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  1. RNA amplification is required for incorporating laser-capture microdissection techniques into microarray assays. However, standard oligonucleotide microarrays contain sense-strand probes, so traditional T7 amp...

    Authors: Loyal A Goff, Jessica Bowers, Jaime Schwalm, Kevin Howerton, Robert C Getts and Ronald P Hart
    Citation: BMC Genomics 2004 5:76
  2. Homeotic gene complexes determine the anterior-posterior body axis in animals. The expression pattern and function of hox genes along this axis is colinear with the order in which they are organized in the comple...

    Authors: Chilaka Sabarinadh, Subbaya Subramanian, Anshuman Tripathi and Rakesh K Mishra
    Citation: BMC Genomics 2004 5:75
  3. Microarrays are an important tool with which to examine coordinated gene expression. Soybean (Glycine max) is one of the most economically valuable crop species in the world food supply. In order to accelerate bo...

    Authors: Lila O Vodkin, Anupama Khanna, Robin Shealy, Steven J Clough, Delkin Orlando Gonzalez, Reena Philip, Gracia Zabala, Françoise Thibaud-Nissen, Mark Sidarous, Martina V Strömvik, Elizabeth Shoop, Christina Schmidt, Ernest Retzel, John Erpelding, Randy C Shoemaker, Alicia M Rodriguez-Huete…
    Citation: BMC Genomics 2004 5:73
  4. Alternative splicing contributes significantly to the complexity of the human transcriptome and proteome. Computational prediction of alternative splice isoforms are usually based on EST sequences that also al...

    Authors: Shobhit Gupta, Dorothea Zink, Bernhard Korn, Martin Vingron and Stefan A Haas
    Citation: BMC Genomics 2004 5:72
  5. Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy and has been the poster-child for improved therapeutics in cancer, with life time disease-free survival (LTDFS) rates improving from <...

    Authors: Stephanie A Mitchell, Kevin M Brown, Michael M Henry, Michelle Mintz, Daniel Catchpoole, Bonnie LaFleur and Dietrich A Stephan
    Citation: BMC Genomics 2004 5:71
  6. Recurrent non-random genomic alterations are the hallmarks of cancer and the characterization of these imbalances is critical to our understanding of tumorigenesis and cancer progression.

    Authors: Qing-Rong Chen, Sven Bilke, Jun S Wei, Craig C Whiteford, Nicola Cenacchi, Alexei L Krasnoselsky, Braden T Greer, Chang-Gue Son, Frank Westermann, Frank Berthold, Manfred Schwab, Daniel Catchpoole and Javed Khan
    Citation: BMC Genomics 2004 5:70
  7. Proteomics is rapidly evolving into a high-throughput technology, in which substantial and systematic studies are conducted on samples from a wide range of physiological, developmental, or pathological conditi...

    Authors: Kevin Garwood, Thomas McLaughlin, Chris Garwood, Scott Joens, Norman Morrison, Christopher F Taylor, Kathleen Carroll, Caroline Evans, Anthony D Whetton, Sarah Hart, David Stead, Zhikang Yin, Alistair JP Brown, Andrew Hesketh, Keith Chater, Lena Hansson…
    Citation: BMC Genomics 2004 5:68
  8. The resolution of radiation hybrid (RH) maps is intermediate between that of the genetic and BAC (Bacterial Artificial Chromosome) contig maps. Moreover, once framework RH maps of a genome have been constructe...

    Authors: Frédérique Pitel, Behnam Abasht, Mireille Morisson, Richard PMA Crooijmans, Florence Vignoles, Sophie Leroux, Katia Feve, Suzanne Bardes, Denis Milan, Sandrine Lagarrigue, Martien AM Groenen, Madeleine Douaire and Alain Vignal
    Citation: BMC Genomics 2004 5:66
  9. The 156 breeds of dog recognized by the American Kennel Club offer a unique opportunity to map genes important in genetic variation. Each breed features a defining constellation of morphological and behavioral...

    Authors: Matthew Breen, Christophe Hitte, Travis D Lorentzen, Rachael Thomas, Edouard Cadieu, Leah Sabacan, Allyson Scott, Gwenaelle Evanno, Heidi G Parker, Ewen F Kirkness, Ruth Hudson, Richard Guyon, Gregory G Mahairas, Boris Gelfenbeyn, Claire M Fraser, Catherine André…
    Citation: BMC Genomics 2004 5:65
  10. Much of the microarray data published at Stanford is based on mouse and human arrays produced under controlled and monitored conditions at the Brown and Botstein laboratories and at the Stanford Functional Gen...

    Authors: I-Ping Tu, Marci Schaner, Maximilian Diehn, Branimir I Sikic, Patrick O Brown, David Botstein and Michael J Fero
    Citation: BMC Genomics 2004 5:64
  11. Among functional elements of a metazoan gene, enhancers are particularly difficult to find and annotate. Pioneering experiments in Drosophila have demonstrated the value of enhancer "trapping" using an invertebra...

    Authors: Darius Balciunas, Ann E Davidson, Sridhar Sivasubbu, Spencer B Hermanson, Zachary Welle and Stephen C Ekker
    Citation: BMC Genomics 2004 5:62
  12. Despite the widespread use of microarrays, much ambiguity regarding data analysis, interpretation and correlation of the different technologies exists. There is a considerable amount of interest in correlating...

