Emma S Mace, Ling Xia, David R Jordan, Kirsten Halloran, Dipal K Parh, Eric Huttner, Peter Wenzl and Andrzej Kilian
    Citation: BMC Genomics 2008 9:26

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