Articles
Volume 5 (2004) - October 2004
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Software
Sierra Stoneberg Holt, Jason A Holt BMC Bioinformatics 2004, 5:173 (29 October 2004) |
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Methodology article
Incremental genetic K-means algorithm and its application in gene expression data analysis Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng, Susan J Brown BMC Bioinformatics 2004, 5:172 (28 October 2004) |
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Software
SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters Chunlin Wang, Elliot J Lefkowitz BMC Bioinformatics 2004, 5:171 (28 October 2004) |
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Research article
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences Saurabh Sinha, Mathieu Blanchette, Martin Tompa BMC Bioinformatics 2004, 5:170 (28 October 2004) An algorithm that searches for regulatory sequences combines the overrepresentation and cross-species conservation of a motif into one probablistic score.
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Methodology article
Peter Meinicke, Maike Tech, Burkhard Morgenstern, Rainer Merkl BMC Bioinformatics 2004, 5:169 (28 October 2004) |
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Software
d-matrix – database exploration, visualization and analysis Dominik Seelow, Raffaello Galli, Siegrun Mebus, Hans-Peter Sperling, Hans Lehrach, Silke Sperling BMC Bioinformatics 2004, 5:168 (28 October 2004) d-matrix, a generic database front-end, provides a powerful tool for data mining, using a new visualization strategy and a high level of interactivity.
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Software
Improvement of alignment accuracy utilizing sequentially conserved motifs Saikat Chakrabarti, Nitin Bhardwaj, Prem A Anand, Ramanathan Sowdhamini BMC Bioinformatics 2004, 5:167 (28 October 2004) |
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Methodology article
A probabilistic model for the evolution of RNA structure Ian Holmes BMC Bioinformatics 2004, 5:166 (26 October 2004) A simplified model of RNA evolution models base-pair substitutions, base-pair indels and whole-stem indels, and may form the basis of an alignment and genefinding tool.
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Methodology article
Zhining Wang, Mark G Lewis, Martin E Nau, Alma Arnold, Maryanne T Vahey BMC Bioinformatics 2004, 5:165 (26 October 2004) Probesets from the Affymetrix GeneChip(R) platforms can be useful in detecting gene expression patterns in non-human primates and even in interspecies comparisons if a conserved probeset is used and normalization applied.
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Methodology article
Multivariate search for differentially expressed gene combinations Yuanhui Xiao, Robert Frisina, Alexander Gordon, Lev Klebanov, Andrei Yakovlev BMC Bioinformatics 2004, 5:164 (26 October 2004) |
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Software
Hanno Teeling, Jost Waldmann, Thierry Lombardot, Margarete Bauer, Frank Glöckner BMC Bioinformatics 2004, 5:163 (26 October 2004) |
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Software
Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing Andreas M Boehm, Robert P Galvin, Albert Sickmann BMC Bioinformatics 2004, 5:162 (26 October 2004) |
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Research article
Implications for domain fusion protein-protein interactions based on structural information Jer-Ming Chia, Prasanna R Kolatkar BMC Bioinformatics 2004, 5:161 (26 October 2004) |
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Methodology article
Reuse of imputed data in microarray analysis increases imputation efficiency Ki-Yeol Kim, Byoung-Jin Kim, Gwan-Su Yi BMC Bioinformatics 2004, 5:160 (26 October 2004) |
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Research article
Combining gene expression data from different generations of oligonucleotide arrays Kyu-Baek Hwang, Sek Kong, Steve A Greenberg, Peter J Park BMC Bioinformatics 2004, 5:159 (25 October 2004) |
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Research article
Yin Liu, Hongyu Zhao BMC Bioinformatics 2004, 5:158 (25 October 2004) |
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Methodology article
Andrew F Neuwald, Jun S Liu BMC Bioinformatics 2004, 5:157 (25 October 2004) |
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Methodology article
Modeling of cell signaling pathways in macrophages by semantic networks Michael Hsing, Joel L Bellenson, Conor Shankey, Artem Cherkasov BMC Bioinformatics 2004, 5:156 (19 October 2004) |
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Research article
PASBio: predicate-argument structures for event extraction in molecular biology Tuangthong Wattarujeekrit, Parantu K Shah, Nigel Collier BMC Bioinformatics 2004, 5:155 (19 October 2004) |
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Research article
Information assessment on predicting protein-protein interactions Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao BMC Bioinformatics 2004, 5:154 (18 October 2004) |
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Research article
Gareth Williams, Patrick Doherty BMC Bioinformatics 2004, 5:153 (18 October 2004) |
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Methodology article
Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE) Sergey V Anisimov, Alexei A Sharov BMC Bioinformatics 2004, 5:152 (18 October 2004) |
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Software
Caryoscope: An Open Source Java application for viewing microarray data in a genomic context Ihab AB Awad, Christian A Rees, Tina Hernandez-Boussard, Catherine A Ball, Gavin Sherlock BMC Bioinformatics 2004, 5:151 (15 October 2004) |
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Software
Florian Meereis, Michael Kaufmann BMC Bioinformatics 2004, 5:150 (15 October 2004) |
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Methodology article
Improved hit criteria for DNA local alignment Laurent Noé, Gregory Kucherov BMC Bioinformatics 2004, 5:149 (14 October 2004) |
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Methodology article
Dietmar E Martin, Philippe Demougin, Michael N Hall, Michel Bellis BMC Bioinformatics 2004, 5:148 (11 October 2004) |
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Research article
Content-rich biological network constructed by mining PubMed abstracts Hao Chen, Burt M Sharp BMC Bioinformatics 2004, 5:147 (8 October 2004) Chilibot, a new data-mining tool using natural language processing, extracts gene and protein interaction information from the PubMed database and presents them in a context-rich graphical format.
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Software
Tools for loading MEDLINE into a local relational database Diane E Oliver, Gaurav Bhalotia, Ariel S Schwartz, Russ B Altman, Marti A Hearst BMC Bioinformatics 2004, 5:146 (7 October 2004) |
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Research article
Extending the mutual information measure to rank inferred literature relationships Jonathan D Wren BMC Bioinformatics 2004, 5:145 (7 October 2004) An extension to the Mutual Information Measure (MIM) improves the accuracy of identifying functionally significant relationships among MEDLINE records.
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Research article
Overdispersed logistic regression for SAGE: Modelling multiple groups and covariates Keith A Baggerly, Li Deng, Jeffrey S Morris, C Marcelo Aldaz BMC Bioinformatics 2004, 5:144 (6 October 2004) |
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Software
Céline Keime, Francesca Damiola, Dominique Mouchiroud, Laurent Duret, Olivier Gandrillon BMC Bioinformatics 2004, 5:143 (6 October 2004) |
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Software
ArrayD: A general purpose software for Microarray design Anu Sharma, Gyan Srivastava, Vineet K Sharma, Srinivasan Ramachandran BMC Bioinformatics 2004, 5:142 (2 October 2004) |
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Software
GeneXplorer: an interactive web application for microarray data visualization and analysis Christian A Rees, Janos Demeter, John C Matese, David Botstein, Gavin Sherlock BMC Bioinformatics 2004, 5:141 (1 October 2004) |
