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  1. Presently, multiple options exist for conducting gene expression profiling studies in swine. In order to determine the performance of some of the existing microarrays, Affymetrix Porcine, Affymetrix Human U133...

    Authors: Shengdar Tsai, Bashir Mir, Amy C Martin, Jose L Estrada, Steve R Bischoff, Wen-ping Hsieh, Joseph P Cassady, Bradley A Freking, Dan J Nonneman, Gary A Rohrer and Jorge A Piedrahita
    Citation: BMC Genomics 2006 7:328
    Content type: Research article Published on:

  2. Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice) and Arabidopsis thaliana (Arabidopsis). Additionally, these two plant species have extensive cDNA and expressed sequence tag (...

    Authors: Matthew A Campbell, Brian J Haas, John P Hamilton, Stephen M Mount and C Robin Buell
    Citation: BMC Genomics 2006 7:327
    Content type: Research article Published on:

  3. Alternative splicing is a mechanism for increasing protein diversity by excluding or including exons during post-transcriptional processing. Alternatively spliced proteins are particularly relevant in oncology...

    Authors: Paul J Gardina, Tyson A Clark, Brian Shimada, Michelle K Staples, Qing Yang, James Veitch, Anthony Schweitzer, Tarif Awad, Charles Sugnet, Suzanne Dee, Christopher Davies, Alan Williams and Yaron Turpaz
    Citation: BMC Genomics 2006 7:325
    Content type: Research article Published on:

  4. The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the p...

    Authors: Raj Chari, William W Lockwood, Bradley P Coe, Anna Chu, Devon Macey, Andrew Thomson, Jonathan J Davies, Calum MacAulay and Wan L Lam
    Citation: BMC Genomics 2006 7:324
    Content type: Research article Published on:

  5. Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. Although some 5' noncoding microsatellites involved in gene regulation hav...

    Authors: Lida Zhang, Kaijing Zuo, Fei Zhang, Youfang Cao, Jiang Wang, Yidong Zhang, Xiaofen Sun and Kexuan Tang
    Citation: BMC Genomics 2006 7:323
    Content type: Research article Published on:

  6. The quail and chicken major histocompatibility complex (Mhc) genomic regions have a similar overall organization but differ markedly in that the quail has an expanded number of duplicated class I, class IIB, natu...

    Authors: Kazuyoshi Hosomichi, Takashi Shiina, Shingo Suzuki, Masayuki Tanaka, Sayoko Shimizu, Shigehisa Iwamoto, Hiromi Hara, Yutaka Yoshida, Jerzy K Kulski, Hidetoshi Inoko and Kei Hanzawa
    Citation: BMC Genomics 2006 7:322
    Content type: Research article Published on:

  9. Up to now, microarray data are mostly assessed in context with only one or few parameters characterizing the experimental conditions under study. More explicit experiment annotations, however, are highly usefu...

    Authors: Kurt Fellenberg, Christian H Busold, Olaf Witt, Andrea Bauer, Boris Beckmann, Nicole C Hauser, Marcus Frohme, Stefan Winter, Jürgen Dippon and Jörg D Hoheisel
    Citation: BMC Genomics 2006 7:319
    Content type: Methodology article Published on:

  11. Many marketed therapeutic agents have been developed to modulate the function of G protein-coupled receptors (GPCRs). The regulators of G-protein signaling (RGS proteins) are also being examined as potential d...

    Authors: Yu-Ching Fang, Wei-Hsin Sun, Li-Cheng Wu, Hsien-Da Huang, Hsueh-Fen Juan and Jorng-Tzong Horng
    Citation: BMC Genomics 2006 7:317
    Content type: Database Published on:

  14. Maturation of spermatozoa, including development of motility and the ability to fertilize the oocyte, occurs during transit through the microenvironment of the epididymis. Comprehensive understanding of sperm ...

    Authors: Jungsu Oh, Jiae Lee, Jong-Min Woo, Eunyoung Choi, Inju Park, Cecil Han, Namhoe Baek, Hoyong Lee, Do Han Kim and Chunghee Cho
    Citation: BMC Genomics 2006 7:314
    Content type: Research article Published on:

  15. Upon exposure to agents that damage DNA, Saccharomyces cerevisiae undergo widespread reprogramming of gene expression. Such a vast response may be due not only to damage to DNA but also damage to proteins, RNA, a...

