PubRank

Tatsuya Akutsu

Author PubWeight™ 69.17‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Protein homology detection using string alignment kernels. Bioinformatics 2004 2.13
2 IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics 2011 1.59
3 KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res 2004 1.43
4 A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Sci 2005 1.38
5 Graph kernels for molecular structure-activity relationship analysis with support vector machines. J Chem Inf Model 2005 1.35
6 Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinformatics 2010 1.34
7 PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites. PLoS One 2012 1.28
8 Enumerating treelike chemical graphs with given path frequency. J Chem Inf Model 2008 1.18
9 Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies. BMC Bioinformatics 2011 1.10
10 An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks. Bioinformatics 2007 1.05
11 RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics 2010 1.04
12 Structural controllability of unidirectional bipartite networks. Sci Rep 2013 1.04
13 Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition. BMC Bioinformatics 2007 1.00
14 Algorithms for finding small attractors in Boolean networks. EURASIP J Bioinform Syst Biol 2007 1.00
15 Correlation between structure and temperature in prokaryotic metabolic networks. BMC Bioinformatics 2007 1.00
16 Breadth-first search approach to enumeration of tree-like chemical compounds. J Bioinform Comput Biol 2013 0.99
17 Efficient tree-matching methods for accurate carbohydrate database queries. Genome Inform 2003 0.97
18 A score matrix to reveal the hidden links in glycans. Bioinformatics 2004 0.96
19 Comparing biological networks via graph compression. BMC Syst Biol 2010 0.96
20 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
21 TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences. PLoS One 2012 0.95
22 Branch-and-bound algorithms for enumerating treelike chemical graphs with given path frequency using detachment-cut. J Chem Inf Model 2010 0.95
23 Optimizing substitution matrices by separating score distributions. Bioinformatics 2004 0.95
24 Optimizing amino acid substitution matrices with a local alignment kernel. BMC Bioinformatics 2006 0.94
25 Improved algorithms for enumerating tree-like chemical graphs with given path frequency. Genome Inform 2008 0.93
26 FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model. PLoS One 2012 0.92
27 Simulation study in Probabilistic Boolean Network models for genetic regulatory networks. Int J Data Min Bioinform 2007 0.92
28 HSEpred: predict half-sphere exposure from protein sequences. Bioinformatics 2008 0.92
29 Clustering of database sequences for fast homology search using upper bounds on alignment score. Genome Inform 2004 0.91
30 A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures. BMC Bioinformatics 2011 0.90
31 Prediction of RNA secondary structure with pseudoknots using integer programming. BMC Bioinformatics 2009 0.90
32 Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. Bioinformatics 2013 0.89
33 On construction of stochastic genetic networks based on gene expression sequences. Int J Neural Syst 2005 0.88
34 A mathematical model for the detection mechanism of DNA double-strand breaks depending on autophosphorylation of ATM. PLoS One 2009 0.88
35 Prodepth: predict residue depth by support vector regression approach from protein sequences only. PLoS One 2009 0.87
36 Network completion using dynamic programming and least-squares fitting. ScientificWorldJournal 2012 0.87
37 A simple method for inferring strengths of protein-protein interactions. Genome Inform 2004 0.87
38 Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology. BMC Bioinformatics 2009 0.87
39 Clustering under the line graph transformation: application to reaction network. BMC Bioinformatics 2004 0.86
40 Inferring strengths of protein-protein interactions from experimental data using linear programming. Bioinformatics 2003 0.86
41 Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. Bioinformatics 2013 0.85
42 On control of singleton attractors in multiple Boolean networks: integer programming-based method. BMC Syst Biol 2014 0.85
43 Bioinformatic approaches for predicting substrates of proteases. J Bioinform Comput Biol 2011 0.84
44 Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach. J Bioinform Comput Biol 2005 0.83
45 Conditional random field approach to prediction of protein-protein interactions using domain information. BMC Syst Biol 2011 0.82
