研究成果 2012 2017

2017
11 引用 (Scopus)

Elucidating the modes of action for bioactive compounds in a cell-specific manner by large-scale chemically-induced transcriptomics

Iwata, M., Sawada, R., Iwata, H., Kotera, M. & Yamanishi, Y., 1 10 2017, : : Scientific reports. 7, 40164.

研究成果: ジャーナルへの寄稿記事

Drug Repositioning
Cell Line
Proteins
Systems Biology
Drug Discovery
2016
4 引用 (Scopus)

GGIP: Structure and sequence-based GPCR–GPCR interaction pair predictor

Nemoto, W., Yamanishi, Y., Limviphuvadh, V., Saito, A. & Toh, H., 9 1 2016, : : Proteins: Structure, Function and Bioinformatics. 84, 9, p. 1224-1233 10 p.

研究成果: ジャーナルへの寄稿記事

G-Protein-Coupled Receptors
Oligomerization
Dimers
Biological Phenomena
ROC Curve
7 引用 (Scopus)

Scalable partial least squares regression on grammar-compressed data matrices

Tabei, Y., Saigo, H., Yamanishi, Y. & Puglisi, S. J., 8 13 2016, KDD 2016 - Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. Association for Computing Machinery, p. 1875-1884 10 p. (Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining; 巻数 13-17-August-2016).

研究成果: 著書/レポートタイプへの貢献会議での発言

Data mining
Scalability
Feature extraction
Costs
Industry
5 引用 (Scopus)

Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction

Tabei, Y., Yamanishi, Y. & Kotera, M., 6 15 2016, : : Bioinformatics. 32, 12, p. i278-i287

研究成果: ジャーナルへの寄稿記事

Metabolic Networks and Pathways
Pathway
Enzymes
Prediction
Substrate
2015
9 引用 (Scopus)

Large-Scale Prediction of Beneficial Drug Combinations Using Drug Efficacy and Target Profiles

Iwata, H., Sawada, R., Mizutani, S., Kotera, M. & Yamanishi, Y., 12 28 2015, : : Journal of Chemical Information and Modeling. 55, 12, p. 2705-2716 12 p.

研究成果: ジャーナルへの寄稿記事

Drug Combinations
drug
Pharmaceutical Preparations
Drug therapy
Computational methods
6 引用 (Scopus)

Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments

Yamanishi, Y., Tabei, Y. & Kotera, M., 6 15 2015, : : Bioinformatics. 31, 12, p. i161-i170

研究成果: ジャーナルへの寄稿記事

Metabolome
Pathway
Alignment
Metabolic Networks and Pathways
Graph in graph theory
3 引用 (Scopus)

Mining Discriminative Patterns from Graph Data with Multiple Labels and Its Application to Quantitative Structure-Activity Relationship (QSAR) Models

Shao, Z., Hirayama, Y., Yamanishi, Y. & Saigo, H., 12 28 2015, : : Journal of Chemical Information and Modeling. 55, 12, p. 2519-2527 9 p.

研究成果: ジャーナルへの寄稿記事

activity structure
Functional groups
Labels
Bioinformatics
Pharmaceutical Preparations
11 引用 (Scopus)

Predicting target proteins for drug candidate compounds based on drug-induced gene expression data in a chemical structure-independent manner

Hizukuri, Y., Sawada, R. & Yamanishi, Y., 12 18 2015, : : BMC Medical Genomics. 8, 1, 82.

研究成果: ジャーナルへの寄稿記事

Gene Expression
Phenotype
Pharmaceutical Preparations
Proteins
Benchmarking
25 引用 (Scopus)

Systematic drug repositioning for a wide range of diseases with integrative analyses of phenotypic and molecular data

Iwata, H., Sawada, R., Mizutani, S. & Yamanishi, Y., 2 23 2015, : : Journal of Chemical Information and Modeling. 55, 2, p. 446-459 14 p.

研究成果: ジャーナルへの寄稿記事

drug
Disease
Pharmaceutical Preparations
indication
Computational methods
19 引用 (Scopus)

Target-Based Drug Repositioning Using Large-Scale Chemical-Protein Interactome Data

Sawada, R., Iwata, H., Mizutani, S. & Yamanishi, Y., 12 28 2015, : : Journal of Chemical Information and Modeling. 55, 12, p. 2717-2730 14 p.

研究成果: ジャーナルへの寄稿記事

drug
Proteins
Pharmaceutical Preparations
Computational methods
indication
2014
19 引用 (Scopus)

Benchmarking a wide range of chemical descriptors for drug-target interaction prediction using a chemogenomic approach

Sawada, R., Kotera, M. & Yamanishi, Y., 11 24 2014, : : Molecular Informatics. 33, 11-12, p. 719-731 13 p.

研究成果: ジャーナルへの寄稿評論記事

Benchmarking
Drug Interactions
Proteins
Pharmaceutical Preparations
Drug interactions
56 引用 (Scopus)

DINIES: Drug-target interaction network inference engine based on supervised analysis

Yamanishi, Y., Kotera, M., Moriya, Y., Sawada, R., Kanehisa, M. & Goto, S., 7 1 2014, : : Nucleic acids research. 42, W1

研究成果: ジャーナルへの寄稿記事

Drug Interactions
Genome
Databases
Drug-Related Side Effects and Adverse Reactions
Amino Acid Sequence
8 引用 (Scopus)

Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach

Kotera, M., Tabei, Y., Yamanishi, Y., Muto, A., Moriya, Y., Tokimatsu, T. & Goto, S., 6 15 2014, : : Bioinformatics. 30, 12

研究成果: ジャーナルへの寄稿記事

Metabolome
Metabolic Networks and Pathways
Pathway
Prediction
Reaction Network
2013
4 引用 (Scopus)

Inferring chemogenomic features from drug-target interaction networks

Yamanishi, Y., 12 1 2013, : : Molecular Informatics. 32, 11-12, p. 991-999 9 p.

