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  1. Involvement of conservative molecular modules and cellular mechanisms in the widely diversified processes of eukaryotic cell morphogenesis leads to the intriguing question: how do similar proteins contribute t...

    Authors: Fatima Cvrčková, Marian Novotný, Denisa Pícková and Viktor Žárský

    Citation: BMC Genomics 2004 5:44

    Content type: Research article

    Published on:

  2. Synaptotagmins exist as a large gene family in mammals. There is much interest in the function of certain family members which act crucially in the regulated synaptic vesicle exocytosis required for efficient ...

    Authors: Molly Craxton

    Citation: BMC Genomics 2004 5:43

    Content type: Research article

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  3. Unravelling the path from genotype to phenotype, as it is influenced by an organism's environment, is one of the central goals in biology. Gene expression profiling by means of microarrays has become very prom...

    Authors: Susan CP Renn, Nadia Aubin-Horth and Hans A Hofmann

    Citation: BMC Genomics 2004 5:42

    Content type: Methodology article

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  4. The stromal component of the thymic microenvironment is critical for T lymphocyte generation. Thymocyte differentiation involves a cascade of coordinated stromal genes controlling thymocyte survival, lineage c...

    Authors: Magali Irla, Denis Puthier, Samuel Granjeaud, Murielle Saade, Geneviève Victorero, Marie-Geneviève Mattei and Catherine Nguyen

    Citation: BMC Genomics 2004 5:41

    Content type: Research article

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  5. High-density DNA microarrays require automatic feature extraction methodologies and softwares. These can be a potential source of non-reproducibility of gene expression measurements. Variation in feature locat...

    Authors: F Lopez, J Rougemont, B Loriod, A Bourgeois, L Loï, F Bertucci, P Hingamp, R Houlgatte and S Granjeaud

    Citation: BMC Genomics 2004 5:38

    Content type: Methodology article

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  6. N-terminal myristoylation plays a vital role in membrane targeting and signal transduction in plant responses to environmental stress. Although N-myristoyltransferase enzymatic function is conserved across pla...

    Authors: Sheila Podell and Michael Gribskov

    Citation: BMC Genomics 2004 5:37

    Content type: Methodology article

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  7. cDNA libraries are widely used to identify genes and splice variants, and as a physical resource for full-length clones. Conventionally-generated cDNA libraries contain a high percentage of 5'-truncated clones...

    Authors: Ruth Wellenreuther, Ingo Schupp, Annemarie Poustka and Stefan Wiemann

    Citation: BMC Genomics 2004 5:36

    Content type: Methodology article

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  8. DNA microarrays using long oligonucleotide probes are widely used to evaluate gene expression in biological samples. These oligonucleotides are pre-synthesized and sequence-optimized to represent specific gene...

    Authors: Latha Ramdas, David E Cogdell, Jack Y Jia, Ellen E Taylor, Valerie R Dunmire, Limei Hu, Stanley R Hamilton and Wei Zhang

    Citation: BMC Genomics 2004 5:35

    Content type: Research article

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  9. The transcription start site of a metazoan gene remains poorly understood, mostly because there is no clear signal present in all genes. Now that several sequenced metazoan genomes have been annotated, we have...

    Authors: Stein Aerts, Gert Thijs, Michal Dabrowski, Yves Moreau and Bart De Moor

    Citation: BMC Genomics 2004 5:34

    Content type: Research article

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  10. Heterocellular hereditary persistence of fetal hemoglobin (HPFH) is a common multifactorial trait characterized by a modest increase of fetal hemoglobin levels in adults. We previously localized a Quantitative...

    Authors: James Close, Laurence Game, Barnaby Clark, Jean Bergounioux, Ageliki Gerovassili and Swee Lay Thein

    Citation: BMC Genomics 2004 5:33

    Content type: Research article

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  11. Intracellular zinc concentration and localization are strictly regulated by two main protein components, metallothioneins and membrane transporters. In mammalian cells, two membrane transporters family are inv...

