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  1. 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:

  2. 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

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  3. 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

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  6. 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

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  8. 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

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  12. 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

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  14. 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

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  15. 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

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  16. 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

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  18. 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

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  19. 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

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  20. 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

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  21. 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

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  22. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  31. 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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  32. 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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  33. 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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  34. 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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  38. 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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  39. 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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  41. 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

    Published on:

  42. 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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  43. 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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  45. 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

    Published on:

  46. 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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  47. 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

    Published on:

  48. 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:

  50. 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

    Published on:

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