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※ ゲノム機能情報研究グループは、人工知能研究センター インテリジェントバイオインフォマティクス研究チーム へ異動となりました。(2016年4月1日付)
ゲノム機能情報研究グループ [ 所在地:臨海副都心センター ] 

ゲノム機能情報研究グループがこれまでに発表した、論文の発行年月、タイトル、著者、掲載誌等の一覧です。

原著論文

2016


COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples
Yamagata K, Yamanishi A, Kokubu C, Takeda J, Sese J
Nucleic Acids Res. 2016 May 5;44(8):e78

2015


Molecular architecture of the active mitochondrial protein gate
Shiota T, Imai K, Qiu J, Hewitt VL, Tan K, Shen H, Sakiyama N, Fukasawa Y, Hayat S, Kamiya M, Elofsson A, Tomii K, Horton P, Wiedemann N, Pfanner N, Lithgow T, Endo T
Science. 2015 Sep 25;349(6255):1544-8
Conservation of structure and function in vertebrate c-FLIP proteins despite rapid evolutionary change
Sakamaki K, Iwabe N, Iwata H, Imai K, Takagi C, Chiba K, Shukunami C, Tomii K, Ueno N
Biochem Biophys Rep. 2015 Sep;3:175-89
A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein
Kakisaka M, Sasaki Y, Yamada K, Kondoh Y, Hikono H, Osada H, Tomii K, Saito T, Aida Y
PLoS Pathog. 2015 Jul 29;11(7):e1005062
A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR
Goda N, Shimizu K, Kuwahara Y, Tenno T, Noguchi T, Ikegami T, Ota M, Hiroaki H
Int J Mol Sci. 2015 Jul 10;16(7):15743-60
Evolutionary analyses of caspase-8 and its paralogs: Deep origins of the apoptotic signaling pathways
Sakamaki K, Imai K, Tomii K, Miller DJ
Bioessays. 2015 Jul;37(7):767-76
Key challenges for the creation and maintenance of specialist protein resources
Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A
Proteins. 2015 Jun;83(6):1005-13
Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae)
Tedder A, Helling M, Pannell JR, Shimizu-Inatsugi R, Kawagoe T, van Campen J, Sese J, Shimizu KK
Ann Bot. 2015 Apr;115(5):763-76
MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites
Fukasawa Y, Tsuji J, Fu SC, Tomii K, Horton P, Imai K
Mol Cell Proteomics. 2015 Apr;14(4):1113-26
Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens
Tsukui T, Nagano N, Umemura M, Kumagai T, Terai G, Machida M, Asai K
Bioinformatics. 2015 Apr 1;31(7):981-5
A Novel Mitosomal β-Barrel Outer Membrane Protein in Entamoeba
Santos HJ, Imai K, Makiuchi T, Tomii K, Horton P, Nozawa A, Ibrahim M, Tozawa Y, Nozaki T
Sci Rep. 2015 Feb 25;5:8545
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs
Ito J, Ikeda K, Yamada K, Mizuguchi K, Tomii K
Nucleic Acids Res. 2015 Jan 28;43(D1):D392-8
EzCatDB: the enzyme reaction database, 2015 update
Nagano N, Nakayama N, Ikeda K, Fukuie M, Yokota K, Doi T, Kato T, Tomii K
Nucleic Acids Res. 2015 Jan 28;43(D1):D453-8
Privacy-preserving search for chemical compound databases
Shimizu K, Nuida K, Arai H, Mitsunari S, Attrapadung N, Hamada M, Tsuda K, Hirokawa T, Sakuma J, Hanaoka G, Asai K
BMC Bioinformatics. 2015;16 Suppl 18:S6

