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CORR
2006
Springer
118views Education» more  CORR 2006»
13 years 11 months ago
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge s
The organization and mining of malaria genomic and post-genomic data is important to significantly increase the knowledge of the biology of its causative agents, and is motivated,...
L.-M. Birkholtz, Olivier Bastien, G. Wells, D. Gra...
BMCBI
2006
129views more  BMCBI 2006»
13 years 11 months ago
A literature-based similarity metric for biological processes
Background: Recent analyses in systems biology pursue the discovery of functional modules within the cell. Recognition of such modules requires the integrative analysis of genome-...
Monica Chagoyen, Pedro Carmona-Saez, Concha Gil, J...
BMCBI
2006
130views more  BMCBI 2006»
13 years 11 months ago
Identifying biological concepts from a protein-related corpus with a probabilistic topic model
Background: Biomedical literature, e.g., MEDLINE, contains a wealth of knowledge regarding functions of proteins. Major recurring biological concepts within such text corpora repr...
Bin Zheng, David C. McLean Jr, Xinghua Lu
BMCBI
2006
195views more  BMCBI 2006»
13 years 11 months ago
Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities
Background: Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instance...
Paul Shafer, Timothy Isganitis, Golan Yona
CN
2010
109views more  CN 2010»
13 years 11 months ago
A taxonomy of biologically inspired research in computer networking
The natural world is enormous, dynamic, incredibly diverse, and highly complex. Despite the inherent challenges of surviving in such a world, biological organisms evolve, self-org...
Michael Meisel, Vasileios Pappas, Lixia Zhang
BMCBI
2008
91views more  BMCBI 2008»
13 years 11 months ago
Presenting and exploring biological pathways with PathVisio
nd: Biological pathways are a useful abstraction of biological concepts, and software tools to deal with pathway diagrams can help biological research. PathVisio is a new visualiz...
Martijn P. van Iersel, Thomas Kelder, Alexander R....
BMCBI
2008
131views more  BMCBI 2008»
13 years 11 months ago
K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space
Background: Kernel-based classification and regression methods have been successfully applied to modelling a wide variety of biological data. The Kernel-based Orthogonal Projectio...
Max Bylesjö, Mattias Rantalainen, Jeremy K. N...
BMCBI
2008
163views more  BMCBI 2008»
13 years 11 months ago
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Background: High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpre...
Frédéric Chalmel, Michael Primig
BMCBI
2007
134views more  BMCBI 2007»
13 years 11 months ago
Nearest Neighbor Networks: clustering expression data based on gene neighborhoods
Background: The availability of microarrays measuring thousands of genes simultaneously across hundreds of biological conditions represents an opportunity to understand both indiv...
Curtis Huttenhower, Avi I. Flamholz, Jessica N. La...
BMCBI
2008
138views more  BMCBI 2008»
13 years 11 months ago
CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions
Background: Quantitative characterization of the topological characteristics of protein-protein interaction (PPI) networks can enable the elucidation of biological functional modu...
Woochang Hwang, Young-Rae Cho, Aidong Zhang, Mural...