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  1. Modern developmental biology relies heavily on the analysis of embryonic gene expression patterns. Investigators manually inspect hundreds or thousands of expression patterns to identify those that are spatial...

    Authors: Rajalakshmi Gurunathan, Bernard Van Emden, Sethuraman Panchanathan and Sudhir Kumar
    Citation: BMC Bioinformatics 2004 5:202
    Content type: Software Published on:

  2. An increasing number of microbial genomes are being sequenced and deposited in public databases. In addition, several closely related strains are also being sequenced in order to understand the genetic basis o...

    Authors: Rohit Ghai, Torsten Hain and Trinad Chakraborty
    Citation: BMC Bioinformatics 2004 5:198
    Content type: Software Published on:

  4. It is a major challenge of computational biology to provide a comprehensive functional classification of all known proteins. Most existing methods seek recurrent patterns in known proteins based on manually-va...

    Authors: Noam Kaplan, Moriah Friedlich, Menachem Fromer and Michal Linial
    Citation: BMC Bioinformatics 2004 5:196
    Content type: Research article Published on:

  5. Gecko (Gene Expression: Computation and Knowledge Organization) is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.

    Authors: Joachim Theilhaber, Anatoly Ulyanov, Anish Malanthara, Jack Cole, Dapeng Xu, Robert Nahf, Michael Heuer, Christoph Brockel and Steven Bushnell
    Citation: BMC Bioinformatics 2004 5:195
    Content type: Software Published on:

  6. Microarray data normalization is an important step for obtaining data that are reliable and usable for subsequent analysis. One of the most commonly utilized normalization techniques is the locally weighted sc...

    Authors: John A Berger, Sampsa Hautaniemi, Anna-Kaarina Järvinen, Henrik Edgren, Sanjit K Mitra and Jaakko Astola
    Citation: BMC Bioinformatics 2004 5:194
    Content type: Methodology article Published on:

  7. Ranked gene lists from microarray experiments are usually analysed by assigning significance to predefined gene categories, e.g., based on functional annotations. Tools performing such analyses are often restrict...

    Authors: Thomas Breslin, Patrik Edén and Morten Krogh
    Citation: BMC Bioinformatics 2004 5:193
    Content type: Methodology article Published on:

  9. Expression microarrays are increasingly used to characterize environmental responses and host-parasite interactions for many different organisms. Probe selection for cDNA microarrays using expressed sequence t...

    Authors: Yian A Chen, David J Mckillen, Shuyuan Wu, Matthew J Jenny, Robert Chapman, Paul S Gross, Gregory W Warr and Jonas S Almeida
    Citation: BMC Bioinformatics 2004 5:191
    Content type: Research article Published on:

  14. The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The prot...

    Authors: Alessandro Dal Palù, Agostino Dovier and Federico Fogolari
    Citation: BMC Bioinformatics 2004 5:186
    Content type: Research article Published on:

  15. A major goal of cancer research is to identify discrete biomarkers that specifically characterize a given malignancy. These markers are useful in diagnosis, may identify potential targets for drug development,...

    Authors: Virginie M Aris, Michael J Cody, Jeff Cheng, James J Dermody, Patricia Soteropoulos, Michael Recce and Peter P Tolias
    Citation: BMC Bioinformatics 2004 5:185
    Content type: Methodology article Published on:

  16. Anatomy ontologies play an increasingly important role in developing integrated bioinformatics applications. One of the primary relationships between anatomical tissues represented in such ontologies is part-of. ...

    Authors: Albert Burger, Duncan Davidson, Yiya Yang and Richard Baldock
    Citation: BMC Bioinformatics 2004 5:184
    Content type: Research article Published on:

  19. Recent genomic and bioinformatic advances have motivated the development of numerous network models intending to describe graphs of biological, technological, and sociological origin. In most cases the success...

    Authors: Manuel Middendorf, Etay Ziv, Carter Adams, Jen Hom, Robin Koytcheff, Chaya Levovitz, Gregory Woods, Linda Chen and Chris Wiggins
    Citation: BMC Bioinformatics 2004 5:181
    Content type: Research article Published on:

  21. Public repositories of microarray data contain an incredible amount of information that is potentially relevant to explore functional relationships among genes by meta-analysis of expression profiles. However,...

    Authors: Maurizio Pellegrino, Paolo Provero, Lorenzo Silengo and Ferdinando Di Cunto
    Citation: BMC Bioinformatics 2004 5:179
    Content type: Methodology article Published on:

  22. The function of a novel gene product is typically predicted by transitive assignment of annotation from similar sequences. We describe a novel method, GOtcha, for predicting gene product function by annotation...

