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  1. Content type: Research article

    HMG-box proteins are a large and diverse superfamily of architectural factors that share one or more copies of a sequence- and structurally-related DNA binding domain. These proteins can modify chromatin struc...

    Authors: Emmett O'Flaherty and Jonathan Kaye

    Citation: BMC Genomics 2003 4:13

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  2. Content type: Research article

    For most sequenced prokaryotic genomes, about a third of the protein coding genes annotated are "orphan proteins", that is, they lack homology to known proteins. These hypothetical genes are typically short an...

    Authors: Lars Juhl Jensen, Marie Skovgaard, Thomas Sicheritz-Pontén, Merete Kjær Jørgensen, Christiane Lundegaard, Corinna Cavan Pedersen, Nanna Petersen and David Ussery

    Citation: BMC Genomics 2003 4:12

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  3. Content type: Research article

    A limiting factor of cDNA microarray technology is the need for a substantial amount of RNA per labeling reaction. Thus, 20–200 micro-grams total RNA or 0.5–2 micro-grams poly (A) RNA is typically required for...

    Authors: Vigdis Nygaard, Anders Løland, Marit Holden, Mette Langaas, Håvard Rue, Fang Liu, Ola Myklebost, Øystein Fodstad, Eivind Hovig and Birgitte Smith-Sørensen

    Citation: BMC Genomics 2003 4:11

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  4. Content type: Research article

    Chromosome band 10q24 is a gene-rich domain and host to a number of cancer, developmental, and neurological genes. Recurring translocations, deletions and mutations involving this chromosome band have been obs...

    Authors: Sheryl M Gough, Margaret McDonald, Xiao-Ning Chen, Julie R Korenberg, Antonino Neri, Tomas Kahn, Michael R Eccles and Christine M Morris

    Citation: BMC Genomics 2003 4:9

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  5. Content type: Research article

    Microarray profiling has the potential to illuminate the molecular processes that govern the phenotypic characteristics of porcine skeletal muscles, such as hypertrophy or atrophy, and the expression of specif...

    Authors: Qianfan Bai, Christine McGillivray, Nuno da Costa, Saffron Dornan, Gary Evans, Michael James Stear and Kin-Chow Chang

    Citation: BMC Genomics 2003 4:8

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  6. Content type: Research article

    Differential polyadenylation is a widespread mechanism in higher eukaryotes producing mRNAs with different 3' ends in different contexts. This involves several alternative polyadenylation sites in the 3' UTR, ...

    Authors: Matthieu Legendre and Daniel Gautheret

    Citation: BMC Genomics 2003 4:7

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  7. Content type: Research article

    Short tandem repeat polymorphisms (STRPs) are powerful tools for gene mapping and other applications. A STRP genome scan of 10 cM is usually adequate for mapping single gene disorders. However mapping studies ...

    Authors: Nader Ghebranious, David Vaske, Adong Yu, Chengfeng Zhao, Gabor Marth and James L Weber

    Citation: BMC Genomics 2003 4:6

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  8. Content type: Research article

    Low RNA yields from small tissue samples can limit the use of oligonucleotide microarrays (Affymetrix GeneChips®). Methods using less cRNA for hybridization or amplifying the cRNA have been reported to reduce the...

    Authors: Jeanette N McClintick, Ronald E Jerome, Charles R Nicholson, David W Crabb and Howard J Edenberg

    Citation: BMC Genomics 2003 4:4

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  9. Content type: Research article

    The vertebrate opsins are proteins which utilise a retinaldehyde chromophore in their photosensory or photoisomerase roles in the visual/irradiance detection cycle. The majority of the opsins, such as rod and ...

    Authors: James Bellingham, Dominic J Wells and Russell G Foster

    Citation: BMC Genomics 2003 4:3

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  10. Content type: Research article

    Tagged sequence mutagenesis is a process for constructing libraries of sequenced insertion mutations in embryonic stem cells that can be transmitted into the mouse germline. To better predict the functional co...

    Authors: Michael Roshon, James V DeGregori and H Earl Ruley

    Citation: BMC Genomics 2003 4:2

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  11. Content type: Research article

    Methylation at CpG dinucleotides in genomic DNA is a fundamental epigenetic mechanism of gene expression control in vertebrates. Proteins with a methyl-CpG-binding domain (MBD) can bind to single methylated Cp...

    Authors: Tim C Roloff, H Hilger Ropers and Ulrike A Nuber

    Citation: BMC Genomics 2003 4:1

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  12. Content type: Research article

    In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcr...

    Authors: Naoki Osada, Munetomo Hida, Jun Kusuda, Reiko Tanuma, Makoto Hirata, Yumiko Suto, Momoki Hirai, Keiji Terao, Sumio Sugano and Katsuyuki Hashimoto

    Citation: BMC Genomics 2002 3:36

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  13. Content type: Research article

    Complete sequencing and annotation of the 96.2 kb Bacillus anthracis plasmid, pXO2, predicted 85 open reading frames (ORFs). Bacillus cereus and Bacillus thuringiensis isolates that ranged in genomic similarity t...

