Masaaki Kotera

Masaaki Kotera

UNVERIFIED PROFILE

Are you Masaaki Kotera?   Register this Author

Register author
Masaaki Kotera

Masaaki Kotera

Publications by authors named "Masaaki Kotera"

Are you Masaaki Kotera?   Register this Author

41Publications

623Reads

21Profile Views

Metabolic disassembler for understanding and predicting the biosynthetic units of natural products.

BMC Bioinformatics 2019 Dec 23;20(1):728. Epub 2019 Dec 23.

Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-019-3183-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6929434PMC
December 2019

Novel Electrotopological Atomic Descriptors for the Prediction of Xenobiotic Cytochrome P450 Reactions.

Mol Inform 2019 10 12;38(10):e1900010. Epub 2019 Jun 12.

Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/minf.201900010DOI Listing
October 2019

Physicochemical Property Labels as Molecular Descriptors for Improved Analysis of Compound-Protein and Compound-Compound Networks.

Authors:
Masaaki Kotera

Methods Mol Biol 2018 ;1825:211-225

Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-8639-2_6DOI Listing
April 2019

De novo design of anticancer peptides by ensemble artificial neural networks.

J Mol Model 2019 Apr 5;25(5):112. Epub 2019 Apr 5.

Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00894-019-4007-6DOI Listing
April 2019

Network-based characterization of drug-protein interaction signatures with a space-efficient approach.

BMC Syst Biol 2019 04 5;13(Suppl 2):39. Epub 2019 Apr 5.

Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Lizuka, Fukuoka, 820-8502, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12918-019-0691-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449886PMC
April 2019

Data integration aids understanding of butterfly-host plant networks.

Sci Rep 2017 03 6;7:43368. Epub 2017 Mar 6.

School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep43368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338290PMC
March 2017

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

Sci Rep 2017 01 10;7:40164. Epub 2017 Jan 10.

Division of System Cohort, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep40164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5223214PMC
January 2017

Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis.

Biophys Physicobiol 2016 15;13:195-205. Epub 2016 Jul 15.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2142/biophysico.13.0_195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042172PMC
July 2016

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

Bioinformatics 2016 06;32(12):i278-i287

School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8550, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btw260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908344PMC
June 2016

Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

J Chem Inf Model 2016 Mar 17;56(3):510-6. Epub 2016 Feb 17.

Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jcim.5b00216DOI Listing
March 2016

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

J Chem Inf Model 2015 Dec 16;55(12):2705-16. Epub 2015 Dec 16.

Division of System Cohort, Multi-Scale Research Center for Medical Science, Medical Institute of Bioregulation, Kyushu University , 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jcim.5b00444DOI Listing
December 2015

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

Bioinformatics 2015 Jun;31(12):i161-70

Division of System Cohort, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Fukuoka 812-8582, Institute for Advanced Study, Kyushu University, Higashi-ku, Fukuoka, Fukuoka 812-8581, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012 and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btv224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765868PMC
June 2015

Benchmarking a Wide Range of Chemical Descriptors for Drug-Target Interaction Prediction Using a Chemogenomic Approach.

Mol Inform 2014 Dec 24;33(11-12):719-31. Epub 2014 Nov 24.

Division of System Cohort, Multi-scale Research Center for Medical Science, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan phone/fax:+81-92-642-6699/+81-92-642-6692.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/minf.201400066DOI Listing
December 2014

Virus proteins similar to human proteins as possible disturbance on human pathways.

Syst Synth Biol 2014 Dec 24;8(4):283-95. Epub 2014 May 24.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 Japan.

View Article

Download full-text PDF

Source
http://link.springer.com/content/pdf/10.1007%2Fs11693-014-91
Web Search
http://link.springer.com/10.1007/s11693-014-9141-y
Publisher Site
http://dx.doi.org/10.1007/s11693-014-9141-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571721PMC
December 2014

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

Nucleic Acids Res 2014 Jul 16;42(Web Server issue):W39-45. Epub 2014 May 16.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gku337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086078PMC
July 2014

Pharmacoepidemiological characterization of drug-induced adverse reaction clusters towards understanding of their mechanisms.