    Authors: David MA Martin, Matthew Berriman and Geoffrey J Barton
    Citation: BMC Bioinformatics 2004 5:178
    Content type: Methodology article Published on:

  23. Non-linearities in observed log-ratios of gene expressions, also known as intensity dependent log-ratios, can often be accounted for by global biases in the two channels being compared. Any step in a microarra...

    Authors: Henrik Bengtsson, Göran Jönsson and Johan Vallon-Christersson
    Citation: BMC Bioinformatics 2004 5:177
    Content type: Research article Published on:

  24. Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs r...

    Authors: Charu G Kumar, Richard LeDuc, George Gong, Levan Roinishivili, Harris A Lewin and Lei Liu
    Citation: BMC Bioinformatics 2004 5:176
    Content type: Software Published on:

  27. The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) in newly determined Poaceae trn L-F sequences...

    Authors: Sierra D Stoneberg Holt and Jason A Holt
    Citation: BMC Bioinformatics 2004 5:173
    Content type: Software Published on:

  28. In recent years, clustering algorithms have been effectively applied in molecular biology for gene expression data analysis. With the help of clustering algorithms such as K-means, hierarchical clustering, SOM...

    Authors: Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng and Susan J Brown
    Citation: BMC Bioinformatics 2004 5:172
    Content type: Methodology article Published on:

  31. Kernel-based learning algorithms are among the most advanced machine learning methods and have been successfully applied to a variety of sequence classification tasks within the field of bioinformatics. Conven...

    Authors: Peter Meinicke, Maike Tech, Burkhard Morgenstern and Rainer Merkl
    Citation: BMC Bioinformatics 2004 5:169
    Content type: Methodology article Published on:

  32. Motivated by a biomedical database set up by our group, we aimed to develop a generic database front-end with embedded knowledge discovery and analysis features. A major focus was the human-oriented representa...

    Authors: Dominik Seelow, Raffaello Galli, Siegrun Mebus, Hans-Peter Sperling, Hans Lehrach and Silke Sperling
    Citation: BMC Bioinformatics 2004 5:168
    Content type: Software Published on:

  34. For the purposes of finding and aligning noncoding RNA gene- and cis-regulatory elements in multiple-genome datasets, it is useful to be able to derive multi-sequence stochastic grammars (and hence multiple align...

    Authors: Ian Holmes
    Citation: BMC Bioinformatics 2004 5:166
    Content type: Methodology article Published on:

  35. While researchers have utilized versions of the Affymetrix human GeneChip® for the assessment of expression patterns in non human primate (NHP) samples, there has been no comprehensive sequence analysis study und...

    Authors: Zhining Wang, Mark G Lewis, Martin E Nau, Alma Arnold and Maryanne T Vahey
    Citation: BMC Bioinformatics 2004 5:165
    Content type: Methodology article Published on:

  36. To identify differentially expressed genes, it is standard practice to test a two-sample hypothesis for each gene with a proper adjustment for multiple testing. Such tests are essentially univariate and disreg...

    Authors: Yuanhui Xiao, Robert Frisina, Alexander Gordon, Lev Klebanov and Andrei Yakovlev
    Citation: BMC Bioinformatics 2004 5:164
    Content type: Methodology article Published on:

  37. In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge...

    Authors: Hanno Teeling, Jost Waldmann, Thierry Lombardot, Margarete Bauer and Frank Oliver Glöckner
    Citation: BMC Bioinformatics 2004 5:163
    Content type: Software Published on:

  44. Substantial amounts of data on cell signaling, metabolic, gene regulatory and other biological pathways have been accumulated in literature and electronic databases. Conventionally, this information is stored ...

    Authors: Michael Hsing, Joel L Bellenson, Conor Shankey and Artem Cherkasov
    Citation: BMC Bioinformatics 2004 5:156
    Content type: Methodology article Published on:

  46. Identifying protein-protein interactions is fundamental for understanding the molecular machinery of the cell. Proteome-wide studies of protein-protein interactions are of significant value, but the high-throu...

    Authors: Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein and Hongyu Zhao
    Citation: BMC Bioinformatics 2004 5:154
    Content type: Research article Published on:

  49. Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context.

    Authors: Ihab AB Awad, Christian A Rees, Tina Hernandez-Boussard, Catherine A Ball and Gavin Sherlock
    Citation: BMC Bioinformatics 2004 5:151
    Content type: Software Published on:

  50. The rapidly increasing number of completely sequenced genomes led to the establishment of the COG-database which, based on sequence homologies, assigns similar proteins from different organisms to clusters of ...

    Authors: Florian Meereis and Michael Kaufmann
    Citation: BMC Bioinformatics 2004 5:150
    Content type: Software Published on:

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