    Authors: Rebecca C Fry, Michael S DeMott, Joseph P Cosgrove, Thomas J Begley, Leona D Samson and Peter C Dedon
    Citation: BMC Genomics 2006 7:313
    Content type: Research article Published on:

  16. Formalin-fixed paraffin-embedded (FFPE) tissues represent the largest source of archival biological material available for genomic studies of human cancer. Therefore, it is desirable to develop methods that en...

    Authors: Sarit Aviel-Ronen, Chang Qi Zhu, Bradley P Coe, Ni Liu, Spencer K Watson, Wan L Lam and Ming Sound Tsao
    Citation: BMC Genomics 2006 7:312
    Content type: Methodology article Published on:

  17. The signals that determine the specificity and efficiency of splicing are multiple and complex, and are not fully understood. Among other factors, the relative contributions of different mechanisms appear to d...

    Authors: Colin N Dewey, Igor B Rogozin and Eugene V Koonin
    Citation: BMC Genomics 2006 7:311
    Content type: Research article Published on:

  18. Rice blast, caused by the fungal pathogen Magnaporthe grisea, is a devastating disease causing tremendous yield loss in rice production. The public availability of the complete genome sequence of M. grisea provid...

    Authors: Malali Gowda, RC Venu, Mohan B Raghupathy, Kan Nobuta, Huameng Li, Rod Wing, Eric Stahlberg, Sean Couglan, Christian D Haudenschild, Ralph Dean, Baek-Hie Nahm, Blake C Meyers and Guo-Liang Wang
    Citation: BMC Genomics 2006 7:310
    Content type: Research article Published on:

  23. One of the most crucial tasks for a cell to ensure its long term survival is preserving the integrity of its genetic heritage via maintenance of DNA structure and sequence. While the DNA damage response in the...

    Authors: Michael G Benton, Swetha Somasundaram, Jeremy D Glasner and Sean P Palecek
    Citation: BMC Genomics 2006 7:305
    Content type: Research article Published on:

  24. Repetitive elements comprise ~45% of mammalian genomes and are increasingly known to impact genomic function by contributing to the genomic architecture, by direct regulation of gene expression and by affectin...

    Authors: Ralph T Wiedmann, Dan J Nonneman and John W Keele
    Citation: BMC Genomics 2006 7:304
    Content type: Research article Published on:

  25. Fission yeast cells undergo sexual differentiation in response to nitrogen starvation. In this process haploid M and P cells first mate to form diploid zygotes, which then enter meiosis and sporulate. Prior to...

    Authors: Yongtao Xue-Franzén, Søren Kjærulff, Christian Holmberg, Anthony Wright and Olaf Nielsen
    Citation: BMC Genomics 2006 7:303
    Content type: Research article Published on:

  26. The development of large genomic resources has become a prerequisite to elucidate the wide-scale evolution of genomes and the molecular basis of complex traits. Linkage maps represent a first level of integrat...

    Authors: René Guyomard, Stéphane Mauger, Kamila Tabet-Canale, Sylvain Martineau, Carine Genet, Francine Krieg and Edwige Quillet
    Citation: BMC Genomics 2006 7:302
    Content type: Research article Published on:

  27. The replication of mammalian genomic DNA during the S phase is a highly coordinated process that occurs in a programmed manner. Recent studies have begun to elucidate the pattern of replication timing on a gen...

    Authors: Stephanie M Cohen, Terrence S Furey, Norman A Doggett and David G Kaufman
    Citation: BMC Genomics 2006 7:301
    Content type: Research article Published on:

  29. Esophageal squamous cell carcinoma (ESCC) is a common malignancy worldwide. Comprehensive genomic characterization of ESCC will further our understanding of the carcinogenesis process in this disease.

    Authors: Nan Hu, Chaoyu Wang, Ying Hu, Howard H Yang, Li-Hui Kong, Ning Lu, Hua Su, Quan-Hong Wang, Alisa M Goldstein, Kenneth H Buetow, Michael R Emmert-Buck, Philip R Taylor and Maxwell P Lee
    Citation: BMC Genomics 2006 7:299
    Content type: Research article Published on:

  30. Single nucleotide polymorphisms (SNPs) are an abundant form of genetic variation in the genome of every species and are useful for gene mapping and association studies. Of particular interest are non-synonymou...

