About: COMPUTATIONAL BIOLOGY

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Attributs	Valeurs
type	Concept
rdfs:label	COMPUTATIONAL BIOLOGY Computational Biology
skos:inScheme	http://hub.abes.fr/referentiel/ouparticlecategories
is Subject of	Problems related to the interpretation of autoradiographic data on gene expression using common constitutive transcripts as controls Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human RNAmmer: consistent and rapid annotation of ribosomal RNA genes Efficient siRNA selection using hybridization thermodynamics Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms Fine-grained annotation and classification of de novo predicted LTR retrotransposons Up-to-date catalogues of yeast protein complexes A nonlinear dynamic model of DNA with a sequence-dependent stacking term A frameshift error detection algorithm for DNA sequencing projects Codon conservation in the influenza A virus genome defines RNA packaging signals Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans Empirical comparison of ab initio repeat finding programs Topological origins of chromosomal territories Comparative DNA sequence features in two long Escherichia coli contigs A method for fast database search for all k-nucleotide repeats Dynamics of transfer RNAs analyzed by normal mode calculation A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis Organismal complexity, cell differentiation and gene expression: human over mouse Modeling DNA-binding of Escherichia coli σ70 exhibits a characteristic energy landscape around strong promoters TREMOR—a tool for retrieving transcriptional modules by incorporating motif covariance CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data High-throughput functional annotation and data mining with the Blast2GO suite MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs PROMALS3D: a tool for multiple protein sequence and structure alignments Prediction of novel microRNA genes in cancer-associated genomic regions—a combined computational and experimental approach Gains and unexpected lessons from genome-scale promoter mapping Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies Prediction of alternative RNA secondary structures based on fluctuating thermodynamic parameters The identification of complete domains within protein sequences using accurate E-values for semi-global alignment Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments A model of base-call resolution on broad-spectrum pathogen detection resequencing DNA microarrays Associating transcription factor-binding site motifs with target GO terms and target genes Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases Engineering transcription factors with novel DNA-binding specificity using comparative genomics A quality control algorithm for DNA sequencing projects Discovering active motifs in sets of related protein sequences and using them for classification Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix anaylsis of transcriptional control regions Detection of new genes in a bacterial genome using Markov models for three gene classes More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature Anatomy of Escherichia coli σ70 promoters Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach A new pheromone trail-based genetic algorithm for comparative genome assembly Phylogenetic classification of short environmental DNA fragments Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components Structural implication of splicing stochastics Stochastic noise in splicing machinery Cavities in protein-DNA and protein-RNA interfaces Importance of randomization in microarray experimental designs with Illumina platforms Multiplex primer prediction software for divergent targets PSI-BLAST pseudocounts and the minimum description length principle Structural basis for the sequence-dependent effects of platinum-DNA adducts A feature-based approach to modeling protein-protein interaction hot spots A fast word search algorithm for the representation of sequence similarity in genomic DNA Divergence in codon usage of Lactobacillus species Evolutionary rates vary among rRNA structural elements Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements Energetics of protein-DNA interactions Accuracy and application of the motif expression decomposition method in dissecting transcriptional regulation DNA supercoiling inhibits DNA knotting Identifying foldable regions in protein sequence from the hydrophobic signal Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface Using genome-wide measurements for computational prediction of SH2-peptide interactions Detection of genomic islands via segmental genome heterogeneity FIGfams: yet another set of protein families RNA structure prediction from evolutionary patterns of nucleotide composition Operon prediction in Pyrococcus furiosus Dissecting the action of an evolutionary conserved non-coding region on renin promoter activity Localizing hotspots of antisense transcription Revealing unique properties of the ribosome using a network based analysis Accurate statistical model of comparison between multiple sequence alignments Stochastic sampling of the RNA structural alignment space FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator High DNA melting temperature predicts transcription start site location in human and mouse Allegro: Analyzing expression and sequence in concert to discover regulatory programs Biological origins of long-range correlations and compositional variations in DNA ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures An adaptive, object oriented strategy for base calling in DNA sequence analysis Tandemly repeated pentanucleotides in DNA sequences of eucaryotes Automated recognition of retroviral sequences in genomic data—RetroTector© Spatial effects on the speed and reliability of protein-DNA search Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design MultiPriDe: automated batch development of quantitative real-time PCR primers The relationship between mutation rates for the (C-G) → (T-A) transition and features of T-G mispair structures in different neighbor environments, determined by free energy molecular mechanics Analysis of eukaryotic promoter sequences reveals a systematically occurring CT-signal Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions Quantitative analysis of electrophoresis data: novel curve fitting methodology and its application to the determination of a protein—DNA binding constant Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae A new systematic computational approach to predicting target genes of transcription factors Tissue-specific splicing factor gene expression signatures Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data Patterns of co-expression for protein complexes by size in Saccharomyces cerevisiae

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