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  1. Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mec...

    Authors: Jiří Macas, Pavel Neumann and Alice Navrátilová
    Citation: BMC Genomics 2007 8:427
    Content type: Research article Published on:

  2. The number of sequenced fungal genomes is ever increasing, with about 200 genomes already fully sequenced or in progress. Only a small percentage of those genomes have been comprehensively studied, for example...

    Authors: Cornelia Hedeler, Han Min Wong, Michael J Cornell, Intikhab Alam, Darren M Soanes, Magnus Rattray, Simon J Hubbard, Nicholas J Talbot, Stephen G Oliver and Norman W Paton
    Citation: BMC Genomics 2007 8:426
    Content type: Database Published on:

  4. Single-nucleotide polymorphisms (SNPs) are the most abundant type of DNA sequence polymorphisms. Their higher availability and stability when compared to simple sequence repeats (SSRs) provide enhanced possibi...

    Authors: Diego Lijavetzky, José Antonio Cabezas, Ana Ibáñez, Virginia Rodríguez and José M Martínez-Zapater
    Citation: BMC Genomics 2007 8:424
    Content type: Research article Published on:

  5. The green peach aphid, Myzus persicae (Sulzer), is a world-wide insect pest capable of infesting more than 40 plant families, including many crop species. However, despite the significant damage inflicted by M. p...

    Authors: John S Ramsey, Alex CC Wilson, Martin de Vos, Qi Sun, Cecilia Tamborindeguy, Agnese Winfield, Gaynor Malloch, Dawn M Smith, Brian Fenton, Stewart M Gray and Georg Jander
    Citation: BMC Genomics 2007 8:423
    Content type: Research article Published on:

  6. Several genome duplications have occurred in the evolutionary history of teleost fish. In returning to a stable diploid state, the polyploid genome reorganized, and large portions are lost, while the fish line...

    Authors: Johan G de Boer, Ryosuke Yazawa, William S Davidson and Ben F Koop
    Citation: BMC Genomics 2007 8:422
    Content type: Research article Published on:

  7. Toll-like receptor-2 (TLR2) and Caspase Recruitment Domain 15 (CARD15) are important pattern recognition receptors that play a role in the initiation of the inflammatory and subsequent immune response. They ha...

    Authors: Sameer D Pant, Flavio S Schenkel, Ivan Leyva-Baca, Bhawani S Sharma and Niel A Karrow
    Citation: BMC Genomics 2007 8:421
    Content type: Research article Published on:

  8. Iron-deficiency leads to the induction of genes related to intestinal iron absorption and homeostasis. By analyzing a large GeneChip® dataset from the rat intestine, we identified a large cluster of 228 genes tha...

    Authors: James F Collins and Zihua Hu
    Citation: BMC Genomics 2007 8:420
    Content type: Research article Published on:

  11. Lactation is an important aspect of mammalian biology and, amongst mammals, marsupials show one of the most complex lactation cycles. Marsupials, such as the tammar wallaby (Macropus eugenii) give birth to a rela...

    Authors: Christophe M Lefèvre, Matthew R Digby, Jane C Whitley, Yvan Strahm and Kevin R Nicholas
    Citation: BMC Genomics 2007 8:417
    Content type: Research article Published on:

  12. The enormous amount of sequence data available in the public domain database has been a gold mine for researchers exploring various themes in life sciences, and hence the quality of such data is of serious con...

    Authors: Yi-An Chen, Chang-Chun Lin, Chin-Di Wang, Huan-Bin Wu and Pei-Ing Hwang
    Citation: BMC Genomics 2007 8:416
    Content type: Methodology article Published on:

  13. Differential expression of genes can be regulated on many different levels. Most global studies of gene regulation concentrate on transcript level regulation, and very few global analyses of differential trans...

    Authors: Christian Lange, Alexander Zaigler, Mathias Hammelmann, Jens Twellmeyer, Günter Raddatz, Stephan C Schuster, Dieter Oesterhelt and Jörg Soppa
    Citation: BMC Genomics 2007 8:415
    Content type: Research article Published on:

  14. Several high-throughput technologies can measure in parallel the abundance of many mRNA transcripts within a sample. These include the widely-used microarray as well as the more recently developed methods base...

    Authors: Junfeng Chen, Vikas Agrawal, Magnus Rattray, Marilyn AL West, Dina A St Clair, Richard W Michelmore, Sean J Coughlan and Blake C Meyers
    Citation: BMC Genomics 2007 8:414
    Content type: Research article Published on:

  15. Suicide is an important and potentially preventable consequence of serious mental disorders of unknown etiology. Gene expression profiling technology provides an unbiased approach to identifying candidate gene...