Comput Biol Chem 2014 Jun 24;50:50-9. Epub 2014 Jan 24.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.compbiolchem.2014.01.006DOI Listing
June 2014

WURCS: the Web3 unique representation of carbohydrate structures.

J Chem Inf Model 2014 Jun 4;54(6):1558-66. Epub 2014 Jun 4.

Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba, Ibaraki 305-8568, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci400571eDOI Listing
June 2014

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

Bioinformatics 2014 Jun;30(12):i165-74

Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan, Division of System Cohort, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan, Institute for Advanced Study, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan and Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btu265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058936PMC
June 2014

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

Comprehensive genomic analysis of sulfur-relay pathway genes.

Genome Inform 2010 ;24:104-15

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan.

View Article

Download full-text PDF

Source
January 2014

Genome-wide analysis of plant UGT family based on sequence and substrate information.

Genome Inform 2010 ;24:127-38

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
January 2014

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

Bioinformatics 2013 Jul;29(13):i135-44

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btt244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694648PMC
July 2013

Modular architecture of metabolic pathways revealed by conserved sequences of reactions.

J Chem Inf Model 2013 Mar 19;53(3):613-22. Epub 2013 Feb 19.

Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci3005379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632090PMC
March 2013

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

J Chem Inf Model 2012 Dec 4;52(12):3284-92. Epub 2012 Dec 4.

Division of System Cohort, Multi-scale Research Center for Medical Science, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci2005548DOI Listing
December 2012

Drug target prediction using adverse event report systems: a pharmacogenomic approach.

Bioinformatics 2012 Sep;28(18):i611-i618

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/bts413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436840PMC
September 2012

GENIES: gene network inference engine based on supervised analysis.

Nucleic Acids Res 2012 Jul 18;40(Web Server issue):W162-7. Epub 2012 May 18.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gks459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394336PMC
July 2012

The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals.

Methods Mol Biol 2012 ;802:19-39

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/978-1-61779-400-1_2
Publisher Site
http://dx.doi.org/10.1007/978-1-61779-400-1_2DOI Listing
April 2012

MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites.

BMC Bioinformatics 2011 Dec 14;12 Suppl 14:S1. Epub 2011 Dec 14.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
Publisher Site
http://dx.doi.org/10.1186/1471-2105-12-S14-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287465PMC
December 2011

Network-based analysis and characterization of adverse drug-drug interactions.

J Chem Inf Model 2011 Nov 11;51(11):2977-85. Epub 2011 Oct 11.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci200367wDOI Listing
November 2011

PathPred: an enzyme-catalyzed metabolic pathway prediction server.

Nucleic Acids Res 2010 Jul 30;38(Web Server issue):W138-43. Epub 2010 Apr 30.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkq318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896155PMC
July 2010

Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework.

Bioinformatics 2010 Jun;26(12):i246-54

Mines ParisTech, Centre for Computational Biology, 35 rue Saint-Honore, F-77305 Fontainebleau Cedex, Institut Curie, F-75248, INSERM U900, F-75248, Paris, France.

View Article

Download full-text PDF

Source
http://iiis.tsinghua.edu.cn/~compbio/papers/psb2014.pdf
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btq176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881361PMC
June 2010

Characterization and classification of adverse drug interactions.

Genome Inform 2010 Jan;22:167-75

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
January 2010

E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.

Bioinformatics 2009 Jun;25(12):i179-86

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btp223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687977PMC
June 2009

Eliciting possible reaction equations and metabolic pathways involving orphan metabolites.

J Chem Inf Model 2008 Dec;48(12):2335-49

School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/abs/10.1021/ci800213g
Publisher Site
http://dx.doi.org/10.1021/ci800213gDOI Listing
December 2008

Functional group and substructure searching as a tool in metabolomics.

PLoS One 2008 Feb 6;3(2):e1537. Epub 2008 Feb 6.

School of Biochemistry and Immunology, Trinity College, Dublin, Ireland.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001537PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2212108PMC
February 2008

Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions.

J Am Chem Soc 2004 Dec;126(50):16487-98

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ja0466457DOI Listing
December 2004