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  1. Numerous tools have been developed to align genomic sequences. However, their relative performance in specific applications remains poorly characterized. Alignments of protein-coding sequences typically have b...

    Authors: Daniel A Pollard, Casey M Bergman, Jens Stoye, Susan E Celniker and Michael B Eisen
    Citation: BMC Bioinformatics 2004 5:6
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2004 5:73

  2. To cancel experimental variations, microarray data must be normalized prior to analysis. Where an appropriate model for statistical data distribution is available, a parametric method can normalize a group of ...

    Authors: Tomokazu Konishi
    Citation: BMC Bioinformatics 2004 5:5
    Content type: Methodology article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2004 5:82

  3. Polymorphic tandem repeat typing is a new generic technology which has been proved to be very efficient for bacterial pathogens such as B. anthracis, M. tuberculosis, P. aeruginosa, L. pneumophila, Y. pestis. The...

    Authors: France Denœud and Gilles Vergnaud
    Citation: BMC Bioinformatics 2004 5:4
    Content type: Database Published on:

  4. The family of voltage-gated potassium channels comprises a functionally diverse group of membrane proteins. They help maintain and regulate the potassium ion-based component of the membrane potential and are t...

    Authors: Bin Li and Warren J Gallin
    Citation: BMC Bioinformatics 2004 5:3
    Content type: Database Published on:

  6. Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the con...

    Authors: Andrew Butterfield, Vivek Vedagiri, Edward Lang, Cath Lawrence, Matthew J Wakefield, Alexander Isaev and Gavin A Huttley
    Citation: BMC Bioinformatics 2004 5:1
    Content type: Software Published on:

  7. Genomic sequence alignment is a powerful method for genome analysis and annotation, as alignments are routinely used to identify functional sites such as genes or regulatory elements. With a growing number of ...

    Authors: Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou and Burkhard Morgenstern
    Citation: BMC Bioinformatics 2003 4:66
    Content type: Methodology article Published on:

  8. Transcription regulatory regions in higher eukaryotes are often represented by cis-regulatory modules (CRM) and are responsible for the formation of specific spatial and temporal gene expression patterns. These e...

    Authors: Anna G Nazina and Dmitri A Papatsenko
    Citation: BMC Bioinformatics 2003 4:65
    Content type: Research article Published on:

  11. With the increasing amount of data generated in molecular genetics laboratories, it is often difficult to make sense of results because of the vast number of different outcomes or variables studied. Examples i...

    Authors: Mark A Levenstien, Yaning Yang and Jürg Ott
    Citation: BMC Bioinformatics 2003 4:62
    Content type: Methodology article Published on:

  12. Molecular experiments using multiplex strategies such as cDNA microarrays or proteomic approaches generate large datasets requiring biological interpretation. Text based data mining tools have recently been de...

    Authors: Kevin G Becker, Douglas A Hosack, Glynn Dennis Jr, Richard A Lempicki, Tiffani J Bright, Chris Cheadle and Jim Engel
    Citation: BMC Bioinformatics 2003 4:61
    Content type: Software Published on:

  13. Using DNA microarrays, we have developed two novel models for tumor classification and target gene prediction. First, gene expression profiles are summarized by optimally selected Self-Organizing Maps (SOMs), ...

    Authors: Junbai Wang, Trond Hellem Bø, Inge Jonassen, Ola Myklebost and Eivind Hovig
    Citation: BMC Bioinformatics 2003 4:60
    Content type: Methodology article Published on:

  15. For many applications one wishes to decide whether a certain set of numbers originates from an equiprobability distribution or whether they are unequally distributed. Distributions of relative frequencies may ...

    Authors: Thorsten Pöschel, Cornelius Frömmel and Christoph Gille
    Citation: BMC Bioinformatics 2003 4:58
    Content type: Methodology article Published on:

  17. To date, many genomic and pathway-related tools and databases have been developed to analyze microarray data. In published web-based applications to date, however, complex pathways have been displayed with sta...

    Authors: Deyun Pan, Ning Sun, Kei-Hoi Cheung, Zhong Guan, Ligeng Ma, Matthew Holford, Xingwang Deng and Hongyu Zhao
    Citation: BMC Bioinformatics 2003 4:56
    Content type: Software Published on:

  18. The genome of the avian adenovirus Chicken Embryo Lethal Orphan (CELO) has two terminal regions without detectable homology in mammalian adenoviruses that are left without annotation in the initial analysis. S...

    Authors: Stefan Washietl and Frank Eisenhaber
    Citation: BMC Bioinformatics 2003 4:55
    Content type: Research article Published on:

  19. We describe the E-RFE method for gene ranking, which is useful for the identification of markers in the predictive classification of array data. The method supports a practical modeling scheme designed to avoi...

    Authors: Cesare Furlanello, Maria Serafini, Stefano Merler and Giuseppe Jurman
    Citation: BMC Bioinformatics 2003 4:54
    Content type: Research article Published on:

  20. The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore...

    Authors: Georgios S Vernikos, Christos G Gkogkas, Vasilis J Promponas and Stavros J Hamodrakas
    Citation: BMC Bioinformatics 2003 4:53
    Content type: Software Published on:

  22. 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
    Content type: Software Published on:

  23. 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
    Content type: Software Published on:

  25. 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
    Content type: Research article Published on:

  26. 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
    Content type: Methodology article Published on:

  28. 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
    Content type: Research article Published on:

  29. 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
    Content type: Methodology article Published on:

  32. 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
    Content type: Research article Published on:

  34. 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
    Content type: Software Published on:

  35. 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
    Content type: Software Published on:

  36. 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
    Content type: Research article Published on:

  37. 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
    Content type: Methodology article Published on:

  39. 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
    Content type: Database Published on:

  40. 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
    Content type: Research article Published on:

  45. 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
    Content type: Methodology article Published on:

  46. 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
    Content type: Methodology article Published on:

  47. 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
    Content type: Methodology article Published on:

  48. 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
    Content type: Methodology article Published on:

  50. 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
    Content type: Research article Published on:

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