Lista de obras -

A Gibbs sampling approach to detection of tree motifs.

artículo científico publicado en 2005

A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures

artículo científico publicado en 2011

A clique-based method using dynamic programming for computing edit distance between unordered trees

artículo científico publicado en 2012

A dynamic programming algorithm to predict synthesis processes of tree-structured compounds with graph grammar

artículo científico publicado el 1 de enero de 2010

A mathematical model for the detection mechanism of DNA double-strand breaks depending on autophosphorylation of ATM.

artículo científico publicado en 2009

A novel representation of protein sequences for prediction of subcellular location using support vector machines

artículo científico publicado en 2005

A score matrix to reveal the hidden links in glycans.

artículo científico publicado en 2004

A simple method for inferring strengths of protein-protein interactions.

artículo científico publicado en 2004

Algorithms and complexity analyses for control of singleton attractors in Boolean networks

artículo científico

Algorithms for finding small attractors in Boolean networks

artículo científico

An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data

artículo científico publicado en 2016

An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks

artículo científico publicado en 2007

An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data

artículo científico publicado en 2014

An improved satisfiability algorithm for nested canalyzing functions and its application to determining a singleton attractor of a Boolean network

artículo científico publicado en 2013

An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins

artículo científico publicado en 2012

Analysis and prediction of nutritional requirements using structural properties of metabolic networks and support vector machines

artículo científico publicado en 2010

Analysis of the Effect of Degree Correlation on the Size of Minimum Dominating Sets in Complex Networks

artículo científico publicado en 2016

Analysis of the impact degree distribution in metabolic networks using branching process approximation

Application of a new probabilistic model for recognizing complex patterns in glycans

artículo científico publicado en 2004

Bioinformatic approaches for predicting substrates of proteases

artículo científico publicado en 2011

Branch-and-bound algorithms for enumerating treelike chemical graphs with given path frequency using detachment-cut

artículo científico publicado en 2010

Breadth-first search approach to enumeration of tree-like chemical compounds

artículo científico publicado en 2013

Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets

artículo científico publicado en 2013

Cascleave: towards more accurate prediction of caspase substrate cleavage sites

artículo científico publicado en 2010

Clustering of database sequences for fast homology search using upper bounds on alignment score.

artículo científico publicado en 2004

Clustering under the line graph transformation: application to reaction network

artículo científico publicado en 2004

Comparing biological networks via graph compression ⬇️

artículo científico publicado el 13 de septiembre de 2010

Comparison and enumeration of chemical graphs

artículo científico publicado en 2013

Complex network-based approaches to biomarker discovery

artículo científico publicado en 2016

Compound analysis via graph kernels incorporating chirality

artículo científico publicado en 2010

Computational Methods for Modification of Metabolic Networks

artículo científico publicado en 2015

Computing smallest intervention strategies for multiple metabolic networks in a boolean model

artículo científico publicado en 2015

Conditional random field approach to prediction of protein-protein interactions using domain information

artículo científico publicado en 2011

Control of Boolean networks: hardness results and algorithms for tree structured networks

artículo científico publicado en 2006

Correlation between structure and temperature in prokaryotic metabolic networks

artículo científico publicado en 2007

Critical controllability analysis of directed biological networks using efficient graph reduction

artículo científico publicado en 2017

Critical controllability in proteome-wide protein interaction network integrating transcriptome

artículo científico publicado en 2016

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition

artículo científico publicado en 2012

Determining Associations between Human Diseases and non-coding RNAs with Critical Roles in Network Control

artículo científico publicado en 2015

Determining a singleton attractor of a boolean network with nested canalyzing functions

artículo científico publicado en 2011

Discriminative random field approach to prediction of protein residue contacts

Dynamic programming algorithms and grammatical modeling for protein beta-sheet prediction.

artículo científico publicado en 2009

Dynamic programming algorithms for RNA structure prediction with binding sites.

artículo científico publicado en 2010

Efficient determination of cluster boundaries for analysis of gene expression profile data using hierarchical clustering and wavelet transform

artículo científico publicado en 2005

Efficient enumeration of monocyclic chemical graphs with given path frequencies

artículo científico publicado en 2014

Efficient enumeration of stereoisomers of outerplanar chemical graphs using dynamic programming

artículo científico publicado en 2011

Efficient extraction of mapping rules of atoms from enzymatic reaction data

artículo científico publicado en 2004

Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs

artículo científico publicado en 2016

Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies

artículo científico publicado en 2011

Enumerating treelike chemical graphs with given path frequency

artículo científico publicado en 2008

Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach

artículo científico publicado en 2016

Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order

artículo científico publicado en 2016

Exact and heuristic methods for network completion for time-varying genetic networks

