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  1. Quantitative Polymerase Chain Reaction (qPCR) is a well-established method for quantifying levels of gene expression, but has not been routinely applied to the detection of constitutional copy number alteratio...

    Authors: Rosanna Weksberg, Simon Hughes, Laura Moldovan, Anne S Bassett, Eva WC Chow and Jeremy A Squire

    Citation: BMC Genomics 2005 6:180

    Content type: Research article

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  2. Macrophages play an integral role in the host immune system, bridging innate and adaptive immunity. As such, they are finely attuned to extracellular and intracellular stimuli and respond by rapidly initiating...

    Authors: Graeme R Grimes, Stuart Moodie, John S Beattie, Marie Craigon, Paul Dickinson, Thorsten Forster, Andrew D Livingston, Muriel Mewissen, Kevin A Robertson, Alan J Ross, Garwin Sing and Peter Ghazal

    Citation: BMC Genomics 2005 6:178

    Content type: Database

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  3. Fungi can undergo autophagic- or apoptotic-type programmed cell death (PCD) on exposure to antifungal agents, developmental signals, and stress factors. Filamentous fungi can also exhibit a form of cell death ...

    Authors: Natalie D Fedorova, Jonathan H Badger, Geoff D Robson, Jennifer R Wortman and William C Nierman

    Citation: BMC Genomics 2005 6:177

    Content type: Research article

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  4. Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chl...

    Authors: Amit Dhingra and Kevin M Folta

    Citation: BMC Genomics 2005 6:176

    Content type: Methodology article

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  5. Spiroplasma citri BR3-3X and S. kunkelii CR2-3X cause serious diseases worldwide on citrus and maize species, respectively. S. citri BR3-3X harbors a plasmid, pBJS-Original (pBJS-O), that encodes the s piroplasma...

    Authors: Bharat D Joshi, Michael Berg, Janet Rogers, Jacqueline Fletcher and Ulrich Melcher

    Citation: BMC Genomics 2005 6:175

    Content type: Research article

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  6. Two closely related species Burkholderia mallei (Bm) and Burkholderia pseudomallei (Bp) are serious human health hazards and are potential bio-warfare agents, whereas another closely related species Burkholderia ...

    Authors: H Stanley Kim, Mark A Schell, Yan Yu, Ricky L Ulrich, Saul H Sarria, William C Nierman and David DeShazer

    Citation: BMC Genomics 2005 6:174

    Content type: Research article

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  7. Vertebrate odorant receptors comprise three types of G protein-coupled receptors: the OR, V1R and V2R receptors. The OR superfamily contains over 1,000 genes in some mammalian species, representing the largest...

    Authors: Tyler S Alioto and John Ngai

    Citation: BMC Genomics 2005 6:173

    Content type: Research article

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  8. Members of the M2 family of peptidases, related to mammalian angiotensin converting enzyme (ACE), play important roles in regulating a number of physiological processes. As more invertebrate genomes are sequen...

    Authors: Susan Burnham, Judith A Smith, Alison J Lee, R Elwyn Isaac and Alan D Shirras

    Citation: BMC Genomics 2005 6:172

    Content type: Research article

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  9. The Atlantic salmon is an important aquaculture species and a very interesting species biologically, since it spawns in fresh water and develops through several stages before becoming a smolt, the stage at whi...

    Authors: Heidi Hagen-Larsen, Jon K Laerdahl, Frank Panitz, Alexei Adzhubei and Bjørn Høyheim

    Citation: BMC Genomics 2005 6:171

    Content type: Research article

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  10. The laboratory rat (Rattus norvegicus) is an important model for studying many aspects of human health and disease. Detailed knowledge on genetic variation between strains is important from a biomedical, particul...

    Authors: Bart MG Smits, Victor Guryev, Dimphy Zeegers, Dirk Wedekind, Hans J Hedrich and Edwin Cuppen

    Citation: BMC Genomics 2005 6:170

    Content type: Research article

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  11. The Engrailed Homology 1 (EH1) motif is a small region, believed to have evolved convergently in homeobox and forkhead containing proteins, that interacts with the Drosophila protein groucho (C. elegans unc-37, H...

    Authors: Richard R Copley

    Citation: BMC Genomics 2005 6:169

    Content type: Research article

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  12. Genome assemblies rely on the existence of transcript sequence to stitch together contigs, verify assembly of whole genome shotgun reads, and annotate genes. Functional genomics studies also rely on transcript...

