Topic: Algorithms

Journal: Bioinformatics (Oxford, England)

Documents

A list of abstracts that contain a topic of "Algorithms" and a journal name of "Bioinformatics (Oxford, England)".

• Urec: a System for Unrooted Reconciliation.

  PMID: 17182699

• Sgn Sim, a Stochastic Genetic Networks Simulator.

  PMID: 17267430

• The Impact of Function Perturbations in Boolean Networks.

  PMID: 17379691

• Domainsieve: a Protein Domain-based Screen That Led to the Identification of Dam-associated Genes with Potential Link to Dna Maintenance.

  PMID: 16787973

• Using Gostats to Test Gene Lists for Go Term Association.

  PMID: 17098774

• A Quantitative Model for Linking Two Disparate Sets of Articles in Medline.

  PMID: 17463015

• Cafe: a Computational Tool for the Study of Gene Family Evolution.

  PMID: 16543274

• A Simple Implementation of a Normal Mixture Approach to Differential Gene Expression in Multiclass Microarrays.

  PMID: 16632494

• Robust Smooth Segmentation Approach for Array Cgh Data Analysis.

  PMID: 17660206

• Pychem: a Multivariate Analysis Package for Python.

  PMID: 16882648

• A Novel Pattern Recognition Algorithm to Classify Membrane Protein Unfolding Pathways with High-throughput Single-molecule Force Spectroscopy.

  PMID: 17237097

• An Initial Strategy for Comparing Proteins at the Domain Architecture Level.

  PMID: 16837531

• Alibaba: Pubmed As a Graph.

  PMID: 16870931

• Adding Sequence Context to a Markov Background Model Improves the Identification of Regulatory Elements.

  PMID: 17068091

• Neural Network Prediction of Peptide Separation in Strong Anion Exchange Chromatography.

  PMID: 17092987

• Biomoby Web Services to Support Clustering of Co-regulated Genes Based on Similarity of Promoter Configurations.

  PMID: 17496321

• Refplus: an R Package Extending the Rma Algorithm.

  PMID: 17623700

• Maximum Significance Clustering of Oligonucleotide Microarrays.

  PMID: 16303800

• Motifscorer: Using a Compendium of Microarrays to Identify Regulatory Motifs.

  PMID: 17138590

• Lfm-pro: a Tool for Detecting Significant Local Structural Sites in Proteins.

  PMID: 17237050

• Multiple Alignment by Aligning Alignments.

  PMID: 17646343

• Prodistin Web Site: a Tool for the Functional Classification of Proteins from Interaction Networks.

  PMID: 16269417

• Probe-level Measurement Error Improves Accuracy in Detecting Differential Gene Expression.

  PMID: 16820429

• Inferring Pairwise Regulatory Relationships from Multiple Time Series Datasets.

  PMID: 17237067

• A Non-linear Optimization Procedure to Estimate Distances and Instantaneous Substitution Rate Matrices Under the Gtr Model.

  PMID: 16397009

• Analysis of Internal Loops Within the Rna Secondary Structure in Almost Quadratic Time.

  PMID: 16543280

• Improved Scoring of Functional Groups from Gene Expression Data by Decorrelating Go Graph Structure.

  PMID: 16606683

• Family Relationships: Should Consensus Reign?--consensus Clustering for Protein Families.

  PMID: 17237108

• A Multi-stage Approach to Clustering and Imputation of Gene Expression Profiles.

  PMID: 17308340

• Powercore: a Program Applying the Advanced M Strategy with a Heuristic Search for Establishing Core Sets.

  PMID: 17586551

• Clustering Threshold Gradient Descent Regularization: with Applications to Microarray Studies.

  PMID: 17182700

• Adaptive Torsion-angle Quasi-statics: a General Simulation Method with Applications to Protein Structure Analysis and Design.

  PMID: 17646324

• Ridom Traceedit: a Dna Trace Editor and Viewer.

  PMID: 16357036

• Ebimed--text Crunching to Gather Facts for Proteins from Medline.

  PMID: 17237098

• The Discovery of Transcriptional Modules by a Two-stage Matrix Decomposition Approach.

  PMID: 17189296

• Identifying Clusters of Functionally Related Genes in Genomes.

