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Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework

Briefings in bioinformatics, 2021-03, Vol.22 (2), p.2126-2140

2021

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Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors

Bioinformatics, 2018-08, Vol.34 (15), p.2546-2555

2018

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

Journal of theoretical biology, 2007-02, Vol.244 (4), p.670-679

2007

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Determining the minimum number of protein-protein interactions required to support known protein complexes

PloS one, 2018-04, Vol.13 (4), p.e0195545-e0195545

2018

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Optimal string clustering based on a Laplace-like mixture and EM algorithm on a set of strings

Journal of computer and system sciences, 2019-12, Vol.106, p.94-128

2019

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

BMC bioinformatics, 2015-04, Vol.16 (1), p.128-128, Article 128

2015

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Improving prediction of heterodimeric protein complexes using combination with pairwise kernel

BMC bioinformatics, 2018-02, Vol.19 (Suppl 1), p.39-39, Article 39

2018

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Complex network-based approaches to biomarker discovery

Biomarkers in medicine, 2016-06, Vol.10 (6), p.621-632

2016

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Maximum margin classifier working in a set of strings

Proceedings of the Royal Society. A, Mathematical, physical, and engineering sciences, 2016-03, Vol.472 (2187), p.20150551-20150551

2016

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

Journal of computational biology, 2016-08, Vol.23 (8), p.625

2016

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Volume formula and growth rates of the balls of strings under the edit distances

Applied mathematics and computation, 2023-12, Vol.458, p.128202, Article 128202

2023

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

BMC bioinformatics, 2014, Vol.15 Suppl 2 (S2), p.S6-S6, Article S6

2014

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

PloS one, 2013-06, Vol.8 (6), p.e65265-e65265

2013

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Improving conditional random field model for prediction of protein-RNA residue-base contacts

Quantitative biology, 2018-06, Vol.6 (2), p.155-162

2018

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Prediction of Protein-Protein Interaction Strength Using Domain Features with Supervised Regression

TheScientificWorld, 2014-01, Vol.2014, p.240673-7

2014

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Finding Median and Center Strings for a Probability Distribution on a Set of Strings Under Levenshtein Distance Based on Integer Linear Programming

Biomedical Engineering Systems and Technologies, p.108-121

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

BMC systems biology, 2011-06, Vol.5 Suppl 1 (Suppl 1), p.S8-S8

2011

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

BMC bioinformatics, 2010-12, Vol.11 Suppl 11 (S11), p.S4-S4, Article S4

2010

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

BMC medical genomics, 2015-05, Vol.8 Suppl 2 (S2), p.S15-S15, Article S15

2015

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Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks

IEICE Transactions on Information and Systems, 2012/12/01, Vol.E95.D(12), pp.2960-2970

2012

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Comparing biological networks via graph compression

BMC systems biology, 2010-09, Vol.4 Suppl 2 (S2), p.S13-S13, Article S13

2010

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Measuring the Similarity of Protein Structures Using Image Compression Algorithms

IEICE Transactions on Information and Systems, 2011/12/01, Vol.E94.D(12), pp.2468-2478

2011

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Survival Analysis by Penalized Regression and Matrix Factorization

TheScientificWorld, 2013-01, Vol.2013, p.632030-11

2013

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Algorithms for Finding Small Attractors in Boolean Networks

EURASIP journal on bioinformatics & systems biology, 2007, Vol.2007 (1), p.20180-20180

2007

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Algorithms for Inference, Analysis and Control of Boolean Networks

Algebraic Biology, p.1-15

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Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework

Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors

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

Determining the minimum number of protein-protein interactions required to support known protein complexes

Optimal string clustering based on a Laplace-like mixture and EM algorithm on a set of strings

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

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel

Complex network-based approaches to biomarker discovery

Maximum margin classifier working in a set of strings

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

Volume formula and growth rates of the balls of strings under the edit distances

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

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

Improving conditional random field model for prediction of protein-RNA residue-base contacts

Prediction of Protein-Protein Interaction Strength Using Domain Features with Supervised Regression

Finding Median and Center Strings for a Probability Distribution on a Set of Strings Under Levenshtein Distance Based on Integer Linear Programming

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

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

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

Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks

Comparing biological networks via graph compression

Measuring the Similarity of Protein Structures Using Image Compression Algorithms

Survival Analysis by Penalized Regression and Matrix Factorization

Algorithms for Finding Small Attractors in Boolean Networks

Algorithms for Inference, Analysis and Control of Boolean Networks

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