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  1. The lycophyte Selaginella moellendorffii is a member of one of the oldest lineages of vascular plants on Earth. Fossil records show that the lycophyte clade arose 400 million years ago, 150–200 million years earl...

    Authors: Jing-Ke Weng, Milos Tanurdzic and Clint Chapple
    Citation: BMC Genomics 2005 6:85
    Content type: Research article Published on:

  2. Creation of human gene families was facilitated significantly by gene duplication and diversification. The (TG/CA)n repeats exhibit length variability, display genome-wide distribution, and are abundant in the hu...

    Authors: Vineet K Sharma, Samir K Brahmachari and Srinivasan Ramachandran
    Citation: BMC Genomics 2005 6:83
    Content type: Research article Published on:

  4. The distribution and location of insertion elements in a genome is an excellent tool to track the evolution of bacterial strains and a useful molecular marker to distinguish between closely related bacterial i...

    Authors: Betsy M Martinez-Vaz, Yang Xie, Wei Pan and Arkady B Khodursky
    Citation: BMC Genomics 2005 6:81
    Content type: Methodology article Published on:

  5. Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and pho...

    Authors: Jeremiah D Hackett, Todd E Scheetz, Hwan Su Yoon, Marcelo B Soares, Maria F Bonaldo, Thomas L Casavant and Debashish Bhattacharya
    Citation: BMC Genomics 2005 6:80
    Content type: Research article Published on:

  6. Bcipep is a database of experimentally determined linear B-cell epitopes of varying immunogenicity collected from literature and other publicly available databases.

    Authors: Sudipto Saha, Manoj Bhasin and Gajendra PS Raghava
    Citation: BMC Genomics 2005 6:79
    Content type: Database Published on:

  7. Microarray-based Comparative Genomic Hybridization (M-CGH) has been used to characterize the extensive intraspecies genetic diversity found in bacteria at the whole-genome level. Although conventional microarr...

    Authors: Eduardo N Taboada, Rey R Acedillo, Christian C Luebbert, Wendy A Findlay and John HE Nash
    Citation: BMC Genomics 2005 6:78
    Content type: Research article Published on:

  8. In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data qual...

    Authors: Sacha AFT van Hijum, Anne de Jong, Richard JS Baerends, Harma A Karsens, Naomi E Kramer, Rasmus Larsen, Chris D den Hengst, Casper J Albers, Jan Kok and Oscar P Kuipers
    Citation: BMC Genomics 2005 6:77
    Content type: Methodology article Published on:

  9. Genes specifically expressed in the oocyte play key roles in oogenesis, ovarian folliculogenesis, fertilization and/or early embryonic development. In an attempt to identify novel oocyte-specific genes in the ...

    Authors: Amélie Paillisson, Sébastien Dadé, Isabelle Callebaut, Martine Bontoux, Rozenn Dalbiès-Tran, Daniel Vaiman and Philippe Monget
    Citation: BMC Genomics 2005 6:76
    Content type: Research article Published on:

  10. Microarray technology has become highly valuable for identifying complex global changes in gene expression patterns. The effective correlation of observed changes in gene expression with shared transcription r...

    Authors: Chris Cheadle, Jinshui Fan, Yoon S Cho-Chung, Thomas Werner, Jill Ray, Lana Do, Myriam Gorospe and Kevin G Becker
    Citation: BMC Genomics 2005 6:75
    Content type: Research article Published on:

  11. Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more...

    Authors: Warren M Snelling, Eduardo Casas, Roger T Stone, John W Keele, Gregory P Harhay, Gary L Bennett and Timothy PL Smith
    Citation: BMC Genomics 2005 6:74
    Content type: Research article Published on:

  13. Commercial microarray scanners and software cannot distinguish between spectrally overlapping emission sources, and hence cannot accurately identify or correct for emissions not originating from the labeled cD...

    Authors: Jerilyn A Timlin, David M Haaland, Michael B Sinclair, Anthony D Aragon, M Juanita Martinez and Margaret Werner-Washburne
    Citation: BMC Genomics 2005 6:72
    Content type: Research article Published on:

  15. Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the ...

