eF-site and PDBjViewer: database and viewer for protein functional sites. - Kengo Kinoshita; Haruki Nakamura (Bioinform., 2004)

P-cats: prediction of catalytic residues in proteins from their tertiary structures. - Kengo Kinoshita; Motonori Ota (Bioinform., 2005)

PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. - Yuko Tsuchiya; Kengo Kinoshita; Haruki Nakamura (Bioinform., 2005)

DBTGR: a database of tunicate promoters and their regulatory elements. - Nicolas Sierro; Takehiro Kusakabe; Keun-Joon Park; Riu Yamashita; Kengo Kinoshita; Kenta Nakai (Nucleic Acids Res., 2006)

PreBI: prediction of biological interfaces of proteins in crystals. - Yuko Tsuchiya; Kengo Kinoshita; Nobutoshi Ito; Haruki Nakamura (Nucleic Acids Res., 2006)

PrDOS: prediction of disordered protein regions from amino acid sequence. - Takashi Ishida 002; Kengo Kinoshita (Nucleic Acids Res., 2007)

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. - Kengo Kinoshita; Yoichi Murakami; Haruki Nakamura (Nucleic Acids Res., 2007)

ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. - Takeshi Obayashi; Kengo Kinoshita; Kenta Nakai; Masayuki Shibaoka; Shinpei Hayashi; Motoshi Saeki; Daisuke Shibata; Kazuki Saito; Hiroyuki Ohta (Nucleic Acids Res., 2007)

Protein structure databases with new web services for structural biology and biomedical research. - Daron M. Standley; Akira R. Kinjo; Kengo Kinoshita; Haruki Nakamura (Briefings Bioinform., 2008)

Prediction of disordered regions in proteins based on the meta approach. - Takashi Ishida 002; Kengo Kinoshita (Bioinform., 2008)

COXPRESdb: a database of coexpressed gene networks in mammals. - Takeshi Obayashi; Shinpei Hayashi; Masayuki Shibaoka; Motoshi Saeki; Hiroyuki Ohta; Kengo Kinoshita (Nucleic Acids Res., 2008)

Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. - Kengo Kinoshita; Takeshi Obayashi (Bioinform., 2009)

PiSite: a database of protein interaction sites using multiple binding states in the PDB. - Miho Higurashi; Takashi Ishida 002; Kengo Kinoshita (Nucleic Acids Res., 2009)

ATTED-II provides coexpressed gene networks for Arabidopsis. - Takeshi Obayashi; Shinpei Hayashi; Motoshi Saeki; Hiroyuki Ohta; Kengo Kinoshita (Nucleic Acids Res., 2009)

Ligand-binding site prediction of proteins based on known fragment-fragment interactions. - Kota Kasahara; Kengo Kinoshita; Toshihisa Takagi (Bioinform., 2010)

SAHG, a comprehensive database of predicted structures of all human proteins. - Chie Motono; Junichi Nakata; Ryotaro Koike; Kana Shimizu; Matsuyuki Shirota; Takayuki Amemiya; Kentaro Tomii; Nozomi Nagano; Naofumi Sakaya; Kiyotaka Misoo; Miwa Sato; Akinori Kidera; et al. (Nucleic Acids Res., 2011)

COXPRESdb: a database to compare gene coexpression in seven model animals. - Takeshi Obayashi; Kengo Kinoshita (Nucleic Acids Res., 2011)

Comprehensive Classification and Diversity Assessment of Atomic Contacts in Protein-Small Ligand Interactions. - Kota Kasahara; Matsuyuki Shirota; Kengo Kinoshita (J. Chem. Inf. Model., 2013)

COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. - Takeshi Obayashi; Yasunobu Okamura; Satoshi Ito; Shu Tadaka; Ikuko N. Motoike; Kengo Kinoshita (Nucleic Acids Res., 2013)

GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes. - Kota Kasahara; Kengo Kinoshita (BMC Bioinform., 2014)

COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems. - Yasunobu Okamura; Yuichi Aoki; Takeshi Obayashi; Shu Tadaka; Satoshi Ito; Takafumi Narise; Kengo Kinoshita (Nucleic Acids Res., 2015)

Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population. - Matsuyuki Shirota; Kengo Kinoshita (Database J. Biol. Databases Curation, 2016)

NCMine: Core-peripheral based functional module detection using near-clique mining. - Shu Tadaka; Kengo Kinoshita (Bioinform., 2016)

Security controls in an integrated Biobank to protect privacy in data sharing: rationale and study design. - Takako Takai-Igarashi; Kengo Kinoshita; Masao Nagasaki; Soichi Ogishima; Naoki Nakamura; Sachiko Nagase; Satoshi Nagaie; Tomo Saito; Fuji Nagami; Naoko Minegishi; Yoichi Suzuki; Kichiya Suzuki; et al. (BMC Medical Informatics Decis. Mak., 2017)

Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data. - Yasunobu Okamura; Kengo Kinoshita (BMC Bioinform., 2018)

De novo profile generation based on sequence context specificity with the long short-term memory network. - Kazunori D. Yamada; Kengo Kinoshita (BMC Bioinform., 2018)

jMorp: Japanese Multi Omics Reference Panel. - Shu Tadaka; Daisuke Saigusa; Ikuko N. Motoike; Jin Inoue; Yuichi Aoki; Matsuyuki Shirota; Seizo Koshiba; Masayuki Yamamoto; Kengo Kinoshita (Nucleic Acids Res., 2018)

Relationship between Dynamics of Physiological Signals and Subjective Quality of Life and Its Lifestyle Dependency. - Ryota Amano; Akihiro Karashima; Ikuko N. Motoike; Norihiro Katayama; Kengo Kinoshita; Mitsuyuki Nakao (EMBC, 2019)

COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference. - Takeshi Obayashi; Yuki Kagaya; Yuichi Aoki; Shu Tadaka; Kengo Kinoshita (Nucleic Acids Res., 2019)

Theoretical characterisation of strand cross-correlation in ChIP-seq. - Hayato Anzawa; Hitoshi Yamagata; Kengo Kinoshita (BMC Bioinform., 2020)

A genotype imputation method for de-identified haplotype reference information by using recurrent neural network. - Kaname Kojima; Shu Tadaka; Fumiki Katsuoka; Gen Tamiya; Masayuki Yamamoto; Kengo Kinoshita (PLoS Comput. Biol., 2020)

jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population. - Shu Tadaka; Eiji Hishinuma; Shohei Komaki; Ikuko N. Motoike; Junko Kawashima; Daisuke Saigusa; Jin Inoue; Jun Takayama; Yasunobu Okamura; Yuichi Aoki; Matsuyuki Shirota; Akihito Otsuki; et al. (Nucleic Acids Res., 2021)

Statistical Modeling of Subjective Sleep Quality. - Siwalee Choilek; Akihiro Karashima; Ikuko N. Motoike; Norihiro Katayama; Kengo Kinoshita; Mitsuyuki Nakao (EMBC, 2023)

COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations. - Takeshi Obayashi; Shun Kodate; Himiko Hibara; Yuki Kagaya; Kengo Kinoshita (Nucleic Acids Res., 2023)