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et al: ChEBI: a database and ontology for chemical entities of biological interest
- Nucleic Acids Res
"... biological interest ..."
C: Chemical entities of biological interest: an update
- Nucleic Acids Res
"... Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small ’ chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome-encoded ..."
Abstract
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Cited by 94 (17 self)
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Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small ’ chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome
Modeling and simulation of genetic regulatory systems: A literature review
- JOURNAL OF COMPUTATIONAL BIOLOGY
, 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
Abstract
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Cited by 738 (14 self)
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DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools
Rethinking the emotional brain
, 2012
"... ts fe o th emotion is, and how it differs from other aspects of mind and behavior, in spite of discussion and debate that dates back to emotion, since animal research is essential for identifying cally use these ‘‘feeling words’ ’ as guideposts to explore the terrain of emotion. One set of such phen ..."
Abstract
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Cited by 678 (3 self)
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or in the presence of food when hungry or drink when thirsty. These are fundamental phenomena that haveemotion. But what does this really mean? If we don’t have an agreed-upon definition of emotion that allows us to say what always interested animal behavior scientists, and would be of interest even if the terms
The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling
- BIOINFORMATICS
, 2005
"... Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all re ..."
Abstract
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Cited by 575 (5 self)
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Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all
Paml 4: Phylogenetic analysis by maximum likelihood
- Mol. Biol. Evol
, 2007
"... PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which ..."
Abstract
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Cited by 1201 (28 self)
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can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (dN and dS) between two protein-coding DNA sequences, inference of positive Darwinian selection through
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
- Nucleic Acids Res.
, 1997
"... ABSTRACT The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantia ..."
Abstract
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Cited by 8572 (88 self)
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BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
Model-Based Analysis of Oligonucleotide Arrays: Model Validation, Design Issues and Standard Error Application
, 2001
"... Background: A model-based analysis of oligonucleotide expression arrays we developed previously uses a probe-sensitivity index to capture the response characteristic of a specific probe pair and calculates model-based expression indexes (MBEI). MBEI has standard error attached to it as a measure of ..."
Abstract
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Cited by 775 (28 self)
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better ranking statistic for filtering genes. We can assign reliability indexes for genes in a specific cluster of interest in hierarchical clustering by resampling clustering trees. A software dChip implementing many of these analysis methods is made available. Conclusions: The model-based approach
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
- STATISTICA SINICA
, 2002
"... DNA microarrays are a new and promising biotechnology whichallows the monitoring of expression levels in cells for thousands of genes simultaneously. The present paper describes statistical methods for the identification of differentially expressed genes in replicated cDNA microarray experiments. A ..."
Abstract
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Cited by 438 (12 self)
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. Although it is not the main focus of the paper, new methods for the important pre-processing steps of image analysis and normalization are proposed. Given suitably normalized data, the biological question of differential expression is restated as a problem in multiple hypothesis testing: the simultaneous
Evolution of networks
- Adv. Phys
, 2002
"... We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of such a kind came into existence rece ..."
Abstract
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Cited by 419 (3 self)
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We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of such a kind came into existence
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