    Authors: Gregory P Harhay, Tad S Sonstegard, John W Keele, Michael P Heaton, Michael L Clawson, Warren M Snelling, Ralph T Wiedmann, Curt P Van Tassell and Timothy PL Smith

    Citation: BMC Genomics 2005 6:166

    Content type: Methodology article

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  13. The mosaic sperm protein zonadhesin (ZAN) has been characterized in mammals and is implicated in species-specific egg-sperm binding interactions. The genomic structure and testes-specific expression of zonadhe...

    Authors: Peter ND Hunt, Michael D Wilson, Kristian R von Schalburg, William S Davidson and Ben F Koop

    Citation: BMC Genomics 2005 6:165

    Content type: Research article

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  14. Analysis of an allelic series of point mutations in a gene, generated by N-ethyl-N-nitrosourea (ENU) mutagenesis, is a valuable method for discovering the full scope of its biological function. Here we present an...

    Authors: Edward J Michaud, Cymbeline T Culiat, Mitchell L Klebig, Paul E Barker, KT Cain, Debra J Carpenter, Lori L Easter, Carmen M Foster, Alysyn W Gardner, ZY Guo, Kay J Houser, Lori A Hughes, Marilyn K Kerley, Zhaowei Liu, Robert E Olszewski, Irina Pinn…

    Citation: BMC Genomics 2005 6:164

    Content type: Research article

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  15. Recent analyses of prokaryotic genome sequences have demonstrated the important force horizontal gene transfer constitutes in genome evolution. Horizontally acquired sequences are detectable by, among others, ...

    Authors: MWJ van Passel, A Bart, HH Thygesen, ACM Luyf, AHC van Kampen and A van der Ende

    Citation: BMC Genomics 2005 6:163

    Content type: Research article

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  16. Identification of a bacterial protein's subcellular localization (SCL) is important for genome annotation, function prediction and drug or vaccine target identification. Subcellular fractionation techniques co...

    Authors: Sébastien Rey, Jennifer L Gardy and Fiona SL Brinkman

    Citation: BMC Genomics 2005 6:162

    Content type: Research article

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  17. The genome of classical laboratory strains of mice is an artificial mosaic of genomes originated from several mouse subspecies with predominant representation (>90%) of the Mus m. domesticus component. Mice of an...

    Authors: Petr Jansa, Petr Divina and Jiří Forejt

    Citation: BMC Genomics 2005 6:161

    Content type: Research article

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  18. Nonhuman primates (NHPs) are essential for biomedical research due to their similarities to humans. The utility of NHPs will be greatly increased by the application of genomics-based approaches such as gene ex...

    Authors: Eliot R Spindel, Mark A Pauley, Yibing Jia, Courtney Gravett, Shaun L Thompson, Nicholas F Boyle, Sergio R Ojeda and Robert B Norgren Jr

    Citation: BMC Genomics 2005 6:160

    Content type: Research article

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  19. Many biological networks show some characteristics of scale-free networks. Scale-free networks can evolve through preferential attachment where new nodes are preferentially attached to well connected nodes. In...

    Authors: Sara Light, Per Kraulis and Arne Elofsson

    Citation: BMC Genomics 2005 6:159

    Content type: Research article

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  20. Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (Medicago sativa). This species occupies different ecological niches, being present ...

    Authors: Elisa Giuntini, Alessio Mengoni, Carlotta De Filippo, Duccio Cavalieri, Nadia Aubin-Horth, Christian R Landry, Anke Becker and Marco Bazzicalupo

    Citation: BMC Genomics 2005 6:158

    Content type: Research article

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  21. Prader-Willi and Angelman syndrome (PWS and AS) patients typically have an ~5 Mb deletion of human chromosome 15q11-q13, of opposite parental origin. A mouse model of PWS and AS has a transgenic insertion-dele...

    Authors: Mihaela Stefan, Kathryn C Claiborn, Edyta Stasiek, Jing-Hua Chai, Tohru Ohta, Richard Longnecker, John M Greally and Robert D Nicholls

    Citation: BMC Genomics 2005 6:157

    Content type: Research article

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  22. Progranulin is an epithelial tissue growth factor (also known as proepithelin, acrogranin and PC-cell-derived growth factor) that has been implicated in development, wound healing and in the progression of man...

    Authors: Benoît Cadieux, Babykumari P Chitramuthu, David Baranowski and Hugh PJ Bennett

    Citation: BMC Genomics 2005 6:156

    Content type: Research article

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  23. SSH has emerged as a widely used technology to identify genes that are differentially regulated between two biological situations. Because it includes a normalisation step, it is used for preference to clone l...