artículo científico publicado en 2014

Extensions of marginalized graph kernels

Fast and accurate database homology search using upper bounds of local alignment scores

artículo científico publicado en 2004

Feature weight estimation for gene selection: a local hyperlinear learning approach

artículo científico publicado en 2014

Finding a periodic attractor of a Boolean network

artículo científico publicado en 2012

Finding and analysing the minimum set of driver nodes required to control multilayer networks

artículo científico publicado en 2019

Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming

artículo científico publicado en 2013

Finding optimal degenerate patterns in DNA sequences

artículo científico publicado en 2003

Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks

artículo científico publicado en 2013

Genetic regulatory networks

artículo científico publicado en 2007

Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs

artículo científico publicado en 2015

Graph kernels for molecular structure-activity relationship analysis with support vector machines

artículo científico publicado en 2005

HSEpred: predict half-sphere exposure from protein sequences

artículo científico publicado en 2008

Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

artículo científico publicado en 2011

Identification of metabolic units induced by environmental signals

artículo científico publicado en 2006

Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology

artículo científico publicado en 2009

Identifying a Probabilistic Boolean Threshold Network From Samples

artículo científico publicado en 2017

Improved algorithms for enumerating tree-like chemical graphs with given path frequency.

artículo científico publicado en 2008

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel

artículo científico publicado en 2018

Inferring strengths of protein-protein interactions from experimental data using linear programming

artículo científico publicado en 2003

Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer.

artículo científico publicado en 2010

Integer programming-based method for designing synthetic metabolic networks by Minimum Reaction Insertion in a Boolean model

artículo científico publicado en 2014

Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures

artículo científico publicado en 2010

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains

artículo científico publicado en 2004

LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length

artículo científico publicado en 2016

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites

Maximum margin classifier working in a set of strings.

artículo científico publicado en 2016

Measuring Structural Robustness of Metabolic Networks under a Boolean Model Using Integer Programming and Feedback Vertex Sets

Minimum dominating set-based methods for analyzing biological networks

artículo científico publicado en 2016

Multiple methods for protein side chain packing using maximum weight cliques

artículo científico publicado en 2006

Network completion for static gene expression data

artículo científico publicado en 2014

Network completion using dynamic programming and least-squares fitting

artículo científico publicado en 2012

On construction of stochastic genetic networks based on gene expression sequences

artículo científico publicado en 2005

On control of singleton attractors in multiple Boolean networks: integer programming-based method

artículo científico publicado en 2014

Optimizing amino acid substitution matrices with a local alignment kernel

artículo científico publicado en 2006

Optimizing substitution matrices by separating score distributions

artículo científico publicado en 2004

Origin of structural difference in metabolic networks with respect to temperature

artículo científico publicado en 2008

PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework

artículo científico publicado en 2018

PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites

artículo científico publicado en 2012

Parallelization of enumerating tree-like chemical compounds by breadth-first search order

artículo científico publicado en 2015

Point matching under non-uniform distortions and protein side chain packing based on an efficient maximum clique algorithm

artículo científico publicado el 1 de enero de 2002

Predicting functional impact of single amino acid polymorphisms by integrating sequence and structural features

Predicting protein-RNA residue-base contacts using two-dimensional conditional random field

Prediction of Protein Folding Rates from Structural Topology and Complex Network Properties

Prediction of RNA secondary structure with pseudoknots using integer programming

artículo científico publicado en 2009

Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions

artículo científico publicado en 2013

Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels

Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso

artículo científico publicado en 2013

Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features

artículo científico publicado en 2011

Prodepth: predict residue depth by support vector regression approach from protein sequences only

artículo científico publicado en 2009

Protein complex prediction via improved verification methods using constrained domain-domain matching

artículo científico publicado en 2012

Protein homology detection using string alignment kernels

artículo científico publicado en 2004

Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach

artículo científico publicado en 2005

Protein threading with profiles and distance constraints using clique based algorithms

artículo científico publicado en 2006

Proteome compression via protein domain compositions

artículo científico publicado en 2014

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming

artículo científico publicado en 2010

Recent Advances in Predicting Functional Impact of Single Amino Acid Polymorphisms: A Review of Useful Features, Computational Methods and Available Tools

article

Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming

artículo científico publicado en 2012

SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems

artículo científico publicado en 2017

Selected Papers from the 16th International Conference on Bioinformatics (InCoB 2017).

