Bioinformatics (Oxford, England)
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Relational patterns of gene expression via non-metric multidimensional scaling analysis
Bioinformatics (Oxford, England) - Tập 21 Số 6 - Trang 730-740 - 2005
Abstract Motivation: Microarray experiments result in large-scale data sets that
require extensive mining and refining to extract useful information. We
demonstrate the usefulness of (non-metric) multidimensional scaling (MDS) method
in analyzing a large number of genes. Applying MDS to the microarray data is
certainly not new, but the existing works are all on small numbers (<100) of
points to...
MissForest—non-parametric missing value imputation for mixed-type data
Bioinformatics (Oxford, England) - Tập 28 Số 1 - Trang 112-118 - 2012
Abstract Motivation: Modern data acquisition based on high-throughput technology
is often facing the problem of missing data. Algorithms commonly used in the
analysis of such large-scale data often depend on a complete set. Missing value
imputation offers a solution to this problem. However, the majority of available
imputation methods are restricted to one type of variable only: continuous or
cat...
Modelling cellular systems with PySCeS
Bioinformatics (Oxford, England) - Tập 21 Số 4 - Trang 560-561 - 2005
Abstract Summary: The Python Simulator for Cellular Systems (PySCeS) is an
extendable research tool for the numerical analysis and investigation of
cellular systems. Availability: PySCeS is distributed as Open Source Software
under the GNU General Public Licence and is available for download from
http://pysces.sourceforge.net Contact: [email protected]
PySCeSToolbox: a collection of metabolic pathway analysis tools
Bioinformatics (Oxford, England) - Tập 34 Số 1 - Trang 124-125 - 2018
Abstract Summary PySCeSToolbox is an extension to the Python Simulator for
Cellular Systems (PySCeS) that includes tools for performing generalized
supply–demand analysis, symbolic metabolic control analysis, and a framework for
investigating the kinetic and thermodynamic aspects of enzyme-catalyzed
reactions. Each tool addresses a different aspect of metabolic behaviour,
control, and regulation; ...
Multi-class protein fold recognition using support vector machines and neural networks
Bioinformatics (Oxford, England) - Tập 17 Số 4 - Trang 349-358 - 2001
Abstract Motivation: Protein fold recognition is an important approach to
structure discovery without relying on sequence similarity. We study this
approach with new multi-class classification methods and examined many issues
important for a practical recognition system. Results: Most current
discriminative methods for protein fold prediction use the one-against-others
method, which has the well-k...
Causal analysis approaches in Ingenuity Pathway Analysis
Bioinformatics (Oxford, England) - Tập 30 Số 4 - Trang 523-530 - 2014
Abstract Motivation: Prior biological knowledge greatly facilitates the
meaningful interpretation of gene-expression data. Causal networks constructed
from individual relationships curated from the literature are particularly
suited for this task, since they create mechanistic hypotheses that explain the
expression changes observed in datasets. Results: We present and discuss a suite
of algorithms...
ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers
Bioinformatics (Oxford, England) - Tập 30 Số 12 - Trang 1771-1773 - 2014
Abstract Summary: Protein–protein interactions are essential to cellular and
immune function, and in many cases, because of the absence of an experimentally
determined structure of the complex, these interactions must be modeled to
obtain an understanding of their molecular basis. We present a user-friendly
protein docking server, based on the rigid-body docking programs ZDOCK and
M-ZDOCK, to pred...
InterProSurf: a web server for predicting interacting sites on protein surfaces
Bioinformatics (Oxford, England) - Tập 23 Số 24 - Trang 3397-3399 - 2007
AbstractSummary: A new web server, InterProSurf, predicts interacting amino acid
residues in proteins that are most likely to interact with other proteins, given
the 3D structures of subunits of a protein complex. The prediction method is
based on solvent accessible surface area of residues in the isolated subunits, a
propensity scale for interface residues and a clustering algorithm to identify
s...
A multi-algorithm, multi-timescale method for cell simulation
Bioinformatics (Oxford, England) - Tập 20 Số 4 - Trang 538-546 - 2004
Abstract Motivation: Many important problems in cell biology require the dense
nonlinear interactions between functional modules to be considered. The
importance of computer simulation in understanding cellular processes is now
widely accepted, and a variety of simulation algorithms useful for studying
certain subsystems have been designed. Many of these are already widely used,
and a large number...
E-CELL: software environment for whole-cell simulation.
Bioinformatics (Oxford, England) - Tập 15 Số 1 - Trang 72-84 - 1999
Abstract MOTIVATION: Genome sequencing projects and further systematic
functional analyses of complete gene sets are producing an unprecedented mass of
molecular information for a wide range of model organisms. This provides us with
a detailed account of the cell with which we may begin to build models for
simulating intracellular molecular processes to predict the dynamic behavior of
living cells...
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