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  1. Over 4 million single nucleotide polymorphisms (SNPs) are currently reported to exist within the human genome. Only a small fraction of these SNPs alter gene function or expression, and therefore might be asso...

    Authors: Salim Mottagui-Tabar, Mohammad A Faghihi, Yosuke Mizuno, Pär G Engström, Boris Lenhard, Wyeth W Wasserman and Claes Wahlestedt
    Citation: BMC Genomics 2005 6:18
  2. Various analytical methods exist that first quantify gene expression and then analyze differentially expressed genes from Affymetrix GeneChip® gene expression analysis array data. These methods differ in the choi...

    Authors: Wenhong Fan, Joel I Pritchard, James M Olson, Najma Khalid and Lue Ping Zhao
    Citation: BMC Genomics 2005 6:16
  3. In human carcinomas, overexpression of cortactin correlates with poor prognosis. Cortactin is an F-actin-binding protein involved in cytoskeletal rearrangements and cell migration by promoting actin-related pr...

    Authors: Agnes GSH van Rossum, Ellen Schuuring-Scholtes, Vera van Buuren-van Seggelen, Philip M Kluin and Ed Schuuring
    Citation: BMC Genomics 2005 6:15
  4. The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of rel...

    Authors: Gang Fang, Christine Ho, Yaowu Qiu, Virginie Cubas, Zhou Yu, Cédric Cabau, Frankie Cheung, Ivan Moszer and Antoine Danchin
    Citation: BMC Genomics 2005 6:14
  5. The application of microarray technology to functional genomic analysis in the chicken has been limited by the lack of arrays containing large numbers of genes.

    Authors: Joan Burnside, Paul Neiman, Jianshan Tang, Ryan Basom, Richard Talbot, Mark Aronszajn, David Burt and Jeff Delrow
    Citation: BMC Genomics 2005 6:13
  6. The ChickRH6 whole chicken genome radiation hybrid (RH) panel recently produced has already been used to build radiation hybrid maps for several chromosomes, generating comparative maps with the human and mous...

    Authors: Sophie Leroux, Mélanie Dottax, Suzanne Bardes, Florence Vignoles, Katia Fève, Frédérique Pitel, Mireille Morisson and Alain Vignal
    Citation: BMC Genomics 2005 6:12
  7. Hematopoiesis is a complex developmental process controlled by a large number of factors that regulate stem cell renewal, lineage commitment and differentiation. Secreted proteins, including the hematopoietic ...

    Authors: Demet Nalbant, Hyewon Youn, S Isil Nalbant, Savitha Sharma, Everardo Cobos, Elmus G Beale, Yang Du and Simon C Williams
    Citation: BMC Genomics 2005 6:11
  8. Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism...

    Authors: Nigel J Saunders, Prawit Boonmee, John F Peden and Stephen A Jarvis
    Citation: BMC Genomics 2005 6:9
  9. In Aedes and Anopheles mosquitoes, ribosomal protein RPS6 has an unusual C-terminal extension that resembles histone H1 proteins. To explore homology between a mosquito H1 histone and the RPS6 tail, we took advan...

    Authors: Yongjiao Zhai and Ann M Fallon
    Citation: BMC Genomics 2005 6:8
  10. During excessive pressure or volume overload, cardiac cells are subjected to increased mechanical stress (MS). We set out to investigate how the stress response of cardiac cells to MS can be compared to genoto...

    Authors: Marjan Boerma, Caroline GC van der Wees, Harry Vrieling, J Peter Svensson, Jan Wondergem, Arnoud van der Laarse, Leon HF Mullenders and Albert A van Zeeland
    Citation: BMC Genomics 2005 6:6
  11. Blood feeding, or hematophagy, is a behavior exhibited by female mosquitoes required both for reproduction and for transmission of pathogens. We determined the expression patterns of 3,068 ESTs, representing ~...

    Authors: Ali N Dana, Young S Hong, Marcia K Kern, Maureen E Hillenmeyer, Brent W Harker, Neil F Lobo, James R Hogan, Patricia Romans and Frank H Collins
    Citation: BMC Genomics 2005 6:5
  12. The pregnancy-specific glycoprotein (Psg) genes encode proteins of unknown function, and are members of the carcinoembryonic antigen (Cea) gene family, which is a member of the immunoglobulin gene (Ig) superfamil...

    Authors: Andrew S McLellan, Beate Fischer, Gabriela Dveksler, Tomomi Hori, Freda Wynne, Melanie Ball, Katsuzumi Okumura, Tom Moore and Wolfgang Zimmermann
    Citation: BMC Genomics 2005 6:4
  13. Microarray technologies are rapidly becoming available for new species including teleost fishes. We constructed a rainbow trout cDNA microarray targeted at the identification of genes which are differentially ...

    Authors: Aleksei Krasnov, Heikki Koskinen, Petri Pehkonen, Caird E Rexroad III, Sergey Afanasyev and Hannu Mölsä
    Citation: BMC Genomics 2005 6:3
  14. Basic manufacturing principles are becoming increasingly important in high-throughput sequencing facilities where there is a constant drive to increase quality, increase efficiency, and decrease operating cost...

    Authors: George S Yang, Jeffery M Stott, Duane Smailus, Sarah A Barber, Miruna Balasundaram, Marco A Marra and Robert A Holt
    Citation: BMC Genomics 2005 6:2
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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

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