    Authors: Michel Seve, Fabrice Chimienti, Séverine Devergnas and Alain Favier

    Citation: BMC Genomics 2004 5:32

    Content type: Research article

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  12. The elastin gene (ELN) is implicated as a factor in both supravalvular aortic stenosis (SVAS) and Williams Beuren Syndrome (WBS), two diseases involving pronounced complications in mental or physical developme...

    Authors: Helen Piontkivska, Yi Zhang, Eric D Green and Laura Elnitski

    Citation: BMC Genomics 2004 5:31

    Content type: Research article

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  13. Various methods for estimating protein expression levels are known. The level of correlation between these methods is only fair, and systematic biases in each of the methods cannot be ruled out. We here invest...

    Authors: Enrique T Munoz, Leonard D Bogarad and Michael W Deem

    Citation: BMC Genomics 2004 5:30

    Content type: Research article

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  14. The requirement of a large amount of high-quality RNA is a major limiting factor for microarray experiments using biopsies. An average microarray experiment requires 10–100 μg of RNA. However, due to their sma...

    Authors: Jörg Schneider, Andreas Buneß, Wolfgang Huber, Joachim Volz, Petra Kioschis, Mathias Hafner, Annemarie Poustka and Holger Sültmann

    Citation: BMC Genomics 2004 5:29

    Content type: Research article

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  15. A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar gen...

    Authors: Diego G Silva, Christian Schönbach, Vladimir Brusic, Luis A Socha, Takeshi Nagashima and Nikolai Petrovsky

    Citation: BMC Genomics 2004 5:28

    Content type: Research article

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  16. Our increasing use of genetic and genomic strategies to understand human prostate cancer means that we need access to simplified and integrated information present in the associated biomedical literature. In p...

    Authors: Ann Etim, Guohui Zhou, Xinyu Wen, Hang Liu, Victor Ruotti, Simon Twigger, Weihong Jin, Brian Matysiak, Jedidiah Mathis, Peter J Tonellato and Milton W Datta

    Citation: BMC Genomics 2004 5:27

    Content type: Database

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  17. Several high throughput technologies have been employed to identify differentially regulated genes that may be molecular targets for drug discovery. Here we compared the sets of differentially regulated genes ...

    Authors: Wuxiong Cao, Charles Epstein, Hong Liu, Craig DeLoughery, Nanxiang Ge, Jieyi Lin, Rong Diao, Hui Cao, Fan Long, Xin Zhang, Yangde Chen, Paul S Wright, Steve Busch, Michelle Wenck, Karen Wong, Alan G Saltzman…

    Citation: BMC Genomics 2004 5:26

    Content type: Methodology article

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  18. Two-dimensional gel electrophoresis (2D-PAGE) has proven over the years to be a reliable and efficient method for separation of hundreds of proteins based on charge and mass. Nevertheless, the complexity of ev...

    Authors: Mary Kathryn Doud, Michael W Schmidt, David Hines, Claudia Naumann, Andreas Kocourek, Noushin Kashani-Poor, Robert Zeidler and Dieter A Wolf

    Citation: BMC Genomics 2004 5:25

    Content type: Methodology article

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  19. Mutations and gene expression alterations in brain tumors have been extensively investigated, however the causes of brain tumorigenesis are largely unknown. Animal models are necessary to correlate altered tra...

    Authors: Thomas Loop, Ronny Leemans, Urs Stiefel, Leandro Hermida, Boris Egger, Fukang Xie, Michael Primig, Ulrich Certa, Karl-Friedrich Fischbach, Heinrich Reichert and Frank Hirth

    Citation: BMC Genomics 2004 5:24

    Content type: Research article

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  20. 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

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  21. 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

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  22. 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

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  23. 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

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  24. 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

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  25. 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

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  26. 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

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  27. 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

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  28. 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

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  29. 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

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  30. 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

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  31. 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

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  32. 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

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  33. 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

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  34. 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

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  35. 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

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  36. 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

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  37. 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

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  38. 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

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  39. 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

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  40. 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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  41. 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:

  42. 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:

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