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  1. AlkB-like proteins are members of the 2-oxoglutarate- and Fe(II)-dependent oxygenase superfamily. In Escherichia coli the protein protects RNA and DNA against damage from methylating agents. 1-methyladenine and 3...

    Authors: Marit S Bratlie and Finn Drabløs
    Citation: BMC Genomics 2005 6:1
  2. Evolutionarily conserved sequences within or adjoining orthologous genes often serve as critical cis-regulatory regions. Recent studies have identified long, non-coding genomic regions that are perfectly conserve...

    Authors: Albin Sandelin, Peter Bailey, Sara Bruce, Pär G Engström, Joanna M Klos, Wyeth W Wasserman, Johan Ericson and Boris Lenhard
    Citation: BMC Genomics 2004 5:99
  3. The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames (OR...

    Authors: Matthias B Wahl, Randolph B Caldwell, Andrzej M Kierzek, Hiroshi Arakawa, Eduardo Eyras, Nina Hubner, Christian Jung, Manuel Soeldenwagner, Manuela Cervelli, Yan-Dong Wang, Volkmar Liebscher and Jean-Marie Buerstedde
    Citation: BMC Genomics 2004 5:98
  4. A significant portion (about 8% in the human genome) of mammalian mRNA sequences contains AU (Adenine and Uracil) rich elements or AREs at their 3' untranslated regions (UTR). These mRNA sequences are usually ...

    Authors: Hyeong Jun An, Doheon Lee, Kwang Hyung Lee and Jonghwa Bhak
    Citation: BMC Genomics 2004 5:97
  5. While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational ...

    Authors: Justin E Paschall, Marjorie F Oleksiak, Jeffrey D VanWye, Jennifer L Roach, J Andrew Whitehead, Gerald J Wyckoff, Kevin J Kolell and Douglas L Crawford
    Citation: BMC Genomics 2004 5:96
  6. DNA homopolymer tracts, poly(dA).poly(dT) and poly(dG).poly(dC), are the simplest of simple sequence repeats. Homopolymer tracts have been systematically examined in the coding, intron and flanking regions of ...

    Authors: Yue Zhou, Jeffrey W Bizzaro and Kenneth A Marx
    Citation: BMC Genomics 2004 5:95
  7. The GOLD.db (Genomics of Lipid-Associated Disorders Database) was developed to address the need for integrating disparate information on the function and properties of genes and their products that are particu...

    Authors: Hubert Hackl, Michael Maurer, Bernhard Mlecnik, Jürgen Hartler, Gernot Stocker, Diego Miranda-Saavedra and Zlatko Trajanoski
    Citation: BMC Genomics 2004 5:93
  8. Defensins are important components of innate immunity to combat bacterial and viral infections, and can even elicit antitumor responses. Clusters of defensin (DEF) genes are located in a 2 Mb range of the huma...

    Authors: Stefan Taudien, Petra Galgoczy, Klaus Huse, Kathrin Reichwald, Markus Schilhabel, Karol Szafranski, Atsushi Shimizu, Shuichi Asakawa, Adam Frankish, Ivan F Loncarevic, Nobuyoshi Shimizu, Roman Siddiqui and Matthias Platzer
    Citation: BMC Genomics 2004 5:92
  9. We have surveyed, compiled and annotated nucleotide variations in 338 human 7-transmembrane receptors (G-protein coupled receptors). In a sample of 32 chromosomes from a Nordic population, we attempted to dete...

    Authors: Claes Wahlestedt, Anthony J Brookes and Salim Mottagui-Tabar
    Citation: BMC Genomics 2004 5:91
  10. Inward rectifier potassium channels (IRK) contribute to the normal function of skeletal and cardiac muscle cells. The chick inward rectifier K+ channel cIRK1/Kir2.1 is expressed in skeletal muscle, heart, brain, ...

    Authors: Hideki Mutai, Lawrence C Kenyon, Emily Locke, Nami Kikuchi and John Carl Oberholtzer
    Citation: BMC Genomics 2004 5:90
  11. The cellular response of plants to water-deficits has both economic and evolutionary importance directly affecting plant productivity in agriculture and plant survival in the natural environment. Genes induced...

    Authors: Melvin J Oliver, Scot E Dowd, Joaquin Zaragoza, Steven A Mauget and Paxton R Payton
    Citation: BMC Genomics 2004 5:89
  12. Primary human tissues are an invaluable widely used tool for discovery of gene expression patterns which characterize disease states. Tissue processing methods remain unstandardized, leading to unanswered conc...