46 Feature weight estimation for gene selection: a local hyperlinear learning approach. BMC Bioinformatics 2014 0.82
47 Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer. Genome Inform 2010 0.81
48 Origin of structural difference in metabolic networks with respect to temperature. BMC Syst Biol 2008 0.81
49 Finding optimal degenerate patterns in DNA sequences. Bioinformatics 2003 0.81
50 Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions. PLoS One 2013 0.81
51 Application of a new probabilistic model for recognizing complex patterns in glycans. Bioinformatics 2004 0.81
52 DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinformatics 2012 0.81
53 Efficient enumeration of stereoisomers of outerplanar chemical graphs using dynamic programming. J Chem Inf Model 2011 0.81
54 Compound analysis via graph kernels incorporating chirality. J Bioinform Comput Biol 2010 0.80
55 Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures. BMC Bioinformatics 2010 0.80
56 Parallelization of enumerating tree-like chemical compounds by breadth-first search order. BMC Med Genomics 2015 0.80
57 Dynamic programming algorithms and grammatical modeling for protein beta-sheet prediction. J Comput Biol 2009 0.79
58 Using binding profiles to predict binding sites of target RNAs. J Bioinform Comput Biol 2011 0.79
59 Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. Nucleic Acids Res 2012 0.78
60 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
61 Computing smallest intervention strategies for multiple metabolic networks in a boolean model. J Comput Biol 2015 0.78
62 Survival analysis by penalized regression and matrix factorization. ScientificWorldJournal 2013 0.78
63 Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features. BMC Bioinformatics 2011 0.78
64 Dynamic programming algorithms for RNA structure prediction with binding sites. Pac Symp Biocomput 2010 0.78
65 Fast and accurate database homology search using upper bounds of local alignment scores. Bioinformatics 2004 0.77
66 An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data. J Comput Biol 2014 0.77
67 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
68 Multiple methods for protein side chain packing using maximum weight cliques. Genome Inform 2006 0.77
69 Point matching under non-uniform distortions and protein side chain packing based on an efficient maximum clique algorithm. Genome Inform 2002 0.76
70 Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. Brief Bioinform 2015 0.76
71 Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso. BMC Syst Biol 2013 0.76
72 Algorithms and complexity analyses for control of singleton attractors in Boolean networks. EURASIP J Bioinform Syst Biol 2008 0.75
73 Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels. BMC Bioinformatics 2014 0.75
74 A clique-based method using dynamic programming for computing edit distance between unordered trees. J Comput Biol 2012 0.75
75 Integer programming-based approach to allocation of reporter genes for cell array analysis. Int J Bioinform Res Appl 2008 0.75
76 Identifying a Probabilistic Boolean Threshold Network From Samples. IEEE Trans Neural Netw Learn Syst 2017 0.75
77 Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs. IEEE/ACM Trans Comput Biol Bioinform 2016 0.75
78 Exact Identification of the Structure of a Probabilistic Boolean Network from Samples. IEEE/ACM Trans Comput Biol Bioinform 2015 0.75
79 Genetic regulatory networks. EURASIP J Bioinform Syst Biol 2007 0.75
80 A dynamic programming algorithm to predict synthesis processes of tree-structured compounds with graph grammar. Genome Inform 2010 0.75
81 Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs. IEEE/ACM Trans Comput Biol Bioinform 2016 0.75
82 Analysis and prediction of nutritional requirements using structural properties of metabolic networks and support vector machines. Genome Inform 2010 0.75
83 A Gibbs sampling approach to detection of tree motifs. Genome Inform 2005 0.75
84 Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. Brief Bioinform 2017 0.75
85 Protein complex prediction via improved verification methods using constrained domain-domain matching. Int J Bioinform Res Appl 2012 0.75
86 Identification of metabolic units induced by environmental signals. Bioinformatics 2006 0.75
87 Protein threading with profiles and distance constraints using clique based algorithms. J Bioinform Comput Biol 2006 0.75
88 Efficient determination of cluster boundaries for analysis of gene expression profile data using hierarchical clustering and wavelet transform. Genome Inform 2005 0.75