    Authors: LC Bui, RD Léandri, JP Renard and V Duranthon

    Citation: BMC Genomics 2005 6:155

    Content type: Methodology article

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  24. It is becoming apparent that perhaps as much as half of the genome of the human blood fluke Schistosoma mansoni is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR) retrotran...

    Authors: Thewarach Laha, Nonglack Kewgrai, Alex Loukas and Paul J Brindley

    Citation: BMC Genomics 2005 6:154

    Content type: Research article

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  25. large scale and reliable proteins' functional annotation is a major challenge in modern biology. Phylogenetic analyses have been shown to be important for such tasks. However, up to now, phylogenetic annotatio...

    Authors: N Balandraud, P Gouret, EGJ Danchin, M Blanc, D Zinn, J Roudier and P Pontarotti

    Citation: BMC Genomics 2005 6:153

    Content type: Methodology article

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  26. Regulatory functions of nitric oxide (NO) that bypass the second messenger cGMP are incompletely understood. Here, cGMP-independent effects of NO on gene expression were globally examined in U937 cells, a human...

    Authors: Xiaolin Cui, Jianhua Zhang, Penglin Ma, Daniela E Myers, Ilana G Goldberg, Kelly J Sittler, Jennifer J Barb, Peter J Munson, Ana del Pilar Cintron, J Philip McCoy, Shuibang Wang and Robert L Danner

    Citation: BMC Genomics 2005 6:151

    Content type: Research article

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  27. High throughput microarray-based single nucleotide polymorphism (SNP) genotyping has revolutionized the way genome-wide linkage scans and association analyses are performed. One of the key features of the arra...

    Authors: Matthew J Huentelman, David W Craig, Albert D Shieh, Jason J Corneveaux, Diane Hu-Lince, John V Pearson and Dietrich A Stephan

    Citation: BMC Genomics 2005 6:149

    Content type: Research article

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  28. Global mRNA amplification has become a widely used approach to obtain gene expression profiles from limited material. An important concern is the reliable reflection of the starting material in the results obt...

    Authors: Vigdis Nygaard, Marit Holden, Anders Løland, Mette Langaas, Ola Myklebost and Eivind Hovig

    Citation: BMC Genomics 2005 6:147

    Content type: Research article

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  29. In contrast to other agents able to induce apoptosis of cultured cells, Ca2+ ionophore A23187 was shown to elicit direct activation of intracellular signal(s). The phenotype of the cells derived from patients hav...

    Authors: Detlef Kozian, Valérie Proulle, Almut Nitsche, Marie Galitzine, Marie-Carmen Martinez, Beatrice Schumann, Dominique Meyer, Matthias Herrmann, Jean-Marie Freyssinet and Danièle Kerbiriou-Nabias

    Citation: BMC Genomics 2005 6:146

    Content type: Research article

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  30. iTRAQ™ technology for protein quantitation using mass spectrometry is a recent, powerful means of determining relative protein levels in up to four samples simultaneously. Although protein identification of sa...

    Authors: Ian P Shadforth, Tom PJ Dunkley, Kathryn S Lilley and Conrad Bessant

    Citation: BMC Genomics 2005 6:145

    Content type: Software

    Published on:

  31. The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near fu...

    Authors: Nathalie Pavy, Charles Paule, Lee Parsons, John A Crow, Marie-Josee Morency, Janice Cooke, James E Johnson, Etienne Noumen, Carine Guillet-Claude, Yaron Butterfield, Sarah Barber, George Yang, Jerry Liu, Jeff Stott, Robert Kirkpatrick, Asim Siddiqui…

    Citation: BMC Genomics 2005 6:144

    Content type: Research article

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  32. Ginkgo biloba L. is the only surviving member of one of the oldest living seed plant groups with medicinal, spiritual and horticultural importance worldwide. As an evolutionary relic, it displays many characters ...

    Authors: Eric D Brenner, Manpreet S Katari, Dennis W Stevenson, Stephen A Rudd, Andrew W Douglas, Walter N Moss, Richard W Twigg, Suzan J Runko, Giulia M Stellari, WR McCombie and Gloria M Coruzzi

    Citation: BMC Genomics 2005 6:143

    Content type: Research article

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  33. The molecular determinants of carcinogenesis, tumor progression and patient prognosis can be deduced from simultaneous comparison of thousands of genes by microarray analysis. However, the presence of stroma c...

