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  1. Content type: Research article

    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

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  2. Content type: Research article

    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

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  3. Content type: Research article

    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

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  4. Content type: Research article

    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

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  5. Content type: Research article

    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

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  6. Content type: Research article

    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

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  7. Content type: Research article

    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

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  8. Content type: Research article

    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

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  9. Content type: Research article

    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

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  10. Content type: Research article

    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

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  11. Content type: Research article

    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

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  12. Content type: Research article

    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

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  13. Content type: Research article

    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

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  14. Content type: Research article

    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

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  15. Content type: Database

    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

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  16. Content type: Research article

    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

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  17. Content type: Research article

    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

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  18. Content type: Research article

    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

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  19. Content type: Research article

    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

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  20. Content type: Research article

    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

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  21. Content type: Research article

    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

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  22. Content type: Research article

    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

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  23. Content type: Research article

    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

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  24. Content type: Research article

    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

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  25. Content type: Software

    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

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  26. Content type: Research article

    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

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  27. Content type: Research article

    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

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  28. Content type: Database

    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

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  29. Content type: Research article

    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

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  30. Content type: Methodology article

    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

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  31. Content type: Research article

    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

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  32. Content type: Research article

    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

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  33. Content type: Methodology article

    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

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  34. Content type: Research article

    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

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  35. Content type: Research article

    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

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  36. Content type: Database

    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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  37. Content type: Research article

    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

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  38. Content type: Research article

    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

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  39. Content type: Software

    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

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  40. Content type: Research article

    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

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  41. Content type: Research article

    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

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