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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. Traditionally, housekeeping and tissue specific genes have been classified using direct assay of mRNA presence across different tissues, but these experiments are costly and the results not easy to compare and...

    Authors: Luna De Ferrari and Stuart Aitken
    Citation: BMC Genomics 2006 7:277
    Content type: Research article Published on:

  24. Eukaryotic replication origins exhibit different initiation efficiencies and activation times within S-phase. Although local chromatin structure and function influences origin activity, the exact mechanisms re...

    Authors: Weihong Xu, Jennifer G Aparicio, Oscar M Aparicio and Simon Tavaré
    Citation: BMC Genomics 2006 7:276
    Content type: Research article Published on:

  25. During the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, ...

    Authors: Thomas Wicker, Edith Schlagenhauf, Andreas Graner, Timothy J Close, Beat Keller and Nils Stein
    Citation: BMC Genomics 2006 7:275
    Content type: Research article Published on:

  26. Body weight and length are economically important traits in foodfish species influenced by quantitative trait loci (QTL) and environmental factors. It is usually difficult to dissect the genetic and environmen...

    Authors: Chun Ming Wang, Loong Chueng Lo, Ze Yuan Zhu and Gen Hua Yue
    Citation: BMC Genomics 2006 7:274
    Content type: Research article Published on:

  28. In this study, we addressed whether a single 454 Life Science GS20 sequencing run provides new gene discovery from a normalized cDNA library, and whether the short reads produced via this technology are of val...

    Authors: Foo Cheung, Brian J Haas, Susanne MD Goldberg, Gregory D May, Yongli Xiao and Christopher D Town
    Citation: BMC Genomics 2006 7:272
    Content type: Research article Published on:

  29. Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Comparison of genomic organisation in different lineag...

    Authors: Karl R Wotton and Sebastian M Shimeld
    Citation: BMC Genomics 2006 7:271
    Content type: Research article Published on:

  30. Bacillus thuringiensis belongs to the Bacillus cereus sensu lato group of Gram-positive and spore-forming bacteria. Most isolates of B. thuringiensis can bear many endogenous plasmids, and the number and size of ...

    Authors: Junyan Huang, Suxia Guo, Jacques Mahillon, Géraldine A Van der Auwera, Li Wang, Dongmei Han, Ziniu Yu and Ming Sun
    Citation: BMC Genomics 2006 7:270
    Content type: Research article Published on:

  31. The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and dist...

    Authors: Francesc López-Giráldez, Olga Andrés, Xavier Domingo-Roura and Montserrat Bosch
    Citation: BMC Genomics 2006 7:269
    Content type: Research article Published on:

  32. A better understanding of the development of metastatic disease and the identification of molecular markers for cancer spread would be useful for the design of improved treatment strategies. This study was con...

    Authors: Heidi Lyng, Runar S Brøvig, Debbie H Svendsrud, Ruth Holm, Olav Kaalhus, Kjetil Knutstad, Halldis Oksefjell, Kolbein Sundfør, Gunnar B Kristensen and Trond Stokke
    Citation: BMC Genomics 2006 7:268
    Content type: Research article Published on:

  33. Our understanding of the mechanisms that govern the cellular process of meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chr...

    Authors: Wayne Crismani, Ute Baumann, Tim Sutton, Neil Shirley, Tracie Webster, German Spangenberg, Peter Langridge and Jason A Able
    Citation: BMC Genomics 2006 7:267
    Content type: Research article Published on:

  34. Microarray normalizations typically apply methods that assume absence of global transcript shifts, or absence of changes in internal control features such as housekeeping genes. These normalization approaches ...

    Authors: Carole L Yauk, Andrew Williams, Sherri Boucher, Lynn M Berndt, Gu Zhou, Jenny L Zheng, Andrea Rowan-Carroll, Hongyan Dong, Iain B Lambert, George R Douglas and Craig L Parfett
    Citation: BMC Genomics 2006 7:266
    Content type: Methodology article Published on:

  35. The identification of genes essential for survival is of theoretical importance in the understanding of the minimal requirements for cellular life, and of practical importance in the identification of potentia...

    Authors: Adam M Gustafson, Evan S Snitkin, Stephen CJ Parker, Charles DeLisi and Simon Kasif
    Citation: BMC Genomics 2006 7:265
    Content type: Research article Published on:

  36. Little is known about the genome sequences of lepidopteran insects, although this group of insects has been studied extensively in the fields of endocrinology, development, immunity, and pathogen-host interact...

    Authors: Youping Deng, Yinghua Dong, Venkata Thodima, Rollie J Clem and A Lorena Passarelli
    Citation: BMC Genomics 2006 7:264
    Content type: Research article Published on:

  37. Aplastic anemia (AA) is a bone marrow failure syndrome mostly characterized by an immune-mediated destruction of marrow hematopoietic progenitor/stem cells. The resulting hypocellularity limits a detailed anal...

    Authors: Anke Franzke, Robert Geffers, J Katrin Hunger, Susanne Pförtner, Wenji Piao, Philipp Ivanyi, Jens Grosse, Michael Probst-Kepper, Arnold Ganser and Jan Buer
    Citation: BMC Genomics 2006 7:263
    Content type: Research article Published on:

  38. TILLING (T argeting I nduced L ocal L esions i n G enomes) is a reverse genetic technique based on the use of a mismatch-specific enzyme that identifies mutations in a target gene through heteroduplex analysis. W...

    Authors: Erin J Gilchrist, Nigel J O'Neil, Ann M Rose, Monique C Zetka and George W Haughn
    Citation: BMC Genomics 2006 7:262
    Content type: Methodology article Published on:

  40. The multi-step process of carcinogenesis can be more fully understood by characterizing gene expression changes induced in cells by carcinogens. In this study, expression microarrays were used to monitor the a...

    Authors: Sarah L Hockley, Volker M Arlt, Daniel Brewer, Ian Giddings and David H Phillips
    Citation: BMC Genomics 2006 7:260
    Content type: Research article Published on:

  41. Post-segregational killing systems are present in a large variety of microorganisms. When found on plasmids, they are described as addiction systems that act to maintain the plasmid during the partitioning of ...

    Authors: Sarah Fico and Jacques Mahillon
    Citation: BMC Genomics 2006 7:259
    Content type: Research article Published on:

  42. Quantitative variation in gene expression has been proposed to underlie phenotypic variation among human individuals. A facilitating step towards understanding the basis for gene expression variability is asso...

    Authors: Vineet K Sharma, Anu Sharma, Naveen Kumar, Mamta Khandelwal, Kiran Kumar Mandapati, Shirley Horn-Saban, Liora Strichman-Almashanu, Doron Lancet, Samir K Brahmachari and Srinivasan Ramachandran
    Citation: BMC Genomics 2006 7:258
    Content type: Database Published on:

  43. The ability to rapidly characterize an unknown microorganism is critical in both responding to infectious disease and biodefense. To do this, we need some way of anticipating an organism's phenotype based on t...

    Authors: Chern-Sing Goh, Tara A Gianoulis, Yang Liu, Jianrong Li, Alberto Paccanaro, Yves A Lussier and Mark Gerstein
    Citation: BMC Genomics 2006 7:257
    Content type: Methodology article Published on:

  45. Dermatophytes are the primary causative agent of dermatophytoses, a disease that affects billions of individuals worldwide. Trichophyton rubrum is the most common of the superficial fungi. Although T. rubrum is a...

    Authors: Lingling Wang, Li Ma, Wenchuan Leng, Tao Liu, Lu Yu, Jian Yang, Li Yang, Wenliang Zhang, Qian Zhang, Jie Dong, Ying Xue, Yafang Zhu, Xingye Xu, Zhe Wan, Guohui Ding, Fudong Yu…
    Citation: BMC Genomics 2006 7:255
    Content type: Research article Published on:

  47. Cross-species primers have been used with moderate success to address a variety of questions concerning genome structure, evolution, and gene function. However, the factors affecting their success have never b...

    Authors: Donna JE Housley, Zachary A Zalewski, Stephanie E Beckett and Patrick J Venta
    Citation: BMC Genomics 2006 7:253
    Content type: Research article Published on:

  48. RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundanc...

    Authors: Ilhem Diboun, Lorenz Wernisch, Christine Anne Orengo and Martin Koltzenburg
    Citation: BMC Genomics 2006 7:252
    Content type: Research article Published on:

  49. Allergy is a common debilitating and occasionally life threatening condition. The fungal kingdom contains a number of species that produce a wide range of well defined protein allergens although the vast major...

    Authors: Paul Bowyer, Marcin Fraczek and David W Denning
    Citation: BMC Genomics 2006 7:251
    Content type: Research article Published on:

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