    Authors: Sanghyeon Kim, Kwang-Ho Choi, Ali Fuat Baykiz and Howard K Gershenfeld
    Citation: BMC Genomics 2007 8:413
    Content type: Research article Published on:

  16. Plant hybrid proline-rich proteins (HyPRPs) are putative cell wall proteins consisting, usually, of a repetitive proline-rich (PR) N-terminal domain and a conserved eight-cysteine motif (8 CM) C-terminal domai...

    Authors: Lenka Dvořáková, Fatima Cvrčková and Lukáš Fischer
    Citation: BMC Genomics 2007 8:412
    Content type: Research article Published on:

  17. Ganoderma lucidum has been widely used as a herbal medicine for promoting health and longevity in China and other Asian countries. Polysaccharide extracts from Ganoderma lucidum have been reported to exhibit immu...

    Authors: Kun-Chieh Cheng, Hsuan-Cheng Huang, Jenn-Han Chen, Jia-Wei Hsu, Hsu-Chieh Cheng, Chern-Han Ou, Wen-Bin Yang, Shui-Tein Chen, Chi-Huey Wong and Hsueh-Fen Juan
    Citation: BMC Genomics 2007 8:411
    Content type: Research article Published on:

  18. We are profoundly ignorant about the diversity of viruses that infect the domain Archaea. Less than 100 have been identified and described and very few of these have had their genomic sequences determined. Here w...

    Authors: Eulyn Pagaling, Richard D Haigh, William D Grant, Don A Cowan, Brian E Jones, Yanhe Ma, Antonio Ventosa and Shaun Heaphy
    Citation: BMC Genomics 2007 8:410
    Content type: Research article Published on:

  19. Transposable elements constitute a significant fraction of plant genomes. The PIF/Harbinger superfamily includes DNA transposons (class II elements) carrying terminal inverted repeats and producing a 3 bp target ...

    Authors: Dariusz Grzebelus, Slawomir Lasota, Tomasz Gambin, Gregory Kucherov and Anna Gambin
    Citation: BMC Genomics 2007 8:409
    Content type: Research article Published on:

  20. Sequencing of the genomes of several Drosophila allows for the first precise analyses of how global sequence patterns change among multiple, closely related animal species. A basic question is whether there are c...

    Authors: Miguel Gallach, Vicente Arnau and Ignacio Marín
    Citation: BMC Genomics 2007 8:408
    Content type: Research article Published on:

  21. Schistosoma mansoni is a blood helminth parasite that causes schistosomiasis, a disease that affects 200 million people in the world. Many orthologs of known mammalian genes have been discovered in this parasite ...

    Authors: Thiago M Venancio, Ricardo DeMarco, Giulliana T Almeida, Katia C Oliveira, João C Setubal and Sergio Verjovski-Almeida
    Citation: BMC Genomics 2007 8:407
    Content type: Research article Published on:

  22. Recent experimental and computational studies have provided overwhelming evidence for a plethora of diverse transcripts that are unrelated to protein-coding genes. One subclass consists of those RNAs that requ...

    Authors: Dominic Rose, Jörg Hackermüller, Stefan Washietl, Kristin Reiche, Jana Hertel, Sven Findeiß, Peter F Stadler and Sonja J Prohaska
    Citation: BMC Genomics 2007 8:406
    Content type: Research article Published on:

  23. Boar taint is a major obstacle when using uncastrated male pigs for swine production. One of the main compounds causing this taint is androstenone, a pheromone produced in porcine testis. Here we use microarra...

    Authors: Maren Moe, Theo Meuwissen, Sigbjørn Lien, Christian Bendixen, Xuefei Wang, Lene Nagstrup Conley, Ingunn Berget, Håvard Tajet and Eli Grindflek
    Citation: BMC Genomics 2007 8:405
    Content type: Research article Published on:

  24. Hypertension is a complex disease with many contributory genetic and environmental factors. We aimed to identify common targets for therapy by gene expression profiling of a resistance artery taken from animal...

    Authors: T Hilton Grayson, Stephen J Ohms, Therese D Brackenbury, Kate R Meaney, Kaiman Peng, Yvonne E Pittelkow, Susan R Wilson, Shaun L Sandow and Caryl E Hill
    Citation: BMC Genomics 2007 8:404
    Content type: Research article Published on:

  25. In the genome of Caenorhabditis elegans, homopolymeric poly-G/poly-C tracts (G/C tracts) exist at high frequency and are maintained by the activity of the DOG-1 protein. The frequency and distribution of G/C trac...

    Authors: Yang Zhao, Nigel J O'Neil and Ann M Rose
    Citation: BMC Genomics 2007 8:403
    Content type: Research article Published on:

  26. A collection of genetic deficiencies covering over 70% of the Caenorhabditis elegans genome exists, however the application of these valuable biological tools has been limited due to the incomplete correlation be...

