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  1. There are four widely used experimental strains of N. gonorrhoeae, one of which has been sequenced and used as the basis for the construction of a multi-strain, mutli-species pan-neisserial microarray. Although t...

    Authors: Lori AS Snyder, John K Davies and Nigel J Saunders
    Citation: BMC Genomics 2004 5:23
    Content type: Research article Published on:

  2. The construction of cDNA libraries is a useful tool to understand gene expression in organisms under different conditions, but random sequencing of unbiased cDNA collections is laborious and can give rise to r...

    Authors: Anamika Ray, Sunita Macwana, Patricia Ayoubi, Leo T Hall, Rolf Prade and Andrew J Mort
    Citation: BMC Genomics 2004 5:22
    Content type: Methodology article Published on:

  3. Asthma pathogenesis and susceptibility involves a complex interplay between genetic and environmental factors. Their interaction modulates the airway inflammation and remodelling processes that are present eve...

    Authors: Catherine Laprise, Robert Sladek, André Ponton, Marie-Claude Bernier, Thomas J Hudson and Michel Laviolette
    Citation: BMC Genomics 2004 5:21
    Content type: Methodology article Published on:

  4. Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design...

    Authors: Natalia Novoradovskaya, Michael L Whitfield, Lee S Basehore, Alexey Novoradovsky, Robert Pesich, Jerry Usary, Mehmet Karaca, Winston K Wong, Olga Aprelikova, Michael Fero, Charles M Perou, David Botstein and Jeff Braman
    Citation: BMC Genomics 2004 5:20
    Content type: Methodology article Published on:

  6. LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to b...

    Authors: Lizhi Gao, Eugene M McCarthy, Eric W Ganko and John F McDonald
    Citation: BMC Genomics 2004 5:18
    Content type: Research article Published on:

  7. Gene microarray technology provides the ability to study the regulation of thousands of genes simultaneously, but its potential is limited without an estimate of the statistical significance of the observed ch...

    Authors: Jason Comander, Sripriya Natarajan, Michael A Gimbrone Jr and Guillermo García-Cardeña
    Citation: BMC Genomics 2004 5:17
    Content type: Methodology article Published on:

  8. Gene expression is regulated mainly by transcription factors (TFs) that interact with regulatory cis-elements on DNA sequences. To identify functional regulatory elements, computer searching can predict TF bindin...

    Authors: Katsuhiko Murakami, Toshio Kojima and Yoshiyuki Sakaki
    Citation: BMC Genomics 2004 5:16
    Content type: Research article Published on:

  9. Bacillus anthracis, Bacillus thuringiensis and Bacillus cereus are closely related members of the B. cereus-group of bacilli. Suppressive subtractive hybridization (SSH) was used to identify specific chromosomal...

    Authors: Kathleen G Dwyer, Janine M Lamonica, Jennifer A Schumacher, Leanne E Williams, Joanne Bishara, Anna Lewandowski, Rajendra Redkar, Guy Patra and Vito G DelVecchio
    Citation: BMC Genomics 2004 5:15
    Content type: Research article Published on:

  10. Four genes designated as PTPRK (PTPκ), PTPRL/U (PCP-2), PTPRM (PTPμ) and PTPRT (PTPρ) code for a subfamily (type R2B) of receptor protein tyrosine phosphatases (RPTPs) uniquely characterized by the presence of...

    Authors: Julie Besco, Magdalena C Popesco, Ramana V Davuluri, Adrienne Frostholm and Andrej Rotter
    Citation: BMC Genomics 2004 5:14
    Content type: Research article Published on:

  11. High-throughput, parallel gene expression analysis by means of microarray technology has become a widely used technique in recent years. There are currently two main dye-labelling strategies for microarray stu...

    Authors: Thorsten Forster, Yael Costa, Douglas Roy, Howard J Cooke and Klio Maratou
    Citation: BMC Genomics 2004 5:13
    Content type: Methodology article Published on:

  12. Spotted 70-mer oligonucleotide arrays offer potentially greater specificity and an alternative to expensive cDNA library maintenance and amplification. Since microarray fabrication is a considerable source of ...

    Authors: Martin J Hessner, Vineet K Singh, Xujing Wang, Shehnaz Khan, Michael R Tschannen and Thomas C Zahrt
    Citation: BMC Genomics 2004 5:12
    Content type: Methodology article Published on:

  13. Activation of proto-oncogenes by DNA amplification is an important mechanism in the development and maintenance of cancer cells. Until recently, identification of the targeted genes relied on labour intensive ...

    Authors: Katleen De Preter, Filip Pattyn, Geert Berx, Kristin Strumane, Björn Menten, Frans Van Roy, Anne De Paepe, Frank Speleman and Jo Vandesompele
    Citation: BMC Genomics 2004 5:11
    Content type: Research article Published on:

  14. High throughput gene expression data from spotted cDNA microarrays are collected by scanning the signal intensities of the corresponding spots by dedicated fluorescence scanners. The major scanner settings for...

    Authors: Heidi Lyng, Azadeh Badiee, Debbie H Svendsrud, Eivind Hovig, Ola Myklebost and Trond Stokke
    Citation: BMC Genomics 2004 5:10
    Content type: Methodology article Published on:

  15. Expression microarrays have evolved into a powerful tool with great potential for clinical application and therefore reliability of data is essential. RNA amplification is used when the amount of starting mate...