研究成果: ジャーナルへの寄稿評論記事

Drug Interactions
Proteins
Pharmaceutical Preparations
Ligands
Drug interactions
17 引用 (Scopus)

Inferring protein domains associated with drug side effects based on drug-target interaction network.

Iwata, H., Mizutani, S., Tabei, Y., Kotera, M., Goto, S. & Yamanishi, Y., 1 1 2013, : : BMC systems biology. 7 Suppl 6

研究成果: ジャーナルへの寄稿記事

Drug-Related Side Effects and Adverse Reactions
Drug Interactions
Drugs
Proteins
Protein
14 引用 (Scopus)

KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics

Kotera, M., Tabei, Y., Yamanishi, Y., Moriya, Y., Tokimatsu, T., Kanehisa, M. & Goto, S., 1 1 2013, : : BMC systems biology. 7, S2.

研究成果: ジャーナルへの寄稿記事

Interpretability
Bioinformatics
Substructure
Computational Biology
Prediction
56 引用 (Scopus)

KEGG OC: A large-scale automatic construction of taxonomy-based ortholog clusters

Nakaya, A., Katayama, T., Itoh, M., Hiranuka, K., Kawashima, S., Moriya, Y., Okuda, S., Tanaka, M., Tokimatsu, T., Yamanishi, Y., Yoshizawa, A. C., Kanehisa, M. & Goto, S., 1 1 2013, : : Nucleic acids research. 41, D1

研究成果: ジャーナルへの寄稿記事

Genome
Databases
Cluster Analysis
Genes
Archaea
21 引用 (Scopus)

Scalable prediction of compound-protein interactions using minwise hashing

Tabei, Y. & Yamanishi, Y., 1 1 2013, : : BMC systems biology. 7, S3.

研究成果: ジャーナルへの寄稿記事

Hashing
Proteins
Protein
Prediction
Interaction
2 引用 (Scopus)

Succinct interval-splitting tree for scalable similarity search of compound-protein pairs with property constraints

Tabei, Y., Kishimoto, A., Kotera, M. & Yamanishi, Y., 8 11 2013, KDD 2013 - 19th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. Association for Computing Machinery, 巻 Part F128815. p. 176-184 9 p. 2487637

研究成果: 著書/レポートタイプへの貢献会議での発言

Proteins
Data structures
Substrates
Drug Discovery
17 引用 (Scopus)

Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets

Kotera, M., Tabei, Y., Yamanishi, Y., Tokimatsu, T. & Goto, S., 7 1 2013, : : Bioinformatics. 29, 13

研究成果: ジャーナルへの寄稿記事

Metabolome
Metabolic Networks and Pathways
Pathway
Metabolomics
Reaction Network
2012
63 引用 (Scopus)

Drug side-effect prediction based on the integration of chemical and biological spaces

Yamanishi, Y., Pauwels, E. & Kotera, M., 12 21 2012, : : Journal of Chemical Information and Modeling. 52, 12, p. 3284-3292 9 p.

研究成果: ジャーナルへの寄稿記事

drug
Proteins
Pharmaceutical Preparations
Molecules
Public health
67 引用 (Scopus)

Drug target prediction using adverse event report systems: A pharmacogenomic approach

Takarabe, M., Kotera, M., Nishimura, Y., Goto, S. & Yamanishi, Y., 9 1 2012, : : Bioinformatics. 28, 18, bts413.

研究成果: ジャーナルへの寄稿記事

Pharmacogenetics
Drugs
Proteins
Target
Prediction
25 引用 (Scopus)

GENIES: Gene network inference engine based on supervised analysis

Kotera, M., Yamanishi, Y., Moriya, Y., Kanehisa, M. & Goto, S., 7 1 2012, : : Nucleic acids research. 40, W1

研究成果: ジャーナルへの寄稿記事

Gene Regulatory Networks
Information Services
Genes
Genome
Metabolic Networks and Pathways
44 引用 (Scopus)

Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers

Tabei, Y., Pauwels, E., Stoven, V., Takemoto, K. & Yamanishi, Y., 9 1 2012, : : Bioinformatics. 28, 18, bts412.

研究成果: ジャーナルへの寄稿記事

Drug Interactions
Drugs
Classifiers
Classifier
Proteins
12 引用 (Scopus)

Network completion using dynamic programming and least-squares fitting

Nakajima, N., Tamura, T., Yamanishi, Y., Horimoto, K. & Akutsu, T., 12 3 2012, : : The Scientific World Journal. 2012, 957620.

研究成果: ジャーナルへの寄稿記事

Least-Squares Analysis
Dynamic programming
Gene expression
Time series
gene expression
87 引用 (Scopus)

Relating drug-protein interaction network with drug side effects

Mizutani, S., Pauwels, E., Stoven, V., Goto, S. & Yamanishi, Y., 9 1 2012, : : Bioinformatics. 28, 18, bts383.

研究成果: ジャーナルへの寄稿記事

Protein Interaction Maps
Protein Interaction Networks
Drug-Related Side Effects and Adverse Reactions
Drug Interactions
Drugs