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2014


The Apoptotic Initiator Caspase-8: Its Functional Ubiquity and Genetic Diversity during Animal Evolution
Sakamaki K, Shimizu K, Iwata H, Imai K, Satou Y, Funayama N, Nozaki M, Yajima M, Nishimura O, Higuchi M, Chiba K, Yoshimoto M, Kimura H, Gracey AY, Shimizu T, Tomii K, Gotoh O, Akasaka K, Sawasaki T, Miller DJ
Mol Biol Evol. 2014 Dec;31(12):3282-301
Simulation and estimation of gene number in a biological pathway using almost complete
saturation mutagenesis screening of haploid mouse cells
Tokunaga M, Kokubu C, Maeda Y, Sese J, Horie K, Sugimoto N, Kinoshita T, Yusa K, Takeda J
BMC Genomics. 2014 Nov 24;15:1016
ScreenCap3: Improving prediction of caspase-3 cleavage sites using experimentally verified noncleavage sites
Fu SC, Imai K, Sawasaki T, Tomii K
Proteomics. 2014 Sep;14(17-18):2042-6
Reference-free prediction of rearrangement breakpoint reads
Wijaya E, Shimizu K, Asai K, Hamada M
Bioinformatics. 2014 Sep 15;30(18):2559-67
Least-squares independence regression for non-linear causal inference under non-Gaussian noise
Yamada M, Sugiyama M, Sese J
Machine Learning. 2014 Sep;96(3):249-67
Ligand heterogeneity of the cysteine protease binding protein family in the parasitic protist Entamoeba histolytica
Marumo K, Nakada-Tsukui K, Tomii K, Nozaki T
Int J Parasitol. 2014 Aug;44(9):625-35
Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus
Umemura M, Nagano N, Koike H, Kawano J, Ishii T, Miyamura Y, Kikuchi M, Tamano K, Yu J, Shin-ya K, Machida M
Fungal Genet Biol. 2014 Jul;68:23-30
Parallelization of Extracting Connected Subgraphs with Common Itemsets
Okuno S, Hiraishi T, Nakashima H, Yasugi M, Sese J
IPSJ Transactions on Programming. 2014 Jul 14;7(3):22-39
Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment
Gotoh O, Morita M, Nelson DR
BMC Bioinformatics. 2014 Jun 14;15:189
Sexual dimorphism and courtship behavior in Drosophila prolongata
Setoguchi S, Takamori H, Aotsuka T, Sese J, Ishikawa Y, Matsuo T
J Ethol. 2014 May;32(2):91-102
Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis
Akama S, Shimizu-Inatsugi R, Shimizu KK, Sese J
Nucleic Acids Res. 2014 Apr;42(6):e46
Revisiting amino acid substitution matrices for identifying distantly related proteins
Yamada K, Tomii K
Bioinformatics. 2014 Feb 1;30(3):317-25
Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests
Nagao C, Nagano N, Mizuguchi K
PLoS One. 2014 Jan 8;9(1):e84623

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2013


MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data
Umemura M, Koike H, Nagano N, Ishii T, Kawano J, Yamane N, Kozone I, Horimoto K, Shin-ya K, Asai K, Yu J, Bennett JW, Machida M
PLoS One. 2013 Dec 31;8(12):e84028
Statistical significance of combinatorial regulations
Terada A, Okada-Hatakeyama M, Tsuda K, Sese J
Proc Natl Acad Sci USA. 2013 Aug 6;110(32):12996-3001
Tam41 Is a CDP-Diacylglycerol Synthase Required for Cardiolipin Biosynthesis in Mitochondria
Tamura Y, Harada Y, Nishikawa S, Yamano K, Kamiya M, Shiota T, Kuroda T, Kuge O, Sesaki H, Imai K, Tomii K, Endo T
Cell Metab. 2013 May 7;17(5):709-18
Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus
Ogura A, Yoshida M, Moritaki T, Okuda Y, Sese J, Shimizu KK, Sousounis K, Tsonis PA
Sci Rep. 2013 Mar 12;3:1432
RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics
Izawa A, Sese J
Source Code Biol Med. 2013 Feb 26;8(1):6
CENP-T provides a structural platform for outer kinetochore assembly
Nishino T, Rago F, Hori T, Tomii K, Cheeseman IM, Fukagawa T
EMBO J. 2013 Feb 6;32(3):424-36
Identification of Cargo Proteins Specific for the Nucleocytoplasmic Transport Carrier Transportin by Combination of an in Vitro Transport System and Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-based Quantitative Proteomics
Kimura M, Kose S, Okumura N, Imai K, Furuta M, Sakiyama N, Tomii K, Horton P, Takao T, Imamoto N
Mol Cell Proteomics. 2013 Jan;12(1):145-57

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2012


Genome-Wide DNA Methylation and Gene Expression Analyses of Monozygotic Twins Discordant for Intelligence Levels
Yu CC, Furukawa M, Kobayashi K, Shikishima C, Cha PC, Sese J, Sugawara H, Iwamoto K, Kato T, Ando J, Toda T
PLoS One. 2012 Oct 17;7(10):e47081
Mammalian NUMT insertion is non-random
Tsuji J, Frith MC, Tomii K, Horton P
Nucleic Acids Res. 2012 Oct;40(18):9073-88
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
Convergent evolution in structural elements of proteins investigated using cross profile analysis
Tomii K, Sawada Y, Honda S

BMC Bioinformatics. 2012 Jan 16;13:11
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