    Authors: George L Mutter, David Zahrieh, Chunmei Liu, Donna Neuberg, David Finkelstein, Heather E Baker and Janet A Warrington
    Citation: BMC Genomics 2004 5:88
  13. The complete genome sequences for human and the nematode Caenorhabditis elegans offer an opportunity to learn more about human gene function through functional characterization of orthologs in the worm. Based on ...

    Authors: Anna Henricson, Erik LL Sonnhammer, David L Baillie and Ana Vaz Gomes
    Citation: BMC Genomics 2004 5:85
  14. The ongoing efforts to sequence the honey bee genome require additional initiatives to define its transcriptome. Towards this end, we employed the Open Reading frame ESTs (ORESTES) strategy to generate profile...

    Authors: Francis MF Nunes, Valeria Valente, Josane F Sousa, Marco AV Cunha, Daniel G Pinheiro, Rafaela M Maia, Daniela D Araujo, Maria CR Costa, Waleska K Martins, Alex F Carvalho, Nadia Monesi, Adriana M Nascimento, Pablo MV Peixoto, Maria FR Silva, Ricardo GP Ramos, Luis FL Reis…
    Citation: BMC Genomics 2004 5:84
  15. Cross-species gene-expression comparison is a powerful tool for the discovery of evolutionarily conserved mechanisms and pathways of expression control. The usefulness of cDNA microarrays in this context is th...

    Authors: James Adjaye, Ralf Herwig, Doris Herrmann, Wasco Wruck, Alia BenKahla, Thore C Brink, Monika Nowak, Joseph W Carnwath, Claus Hultschig, Heiner Niemann and Hans Lehrach
    Citation: BMC Genomics 2004 5:83
  16. In this study we have built and mined a gene expression database composed of 65 diverse mouse tissues for genes preferentially expressed in immune tissues and cell types. Using expression pattern criteria, we ...

    Authors: John J Hutton, Anil G Jegga, Sue Kong, Ashima Gupta, Catherine Ebert, Sarah Williams, Jonathan D Katz and Bruce J Aronow
    Citation: BMC Genomics 2004 5:82
  17. In contrast to gene-mapping studies of simple Mendelian disorders, genetic analyses of complex traits are far more challenging, and high quality data management systems are often critical to the success of the...

    Authors: Elizabeth M Gillanders, Anthony Masiello, Derek Gildea, Lowell Umayam, Priya Duggal, Mary Pat Jones, Alison P Klein, Diana Freas-Lutz, Grace Ibay, Ken Trout, Tyra G Wolfsberg, Jeffrey M Trent, Joan E Bailey-Wilson and Andreas D Baxevanis
    Citation: BMC Genomics 2004 5:81
  18. Plant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. Most of them, with the exception of virus-like sequences, do...

    Authors: Motoyuki Kunii, Masanori Kanda, Hironori Nagano, Ichiro Uyeda, Yuji Kishima and Yoshio Sano
    Citation: BMC Genomics 2004 5:80
  19. Malaria, caused by the parasitic protist Plasmodium falciparum, represents a major public health problem in the developing world. The P. falciparum genome has been sequenced, which provides new opportunities for ...

    Authors: Pauline Ward, Leila Equinet, Jeremy Packer and Christian Doerig
    Citation: BMC Genomics 2004 5:79
  20. Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Compu...

    Authors: Feng-Mao Lin, Hsien-Da Huang, Yu-Chung Chang and Jorng-Tzong Horng
    Citation: BMC Genomics 2004 5:78
  21. Bovine chromosome (BTA) 15 contains a quantitative trait loci (QTL) for meat tenderness, as well as several breaks in synteny with human chromosome (HSA) 11. Both linkage and radiation hybrid (RH) maps of BTA ...

    Authors: Warren M Snelling, Mathieu Gautier, John W Keele, Timothy PL Smith, Roger T Stone, Gregory P Harhay, Gary L Bennett, Naoya Ihara, Akiko Takasuga, Haruko Takeda, Yoshikazu Sugimoto and André Eggen
    Citation: BMC Genomics 2004 5:77
  22. RNA amplification is required for incorporating laser-capture microdissection techniques into microarray assays. However, standard oligonucleotide microarrays contain sense-strand probes, so traditional T7 amp...

    Authors: Loyal A Goff, Jessica Bowers, Jaime Schwalm, Kevin Howerton, Robert C Getts and Ronald P Hart
    Citation: BMC Genomics 2004 5:76
  23. Homeotic gene complexes determine the anterior-posterior body axis in animals. The expression pattern and function of hox genes along this axis is colinear with the order in which they are organized in the comple...