    Authors: Michael A Lee, Orla M Keane, Belinda C Glass, Tim R Manley, Neil G Cullen, Ken G Dodds, Alan F McCulloch, Chris A Morris, Mark Schreiber, Jonathan Warren, Amonida Zadissa, Theresa Wilson and John C McEwan
    Citation: BMC Genomics 2006 7:298
    Content type: Research article Published on:

  31. Peridinin-containing dinoflagellates have a highly reduced chloroplast genome, which is unlike that found in other chloroplast containing organisms. Genome reduction appears to be the result of extensive trans...

    Authors: Adrian C Barbrook, Nicole Santucci, Lindsey J Plenderleith, Roger G Hiller and Christopher J Howe
    Citation: BMC Genomics 2006 7:297
    Content type: Research article Published on:

  32. To unravel molecular targets involved in glycopeptide resistance, three isogenic strains of Staphylococcus aureus with different susceptibility levels to vancomycin or teicoplanin were subjected to whole-genome m...

    Authors: Alexander Scherl, Patrice François, Yvan Charbonnier, Jacques M Deshusses, Thibaud Koessler, Antoine Huyghe, Manuela Bento, Jianru Stahl-Zeng, Adrien Fischer, Alexandre Masselot, Alireza Vaezzadeh, Francesca Gallé, Adriana Renzoni, Pierre Vaudaux, Daniel Lew, Catherine G Zimmermann-Ivol…
    Citation: BMC Genomics 2006 7:296
    Content type: Research article Published on:

  33. The development and outcome of cerebral malaria (CM) reflects a complex interplay between parasite-expressed virulence factors and host response to infection. The murine CM model, Plasmodium berghei ANKA (PbA), w...

    Authors: Fiona E Lovegrove, Lourdes Peña-Castillo, Naveed Mohammad, W Conrad Liles, Timothy R Hughes and Kevin C Kain
    Citation: BMC Genomics 2006 7:295
    Content type: Research article Published on:

  34. The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to p...

    Authors: Wei Liu, Yonghui Zhao, Zhaoliang Liu, Ying Zhang, Zhengxing Lian and Ning Li
    Citation: BMC Genomics 2006 7:294
    Content type: Research article Published on:

  35. Currently available vaccines against leptospirosis are of low efficacy, have an unacceptable side-effect profile, do not induce long-term protection, and provide no cross-protection against the different serov...

    Authors: Hong-Liang Yang, Yong-Zhang Zhu, Jin-Hong Qin, Ping He, Xu-Cheng Jiang, Guo-Ping Zhao and Xiao-Kui Guo
    Citation: BMC Genomics 2006 7:293
    Content type: Research article Published on:

  36. Protein degradation by the ubiquitin system plays a crucial role in numerous cellular signaling pathways. Deubiquitination, a reversal of ubiquitination, has been recognized as an important regulatory step in ...

    Authors: Ju-Mi Shin, Kyong-Jai Yoo, Myung-Sun Kim, Dongku Kim and Kwang-Hyun Baek
    Citation: BMC Genomics 2006 7:292
    Content type: Research article Published on:

  37. There is an imperative need for SNP genotyping technologies that are cost-effective per sample with retained high accuracy, throughput and flexibility. We have developed a microarray-based technique and compar...

    Authors: Max Käller, Emilie Hultin, Kristina Holmberg, Marie-Louise Persson, Jacob Odeberg, Joakim Lundeberg and Afshin Ahmadian
    Citation: BMC Genomics 2006 7:291
    Content type: Methodology article Published on:

  39. Increased focus surrounds identifying patients with advanced non-small cell lung cancer (NSCLC) who will benefit from treatment with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI). EG...

    Authors: Justin M Balko, Anil Potti, Christopher Saunders, Arnold Stromberg, Eric B Haura and Esther P Black
    Citation: BMC Genomics 2006 7:289
    Content type: Research article Published on:

  40. To gain insight into the evolutionary features of the huntingtin (htt) gene in Chordata, we have sequenced and characterized the full-length htt mRNA in the ascidian Ciona intestinalis, a basal chordate emerging ...

