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The consensus string problem and the complexity of comparing hidden Markov models. ⋮ Predicting protein fold pattern with functional domain and sequential evolution information ⋮ Statistical correction for functional metagenomic profiling of a microbial community with short NGS reads ⋮ Refining cellular pathway models using an ensemble of heterogeneous data sources ⋮ Automatic topography of high-dimensional data sets by non-parametric density peak clustering ⋮ On the entropy of protein families ⋮ Elman RNN based classification of proteins sequences on account of their mutual information ⋮ The first peptides: the evolutionary transition between prebiotic amino acids and early proteins ⋮ On application of directons to functional classification of genes in prokaryotes ⋮ Computation of mutual information from hidden Markov models ⋮ Discovering short linear protein motif based on selective training of profile hidden Markov models ⋮ Variational Bayes via propositionalized probability computation in PRISM ⋮ Predicting DNA binding proteins using support vector machine with hybrid fractal features ⋮ Unnamed Item ⋮ Cooperative ``folding transition in the sequence space facilitates function-driven evolution of protein families ⋮ Protein domain hierarchy Gibbs sampling strategies ⋮ Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences ⋮ Non-linear models based on simple topological indices to identify RNase III protein members ⋮ Some remarks on protein attribute prediction and pseudo amino acid composition ⋮ Mathematical basis of improved protein subfamily classification by a HMM-based sequence filter ⋮ Protein model refinement using structural fragment tessellation ⋮ Chou's pseudo amino acid composition improves sequence-based antifreeze protein prediction ⋮ Approximate symbolic pattern matching for protein sequence data ⋮ Bioinformatics. Volume II: structure, function, and applications ⋮ The EM algorithm and the rise of computational biology ⋮ Synergy of multi-label hierarchical ensembles, data fusion, and cost-sensitive methods for gene functional inference ⋮ A hyper-heuristic for the longest common subsequence problem ⋮ Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix ⋮ Gneg-mPLoc: a top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins ⋮ \textit{In silico} analysis of \textit{plasmodium falciparum} CDPK5 protein through molecular modeling, docking and dynamics ⋮ An efficient genomic signature ranking method for genomic island prediction from a single genome ⋮ Fast detection of common sequence structure patterns in RNAs ⋮ Applications of domain-domain interactions in pathway study ⋮ ECS: an automatic enzyme classifier based on functional domain composition ⋮ Neighborhood functions and hill-climbing strategies dedicated to the generalized ungapped local multiple alignment ⋮ Compressing table data with column dependency ⋮ Fast Error-Tolerant Quartet Phylogeny Algorithms ⋮ Some operations research methods for analyzing protein sequences and structures ⋮ Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis ⋮ A proteome-wide analysis of domain architectures of prokaryotic single-spanning transmembrane proteins ⋮ Construction and characterization of a rock-cluster-based EST analysis pipeline ⋮ MoDEL: an efficient strategy for ungapped local multiple alignment ⋮ The iProClass integrated database for protein functional analysis ⋮ Testing statistical hypothesis on random trees and applications to the protein classification problem ⋮ Multiple sequence alignment using the hidden Markov model trained by an improved quantum-behaved particle swarm optimization ⋮ Analyzing functional similarity of protein sequences with discrete wavelet transform ⋮ Pattern-constrained multiple polypeptide sequence alignment ⋮ Operon prediction based on SVM ⋮ A hybrid method for protein sequence modeling with improved accuracy ⋮ Fast embedding methods for clustering tens of thousands of sequences ⋮ The metabolic pH response in Lactococcus lactis: An integrative experimental and modelling approach ⋮ A matrix based algorithm for protein-protein interaction prediction using domain-domain associations ⋮ A hidden Markov model applied to the protein 3D structure analysis ⋮ Comparative protein structure modeling in genomics ⋮ Towards a comprehensive collection of diagnostic patterns for protein sequence classification ⋮ Sequence annotation with HMMs: new problems and their complexity
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