    Authors: Rasmus Wernersson, Mikkel H Schierup, Frank G Jørgensen, Jan Gorodkin, Frank Panitz, Hans-Henrik Stærfeldt, Ole F Christensen, Thomas Mailund, Henrik Hornshøj, Ami Klein, Jun Wang, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Gane KS Wong…
    Citation: BMC Genomics 2005 6:70
    Content type: Research article Published on:

  16. The purpose of this work was to characterize the expression of drug and nutrient carriers along the anterior-posterior and crypt-villus axes of the intestinal epithelium and to study the validity of utilizing ...

    Authors: Pascale Anderle, Thierry Sengstag, David M Mutch, Martin Rumbo, Viviane Praz, Robert Mansourian, Mauro Delorenzi, Gary Williamson and Matthew-Alan Roberts
    Citation: BMC Genomics 2005 6:69
    Content type: Research article Published on:

  17. The expression of gene batteries, genomic units of functionally linked genes which are activated by similar sets of cis- and trans-acting regulators, has been proposed as a major determinant of cell specializatio...

    Authors: Sven Nelander, Erik Larsson, Erik Kristiansson, Robert MÃ¥nsson, Olle Nerman, Mikael Sigvardsson, Petter Mostad and Per Lindahl
    Citation: BMC Genomics 2005 6:68
    Content type: Research article Published on:

  18. Regional expression biases (REBs) are genetic intervals where gene expression is coordinately changed. For example, if a region of the genome is amplified, often the majority of genes that map within the ampli...

    Authors: Kyle A Furge, Karl J Dykema, Coral Ho and Xin Chen
    Citation: BMC Genomics 2005 6:67
    Content type: Methodology article Published on:

  19. DNA microarray is an invaluable tool for gene expression explorations. In the two-dye microarray, fluorescence intensities of two samples, each labeled with a different dye, are compared after hybridization. T...

    Authors: Mugdha Gadgil, Wei Lian, Chetan Gadgil, Vivek Kapur and Wei-Shou Hu
    Citation: BMC Genomics 2005 6:66
    Content type: Methodology article Published on:

  21. Exfoliated cervical cells are used in cytology-based cancer screening and may also be a source for molecular biomarkers indicative of neoplastic changes in the underlying tissue. However, because of keratiniza...

    Authors: Martin Steinau, Daisy R Lee, Mangalathu S Rajeevan, Suzanne D Vernon, Mack T Ruffin and Elizabeth R Unger
    Citation: BMC Genomics 2005 6:64
    Content type: Research article Published on:

  22. Microarrays for the analysis of gene expression are of three different types: short oligonucleotide (25–30 base), long oligonucleotide (50–80 base), and cDNA (highly variable in length). The short oligonucleot...

    Authors: David Petersen, GVR Chandramouli, Joel Geoghegan, Joanne Hilburn, Jonathon Paarlberg, Chang Hee Kim, David Munroe, Lisa Gangi, Jing Han, Raj Puri, Lou Staudt, John Weinstein, J Carl Barrett, Jeffrey Green and Ernest S Kawasaki
    Citation: BMC Genomics 2005 6:63
    Content type: Research article Published on:

  23. Genomic approaches in large animal models (canine, ovine etc) are challenging due to insufficient genomic information for these species and the lack of availability of corresponding microarray platforms. To ad...

    Authors: Dmitry N Grigoryev, Shwu-Fan Ma, Brett A Simon, Rafael A Irizarry, Shui Q Ye and Joe GN Garcia
    Citation: BMC Genomics 2005 6:62
    Content type: Methodology article Published on:

  24. The need to perform microarray experiments with small amounts of tissue has led to the development of several protocols for amplifying the target transcripts. The use of different amplification protocols could...

    Authors: Johan Wadenbäck, David H Clapham, Deborah Craig, Ronald Sederoff, Gary F Peter, Sara von Arnold and Ulrika Egertsdotter
    Citation: BMC Genomics 2005 6:61
    Content type: Research article Published on:

  26. The use of microarray technology to assess gene expression levels is now widespread in biology. The validation of microarray results using independent mRNA quantitation techniques remains a desirable element o...