artículo científico publicado en 2017

Simulation study in Probabilistic Boolean Network models for genetic regulatory networks

artículo científico publicado en 2007

Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks

artículo científico publicado en 2015

Structural controllability of unidirectional bipartite networks

artículo científico publicado en 2013

Structurally robust control of complex networks ⬇️

artículo científico publicado en 2015

Structure of n-clique networks embedded in a complex network

Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition

artículo científico publicado en 2007

Survival analysis by penalized regression and matrix factorization

artículo científico publicado en 2013

TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences

artículo científico publicado en 2012

Theoretical estimation of metabolic network robustness against multiple reaction knockouts using branching process approximation

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods

Using binding profiles to predict binding sites of target RNAs

artículo científico publicado en 2011

iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites

ncRNA-disease association prediction based on sequence information and tripartite network

artículo científico publicado en 2018

Lista de obras de

A Gibbs sampling approach to detection of tree motifs.

A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures

A clique-based method using dynamic programming for computing edit distance between unordered trees

A dynamic programming algorithm to predict synthesis processes of tree-structured compounds with graph grammar

A mathematical model for the detection mechanism of DNA double-strand breaks depending on autophosphorylation of ATM.

A novel representation of protein sequences for prediction of subcellular location using support vector machines

A score matrix to reveal the hidden links in glycans.

A simple method for inferring strengths of protein-protein interactions.

Algorithms and complexity analyses for control of singleton attractors in Boolean networks

Algorithms for finding small attractors in Boolean networks

An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data

An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks

An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data

An improved satisfiability algorithm for nested canalyzing functions and its application to determining a singleton attractor of a Boolean network

An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins

Analysis and prediction of nutritional requirements using structural properties of metabolic networks and support vector machines

Analysis of the Effect of Degree Correlation on the Size of Minimum Dominating Sets in Complex Networks

Analysis of the impact degree distribution in metabolic networks using branching process approximation

Application of a new probabilistic model for recognizing complex patterns in glycans

Bioinformatic approaches for predicting substrates of proteases

Branch-and-bound algorithms for enumerating treelike chemical graphs with given path frequency using detachment-cut

Breadth-first search approach to enumeration of tree-like chemical compounds

Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets

Cascleave: towards more accurate prediction of caspase substrate cleavage sites

Clustering of database sequences for fast homology search using upper bounds on alignment score.

Clustering under the line graph transformation: application to reaction network

Comparing biological networks via graph compression ⬇️

Comparison and enumeration of chemical graphs

Complex network-based approaches to biomarker discovery

Compound analysis via graph kernels incorporating chirality

Computational Methods for Modification of Metabolic Networks

Computing smallest intervention strategies for multiple metabolic networks in a boolean model

Conditional random field approach to prediction of protein-protein interactions using domain information

Control of Boolean networks: hardness results and algorithms for tree structured networks

Correlation between structure and temperature in prokaryotic metabolic networks

Critical controllability analysis of directed biological networks using efficient graph reduction

Critical controllability in proteome-wide protein interaction network integrating transcriptome

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition

Determining Associations between Human Diseases and non-coding RNAs with Critical Roles in Network Control

Determining a singleton attractor of a boolean network with nested canalyzing functions

Discriminative random field approach to prediction of protein residue contacts

Dynamic programming algorithms and grammatical modeling for protein beta-sheet prediction.

Dynamic programming algorithms for RNA structure prediction with binding sites.

Efficient determination of cluster boundaries for analysis of gene expression profile data using hierarchical clustering and wavelet transform

Efficient enumeration of monocyclic chemical graphs with given path frequencies

Efficient enumeration of stereoisomers of outerplanar chemical graphs using dynamic programming

Efficient extraction of mapping rules of atoms from enzymatic reaction data

Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs

Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies

Enumerating treelike chemical graphs with given path frequency

Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach

Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order

Exact and heuristic methods for network completion for time-varying genetic networks

Extensions of marginalized graph kernels

Fast and accurate database homology search using upper bounds of local alignment scores

Feature weight estimation for gene selection: a local hyperlinear learning approach

Finding a periodic attractor of a Boolean network

Finding and analysing the minimum set of driver nodes required to control multilayer networks

Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming

Finding optimal degenerate patterns in DNA sequences

Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks

Genetic regulatory networks

Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs

Graph kernels for molecular structure-activity relationship analysis with support vector machines

HSEpred: predict half-sphere exposure from protein sequences

Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

Identification of metabolic units induced by environmental signals

Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology

Identifying a Probabilistic Boolean Threshold Network From Samples

Improved algorithms for enumerating tree-like chemical graphs with given path frequency.

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel

Inferring strengths of protein-protein interactions from experimental data using linear programming

Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer.

Integer programming-based method for designing synthetic metabolic networks by Minimum Reaction Insertion in a Boolean model

Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains

LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites