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  1. Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are und...

    Authors: Scott D Zuyderduyn and Steven JM Jones
    Citation: BMC Bioinformatics 2003 4:51
  2. Eval is a flexible tool for analyzing the performance of gene annotation systems. It provides summaries and graphical distributions for many descriptive statistics about any set of annotations, regardless of t...

    Authors: Evan Keibler and Michael R Brent
    Citation: BMC Bioinformatics 2003 4:50
  3. Conventionally, the first step in analyzing the large and high-dimensional data sets measured by microarrays is visual exploration. Dendrograms of hierarchical clustering, self-organizing maps (SOMs), and mult...

    Authors: Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna, Petri Törönen and Eero Castrén
    Citation: BMC Bioinformatics 2003 4:48
  4. The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is complet...

    Authors: GPS Raghava, Stephen MJ Searle, Patrick C Audley, Jonathan D Barber and Geoffrey J Barton
    Citation: BMC Bioinformatics 2003 4:47
  5. Large-scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed int...

    Authors: Dan Bolser, Panos Dafas, Richard Harrington, Jong Park and Michael Schroeder
    Citation: BMC Bioinformatics 2003 4:45
  6. For many RNA molecules, secondary structure rather than primary sequence is the evolutionarily conserved feature. No programs have yet been published that allow searching a sequence database for homologs of a ...

    Authors: Robert J Klein and Sean R Eddy
    Citation: BMC Bioinformatics 2003 4:44
  7. The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes fro...

    Authors: Roman L Tatusov, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Boris Kiryutin, Eugene V Koonin, Dmitri M Krylov, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Sergei Smirnov, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin…
    Citation: BMC Bioinformatics 2003 4:41
  8. In the last years several high-throughput cDNA sequencing projects have been funded worldwide with the aim of identifying and characterizing the structure of complete novel human transcripts. However some of t...

    Authors: Coral del Val, Karl-Heinz Glatting and Sandor Suhai
    Citation: BMC Bioinformatics 2003 4:39
  9. We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with inf...

    Authors: Sashidhar Gadiraju, Carrie A Vyhlidal, J Steven Leeder and Peter K Rogan
    Citation: BMC Bioinformatics 2003 4:38
  10. Genomic studies of complex tissues pose unique analytical challenges for assessment of data quality, performance of statistical methods used for data extraction, and detection of differentially expressed genes...

    Authors: Hanga C Galfalvy, Loubna Erraji-Benchekroun, Peggy Smyrniotopoulos, Paul Pavlidis, Steven P Ellis, J John Mann, Etienne Sibille and Victoria Arango
    Citation: BMC Bioinformatics 2003 4:37
  11. A potential benefit of profiling of tissue samples using microarrays is the generation of molecular fingerprints that will define subtypes of disease. Hierarchical clustering has been the primary analytical to...

    Authors: Mark Smolkin and Debashis Ghosh
    Citation: BMC Bioinformatics 2003 4:36
  12. The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome organization that a...

    Authors: Boris E Shakhnovich, John M Harvey, Steve Comeau, David Lorenz, Charles DeLisi and Eugene Shakhnovich
    Citation: BMC Bioinformatics 2003 4:34
  13. Microarray technology allows the monitoring of expression levels for thousands of genes simultaneously. This novel technique helps us to understand gene regulation as well as gene by gene interactions more sys...

    Authors: Taesung Park, Sung-Gon Yi, Sung-Hyun Kang, SeungYeoun Lee, Yong-Sung Lee and Richard Simon
    Citation: BMC Bioinformatics 2003 4:33
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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

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