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Items: 19

1.

Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm.

Iwata M, Yuan L, Zhao Q, Tabei Y, Berenger F, Sawada R, Akiyoshi S, Hamano M, Yamanishi Y.

Bioinformatics. 2019 Jul 15;35(14):i191-i199. doi: 10.1093/bioinformatics/btz313.

2.

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

Tabei Y, Kotera M, Sawada R, Yamanishi Y.

BMC Syst Biol. 2019 Apr 5;13(Suppl 2):39. doi: 10.1186/s12918-019-0691-1.

3.

Predicting inhibitory and activatory drug targets by chemically and genetically perturbed transcriptome signatures.

Sawada R, Iwata M, Tabei Y, Yamato H, Yamanishi Y.

Sci Rep. 2018 Jan 9;8(1):156. doi: 10.1038/s41598-017-18315-9.

4.

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

Tabei Y, Yamanishi Y, Kotera M.

Bioinformatics. 2016 Jun 15;32(12):i278-i287. doi: 10.1093/bioinformatics/btw260.

5.

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

Yamanishi Y, Tabei Y, Kotera M.

Bioinformatics. 2015 Jun 15;31(12):i161-70. doi: 10.1093/bioinformatics/btv224.

6.

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.

Bioinformatics. 2014 Jun 15;30(12):i165-74. doi: 10.1093/bioinformatics/btu265.

7.

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.

BMC Syst Biol. 2013;7 Suppl 6:S18. doi: 10.1186/1752-0509-7-S6-S18. Epub 2013 Dec 13.

8.

Scalable prediction of compound-protein interactions using minwise hashing.

Tabei Y, Yamanishi Y.

BMC Syst Biol. 2013;7 Suppl 6:S3. doi: 10.1186/1752-0509-7-S6-S3. Epub 2013 Dec 13.

9.

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.

BMC Syst Biol. 2013;7 Suppl 6:S2. doi: 10.1186/1752-0509-7-S6-S2. Epub 2013 Dec 13.

10.

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

Kotera M, Tabei Y, Yamanishi Y, Tokimatsu T, Goto S.

Bioinformatics. 2013 Jul 1;29(13):i135-44. doi: 10.1093/bioinformatics/btt244.

11.

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

Tabei Y, Pauwels E, Stoven V, Takemoto K, Yamanishi Y.

Bioinformatics. 2012 Sep 15;28(18):i487-i494. doi: 10.1093/bioinformatics/bts412.

12.

PoSSuM: a database of similar protein-ligand binding and putative pockets.

Ito J, Tabei Y, Shimizu K, Tsuda K, Tomii K.

Nucleic Acids Res. 2012 Jan;40(Database issue):D541-8. doi: 10.1093/nar/gkr1130. Epub 2011 Dec 1.

13.

PDB-scale analysis of known and putative ligand-binding sites with structural sketches.

Ito J, Tabei Y, Shimizu K, Tomii K, Tsuda K.

Proteins. 2012 Mar;80(3):747-63. doi: 10.1002/prot.23232. Epub 2011 Nov 24.

PMID:
22113700
14.

SketchSort: Fast All Pairs Similarity Search for Large Databases of Molecular Fingerprints.

Tabei Y, Tsuda K.

Mol Inform. 2011 Sep;30(9):801-7. doi: 10.1002/minf.201100050. Epub 2011 Jul 12.

PMID:
27467412
15.

A local multiple alignment method for detection of non-coding RNA sequences.

Tabei Y, Asai K.

Bioinformatics. 2009 Jun 15;25(12):1498-505. doi: 10.1093/bioinformatics/btp261. Epub 2009 Apr 17.

PMID:
19376823
16.

Software.ncrna.org: web servers for analyses of RNA sequences.

Asai K, Kiryu H, Hamada M, Tabei Y, Sato K, Matsui H, Sakakibara Y, Terai G, Mituyama T.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W75-8. doi: 10.1093/nar/gkn222. Epub 2008 Apr 25.

17.

A fast structural multiple alignment method for long RNA sequences.

Tabei Y, Kiryu H, Kin T, Asai K.

BMC Bioinformatics. 2008 Jan 23;9:33. doi: 10.1186/1471-2105-9-33.

18.

Murlet: a practical multiple alignment tool for structural RNA sequences.

Kiryu H, Tabei Y, Kin T, Asai K.

Bioinformatics. 2007 Jul 1;23(13):1588-98. Epub 2007 Apr 25.

PMID:
17459961
19.

SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments.

Tabei Y, Tsuda K, Kin T, Asai K.

Bioinformatics. 2006 Jul 15;22(14):1723-9. Epub 2006 May 11.

PMID:
16690634

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