    Authors: James Pannucci, Richard T Okinaka, Erin Williams, Robert Sabin, Lawrence O Ticknor and Cheryl R Kuske

    Citation: BMC Genomics 2002 3:34

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  14. Content type: Research article

    The CyaB protein from Aeromonas hydrophila has been shown to possess adenylyl cyclase activity. While orthologs of this enzyme have been found in some bacteria and archaea, it shows no detectable relationship to ...

    Authors: Lakshminarayan M Iyer and L Aravind

    Citation: BMC Genomics 2002 3:33

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  15. Content type: Research article

    Co-regulation of genes may imply involvement in similar biological processes or related function. Many clusters of co-regulated genes have been identified using microarray experiments. In this study, we examin...

    Authors: Wei Ding, Luquan Wang, Ping Qiu, Mitchel Kostich, Jonathan Greene and Marco Hernandez

    Citation: BMC Genomics 2002 3:32

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  16. Content type: Methodology article

    T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different ampl...

    Authors: Hongjuan Zhao, Trevor Hastie, Michael L Whitfield, Anne-Lise Børresen-Dale and Stefanie S Jeffrey

    Citation: BMC Genomics 2002 3:31

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  17. Content type: Research article

    Multiple candidate regions as sites for Schizophrenia and Bipolar susceptibility genes have been reported, suggesting heterogeneity of susceptibility genes or oligogenic inheritance. Linkage analysis has sugge...

    Authors: Manjula Maheshwari, SL Christian, C Liu, JA Badner, S Detera-Wadleigh, ES Gershon and Richard A Gibbs

    Citation: BMC Genomics 2002 3:30

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  18. Content type: Research article

    The EST database provides a rich resource for gene discovery and in silico expression analysis. We report a novel computational approach to identify co-expressed genes using EST database, and its application to I...

    Authors: Lawrence Benbow, Lynn Wang, Maureen Laverty, Suxing Liu, Ping Qiu, Richard W Bond, Eric Gustafson, Joseph A Hedrick, Mitchell Kostich, Jonathan R Greene and Luquan Wang

    Citation: BMC Genomics 2002 3:29

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  19. Content type: Research article

    Microarray technology is a powerful methodology for identifying differentially expressed genes. However, when thousands of genes in a microarray data set are evaluated simultaneously by fold changes and signif...

    Authors: Yuanyuan Xiao, Mark R Segal, Douglas Rabert, Andrew H Ahn, Praveen Anand, Lakshmi Sangameswaran, Donglei Hu and C Anthony Hunt

    Citation: BMC Genomics 2002 3:28

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  20. Content type: Research article

    Gonadotropin releasing hormone (GnRH) is responsible for stimulation of gonadotropic hormone (GtH) in the hypothalamus-pituitary-gonadal axis (HPG). The regulatory mechanisms responsible for brain specificity ...

    Authors: Jacob Torgersen, Rasoul Nourizadeh-Lillabadi, Harald Husebye and Peter Aleström

    Citation: BMC Genomics 2002 3:25

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  21. Content type: Research article

    The Blau syndrome (MIM 186580), an autosomal dominant granulomatous disease, was previously mapped to chromosome 16p12-q21. However, inconsistent physical maps of the region and consequently an unknown order o...

    Authors: Xiaoju Wang, Helena Kuivaniemi, Gina Bonavita, Charlene J Williams and Gerard Tromp

    Citation: BMC Genomics 2002 3:24

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  22. Content type: Research article

    The dinucleotide relative abundance profile can be regarded as a genomic signature because, despite diversity between species, it varies little between 50 kilobase or longer windows on a given genome. Both the...

    Authors: Robert W Jernigan and Robert H Baran

    Citation: BMC Genomics 2002 3:23

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  23. Content type: Methodology article

    Analysis of cell-selective gene expression for families of proteins of therapeutic interest is crucial when deducing the influence of genes upon complex traits and disease susceptibility. Presently, there is n...

    Authors: Grant Dewson, Edward C Conley and Peter Bradding

    Citation: BMC Genomics 2002 3:22

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  24. Content type: Research article

    Based on sequence similarity, the superfamily of G protein-coupled receptors (GPRs) can be subdivided into several subfamilies, the members of which often share similar ligands. The sequence data provided by t...

    Authors: Timo Wittenberger, Susanne Hellebrand, Antonia Munck, Hans-Jürgen Kreienkamp, H Chica Schaller and Wolfgang Hampe

    Citation: BMC Genomics 2002 3:17

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  25. Content type: Methodology article

    High density cDNA microarray technology provides a powerful tool to survey the activity of thousands of genes in normal and diseased cells, which helps us both to understand the molecular basis of the disease ...

