Journal: Bioinformatics

Found 29 papers in total
Detection of potential enzyme targets by metabolic modelling and optimization: Application to a simple enzymopathy
Detection of potential enzyme targets by metabolic modelling and optimization: Application to a simple enzymopathy
2007,
A very promising approach in drug discovery involves the integration of available...
Recovering metabolic pathways via optimization
Recovering metabolic pathways via optimization
2007,
A metabolic pathway is a coherent set of enzyme catalysed biochemical reactions by...
QOMA: quasi-optimal multiple alignment of protein sequences
QOMA: quasi-optimal multiple alignment of protein sequences
2007,
We consider the problem of multiple alignment of protein sequences with the goal of...
Using dynamic programming to create isotopic distribution maps from mass spectra
Using dynamic programming to create isotopic distribution maps from mass spectra
2007,
This article presents a method to identify the isotopic distributions within a mass...
Locomotif: from graphical motif description to RNA motif search
Locomotif: from graphical motif description to RNA motif search
2007,
Motivated by the recent rise of interest in small regulatory RNAs, we present...
Markers improve clustering of CGH data
Markers improve clustering of CGH data
2007,
We consider the problem of clustering a population of Comparative Genomic...
Peak selection from MALDI-TOF mass spectra using ant colony optimization
Peak selection from MALDI-TOF mass spectra using ant colony optimization
2007,
Due to the large number of peaks in mass spectra of low-molecular-weight enriched...
Alignment of molecular networks by integer quadratic programming
Alignment of molecular networks by integer quadratic programming
2007,
With more and more data on molecular networks (e.g. protein interaction networks, gene...
HMMoC – a compiler for hidden Markov models
HMMoC – a compiler for hidden Markov models
2007,
Hidden Markov models are widely applied within computational biology. The large data...
Optimization of primer design for the detection of variable genomic lesions in cancer
Optimization of primer design for the detection of variable genomic lesions in cancer
2007,
Primer approximation multiplex PCR (PAMP) is a new experimental protocol for...
HapBlock: Haplotype block partitioning and tag single nucleotide polymorphism selection software using a set of dynamic programming algorithms
HapBlock: Haplotype block partitioning and tag single nucleotide polymorphism selection software using a set of dynamic programming algorithms
2005,
Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the...
Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms
Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms
2005,
Motivation: Protein β-sheets play a fundamental role in protein structure,...
Extracting multiple structural alignments from pairwise alignments: A comparison of a rigorous and a heuristic approach
Extracting multiple structural alignments from pairwise alignments: A comparison of a rigorous and a heuristic approach
2005,
Multiple structural alignments (MSTAs) provide position-specific information on the...
Solving and analyzing side-chain positioning problems using linear and integer programming
Solving and analyzing side-chain positioning problems using linear and integer programming
2005,
Motivation: Side-chain positioning is a central component of homology modeling and...
Evaluation of iterative alignment algorithms for multiple alignment
Evaluation of iterative alignment algorithms for multiple alignment
2005,
Motivation: Iteration has been used a number of times as an optimization method to...
A fractional programming approach to efficient DNA melting temperature calculation
A fractional programming approach to efficient DNA melting temperature calculation
2005,
Motivation: In a wide range of experimental techniques in biology, there is a need for...
A linear programming approach for identifying a consensus sequence on DNA sequences
A linear programming approach for identifying a consensus sequence on DNA sequences
2005,
Maximum-likelihood methods for solving the consensus sequence identification (CSI)...
A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes
A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes
2005,
Motivation: It is known that steady-state flux distributions in metabolic networks can...
Sight: automating genomic data-mining without programming skills
Sight: automating genomic data-mining without programming skills
2004,
We created and tested Sight, a Java-based package that provides a user-friendly...
A generalized global alignment algorithm
A generalized global alignment algorithm
2003,
Motivation: Homologous sequences are sometimes similar over some regions but different...
An efficient algorithm for minimal primer set selection
An efficient algorithm for minimal primer set selection
2003,
We have developed U-PRIMER, a primer design program, to compute a minimal primer set...
Dynamic modeling of genetic networks using genetic algorithm and S-system
Dynamic modeling of genetic networks using genetic algorithm and S-system
2003,
Motivation: The modeling of system dynamics of genetic networks, metabolic networks or...
A mathematical programming approach for gene selection and tissue classification
A mathematical programming approach for gene selection and tissue classification
2003,
Motivation: Extracting useful information from expression levels of thousands of genes...
Clustering gene expression data using a graph-theoretic approach: An application of minimum spanning trees
Clustering gene expression data using a graph-theoretic approach: An application of minimum spanning trees
2002,
Motivation: Gene expression data clustering provides a powerful tool for studying...
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