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  1. 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:

  3. 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:

  4. 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:

  6. 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:

  7. 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:

  8. 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:

  11. 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:

  13. 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:

  17. 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:

  19. 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:

  20. 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:

  21. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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 Published on:

  36. 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 Published on:

  37. 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 Published on:

  38. 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 Published on:

  39. 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 Published on:

  43. 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 Published on:

  44. 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 Published on:

  46. 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:

  47. 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 Published on:

  48. 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 Published on:

  50. 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:

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