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BioJava: an opensource framework for bioinformatics in 2012
 Page 10 of 11 Original article Database, Vol. 2013, Article ID bat051, doi:10.1093/database/bat051 ............................................................................................................................................................
, 2012
"... Motivation: BioJava is an opensource project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality. Results: BioJava now consists of several independent mo ..."
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Cited by 20 (3 self)
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Motivation: BioJava is an opensource project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality. Results: BioJava now consists of several independent
BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/bts494 Structural bioinformatics Advance Access publication August 9, 2012 BioJava: an opensource framework for bioinformatics in 2012
"... Motivation: BioJava is an opensource project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality. Results: BioJava now consists of several independent mo ..."
Abstract
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Motivation: BioJava is an opensource project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality. Results: BioJava now consists of several independent
Taverna: A tool for the composition and enactment of bioinformatics workflows
 Bioinformatics
, 2004
"... *To whom correspondence should be addressed. Running head: Composing and enacting workflows using Taverna Motivation: In silico experiments in bioinformatics involve the coordinated use of computational tools and information repositories. A growing number of these resources are being made available ..."
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Cited by 464 (8 self)
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examples are used to illustrate the ease by with which in silico experiments can be represented as Scufl workflows using the workbench application. Availability: The Taverna workflow system is available as open source and can be downloaded with example Scufl workflows from
A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized tTest and Statistical Inferences of Gene Changes
 Bioinformatics
, 2001
"... Motivation: DNA microarrays are now capable of providing genomewide patterns of gene expression across many different conditions. The first level of analysis of these patterns requires determining whether observed differences in expression are significant or not. Current methods are unsatisfactory ..."
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Cited by 485 (6 self)
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test or fold methods, and partly compensate for the lack of replication. Availability: The approach is implemented in a software called CyberT accessible through a Web interface at www.genomics.uci.edu/software.html. The code is available as Open Source and is written in the freely available statistical
Graphical models, exponential families, and variational inference
, 2008
"... The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fiel ..."
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Cited by 800 (26 self)
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The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical
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 ..."
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Cited by 729 (15 self)
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for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations
Application of Phylogenetic Networks in Evolutionary Studies
 SUBMITTED TO MBE 2005
, 2005
"... The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evoluti ..."
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Cited by 867 (15 self)
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both split networks and reticulate networks, how they are defined and how they can be interpreted. Additionally, the paper outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce
The Bioperl Toolkit: Perl Modules for the Life Sciences
, 2002
"... Data Type by defining how a given modul wil behave without specifying the mechanism by which it achieves this end. ..."
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Cited by 484 (11 self)
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Data Type by defining how a given modul wil behave without specifying the mechanism by which it achieves this end.
TopicSensitive PageRank
, 2002
"... In the original PageRank algorithm for improving the ranking of searchquery results, a single PageRank vector is computed, using the link structure of the Web, to capture the relative "importance" of Web pages, independent of any particular search query. To yield more accurate search resu ..."
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Cited by 535 (10 self)
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In the original PageRank algorithm for improving the ranking of searchquery results, a single PageRank vector is computed, using the link structure of the Web, to capture the relative "importance" of Web pages, independent of any particular search query. To yield more accurate search results, we propose computing a set of PageRank vectors, biased using a set of representative topics, to capture more accurately the notion of importance with respect to a particular topic. By using these (precomputed) biased PageRank vectors to generate queryspecific importance scores for pages at query time, we show that we can generate more accurate rankings than with a single, generic PageRank vector. For ordinary keyword search queries, we compute the topicsensitive PageRank scores for pages satisfying the query using the topic of the query keywords. For searches done in context (e.g., when the search query is performed by highlighting words in a Web page), we compute the topicsensitive PageRank scores using the topic of the context in which the query appeared.
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