    Authors: Elza C de Bruin, Simone van de Pas, Esther H Lips, Ronald van Eijk, Minke MC van der Zee, Marcel Lombaerts, Tom van Wezel, Corrie AM Marijnen, J Han JM van Krieken, Jan Paul Medema, Cornelis JH van de Velde, Paul HC Eilers and Lucy TC Peltenburg

    Citation: BMC Genomics 2005 6:142

    Content type: Research article

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  34. A yeast strain lacking the two genes SSA1 and SSA2, which encode cytosolic molecular chaperones, acquires thermotolerance as well as the mild heat-shocked wild-type yeast strain. We investigated the genomic respo...

    Authors: Rena Matsumoto, Kuniko Akama, Randeep Rakwal and Hitoshi Iwahashi

    Citation: BMC Genomics 2005 6:141

    Content type: Research article

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  35. As a result of high-throughput genotyping methods, millions of human genetic variants have been reported in recent years. To efficiently identify those with significant biological functions, a practical strate...

    Authors: Yongjian Guo and D Curtis Jamison

    Citation: BMC Genomics 2005 6:140

    Content type: Research article

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  36. ADP-ribosylation is an enzyme-catalyzed posttranslational protein modification in which mono(ADP-ribosyl)transferases (mARTs) and poly(ADP-ribosyl)transferases (pARTs) transfer the ADP-ribose moiety from NAD o...

    Authors: Helge Otto, Pedro A Reche, Fernando Bazan, Katharina Dittmar, Friedrich Haag and Friedrich Koch-Nolte

    Citation: BMC Genomics 2005 6:139

    Content type: Research article

    Published on:

  37. Pooling genomic DNA samples within clinical classes of disease followed by genotyping on whole-genome SNP microarrays, allows for rapid and inexpensive genome-wide association studies. Key to the success of th...

    Authors: David W Craig, Matthew J Huentelman, Diane Hu-Lince, Victoria L Zismann, Michael C Kruer, Anne M Lee, Erik G Puffenberger, John M Pearson and Dietrich A Stephan

    Citation: BMC Genomics 2005 6:138

    Content type: Methodology article

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  38. Eukaryotic organisms contain mitochondria, organelles capable of producing large amounts of ATP by oxidative phosphorylation. Each cell contains many mitochondria with many copies of mitochondrial DNA in each ...

    Authors: Patrick C Bradshaw, Anand Rathi and David C Samuels

    Citation: BMC Genomics 2005 6:136

    Content type: Research article

    Published on:

  39. Microarray transcript profiling has the potential to illuminate the molecular processes that are involved in the responses of cattle to disease challenges. This knowledge may allow the development of strategie...

    Authors: Laurelea Donaldson, Tony Vuocolo, Christian Gray, Ylva Strandberg, Antonio Reverter, Sean McWilliam, YongHong Wang, Keren Byrne and Ross Tellam

    Citation: BMC Genomics 2005 6:135

    Content type: Research article

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  40. Independent identification of genes in different organisms and assays has led to a multitude of names for each gene. This balkanization makes it difficult to use gene names to locate genomic resources, homolog...

    Authors: Andrew J Olson, Tim Tully and Ravi Sachidanandam

    Citation: BMC Genomics 2005 6:134

    Content type: Software

    Published on:

  41. The gene(s) encoding the ETEC F4ab/ac receptors, involved in neonatal diarrhoea in pigs (a disease not yet described in humans), is located close to the TF locus on Sscr13. In order to reveal and characterize ...

    Authors: Mario Van Poucke, David Bourry, François Piumi, Marc Mattheeuws, Alex Van Zeveren, Patrick Chardon and Luc J Peelman

    Citation: BMC Genomics 2005 6:133

    Content type: Research article

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  42. Severe acute respiratory syndrome (SARS), a recent epidemic human disease, is caused by a novel coronavirus (SARS-CoV). First reported in Asia, SARS quickly spread worldwide through international travelling. A...

    Authors: Yun-Shien Lee, Chun-Houh Chen, Angel Chao, En-Shih Chen, Min-Li Wei, Lung-Kun Chen, Kuender D Yang, Meng-Chih Lin, Yi-Hsi Wang, Jien-Wei Liu, Hock-Liew Eng, Ping-Cherng Chiang, Ting-Shu Wu, Kuo-Chein Tsao, Chung-Guei Huang, Yin-Jing Tien…

    Citation: BMC Genomics 2005 6:132

    Content type: Research article

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