    Authors: Chilaka Sabarinadh, Subbaya Subramanian, Anshuman Tripathi and Rakesh K Mishra
    Citation: BMC Genomics 2004 5:75
  24. Microarrays are an important tool with which to examine coordinated gene expression. Soybean (Glycine max) is one of the most economically valuable crop species in the world food supply. In order to accelerate bo...

    Authors: Lila O Vodkin, Anupama Khanna, Robin Shealy, Steven J Clough, Delkin Orlando Gonzalez, Reena Philip, Gracia Zabala, Françoise Thibaud-Nissen, Mark Sidarous, Martina V Strömvik, Elizabeth Shoop, Christina Schmidt, Ernest Retzel, John Erpelding, Randy C Shoemaker, Alicia M Rodriguez-Huete…
    Citation: BMC Genomics 2004 5:73
  25. Alternative splicing contributes significantly to the complexity of the human transcriptome and proteome. Computational prediction of alternative splice isoforms are usually based on EST sequences that also al...

    Authors: Shobhit Gupta, Dorothea Zink, Bernhard Korn, Martin Vingron and Stefan A Haas
    Citation: BMC Genomics 2004 5:72
  26. Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy and has been the poster-child for improved therapeutics in cancer, with life time disease-free survival (LTDFS) rates improving from <...

    Authors: Stephanie A Mitchell, Kevin M Brown, Michael M Henry, Michelle Mintz, Daniel Catchpoole, Bonnie LaFleur and Dietrich A Stephan
    Citation: BMC Genomics 2004 5:71
  27. Recurrent non-random genomic alterations are the hallmarks of cancer and the characterization of these imbalances is critical to our understanding of tumorigenesis and cancer progression.

    Authors: Qing-Rong Chen, Sven Bilke, Jun S Wei, Craig C Whiteford, Nicola Cenacchi, Alexei L Krasnoselsky, Braden T Greer, Chang-Gue Son, Frank Westermann, Frank Berthold, Manfred Schwab, Daniel Catchpoole and Javed Khan
    Citation: BMC Genomics 2004 5:70
  28. Proteomics is rapidly evolving into a high-throughput technology, in which substantial and systematic studies are conducted on samples from a wide range of physiological, developmental, or pathological conditi...

    Authors: Kevin Garwood, Thomas McLaughlin, Chris Garwood, Scott Joens, Norman Morrison, Christopher F Taylor, Kathleen Carroll, Caroline Evans, Anthony D Whetton, Sarah Hart, David Stead, Zhikang Yin, Alistair JP Brown, Andrew Hesketh, Keith Chater, Lena Hansson…
    Citation: BMC Genomics 2004 5:68
  29. The resolution of radiation hybrid (RH) maps is intermediate between that of the genetic and BAC (Bacterial Artificial Chromosome) contig maps. Moreover, once framework RH maps of a genome have been constructe...

    Authors: Frédérique Pitel, Behnam Abasht, Mireille Morisson, Richard PMA Crooijmans, Florence Vignoles, Sophie Leroux, Katia Feve, Suzanne Bardes, Denis Milan, Sandrine Lagarrigue, Martien AM Groenen, Madeleine Douaire and Alain Vignal
    Citation: BMC Genomics 2004 5:66
  30. The 156 breeds of dog recognized by the American Kennel Club offer a unique opportunity to map genes important in genetic variation. Each breed features a defining constellation of morphological and behavioral...

    Authors: Matthew Breen, Christophe Hitte, Travis D Lorentzen, Rachael Thomas, Edouard Cadieu, Leah Sabacan, Allyson Scott, Gwenaelle Evanno, Heidi G Parker, Ewen F Kirkness, Ruth Hudson, Richard Guyon, Gregory G Mahairas, Boris Gelfenbeyn, Claire M Fraser, Catherine André…
    Citation: BMC Genomics 2004 5:65
  31. Much of the microarray data published at Stanford is based on mouse and human arrays produced under controlled and monitored conditions at the Brown and Botstein laboratories and at the Stanford Functional Gen...

    Authors: I-Ping Tu, Marci Schaner, Maximilian Diehn, Branimir I Sikic, Patrick O Brown, David Botstein and Michael J Fero
    Citation: BMC Genomics 2004 5:64
  32. Among functional elements of a metazoan gene, enhancers are particularly difficult to find and annotate. Pioneering experiments in Drosophila have demonstrated the value of enhancer "trapping" using an invertebra...