    Authors: Richard Shippy, Timothy J Sendera, Randall Lockner, Chockalingam Palaniappan, Tamma Kaysser-Kranich, George Watts and John Alsobrook
    Citation: BMC Genomics 2004 5:61
  13. Capillary DNA sequencing machines allow the generation of vast amounts of data with little hands-on time. With this expansion of data generation, there is a growing need for automated data processing. Most ava...

    Authors: Jan A Aerts, Bart J Jungerius and Martien AM Groenen
    Citation: BMC Genomics 2004 5:60
  14. The analysis of gene expression using DNA microarrays provides genome wide profiles of the genes controlled by the presence or absence of a specific transcription factor. However, the question arises of whethe...

    Authors: Vijayalakshmi H Nagaraj, Ruadhan A O'Flanagan, Adrian R Bruning, Jonathan R Mathias, Andrew K Vershon and Anirvan M Sengupta
    Citation: BMC Genomics 2004 5:59
  15. Gene expression technologies have the ability to generate vast amounts of data, yet there often resides only limited resources for subsequent validation studies. This necessitates the ability to perform sortin...

    Authors: Michael Schlicht, Brian Matysiak, Tracy Brodzeller, Xinyu Wen, Hang Liu, Guohui Zhou, Rajiv Dhir, Martin J Hessner, Peter Tonellato, Mark Suckow, Morris Pollard and Milton W Datta
    Citation: BMC Genomics 2004 5:58
  16. In this study, we investigated the effect of genetic background on expression profiles. We analysed the transcriptome of mouse hindlimb muscle of five frequently used mouse inbred strains using spotted oligonu...

    Authors: Rolf Turk, Peter AC 't Hoen, Ellen Sterrenburg, Renée X de Menezes, Emile J de Meijer, Judith M Boer, Gert-Jan B van Ommen and Johan T den Dunnen
    Citation: BMC Genomics 2004 5:57
  17. Defensins comprise a large family of cationic antimicrobial peptides that are characterized by the presence of a conserved cysteine-rich defensin motif. Based on the spacing pattern of cysteines, these defensi...

    Authors: Yanjing Xiao, Austin L Hughes, Junko Ando, Yoichi Matsuda, Jan-Fang Cheng, Donald Skinner-Noble and Guolong Zhang
    Citation: BMC Genomics 2004 5:56
  18. Endogenous reference genes are commonly used to normalize expression levels of other genes with the assumption that the expression of the former is constant in different tissues and in different physiopatholog...

    Authors: Ping Jin, Yingdong Zhao, Yvonne Ngalame, Monica C Panelli, Dirk Nagorsen, Vladia Monsurró, Kina Smith, Nan Hu, Hua Su, Phil R Taylor, Francesco M Marincola and Ena Wang
    Citation: BMC Genomics 2004 5:55
  19. Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We devel...

    Authors: Srikrishna Putta, Jeramiah J Smith, John A Walker, Mathieu Rondet, David W Weisrock, James Monaghan, Amy K Samuels, Kevin Kump, David C King, Nicholas J Maness, Bianca Habermann, Elly Tanaka, Susan V Bryant, David M Gardiner, David M Parichy and S Randal Voss
    Citation: BMC Genomics 2004 5:54
  20. Global gene expression studies with microarrays can offer biological insights never before possible. However, the technology possesses many sources of technical variability that are an obstacle to obtaining hi...

    Authors: Martin J Hessner, Lisa Meyer, Jennifer Tackes, Sanaa Muheisen and Xujing Wang
    Citation: BMC Genomics 2004 5:53
  21. Annotating genomes remains an hazardous task. Mistakes or gaps in such a complex process may occur when relevant knowledge is ignored, whether lost, forgotten or overlooked. This paper exemplifies an approach ...

    Authors: Daniil G Naumoff, Ying Xu, Nicolas Glansdorff and Bernard Labedan
    Citation: BMC Genomics 2004 5:52
  22. Members of the C-type lectin domain (CTLD) superfamily are metazoan proteins functionally important in glycoprotein metabolism, mechanisms of multicellular integration and immunity. Three genome-level studies ...

    Authors: Alex N Zelensky and Jill E Gready
    Citation: BMC Genomics 2004 5:51
  23. The mammalian retina is a valuable model system to study neuronal biology in health and disease. To obtain insight into intrinsic processes of the retina, great efforts are directed towards the identification ...

    Authors: Heidi L Schulz, Thomas Goetz, Juergen Kaschkoetoe and Bernhard HF Weber
    Citation: BMC Genomics 2004 5:50
  24. FU is the human homologue of the Drosophila gene fused whose product fused is a positive regulator of the transcription factor Cubitus interruptus (Ci). Thus, FU may act as a regulator of the human counterparts ...

    Authors: Torben Østerlund, David B Everman, Regina C Betz, Monica Mosca, Markus M Nöthen, Charles E Schwartz, Peter G Zaphiropoulos and Rune Toftgård
    Citation: BMC Genomics 2004 5:49
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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

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