    Authors: Peter B Dallas, Nicholas G Gottardo, Martin J Firth, Alex H Beesley, Katrin Hoffmann, Philippa A Terry, Joseph R Freitas, Joanne M Boag, Aaron J Cummings and Ursula R Kees
    Citation: BMC Genomics 2005 6:59
    Content type: Research article Published on:

  27. Hookworms, infecting over one billion people, are the mostly closely related major human parasites to the model nematode Caenorhabditis elegans. Applying genomics techniques to these species, we analyzed 3,840 an...

    Authors: Makedonka Mitreva, James P McCarter, Prema Arasu, John Hawdon, John Martin, Mike Dante, Todd Wylie, Jian Xu, Jason E Stajich, Wadim Kapulkin, Sandra W Clifton, Robert H Waterston and Richard K Wilson
    Citation: BMC Genomics 2005 6:58
    Content type: Research article Published on:

  28. The most widely used amplification method for microarray analysis of gene expression uses T7 RNA polymerase-driven in vitro transcription (IVT) to produce complementary RNA (cRNA) that can be hybridized to arrays...

    Authors: Christopher S Barker, Chandi Griffin, Gregory M Dolganov, Kristina Hanspers, Jean Yee Hwa Yang and David J Erle
    Citation: BMC Genomics 2005 6:57
    Content type: Methodology article Published on:

  29. The Major Histocompatibility Complex is the main genetic contributor to susceptibility to type 1 diabetes (T1D); genome-wide scans have consistently mapped increased predisposition to this region. The highest ...

    Authors: Elena Urcelay, José L Santiago, Hermenegildo de la Calle, Alfonso Martínez, Julián Méndez, José M Ibarra, Carlos Maluenda, Miguel Fernández-Arquero and Emilio G de la Concha
    Citation: BMC Genomics 2005 6:56
    Content type: Research article Published on:

  30. Since the early stages of tumorigenesis involve adhesion, escape from immune surveillance, vascularization and angiogenesis, we devised a strategy to study the expression profiles of all publicly known and put...

    Authors: Robert A Stull, Roya Tavassoli, Scot Kennedy, Steve Osborn, Rachel Harte, Yan Lu, Cheryl Napier, Arie Abo and Daniel J Chin
    Citation: BMC Genomics 2005 6:55
    Content type: Research article Published on:

  31. Comparative genomics, through the integration of genetic maps from species of interest with whole genome sequences of other species, will facilitate the identification of genes affecting phenotypes of interest...

    Authors: Caird E Rexroad III, Maria F Rodriguez, Issa Coulibaly, Karim Gharbi, Roy G Danzmann, Jenefer DeKoning, Ruth Phillips and Yniv Palti
    Citation: BMC Genomics 2005 6:54
    Content type: Research article Published on:

  33. Quantitative trait locus (QTL) theory predicts that genetic influence on complex traits involves multiple genes of small effect size. To detect QTL associations of small effect size, large samples and systemat...

    Authors: Emma Meaburn, Lee M Butcher, Lin Liu, Cathy Fernandes, Valerie Hansen, Ammar Al-Chalabi, Robert Plomin, Ian Craig and Leonard C Schalkwyk
    Citation: BMC Genomics 2005 6:52
    Content type: Research article Published on:

  34. Gene expression studies on non-model organisms require open-end strategies for transcription profiling. Gel-based analysis of cDNA fragments allows to detect alterations in gene expression for genes which have...

    Authors: Balakrishnan Venkatesh, Ursula Hettwer, Birger Koopmann and Petr Karlovsky
    Citation: BMC Genomics 2005 6:51
    Content type: Methodology article Published on:

  35. As farming of Atlantic salmon is growing as an aquaculture enterprise, the need to identify the genomic mechanisms for specific traits is becoming more important in breeding and management of the animal. Trait...

    Authors: Jim Thorsen, Baoli Zhu, Eirik Frengen, Kazutoyo Osoegawa, Pieter J de Jong, Ben F Koop, William S Davidson and Bjørn Høyheim
    Citation: BMC Genomics 2005 6:50
    Content type: Research article Published on:

  36. In screening of libraries derived by expression cloning, expression of active proteins in E. coli can be limited by formation of inclusion bodies. In these cases it would be desirable to enrich gene libraries for...

