Published in Genome Inform on January 01, 2005
Protein homology detection using string alignment kernels. Bioinformatics (2004) 2.13
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics (2011) 1.59
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res (2004) 1.43
A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Sci (2005) 1.38
Graph kernels for molecular structure-activity relationship analysis with support vector machines. J Chem Inf Model (2005) 1.35
Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinformatics (2010) 1.34
PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites. PLoS One (2012) 1.28
Enumerating treelike chemical graphs with given path frequency. J Chem Inf Model (2008) 1.18
Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies. BMC Bioinformatics (2011) 1.10
An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks. Bioinformatics (2007) 1.05
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics (2010) 1.04
Structural controllability of unidirectional bipartite networks. Sci Rep (2013) 1.04
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition. BMC Bioinformatics (2007) 1.00
Algorithms for finding small attractors in Boolean networks. EURASIP J Bioinform Syst Biol (2007) 1.00
Correlation between structure and temperature in prokaryotic metabolic networks. BMC Bioinformatics (2007) 1.00
Breadth-first search approach to enumeration of tree-like chemical compounds. J Bioinform Comput Biol (2013) 0.99
Efficient tree-matching methods for accurate carbohydrate database queries. Genome Inform (2003) 0.97
Comparing biological networks via graph compression. BMC Syst Biol (2010) 0.96
A score matrix to reveal the hidden links in glycans. Bioinformatics (2004) 0.96
Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming. Int J Data Min Bioinform (2013) 0.96
TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences. PLoS One (2012) 0.95
Optimizing substitution matrices by separating score distributions. Bioinformatics (2004) 0.95
Branch-and-bound algorithms for enumerating treelike chemical graphs with given path frequency using detachment-cut. J Chem Inf Model (2010) 0.95
Optimizing amino acid substitution matrices with a local alignment kernel. BMC Bioinformatics (2006) 0.94
Improved algorithms for enumerating tree-like chemical graphs with given path frequency. Genome Inform (2008) 0.93
FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model. PLoS One (2012) 0.92
HSEpred: predict half-sphere exposure from protein sequences. Bioinformatics (2008) 0.92
Simulation study in Probabilistic Boolean Network models for genetic regulatory networks. Int J Data Min Bioinform (2007) 0.92
Clustering of database sequences for fast homology search using upper bounds on alignment score. Genome Inform (2004) 0.91
Prediction of RNA secondary structure with pseudoknots using integer programming. BMC Bioinformatics (2009) 0.90
A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures. BMC Bioinformatics (2011) 0.90
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. Bioinformatics (2013) 0.89
On construction of stochastic genetic networks based on gene expression sequences. Int J Neural Syst (2005) 0.88
A mathematical model for the detection mechanism of DNA double-strand breaks depending on autophosphorylation of ATM. PLoS One (2009) 0.88
Prodepth: predict residue depth by support vector regression approach from protein sequences only. PLoS One (2009) 0.87
Network completion using dynamic programming and least-squares fitting. ScientificWorldJournal (2012) 0.87
Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology. BMC Bioinformatics (2009) 0.87
A simple method for inferring strengths of protein-protein interactions. Genome Inform (2004) 0.87
Clustering under the line graph transformation: application to reaction network. BMC Bioinformatics (2004) 0.86
Inferring strengths of protein-protein interactions from experimental data using linear programming. Bioinformatics (2003) 0.86
Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. Bioinformatics (2013) 0.85
On control of singleton attractors in multiple Boolean networks: integer programming-based method. BMC Syst Biol (2014) 0.85
Bioinformatic approaches for predicting substrates of proteases. J Bioinform Comput Biol (2011) 0.84
Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach. J Bioinform Comput Biol (2005) 0.83
Feature weight estimation for gene selection: a local hyperlinear learning approach. BMC Bioinformatics (2014) 0.82
Conditional random field approach to prediction of protein-protein interactions using domain information. BMC Syst Biol (2011) 0.82
Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer. Genome Inform (2010) 0.81
Origin of structural difference in metabolic networks with respect to temperature. BMC Syst Biol (2008) 0.81
Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions. PLoS One (2013) 0.81
Application of a new probabilistic model for recognizing complex patterns in glycans. Bioinformatics (2004) 0.81
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinformatics (2012) 0.81
Efficient enumeration of stereoisomers of outerplanar chemical graphs using dynamic programming. J Chem Inf Model (2011) 0.81
Finding optimal degenerate patterns in DNA sequences. Bioinformatics (2003) 0.81
Compound analysis via graph kernels incorporating chirality. J Bioinform Comput Biol (2010) 0.80
Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures. BMC Bioinformatics (2010) 0.80
Parallelization of enumerating tree-like chemical compounds by breadth-first search order. BMC Med Genomics (2015) 0.80
Using binding profiles to predict binding sites of target RNAs. J Bioinform Comput Biol (2011) 0.79
Dynamic programming algorithms and grammatical modeling for protein beta-sheet prediction. J Comput Biol (2009) 0.79
Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features. BMC Bioinformatics (2011) 0.78
Computing smallest intervention strategies for multiple metabolic networks in a boolean model. J Comput Biol (2015) 0.78
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. Nucleic Acids Res (2012) 0.78
Dynamic programming algorithms for RNA structure prediction with binding sites. Pac Symp Biocomput (2010) 0.78
An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins. PLoS One (2012) 0.78
Survival analysis by penalized regression and matrix factorization. ScientificWorldJournal (2013) 0.78
An improved satisfiability algorithm for nested canalyzing functions and its application to determining a singleton attractor of a Boolean network. J Comput Biol (2013) 0.77
An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data. J Comput Biol (2014) 0.77
Fast and accurate database homology search using upper bounds of local alignment scores. Bioinformatics (2004) 0.77
Multiple methods for protein side chain packing using maximum weight cliques. Genome Inform (2006) 0.77
Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. Brief Bioinform (2015) 0.76
Point matching under non-uniform distortions and protein side chain packing based on an efficient maximum clique algorithm. Genome Inform (2002) 0.76
Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso. BMC Syst Biol (2013) 0.76
Algorithms and complexity analyses for control of singleton attractors in Boolean networks. EURASIP J Bioinform Syst Biol (2008) 0.75
Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels. BMC Bioinformatics (2014) 0.75
A clique-based method using dynamic programming for computing edit distance between unordered trees. J Comput Biol (2012) 0.75
Integer programming-based approach to allocation of reporter genes for cell array analysis. Int J Bioinform Res Appl (2008) 0.75
Exact Identification of the Structure of a Probabilistic Boolean Network from Samples. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.75
Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.75
Identification of metabolic units induced by environmental signals. Bioinformatics (2006) 0.75
Protein threading with profiles and distance constraints using clique based algorithms. J Bioinform Comput Biol (2006) 0.75
A dynamic programming algorithm to predict synthesis processes of tree-structured compounds with graph grammar. Genome Inform (2010) 0.75
Analysis and prediction of nutritional requirements using structural properties of metabolic networks and support vector machines. Genome Inform (2010) 0.75
Genetic regulatory networks. EURASIP J Bioinform Syst Biol (2007) 0.75
Identifying a Probabilistic Boolean Threshold Network From Samples. IEEE Trans Neural Netw Learn Syst (2017) 0.75
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. Brief Bioinform (2017) 0.75
Protein complex prediction via improved verification methods using constrained domain-domain matching. Int J Bioinform Res Appl (2012) 0.75
Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.75
Efficient determination of cluster boundaries for analysis of gene expression profile data using hierarchical clustering and wavelet transform. Genome Inform (2005) 0.75