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  1. Subtractive hybridization methods are valuable tools for identifying differentially regulated genes in a given tissue avoiding redundant sequencing of clones representing the same expressed genes, maximizing d...

    Authors: Paula Fernández, Norma Paniego, Sergio Lew, H Esteban Hopp and Ruth A Heinz
    Citation: BMC Genomics 2003 4:40
  2. In order to facilitate the identification of genes involved in the metastatic phenotype we have previously developed a pair of cell lines from the human breast carcinoma cell line MDA-MB-435, which have diamet...

    Authors: Steve Goodison, Carrie Viars, Maren Grazzini and Virginia Urquidi
    Citation: BMC Genomics 2003 4:39
  3. Numerous DNA microarray hybridization experiments have been performed in yeast over the last years using either synthetic oligonucleotides or PCR-amplified coding sequences as probes. The design and quality of...

    Authors: Emmanuel Talla, Fredj Tekaia, Laurent Brino and Bernard Dujon
    Citation: BMC Genomics 2003 4:38
  4. Cloning of genes in expression libraries, such as the yeast two-hybrid system (Y2H), is based on the assumption that the loss of target genes is minimal, or at worst, managable. However, the expression of gene...

    Authors: Steven A Haney, David Keeney, Lei Chen, Soraya Moghazeh, Steve Projan and Beth Rasmussen
    Citation: BMC Genomics 2003 4:36
  5. Twenty-eight genes putatively encoding cytosolic glutathione transferases have been identified in the Anopheles gambiae genome. We manually annotated these genes and then confirmed the annotation by sequencing of...

    Authors: Yunchuan Ding, Federica Ortelli, Louise C Rossiter, Janet Hemingway and Hilary Ranson
    Citation: BMC Genomics 2003 4:35
  6. A great diversity of multi-pass membrane receptors, typically with 7 transmembrane (TM) helices, is observed in the eukaryote crown group. So far, they are relatively rare in the prokaryotes, and are restricte...

    Authors: Vivek Anantharaman and L Aravind
    Citation: BMC Genomics 2003 4:34
  7. RNA interference (RNAi) is a process triggered by a double-stranded RNA that leads to targeted down-regulation/silencing of gene expression and can be used for functional genomics; i.e. loss-of-function studie...

    Authors: Svetlana Dzitoyeva, Nikola Dimitrijevic and Hari Manev
    Citation: BMC Genomics 2003 4:33
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  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
  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
  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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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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