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総説、その他


On Limitations and Alternatives of Privacy-Preserving Cryptographic Protocols for Genomic Data
Teruya T, Nuida K, Shimizu K, Hanaoka G
Advances in Information and Computer Security, LNCS 2015;9241:242-61
(Proceedings of The 10th International Workshop on Security (IWSEC 2015), Nara, Japan, Aug 26-28, 2015)
遠縁タンパク質検索に適した新規アミノ酸置換行列
山田 和範、富井 健太郎
生物物理、2015 May 25;55(3-通巻319):133-6、(一社)日本生物物理学会
糸状菌におけるリボソームペプチド生合成経路の発見:新規糸状菌二次代謝経路の発見と展望
梅村 舞子、長野 希美
化学と生物、2015 Apr 20;53(5):273-6、(公社)日本農芸化学会
PoSSuM: ポケット類似性情報に基づく合理的薬剤設計支援に向けて [PDF: 6.2MB]
池田 和由、富井 健太郎
SAR News、2015 Apr 14;28:14-20、(公社)日本薬学会構造活性相関部会
ゲノムプライバシ保護を考慮した紛失通信プロトコル
照屋 唯紀、縫田 光司、清水 佳奈、花岡 悟一郎
2015年(第32回)暗号と情報セキュリティシンポジウム (SCIS 2015)、2015 Jan 20;暗号プロトコル(2) 1E2-1、(一社)電子情報通信学会 (Proceedings)
A Fast Method of Statistical Assessment for Combinatorial Hypotheses Based on Frequent Itemset Enumeration
Minato S, Uno T, Tsuda K, Terada A, Sese J
Machine Learning and Knowledge Discovery in Databases Part II, LNCS 2014;8725:422-36
(Proceedings of The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases(ECML PKDD 2014), Nancy, France, September 15-19, 2014)
POODLE: Tools Predicting Intrinsically Disordered Regions of Amino Acid Sequence
Shimizu K
Protein Structure Prediction, Methods Mol Biol. 2014 Mar 19;1137:131-45
Fast Westfall-Young permutation procedure for combinatorial regulation discovery
Terada A, Tsuda K, Sese J
BIBM2013. 2013 Dec:153-8
(Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shanghai, China, December 18-21, 2013)
Bonferroni correction hides significant motif combinations
Terada A, Sese J
BIBE2013. 2013 Nov:1-4
(Proceedings of the 13th IEEE International Conference on BioInformatics and BioEngineering, Chania, Greece, November 10-13, 2013)
クロスプロファイル解析において同定されたタンパク質セグメントの収斂進化
富井 健太郎、本田 真也
生物物理、2013 Mar 25;53(2):101-2、(一社)日本生物物理学会
Localization Prediction and Structure-Based In Silico Analysis of Bacterial Proteins: With Emphasis on Outer Membrane Proteins
Imai K, Hayat S, Sakiyama N, Fujita N, Tomii K, Elofsson A, Horton P
Data Mining for Systems Biology, Methods Mol Biol. 2012 Nov 29;939:115-40
Pattern Recognition in Bioinformatics
Shibuya T, Kashima H, Sese J, Ahmad S (Eds.)
LNCS 2012;7632
(Proceedings of the 7th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB2012), Tokyo, Japan, November 8-10, 2012)
加法準同型暗号を用いた化合物データベースの秘匿検索プロトコル
縫田 光司、清水 佳奈、荒井 ひろみ、浜田 道昭、津田 宏治、広川 貴次、花岡 悟一郎、佐久間 淳、浅井 潔
コンピュータセキュリティシンポジウム2012論文集、2012 Oct 23;2012(3):382-9
Systematic measurement of missmatch effect for designing inter-species microarray
Fukuzaki M, Yoshida M, Ogura A, Sese J
BIBM2012. 2012 Oct:478-81
(Proceedings of The IEEE International Conference on Bioinformatics and Biomedicine, Philadelphia, USA, October 4-7, 2012)
Integrated Visualization of Gene Network and Ontology Applying a Hierarchical Graph Visualization Technique
Nakazawa R, Itoh T, Sese J, Terada A
IV2012. 2012 Jul:81-6
(Proceedings of the 16th International Conference on Information Visualization, Montpellier, France, July 11-13, 2012)
Data Analysis of Large-Scale Glycan-Sample Interactions
大規模糖鎖相互作用情報データの解析
Sese J
Trends Glycosci Glycotechnol. 2012 May; 24(137):122-8
Global Alignment of Protein-Protein Interaction Networks for Analyzing Evolutionary Changes of Network Frameworks [PDF:281KB]
Terada A, Sese J
BICoB-2012. 2012 Mar:196-201
(Proceedings of the 4th International Conference on Bioinformatics and Computational Biology, Las Vegas, USA, March 12-14, 2012)

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