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  1. Appropriate definitionof neural network architecture prior to data analysis is crucialfor successful data mining. This can be challenging when the underlyingmodel of the data is unknown. The goal of this study...

    Authors: Marylyn D Ritchie, Bill C White, Joel S Parker, Lance W Hahn and Jason H Moore
    Citation: BMC Bioinformatics 2003 4:28
  2. The development of large-scale gene expression profiling technologies is rapidly changing the norms of biological investigation. But the rapid pace of change itself presents challenges. Commercial microarrays ...

    Authors: Ashish Nimgaonkar, Despina Sanoudou, Atul J Butte, Judith N Haslett, Louis M Kunkel, Alan H Beggs and Isaac S Kohane
    Citation: BMC Bioinformatics 2003 4:27
  3. Microarray technology has become a very important tool for studying gene expression profiles under various conditions. Biologists often pool RNA samples extracted from different subjects onto a single microarr...

    Authors: Xuejun Peng, Constance L Wood, Eric M Blalock, Kuey Chu Chen, Philip W Landfield and Arnold J Stromberg
    Citation: BMC Bioinformatics 2003 4:26
  4. The gene regulatory information is hardwired in the promoter regions formed by cis-regulatory elements that bind specific transcription factors (TFs). Hence, establishing the architecture of plant promoters is fu...

    Authors: Ramana V Davuluri, Hao Sun, Saranyan K Palaniswamy, Nicole Matthews, Carlos Molina, Mike Kurtz and Erich Grotewold
    Citation: BMC Bioinformatics 2003 4:25
  5. Seattle Biomedical Research Institute (SBRI) as part of the Leishmania Genome Network (LGN) is sequencing chromosomes of the trypanosomatid protozoan species Leishmania major. At SBRI, chromosomal sequence is ann...

    Authors: Gautam Aggarwal, EA Worthey, Paul D McDonagh and Peter J Myler
    Citation: BMC Bioinformatics 2003 4:23
  6. To date, many of the methods for information extraction of biological information from scientific articles are restricted to the abstract of the article. However, full text articles in electronic version, whic...

    Authors: Parantu K Shah, Carolina Perez-Iratxeta, Peer Bork and Miguel A Andrade
    Citation: BMC Bioinformatics 2003 4:20
  7. DNA pooling is a technique to reduce genotyping effort while incurring only minor losses in accuracy of allele frequency estimates for single nucleotide polymorphism (SNP) markers.

    Authors: Josephine Hoh, Fumihiko Matsuda, Xu Peng, Daniela Markovic, Mark G Lathrop and Jurg Ott
    Citation: BMC Bioinformatics 2003 4:14
  8. Genes that are determined to be significantly differentially regulated in microarray analyses often appear to have functional commonalities, such as being components of the same biochemical pathway. This resul...

    Authors: Charles C Kim and Stanley Falkow
    Citation: BMC Bioinformatics 2003 4:12
  9. The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational method...

    Authors: Ian Donaldson, Joel Martin, Berry de Bruijn, Cheryl Wolting, Vicki Lay, Brigitte Tuekam, Shudong Zhang, Berivan Baskin, Gary D Bader, Katerina Michalickova, Tony Pawson and Christopher WV Hogue
    Citation: BMC Bioinformatics 2003 4:11
  10. There are several evolutionarily unrelated and structurally dissimilar superfamilies of S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTases). A new superfamily (SPOUT) has been recently characte...

    Authors: Michal A Kurowski, Joanna M Sasin, Marcin Feder, Janusz Debski and Janusz M Bujnicki
    Citation: BMC Bioinformatics 2003 4:9
  11. Contradicting evidence has been presented in the literature concerning the effectiveness of empirical contact energies for fold recognition. Empirical contact energies are calculated on the basis of informatio...

    Authors: Marco Berrera, Henriette Molinari and Federico Fogolari
    Citation: BMC Bioinformatics 2003 4:8
  12. The analysis of complex cytogenetic databases of distinct leukaemia entities may help to detect rare recurring chromosome aberrations, minimal common regions of gains and losses, and also hot spots of genomic ...

    Authors: Jutta Bradtke, Harald Balz, Christa Fonatsch, Barbara Heinze, Anna Jauch, Brigitte Mohr, Claudia Schoch and Harald Rieder
    Citation: BMC Bioinformatics 2003 4:4
  13. Haplotype based linkage disequilibrium (LD) mapping has become a powerful and cost-effective method for performing genetic association studies, particularly in the search for genetic markers in linkage disequi...

    Authors: Peisen Zhang, Huitao Sheng, Alfredo Morabia and T Conrad Gilliam
    Citation: BMC Bioinformatics 2003 4:3
  14. Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression ...

    Authors: Konrad Büssow, Steve Hoffmann and Volker Sievert
    Citation: BMC Bioinformatics 2002 3:40
  15. An organism's ability to adapt to its particular environmental niche is of fundamental importance to its survival and proliferation. In the largest study of its kind, we sought to identify and exploit the amin...

    Authors: Michel Dumontier, Katerina Michalickova and Christopher WV Hogue
    Citation: BMC Bioinformatics 2002 3:39
  16. Robustness of mathematical models of biochemical networks is important for validation purposes and can be used as a means of selecting between different competing models. Tools for quantifying parametric robus...

    Authors: Lan Ma and Pablo A Iglesias
    Citation: BMC Bioinformatics 2002 3:38
  17. Total sequence decomposition, using the web-based MASIA tool, identifies areas of conservation in aligned protein sequences. By structurally annotating these motifs, the sequence can be parsed into individual ...

    Authors: Catherine H Schein, Numan Özgün, Tadahide Izumi and Werner Braun
    Citation: BMC Bioinformatics 2002 3:37
  18. A method to evaluate and analyze the massive data generated by series of microarray experiments is of utmost importance to reveal the hidden patterns of gene expression. Because of the complexity and the high ...

    Authors: Junbai Wang, Jan Delabie, Hans Christian Aasheim, Erlend Smeland and Ola Myklebost
    Citation: BMC Bioinformatics 2002 3:36
  19. For effective exposition of biological information, especially with regard to analysis of large-scale data types, researchers need immediate access to multiple categorical knowledge bases and need summary info...

    Authors: Mark D Robinson, Jörg Grigull, Naveed Mohammad and Timothy R Hughes
    Citation: BMC Bioinformatics 2002 3:35
  20. Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. U...

    Authors: Martin Steffen, Allegra Petti, John Aach, Patrik D'haeseleer and George Church
    Citation: BMC Bioinformatics 2002 3:34
  21. We describe the development, validation, and use of a highly redundant 120,000 oligonucleotide microarray (MuscleChip) containing 4,601 probe sets representing 1,150 known genes expressed in muscle and 2,075 E...

    Authors: Rehannah HA Borup, Stefano Toppo, Yi-Wen Chen, Tanya M Teslovich, Gerolamo Lanfranchi, Giorgio Valle and Eric P Hoffman
    Citation: BMC Bioinformatics 2002 3:33
  22. SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally...

    Authors: Katerina Michalickova, Gary D Bader, Michel Dumontier, Hao Lieu, Doron Betel, Ruth Isserlin and Christopher WV Hogue
    Citation: BMC Bioinformatics 2002 3:32
  23. Expressed sequence tags (ESTs) are single pass reads from randomly selected cDNA clones. They provide a highly cost-effective method to access and identify expressed genes. However, they are often prone to seq...

    Authors: John Parkinson, David B Guiliano and Mark Blaxter
    Citation: BMC Bioinformatics 2002 3:31
  24. Regulation of gene transcription is crucial for the function and development of all organisms. While gene prediction programs that identify protein coding sequence are used with remarkable success in the annot...

    Authors: Nikolaus Rajewsky, Massimo Vergassola, Ulrike Gaul and Eric D Siggia
    Citation: BMC Bioinformatics 2002 3:30
  25. Gene expression analyses based on complex hybridization measurements have increased rapidly in recent years and have given rise to a huge amount of bioinformatic tools such as image analyses and cluster analys...

    Authors: Christoph K Wierling, Matthias Steinfath, Thorsten Elge, Steffen Schulze-Kremer, Pia Aanstad, Matthew Clark, Hans Lehrach and Ralf Herwig
    Citation: BMC Bioinformatics 2002 3:29
  26. Identifying reliable oligonucleotide sequences for use in microarray experiments is a complex process. Two key issues are the accuracy of the input sequences and the specificity of the oligonucleotide sequences.

    Authors: Hao Chen and Burt M Sharp
    Citation: BMC Bioinformatics 2002 3:27
  27. Molecular characterization has contributed to the understanding of the inception, progression, treatment and prognosis of cancer. Nucleic acid array-based technologies extend molecular characterization of tumo...

    Authors: Michael A Gieseg, Theresa Cody, Michael Z Man, Steven J Madore, Mark A Rubin and Eric P Kaldjian
    Citation: BMC Bioinformatics 2002 3:26
  28. T-cells are key players in regulating a specific immune response. Activation of cytotoxic T-cells requires recognition of specific peptides bound to Major Histocompatibility Complex (MHC) class I molecules. MH...

    Authors: Pierre Dönnes and Arne Elofsson
    Citation: BMC Bioinformatics 2002 3:25
  29. For many years, scientists believed that point mutations in genes are the genetic switches for somatic and inherited diseases such as cystic fibrosis, phenylketonuria and cancer. Some of these mutations likely...

    Authors: Sean D Mooney and Teri E Klein
    Citation: BMC Bioinformatics 2002 3:24

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