  PMID: 17237058

• Application of a Simple Likelihood Ratio Approximant to Protein Sequence Classification.

  PMID: 17090576

• Automatic Recognition and Annotation of Gene Expression Patterns of Fly Embryos.

  PMID: 17237064

• Assessment of Phylogenomic and Orthology Approaches for Phylogenetic Inference.

  PMID: 17237036

• Position Dependencies in Transcription Factor Binding Sites.

  PMID: 17308339

• Modeling Nonlinearity in Dilution Design Microarray Data.

  PMID: 17237040

• A Geometric Approach for the Alignment of Liquid Chromatography-mass Spectrometry Data.

  PMID: 17646306

• Nucleotide Variation of Regulatory Motifs May Lead to Distinct Expression Patterns.

  PMID: 17646329

• A Structure and Evolution-guided Monte Carlo Sequence Selection Strategy for Multiple Alignment-based Analysis of Proteins.

  PMID: 16303797

• The Sbml Ode Solver Library: a Native Api for Symbolic and Fast Numerical Analysis of Reaction Networks.

  PMID: 16527832

• Finding Novel Genes in Bacterial Communities Isolated from the Environment.

  PMID: 16873483

• Protein Classification Using Probabilistic Chain Graphs and the Gene Ontology Structure.

  PMID: 16705013

• Gel: a Novel Genotype Calling Algorithm Using Empirical Likelihood.

  PMID: 16809396

• Tesd: a Transposable Element Dynamics Simulation Environment.

  PMID: 16928734

• Identification of Conserved Protein Complexes Based on a Model of Protein Network Evolution.

  PMID: 17237088

• Protmap2d: Visualization, Comparison and Analysis of 2d Maps of Protein Structure.

  PMID: 17400727

• Sparse Non-negative Matrix Factorizations Via Alternating Non-negativity-constrained Least Squares for Microarray Data Analysis.

  PMID: 17483501

• Iptree-stab: Interpretable Decision Tree Based Method for Predicting Protein Stability Changes Upon Mutations.

  PMID: 17379687

• Family Specific Rates of Protein Evolution.

  PMID: 16510497

• Integrative Array Analyzer: a Software Package for Analysis of Cross-platform and Cross-species Microarray Data.

  PMID: 16672260

• Schism2: Creating Interactive Web Page Annotations of Molecular Structure Models Using Jmol.

  PMID: 17204464

• An Efficient, Versatile and Scalable Pattern Growth Approach to Mine Frequent Patterns in Unaligned Protein Sequences.

  PMID: 17237070

• Pquad--a Visual Analysis Platform for Proteomic Data Exploration of Microbial Organisms.

  PMID: 17483503

• Comparing Association Network Algorithms for Reverse Engineering of Large-scale Gene Regulatory Networks: Synthetic Versus Real Data.

  PMID: 17485431

• Tree Gibbs Sampler: Identifying Conserved Motifs Without Aligning Orthologous Sequences.

  PMID: 17540681

• Mining Complex Genotypic Features for Predicting Hiv-1 Drug Resistance.

  PMID: 17698858

• Assembling Millions of Short Dna Sequences Using Ssake.

  PMID: 17158514

• Msvm-rfe: Extensions of Svm-rfe for Multiclass Gene Selection on Dna Microarray Data.

  PMID: 17494773

• Orderedlist--a Bioconductor Package for Detecting Similarity in Ordered Gene Lists.

  PMID: 16844712

• Unsupervised Segmentation of Continuous Genomic Data.

  PMID: 17384021

• Robust Prediction of Consensus Secondary Structures Using Averaged Base Pairing Probability Matrices.

  PMID: 17182698

• Discovering Gene Expression Patterns in Time Course Microarray Experiments by Anova-sca.

  PMID: 17519250

• Caps: Coevolution Analysis Using Protein Sequences.

  PMID: 17005535

• Murlet: a Practical Multiple Alignment Tool for Structural Rna Sequences.

  PMID: 17459961

• Dependence Network Modeling for Biomarker Identification.

  PMID: 17077095

• Bioweka--extending the Weka Framework for Bioinformatics.

  PMID: 17237069

• De Novo Peptide Sequencing Using Ion Peak Intensity and Amino Acid Cleavage Intensity Ratio.

  PMID: 17341498

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