    Authors: Darius Balciunas, Ann E Davidson, Sridhar Sivasubbu, Spencer B Hermanson, Zachary Welle and Stephen C Ekker
    Citation: BMC Genomics 2004 5:62
  33. Despite the widespread use of microarrays, much ambiguity regarding data analysis, interpretation and correlation of the different technologies exists. There is a considerable amount of interest in correlating...

    Authors: Richard Shippy, Timothy J Sendera, Randall Lockner, Chockalingam Palaniappan, Tamma Kaysser-Kranich, George Watts and John Alsobrook
    Citation: BMC Genomics 2004 5:61
  34. Capillary DNA sequencing machines allow the generation of vast amounts of data with little hands-on time. With this expansion of data generation, there is a growing need for automated data processing. Most ava...

    Authors: Jan A Aerts, Bart J Jungerius and Martien AM Groenen
    Citation: BMC Genomics 2004 5:60
  35. The analysis of gene expression using DNA microarrays provides genome wide profiles of the genes controlled by the presence or absence of a specific transcription factor. However, the question arises of whethe...

    Authors: Vijayalakshmi H Nagaraj, Ruadhan A O'Flanagan, Adrian R Bruning, Jonathan R Mathias, Andrew K Vershon and Anirvan M Sengupta
    Citation: BMC Genomics 2004 5:59
  36. Gene expression technologies have the ability to generate vast amounts of data, yet there often resides only limited resources for subsequent validation studies. This necessitates the ability to perform sortin...

    Authors: Michael Schlicht, Brian Matysiak, Tracy Brodzeller, Xinyu Wen, Hang Liu, Guohui Zhou, Rajiv Dhir, Martin J Hessner, Peter Tonellato, Mark Suckow, Morris Pollard and Milton W Datta
    Citation: BMC Genomics 2004 5:58
  37. In this study, we investigated the effect of genetic background on expression profiles. We analysed the transcriptome of mouse hindlimb muscle of five frequently used mouse inbred strains using spotted oligonu...

    Authors: Rolf Turk, Peter AC 't Hoen, Ellen Sterrenburg, Renée X de Menezes, Emile J de Meijer, Judith M Boer, Gert-Jan B van Ommen and Johan T den Dunnen
    Citation: BMC Genomics 2004 5:57
  38. Defensins comprise a large family of cationic antimicrobial peptides that are characterized by the presence of a conserved cysteine-rich defensin motif. Based on the spacing pattern of cysteines, these defensi...

    Authors: Yanjing Xiao, Austin L Hughes, Junko Ando, Yoichi Matsuda, Jan-Fang Cheng, Donald Skinner-Noble and Guolong Zhang
    Citation: BMC Genomics 2004 5:56
  39. Endogenous reference genes are commonly used to normalize expression levels of other genes with the assumption that the expression of the former is constant in different tissues and in different physiopatholog...

    Authors: Ping Jin, Yingdong Zhao, Yvonne Ngalame, Monica C Panelli, Dirk Nagorsen, Vladia Monsurró, Kina Smith, Nan Hu, Hua Su, Phil R Taylor, Francesco M Marincola and Ena Wang
    Citation: BMC Genomics 2004 5:55
  40. Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We devel...

    Authors: Srikrishna Putta, Jeramiah J Smith, John A Walker, Mathieu Rondet, David W Weisrock, James Monaghan, Amy K Samuels, Kevin Kump, David C King, Nicholas J Maness, Bianca Habermann, Elly Tanaka, Susan V Bryant, David M Gardiner, David M Parichy and S Randal Voss
    Citation: BMC Genomics 2004 5:54
  41. Global gene expression studies with microarrays can offer biological insights never before possible. However, the technology possesses many sources of technical variability that are an obstacle to obtaining hi...

    Authors: Martin J Hessner, Lisa Meyer, Jennifer Tackes, Sanaa Muheisen and Xujing Wang
    Citation: BMC Genomics 2004 5:53
  42. Annotating genomes remains an hazardous task. Mistakes or gaps in such a complex process may occur when relevant knowledge is ignored, whether lost, forgotten or overlooked. This paper exemplifies an approach ...

    Authors: Daniil G Naumoff, Ying Xu, Nicolas Glansdorff and Bernard Labedan
    Citation: BMC Genomics 2004 5:52
  43. Members of the C-type lectin domain (CTLD) superfamily are metazoan proteins functionally important in glycoprotein metabolism, mechanisms of multicellular integration and immunity. Three genome-level studies ...

    Authors: Alex N Zelensky and Jill E Gready
    Citation: BMC Genomics 2004 5:51

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