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  1. The tetranucleotide GATC is methylated in Escherichia. coli by the DNA methyltransferase (Dam) and is known to be implicated in numerous cellular processes. Mutants lacking Dam are characterized by a pleiotropic ...

    Authors: Alessandra Riva, Marie-Odile Delorme, Tony Chevalier, Nicolas Guilhot, Corinne Hénaut and Alain Hénaut
    Citation: BMC Genomics 2004 5:48
  2. To identify the spectrum of malignant attributes maintained outside the host environment, we have compared global gene expression in primary breast tumors and matched short-term epithelial cultures.

    Authors: Shanaz H Dairkee, Youngran Ji, Yong Ben, Dan H Moore, Zhenhang Meng and Stefanie S Jeffrey
    Citation: BMC Genomics 2004 5:47
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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

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