    Authors: Martin R Jones, Jason S Maydan, Stephane Flibotte, Donald G Moerman and David L Baillie
    Citation: BMC Genomics 2007 8:402
    Content type: Methodology article Published on:

  27. Since the finishing of the sequencing of the Arabidopsis thaliana genome, the Arabidopsis community and the annotator centers have been working on the improvement of gene annotation at the structural and function...

    Authors: Sébastien Aubourg, Marie-Laure Martin-Magniette, Véronique Brunaud, Ludivine Taconnat, Frédérique Bitton, Sandrine Balzergue, Pauline E Jullien, Mathieu Ingouff, Vincent Thareau, Thomas Schiex, Alain Lecharny and Jean-Pierre Renou
    Citation: BMC Genomics 2007 8:401
    Content type: Research article Published on:

  28. Bovine tuberculosis is an enduring disease of cattle that has significant repercussions for human health. The advent of high-throughput functional genomics technologies has facilitated large-scale analyses of ...

    Authors: Kieran G Meade, Eamonn Gormley, Mairéad B Doyle, Tara Fitzsimons, Cliona O'Farrelly, Eamon Costello, Joseph Keane, Yingdong Zhao and David E MacHugh
    Citation: BMC Genomics 2007 8:400
    Content type: Research article Published on:

  29. With the completion of the human genome sequence the functional analysis and characterization of the encoded proteins has become the next urging challenge in the post-genome era. The lack of comprehensive ORFe...

    Authors: Stephanie Bechtel, Heiko Rosenfelder, Anny Duda, Christian Peter Schmidt, Ute Ernst, Ruth Wellenreuther, Alexander Mehrle, Claudia Schuster, Andre Bahr, Helmut Blöcker, Dagmar Heubner, Andreas Hoerlein, Guenter Michel, Holger Wedler, Karl Köhrer, Birgit Ottenwälder…
    Citation: BMC Genomics 2007 8:399
    Content type: Methodology article Published on:

  30. The comparison of complete genomes has revealed surprisingly large numbers of conserved non-protein-coding (CNC) DNA regions. However, the biological function of CNC remains elusive. CNC differ in two aspects ...

    Authors: Dorota Retelska, Emmanuel Beaudoing, Cédric Notredame, C Victor Jongeneel and Philipp Bucher
    Citation: BMC Genomics 2007 8:398
    Content type: Research article Published on:

  31. Pseudomonas syringae is a widespread bacterial plant pathogen, and strains of P. syringae may be assigned to different pathovars based on host specificity among different plant species. The genomes of P. syringae

    Authors: José L Lavín, Kristoffer Kiil, Ohiana Resano, David W Ussery and José A Oguiza
    Citation: BMC Genomics 2007 8:397
    Content type: Research article Published on:

  33. Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria...

    Authors: Xiaowen Zhang, Fangqing Zhao, Xiangyu Guan, Yu Yang, Chengwei Liang and Song Qin
    Citation: BMC Genomics 2007 8:395
    Content type: Research article Published on:

  34. The innate immune system is the first line of defense mechanisms protecting the host from invading pathogens such as bacteria and viruses. The innate immunity responses are triggered by recognition of prototyp...

    Authors: Ran Elkon, Chaim Linhart, Yonit Halperin, Yosef Shiloh and Ron Shamir
    Citation: BMC Genomics 2007 8:394
    Content type: Research article Published on:

  35. The use of computational methods for predicting protein interaction networks will continue to grow with the number of fully sequenced genomes available. The Co-Conservation method, also known as the Phylogenet...

    Authors: Anis Karimpour-Fard, Lawrence Hunter and Ryan T Gill
    Citation: BMC Genomics 2007 8:393
    Content type: Research article Published on:

  37. Repeats are present in all genomes, and often have important functions. However, in large genome sequencing projects, many repetitive regions remain uncharacterized. The genome of the protozoan parasite Trypanoso...

    Authors: Erik Arner, Ellen Kindlund, Daniel Nilsson, Fatima Farzana, Marcela Ferella, Martti T Tammi and Björn Andersson
    Citation: BMC Genomics 2007 8:391
    Content type: Research article Published on:

  38. The v-erbA oncogene, carried by the Avian Erythroblastosis Virus, derives from the c-erbAα proto-oncogene that encodes the nuclear receptor for triiodothyronine (T3R). v-ErbA transforms erythroid progenitors in v...

    Authors: Corinne Bresson, Celine Keime, Claudine Faure, Yann Letrillard, Maud Barbado, Sandra Sanfilippo, Najate Benhra, Olivier Gandrillon and Sandrine Gonin-Giraud
    Citation: BMC Genomics 2007 8:390
    Content type: Research article Published on:

  39. Fetal alcohol syndrome (FAS) is a serious global health problem and is observed at high frequencies in certain South African communities. Although in utero alcohol exposure is the primary trigger, there is eviden...