    Authors: Ali Naderi, Ahmed A Ahmed, Nuno L Barbosa-Morais, Samuel Aparicio, James D Brenton and Carlos Caldas
    Citation: BMC Genomics 2004 5:9
    Content type: Methodology article Published on:

  17. We have recently cloned and characterized a novel gene family named ancient conserved domain protein (ACDP) in humans. To facilitate the functional study of this novel gene family, we have cloned and characterize...

    Authors: Cong-Yi Wang, Ping Yang, Jing-Da Shi, Sharad Purohit, Dehuang Guo, Haiqian An, Jian-Guo Gu, Jennifer Ling, Zheng Dong and Jin-Xiong She
    Citation: BMC Genomics 2004 5:7
    Content type: Research article Published on:

  18. The recent development of array based comparative genomic hybridization (CGH) technology provides improved resolution for detection of genomic DNA copy number alterations. In array CGH, generating spotting sol...

    Authors: Spencer K Watson, Ronald J deLeeuw, Adrian S Ishkanian, Chad A Malloff and Wan L Lam
    Citation: BMC Genomics 2004 5:6
    Content type: Methodology article Published on:

  19. The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting proteins to the ER membrane. The SRP of metazoans is well characterized and composed of an RNA molecule and six po...

    Authors: Magnus Alm Rosenblad, Christian Zwieb and Tore Samuelsson
    Citation: BMC Genomics 2004 5:5
    Content type: Research article Published on:

  21. We studied four extremely halophilic archaea by low-pass shotgun sequencing: (1) the metabolically versatile Haloarcula marismortui; (2) the non-pigmented Natrialba asiatica; (3) the psychrophile Halorubrum lacus...

    Authors: Young Ah Goo, Jared Roach, Gustavo Glusman, Nitin S Baliga, Kerry Deutsch, Min Pan, Sean Kennedy, Shiladitya DasSarma, Wailap Victor Ng and Leroy Hood
    Citation: BMC Genomics 2004 5:3
    Content type: Research article Published on:

  22. To generate specific transcript profiles, one must isolate homogenous cell populations using techniques that often yield small amounts of RNA, requiring researchers to employ RNA amplification methods. The dat...

    Authors: David Gold, Kevin Coombes, Dina Medhane, Anitha Ramaswamy, Zhenlin Ju, Louise Strong, Ja Seok Koo and Mini Kapoor
    Citation: BMC Genomics 2004 5:2
    Content type: Methodology article Published on:

  24. We have previously set up an in vitro mesenchymal-epithelial cell co-culture model which mimics the intestinal crypt villus axis biology in terms of epithelial cell differentiation. In this model the fibroblast-i...

    Authors: Katri Lindfors, Keijo M Viiri, Marjo Niittynen, Taisto YK Heinonen, Markku Mäki and Heikki Kainulainen
    Citation: BMC Genomics 2003 4:53
    Content type: Research article Published on:

  25. Non-coding DNA represents a high proportion of all metazoan genomes. Although an undetermined fraction of this DNA may be considered devoid of any function, it also contains important information residing in s...

    Authors: Javier Costas, Cristina P Vieira, Fernando Casares and Jorge Vieira
    Citation: BMC Genomics 2003 4:52
    Content type: Research article Published on:

  26. Acidithiobacillus ferrooxidans is a gamma-proteobacterium that lives at pH2 and obtains energy by the oxidation of sulfur and iron. It is used in the biomining industry for the recovery of metals and is one of th...

    Authors: Jorge Valdés, Felipe Veloso, Eugenia Jedlicki and David Holmes
    Citation: BMC Genomics 2003 4:51
    Content type: Research article Published on:

  29. Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH...

    Authors: Michal A Kurowski, Ashok S Bhagwat, Grzegorz Papaj and Janusz M Bujnicki
    Citation: BMC Genomics 2003 4:48
    Content type: Research article Published on:

  31. Tumor necrosis factor α (TNF) is able to induce a variety of biological responses in the nervous system including inflammation and neuroprotection. Human astrocytoma cells U373 have been widely used as a model...

    Authors: Jens Schwamborn, Antje Lindecke, Margitta Elvers, Volker Horejschi, Martin Kerick, Mehran Rafigh, Julia Pfeiffer, Maria Prüllage, Barbara Kaltschmidt and Christian Kaltschmidt
    Citation: BMC Genomics 2003 4:46
    Content type: Research article Published on:

  35. Many model proteomes or "complete" sets of proteins of given organisms are now publicly available. Much effort has been invested in computational annotation of those "draft" proteomes. Motif or domain based al...

    Authors: Yong Zhang, Yanbin Yin, Yunjia Chen, Ge Gao, Peng Yu, Jingchu Luo and Ying Jiang
    Citation: BMC Genomics 2003 4:42
    Content type: Database Published on:

  37. 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
    Content type: Research article Published on:

  38. 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
    Content type: Research article Published on:

  39. 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
    Content type: Research article Published on:

  41. 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
    Content type: Methodology article Published on:

  42. 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
    Content type: Research article Published on:

  43. 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
    Content type: Research article Published on:

  44. 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
    Content type: Research article Published on:

  45. 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 Published on:

  47. 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 Published on:

  48. 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 Published on:

  49. 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 Published on:

  50. 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 Published on:

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