    Authors: Limei Hu, Jing Wang, Keith Baggerly, Hua Wang, Gregory N Fuller, Stanley R Hamilton, Kevin R Coombes and Wei Zhang

    Citation: BMC Genomics 2002 3:16

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  26. Content type: Research article

    Freshwater planarians are widely used as models for investigation of pattern formation and studies on genetic variation in populations. Despite extensive information on the biology and genetics of planaria, th...

    Authors: Denis V Rebrikov, Maria E Bulina, Ekaterina A Bogdanova, Loura L Vagner and Sergey A Lukyanov

    Citation: BMC Genomics 2002 3:15

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  27. Content type: Research article

    Suppression Subtractive Hybridization PCR (SSH PCR) is a sophisticated cDNA subtraction method to enrich and isolate differentially expressed genes. Despite its popularity, the method has not been thoroughly s...

    Authors: Wan Ji, Matthew B Wright, Li Cai, Angel Flament and Klaus Lindpaintner

    Citation: BMC Genomics 2002 3:12

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  28. Content type: Research article

    The centromere is a specialized locus that mediates chromosome movement during mitosis and meiosis. This chromosomal domain comprises a uniquely packaged form of heterochromatin that acts as a nucleus for the ...

    Authors: Javier Figueroa, Carlos Pendón and Manuel M Valdivia

    Citation: BMC Genomics 2002 3:11

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  29. Content type: Research article

    Genome wide transcriptome maps can provide tools to identify candidate genes that are over-expressed or silenced in certain disease tissue and increase our understanding of the structure and organization of th...

    Authors: Ping Qiu, Lawrence Benbow, Suxing Liu, Jonathan R Greene and Luquan Wang

    Citation: BMC Genomics 2002 3:10

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  30. Content type: Research article

    Animal and yeast proteins containing long coiled-coil domains are involved in attaching other proteins to the large, solid-state components of the cell. One subgroup of long coiled-coil proteins are the nuclea...

    Authors: Frank Gindullis, Annkatrin Rose, Shalaka Patel and Iris Meier

    Citation: BMC Genomics 2002 3:9

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  31. Content type: Methodology article

    Gene expression profiling among different tissues is of paramount interest in various areas of biomedical research. We have developed a novel method (DADA, D igital A nalysis of cD NA A bundance), that calculates...

    Authors: Peter Hof, Claudia Ortmeier, Kirstin Pape, Birgit Reitmaier, Johannes Regenbogen, Andreas Goppelt and Joern-Peter Halle

    Citation: BMC Genomics 2002 3:7

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  32. Content type: Research article

    Familial atrial fibrillation, an autosomal dominant disease, was previously mapped to chromosome 10q22. One of the genes mapped to the 10q22 region is DLG5, a member of the MAGUKs (Membrane Associated Gyanylat...

    Authors: Gopi Shah, Ramon Brugada, Oscar Gonzalez, Grazyna Czernuszewicz, Richard A Gibbs, Linda Bachinski and Robert Roberts

    Citation: BMC Genomics 2002 3:6

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  33. Content type: Research article

    Inhibitor of Apoptosis (IAP) proteins are key intrinsic regulators of apoptosis induced by a variety of triggers. We isolated the rat Inhibitor of Apoptosis genes 1, 2 and 3 and characterized their tissue dist...

    Authors: Martin Holcik, Charles A Lefebvre, Keiko Hicks and Robert G Korneluk

    Citation: BMC Genomics 2002 3:5

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  34. Content type: Research article

    Mucolipidosis type IV (MLIV) is an autosomal recessive lysosomal storage disorder characterized by severe neurologic and ophthalmologic abnormalities. Recently the MLIV gene, MCOLN1, has been identified as a new ...

    Authors: John L Falardeau, John C Kennedy, James S Acierno Jr, Mei Sun, Stefanie Stahl, Ehud Goldin and Susan A Slaugenhaupt

    Citation: BMC Genomics 2002 3:3

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  35. Content type: Research article

    The phospholipase D (PLD) family has been identified in plants by recent molecular studies, fostered by the emerging importance of plant PLDs in stress physiology and signal transduction. However, the presence...

    Authors: Marek Eliáš, Martin Potocký, Fatima Cvrčková and Viktor Žárský

    Citation: BMC Genomics 2002 3:2

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  36. Content type: Research article

    Two-hybrid screening for proteins that interact with the core domain of human topoisomerase I identified two novel proteins, BTBD1 and BTBD2, which share 80% amino acid identities.

    Authors: Lixin Xu, Lihong Yang, Keiko Hashimoto, Melvin Anderson, Glenda Kohlhagen, Yves Pommier and Peter D'Arpa

    Citation: BMC Genomics 2002 3:1

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