    Authors: Markus Koschorreck, Markus Fischer, Sandra Barth and Jürgen Pleiss
    Citation: BMC Genomics 2005 6:49
    Content type: Research article Published on:

  40. Chemokines and their receptors play important roles in host defense, organogenesis, hematopoiesis, and neuronal communication. Forty-two chemokines and 19 cognate receptors have been found in the human genome....

    Authors: Jixin Wang, David L Adelson, Ahmet Yilmaz, Sing-Hoi Sze, Yuan Jin and James J Zhu
    Citation: BMC Genomics 2005 6:45
    Content type: Research article Published on:

  42. The moss Physcomitrella patens is an emerging plant model system due to its high rate of homologous recombination, haploidy, simple body plan, physiological properties as well as phylogenetic position. Available ...

    Authors: Stefan A Rensing, Dana Fritzowsky, Daniel Lang and Ralf Reski
    Citation: BMC Genomics 2005 6:43
    Content type: Research article Published on:

  43. Differential gene expression specifies the highly diverse cell types that constitute the nervous system. With its sequenced genome and simple, well-defined neuroanatomy, the nematode C. elegans is a useful model ...

    Authors: Rebecca M Fox, Stephen E Von Stetina, Susan J Barlow, Christian Shaffer, Kellen L Olszewski, Jason H Moore, Denis Dupuy, Marc Vidal and David M Miller III
    Citation: BMC Genomics 2005 6:42
    Content type: Methodology article Published on:

  44. A chicken egg contains several biotin-binding proteins (BBPs), whose complete DNA and amino acid sequences are not known. In order to identify and characterise these genes and proteins we studied chicken cDNAs...

    Authors: Einari A Niskanen, Vesa P Hytönen, Alessandro Grapputo, Henri R Nordlund, Markku S Kulomaa and Olli H Laitinen
    Citation: BMC Genomics 2005 6:41
    Content type: Research article Published on:

  45. The retina is a well-defined portion of the central nervous system (CNS) that has been used as a model for CNS development and function studies. The full specification of transcripts in an individual tissue or...

    Authors: Samuel Shao-Min Zhang, Xuming Xu, Jinming Li, Mu-Gen Liu, Hongyu Zhao, M Bento Soares, Colin J Barnstable and Xin-Yuan Fu
    Citation: BMC Genomics 2005 6:40
    Content type: Research article Published on:

  46. In Micrococcus luteus growth and resuscitation from starvation-induced dormancy is controlled by the production of a secreted growth factor. This autocrine r esuscitation-p romoting f actor (Rpf) is the founder m...

    Authors: Adriana Ravagnani, Christopher L Finan and Michael Young
    Citation: BMC Genomics 2005 6:39
    Content type: Research article Published on:

  47. Germline mutations or large-scale deletions in the coding region and splice sites of STK11/LKB1 do not account for all cases of Peutz-Jeghers syndrome (PJS). It is conceivable that, on the basis of data from othe...

    Authors: Nicholas CM Hearle, Ian Tomlinson, Wendy Lim, Victoria Murday, Edwin Swarbrick, Guan Lim, Robin Phillips, Peter Lee, John O'Donohue, Richard C Trembath, Patrick J Morrison, Andrew Norman, Rohan Taylor, Shirley Hodgson, Anneke Lucassen and Richard S Houlston
    Citation: BMC Genomics 2005 6:38
    Content type: Research article Published on:

  48. Estrogens are known to regulate the proliferation of breast cancer cells and to modify their phenotypic properties. Identification of estrogen-regulated genes in human breast tumors is an essential step toward...

    Authors: Martín C Abba, Yuhui Hu, Hongxia Sun, Jeffrey A Drake, Sally Gaddis, Keith Baggerly, Aysegul Sahin and C Marcelo Aldaz
    Citation: BMC Genomics 2005 6:37
    Content type: Research article Published on:

  50. The Marine Genomics project is a functional genomics initiative developed to provide a pipeline for the curation of Expressed Sequence Tags (ESTs) and gene expression microarray data for marine organisms. It p...

    Authors: David J McKillen, Yian A Chen, Chuming Chen, Matthew J Jenny, Harold F Trent III, Javier Robalino, David C McLean Jr, Paul S Gross, Robert W Chapman, Gregory W Warr and Jonas S Almeida
    Citation: BMC Genomics 2005 6:34
    Content type: Database Published on:

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