    Authors: Zané Lombard, Nicki Tiffin, Oliver Hofmann, Vladimir B Bajic, Winston Hide and Michèle Ramsay
    Citation: BMC Genomics 2007 8:389
    Content type: Methodology article Published on:

  40. Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Ins...

    Authors: Françoise Thibaud-Nissen, Matthew Campbell, John P Hamilton, Wei Zhu and C Robin Buell
    Citation: BMC Genomics 2007 8:388
    Content type: Software Published on:

  42. Mitochondrial genomes are widely utilized for phylogenetic and population genetic analyses among animals. In addition to sequence data the mitochondrial gene order and RNA secondary structure data are used in ...

    Authors: Kathrin Fahrein, Giovanni Talarico, Anke Braband and Lars Podsiadlowski
    Citation: BMC Genomics 2007 8:386
    Content type: Research article Published on:

  43. The t(12;21)(p13;q22) translocation is found in 20 to 25% of cases of childhood B-lineage acute lymphoblastic leukemia (B-ALL). This rearrangement results in the fusion of ETV6 (TEL) and RUNX1 (AML1) genes and de...

    Authors: Virginie Gandemer, Anne-Gaëlle Rio, Marie de Tayrac, Vonnick Sibut, Stéphanie Mottier, Béatrice Ly Sunnaram, Catherine Henry, Annabelle Monnier, Christian Berthou, Edouard Le Gall, André Le Treut, Claudine Schmitt, Jean-Yves Le Gall, Jean Mosser and Marie-Dominique Galibert
    Citation: BMC Genomics 2007 8:385
    Content type: Research article Published on:

  44. The differentiation of hematopoietic stem cells into platelet-forming megakaryocytes is of fundamental importance to hemostasis. Constitutive apoptosis is an integral, yet poorly understood, facet of megakaryo...

    Authors: Chi Chen, Peter G Fuhrken, Li Ting Huang, Pani Apostolidis, Min Wang, Carlos J Paredes, William M Miller and Eleftherios T Papoutsakis
    Citation: BMC Genomics 2007 8:384
    Content type: Research article Published on:

  45. Understanding how mesenchymal cells arise from epithelial cells could have a strong impact in unveiling mechanisms of epithelial cell plasticity underlying kidney regeneration and repair.

    Authors: Stefano Campanaro, Simone Picelli, Rossella Torregrossa, Laura Colluto, Monica Ceol, Dorella Del Prete, Angela D'Angelo, Giorgio Valle and Franca Anglani
    Citation: BMC Genomics 2007 8:383
    Content type: Research article Published on:

  46. High-resolution microarray-based comparative genomic hybridization (CGH) techniques have successfully been applied to study copy number imbalances in a number of settings such as the analysis of cancer genomes...

    Authors: Johan Staaf, Göran Jönsson, Markus Ringnér and Johan Vallon-Christersson
    Citation: BMC Genomics 2007 8:382
    Content type: Methodology article Published on:

  47. Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation...

    Authors: Chai-Ling Ho, Yen-Yen Kwan, Mei-Chooi Choi, Sue-Sean Tee, Wai-Har Ng, Kok-Ang Lim, Yang-Ping Lee, Siew-Eng Ooi, Weng-Wah Lee, Jin-Ming Tee, Siang-Hee Tan, Harikrishna Kulaveerasingam, Sharifah Shahrul Rabiah Syed Alwee and Meilina Ong Abdullah
    Citation: BMC Genomics 2007 8:381
    Content type: Research article Published on:

  48. Recently, we demonstrated that human mesenchymal stem cells (hMSC) stimulated with dexamethazone undergo gene focusing during osteogenic differentiation (Stem Cells Dev 14(6): 1608–20, 2005). Here, we examine the...

    Authors: Kristin P Bennett, Charles Bergeron, Evrim Acar, Robert F Klees, Scott L Vandenberg, Bülent Yener and George E Plopper
    Citation: BMC Genomics 2007 8:380
    Content type: Research article Published on:

  49. Hereditary hemochromatosis (HH) encompasses genetic disorders of iron overload characterized by deficient expression or function of the iron-regulatory hormone hepcidin. Mutations in 5 genes have been linked t...

    Authors: Alejandra Rodriguez, Mika Hilvo, Leena Kytömäki, Robert E Fleming, Robert S Britton, Bruce R Bacon and Seppo Parkkila
    Citation: BMC Genomics 2007 8:379
    Content type: Research article Published on:

  50. The measurement of gene expression using microarray technology is a complicated process in which a large number of factors can be varied. Due to the lack of standard calibration samples such as are used in tra...

    Authors: Torunn Bruland, Endre Anderssen, Berit Doseth, Hallgeir Bergum, Vidar Beisvag and Astrid Lægreid
    Citation: BMC Genomics 2007 8:377
    Content type: Methodology article Published on:

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