    Authors: Carmela Gissi, Graziano Pesole, Elena Cattaneo and Marzia Tartari
    Citation: BMC Genomics 2006 7:288
    Content type: Research article Published on:

  41. Rhabdomyosarcoma is a highly malignant soft tissue sarcoma in childhood and arises as a consequence of regulatory disruption of the growth and differentiation pathways of myogenic precursor cells. The pathogen...

    Authors: Chiara Romualdi, Cristiano De Pittà, Lucia Tombolan, Stefania Bortoluzzi, Francesca Sartori, Angelo Rosolen and Gerolamo Lanfranchi
    Citation: BMC Genomics 2006 7:287
    Content type: Research article Published on:

  42. Alzheimer's disease (AD) is a complex disorder that involves multiple biological processes. Many genes implicated in these processes may be present in low abundance in the human brain. DNA microarray analysis ...

    Authors: Qing Yan Liu, Roy R Sooknanan, Lawrence T Malek, Maria Ribecco-Lutkiewicz, Joy X Lei, Hui Shen, Boleslaw Lach, P Roy Walker, Joel Martin and Marianna Sikorska
    Citation: BMC Genomics 2006 7:286
    Content type: Methodology article Published on:

  43. MicroRNAs (miRNAs) have been shown to play important roles in regulating gene expression. Since miRNAs are often evolutionarily conserved and their precursors can be folded into stem-loop hairpins, many miRNAs...

    Authors: Xijin Ge, Qingfa Wu and San Ming Wang
    Citation: BMC Genomics 2006 7:285
    Content type: Research article Published on:

  45. Several approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from technical deficiencies...

    Authors: Oliver C Jann, Jan Aerts, Michelle Jones, Nicola Hastings, Andy Law, Stephanie McKay, Elisa Marques, Aparna Prasad, Jody Yu, Stephen S Moore, Sandrine Floriot, Marie-Françoise Mahé, André Eggen, Licia Silveri, Riccardo Negrini, Elisabetta Milanesi…
    Citation: BMC Genomics 2006 7:283
    Content type: Research article Published on:

  46. The completed genome sequences of the malaria parasites P. falciparum, P. y. yoelii and P. vivax have revealed some unusual features. P. falciparum contains the most AT rich genome sequenced so far – over 90% in ...

    Authors: Pierre M Durand, Andries J Oelofse and Theresa L Coetzer
    Citation: BMC Genomics 2006 7:282
    Content type: Research article Published on:

  47. The Major Histocompatibility Complex (MHC) is essential for immune function. Historically, it has been subdivided into three regions (Class I, II, and III), but a cluster of functionally related genes within t...

    Authors: Janine E Deakin, Anthony T Papenfuss, Katherine Belov, Joseph GR Cross, Penny Coggill, Sophie Palmer, Sarah Sims, Terence P Speed, Stephan Beck and Jennifer A Marshall Graves
    Citation: BMC Genomics 2006 7:281
    Content type: Research article Published on:

  48. The Caenorhabditis elegans genome encodes ten proteins that share sequence similarity with the Hedgehog signaling molecule through their C-terminal autoprocessing Hint/Hog domain. These proteins contain novel N-t...

    Authors: Limin Hao, Robert Johnsen, Gilbert Lauter, David Baillie and Thomas R Bürglin
    Citation: BMC Genomics 2006 7:280
    Content type: Research article Published on:

  49. The TGFβ1-induced signal transduction processes involved in growth and differentiation are only partly known. The three-dimensional epithelial differentiation model, in which T84 epithelial cells are induced t...

    Authors: Kati M Juuti-Uusitalo, Katri Kaukinen, Markku Mäki, Jarno Tuimala and Heikki Kainulainen
    Citation: BMC Genomics 2006 7:279
    Content type: Research article Published on:

  50. A 70-gene tumor expression profile was established as a powerful predictor of disease outcome in young breast cancer patients. This profile, however, was generated on microarrays containing 25,000 60-mer oligo...

    Authors: Annuska M Glas, Arno Floore, Leonie JMJ Delahaye, Anke T Witteveen, Rob CF Pover, Niels Bakx, Jaana ST Lahti-Domenici, Tako J Bruinsma, Marc O Warmoes, René Bernards, Lodewyk FA Wessels and Laura J Van 't Veer
    Citation: BMC Genomics 2006 7:278
    Content type: Methodology article Published on:

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BMC Genomics

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