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  1. As part of our investigation into the genetic basis of tumor cell radioresponse, we have isolated several clones with a wide range of responses to X-radiation (XR) from an unirradiated human colorectal tumor c...

    Authors: Felix M Mesak, Naoki Osada, Katsuyuki Hashimoto, Qing Y Liu and Cheng E Ng

    Citation: BMC Genomics 2003 4:32

    Content type: Research article

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  3. The pufferfish Fugu rubripes (Fugu) with its compact genome is increasingly recognized as an important vertebrate model for comparative genomic studies. In particular, large regions of conserved synteny between h...

    Authors: Alexandre Montpetit, Michael D Wilson, Mario Chevrette, Ben F Koop and Daniel Sinnett

    Citation: BMC Genomics 2003 4:30

    Content type: Research article

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  4. The high degree of sequence conservation between coding regions in fish and mammals can be exploited to identify genes in mammalian genomes by comparison with the sequence of similar genes in fish. Conversely,...

    Authors: Georges Lutfalla, Hugues Roest Crollius, Nicole Stange-thomann, Olivier Jaillon, Knud Mogensen and Danièle Monneron

    Citation: BMC Genomics 2003 4:29

    Content type: Research article

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  5. The ADGE technique is a method designed to magnify the ratios of gene expression before detection. It improves the detection sensitivity to small change of gene expression and requires small amount of starting...

    Authors: Zhijian J Chen, Laurent Gaté, Warren Davis, Kristina E Ile and Kenneth D Tew

    Citation: BMC Genomics 2003 4:28

    Content type: Methodology article

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  6. The genome of the fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genomic era of this increasingly popular model organism. We have built fission yeast microarra...

    Authors: Rachel Lyne, Gavin Burns, Juan Mata, Chris J Penkett, Gabriella Rustici, Dongrong Chen, Cordelia Langford, David Vetrie and Jürg Bähler

    Citation: BMC Genomics 2003 4:27

    Content type: Research article

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  7. In order to identify rice genes involved in nutrient partitioning, microarray experiments have been done to quantify genomic scale gene expression. Genes involved in nutrient partitioning, specifically grain f...

    Authors: Abraham Anderson, Matthew Hudson, Wenqiong Chen and Tong Zhu

    Citation: BMC Genomics 2003 4:26

    Content type: Research article

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  10. DNA microarrays are a powerful tool with important applications such as global gene expression profiling. Construction of bacterial DNA microarrays from genomic sequence data using a two-stage PCR amplificatio...

    Authors: Bradley L Postier, Hong-Liang Wang, Abhay Singh, Lori Impson, Heather L Andrews, Jessica Klahn, Hong Li, George Risinger, David Pesta, Michael Deyholos, David W Galbraith, Louis A Sherman and Robert L Burnap

    Citation: BMC Genomics 2003 4:23

    Content type: Methodology article

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  11. Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of indi...

    Authors: Sreedhar Oduru, Janee L Campbell, SriTulasi Karri, William J Hendry, Shafiq A Khan and Simon C Williams

    Citation: BMC Genomics 2003 4:22

    Content type: Research article

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  12. Rolling circle amplification of ligated probes is a simple and sensitive means for genotyping directly from genomic DNA. SNPs and mutations are interrogated with open circle probes (OCP) that can be circulariz...

    Authors: Osama A Alsmadi, Carole J Bornarth, Wanmin Song, Michele Wisniewski, Jing Du, Joel P Brockman, A Fawad Faruqi, Seiyu Hosono, Zhenyu Sun, Yuefen Du, Xiaohong Wu, Michael Egholm, Patricio Abarzúa, Roger S Lasken and Mark D Driscoll

    Citation: BMC Genomics 2003 4:21

    Content type: Methodology article

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  13. The generation of BAC/PAC contigs in targeted genome regions is a powerful method to establish high-resolution physical maps. In domestic animal species the generation of such contigs is typically initiated wi...

    Authors: Flávia Martins-Wess, Denis Milan, Cord Drögemüller, Rodja Voβ-Nemitz, Bertram Brenig, Annie Robic, Martine Yerle and Tosso Leeb

    Citation: BMC Genomics 2003 4:20

    Content type: Research article

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  17. Transformation-associated recombination (TAR) cloning in yeast is a unique method for selective isolation of large chromosomal fragments or entire genes from complex genomes. The technique involves homologous ...

    Authors: Vladimir N Noskov, Natalay Kouprina, Sun-Hee Leem, Ilia Ouspenski, J Carl Barrett and Vladimir Larionov

    Citation: BMC Genomics 2003 4:16

    Content type: Methodology article

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  18. Chromosomal abnormalities affecting human chromosome 15q11-q13 underlie multiple genomic disorders caused by deletion, duplication and triplication of intervals in this region. These events are mediated by hig...

    Authors: James S Sutcliffe, Michael K Han, Taneem Amin, Robert A Kesterson and Erika L Nurmi

    Citation: BMC Genomics 2003 4:15

    Content type: Research article

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  20. 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

    Content type: Research article

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  21. 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

    Content type: Research article

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  22. 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

    Content type: Research article

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  24. 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

    Content type: Research article

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  25. 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

    Content type: Research article

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  26. 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

    Content type: Research article

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  27. 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

    Content type: Research article

    Published on:

  29. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

    Published on:

  37. 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

    Content type: Research article

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  38. 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

    Content type: Methodology article

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  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

    Published on:

  41. 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

    Content type: Research article

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  44. 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

    Content type: Research article

    Published on:

  45. 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

    Content type: Research article

    Published on:

  46. 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

    Content type: Research article

    Published on:

  47. 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

    Content type: Methodology article

    Published on:

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