NIG Supercomputer
日本語 English

論文のリスト(2016)

2016.01.01 -- 2016.12.31にユーザによって発表された論文のリスト

2016年度の年度末アカウント継続申請時に集計した論文

Supercomputer users in authors list (Japanese) Supercomputer users in authors list Title Journal, Volume, Number, Pages PMID DOI
1 林 正康 Masayasu Hayashi Chd5 Regulates MuERV-L/MERVL Expression in Mouse Embryonic Stem Cells Via H3K27me3 Modification and Histone H3.1/H3.2. J Cell Biochem. 2016 Mar;117(3):780-92. 26359639 doi: 10.1002/jcb.25368.
2 大柳 一 Hajime Ohyanagi OryzaGenome: Genome Diversity Database of Wild Oryza Species Plant Cell Physiol. 2016 Jan;57(1):e1. 26578696 doi: 10.1093/pcp/pcv171.
3 石井 孝司 Koji Ishii An Outbreak of Acute Hepatitis Caused by Genotype IB Hepatitis A Viruses Contaminating the Water Supply in Thailand. ervirology. 2016;59(4):197-203. 28208132 doi: 10.1159/000455856.
4 Rai Amit,高橋弘喜 Amit Rai,Hiroki Takahashi RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis. Front Plant Sci. 2016 Apr 12;7:481. 27148308 doi: 10.3389/fpls.2016.00481.
5 斎藤 成也 Naruya Saitou Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences. Genome Biol Evol. 2016 Jul 12;8(7):2076-92. 27289096 doi: 10.1093/gbe/evw132.
6 Babarinde IA, 斎藤 成也 Isaac Adeyemi Babarinde,Naruya Saitou Genomic Locations of Conserved Noncoding Sequences and Their Proximal Protein-Coding Genes in Mammalian Expression Dynamics. Mol Biol Evol. 2016 Jul;33(7):1807-17. 27017584 doi: 10.1093/molbev/msw058.
7 Tsai Isheng Jason, 菊地 泰生 Isheng J Tsai, Taisei Kikuchi The genomic basis of parasitism in the Strongyloides clade of nematodes. Nat Genet. 2016 Mar;48(3):299-307. 26829753 doi: 10.1038/ng.3495.
8 菊地 泰生 Taisei Kikuchi Transcriptional and morphological changes in the transition from mycetophagous to phytophagous phase in the plant-parasitic nematode Bursaphelenchus xylophilus. Mol Plant Pathol. 2016 Jan;17(1):77-83. 25831996 doi: 10.1111/mpp.12261.
9 菊地 泰生 Taisei Kikuchi Genome-Wide Analyses of Individual Strongyloides stercoralis (Nematoda: Rhabditoidea) Provide Insights into Population Structure and Reproductive Life Cycles. PLoS Negl Trop Dis. 2016 Dec 29;10(12):e0005253. 28033376 doi: 10.1371/journal.pntd.0005253.
10 菊地 泰生 Taisei Kikuchi Complete mitochondrial genomes of four entomopathogenic nematode species of the genus Steinernema. Parasit Vectors. 2016 Aug 5;9(1):430. 27494995 doi: 10.1186/s13071-016-1730-z.
11 菊地 泰生 Taisei Kikuchi An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus. Sci Rep. 2016 Dec 22;6:39749. 28004836 doi: 10.1038/srep39749.
12 門田 有希 Yuki Monden 色素原料用サツマイモ品種の識別に利用可能なレトロトランスポゾンRtsp-1挿入箇所の選定 DNA多型 24, p115-118 (2016) NULL NULL
13 門田 有希 Yuki Monden レトロトランスポゾン挿入多型を利用したリンゴの品種識別マーカー開発 DNA多型 24, 101-107 (2016) NULL NULL
14 小林 和也 Kazuya Kobayashi Caste-Specific and Sex-Specific Expression of Chemoreceptor Genes in a Termite. PLoS One. 2016 Jan 13;11(1):e0146125. 26760975 doi: 10.1371/journal.pone.0146125.
15 小林 和也 Kazuya Kobayashi A female-biased sex ratio reduces the twofold cost of sex. Sci Rep. 2016 Apr 1;6:23982. 27035400 doi: 10.1038/srep23982.
16 小林 和也 Kazuya Kobayashi Difference in evolutionary patterns of strongly or weakly selected characters among ant populations. Sci Rep. 2016 Dec 20;6:39451. 27995972 doi: 10.1038/srep39451.
17 高橋 佑磨 Yuma Takahashi Lack of genetic variation prevents adaptation at the geographic range margin in a damselfly. Mol Ecol. 2016 Sep;25(18):4450-60. 27501054 doi: 10.1111/mec.13782.
18 土橋 映仁 Akito Dobashi Frequent BCOR aberrations in extranodal NK/T-Cell lymphoma, nasal type. Genes Chromosomes Cancer. 2016 May;55(5):460-71. 26773734 doi: 10.1002/gcc.22348.
19 成相 直樹 Naoki Nariai A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes. BMC Genomics. 2016 Jan 11;17 Suppl 1(Suppl 1):2. 26818838 doi: 10.1186/s12864-015-2295-5.
20 山田 洋一 Yoichi Yamada Myeloid Differentiation Factor 88 Signaling in Bone Marrow-Derived Cells Promotes Gastric Tumorigenesis by Generation of Inflammatory Microenvironment. Cancer Prev Res (Phila). 2016 Mar;9(3):253-63. 26888865 doi: 10.1158/1940-6207.CAPR-15-0315.
21 中尾 稔 Minoru Nakao Reappraisal of Hydatigera taeniaeformis (Batsch, 1786) (Cestoda: Taeniidae) sensu lato with description of Hydatigera kamiyai n. sp. Int J Parasitol. 2016 May;46(5-6):361-74. 26956060 doi: 10.1016/j.ijpara.2016.01.009.
22 工藤 徹 Toru Kudo Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants. Genes Genet Syst. 2016 Oct 13;91(2):111-125. 27040147 doi: 10.1266/ggs.15-00065.
23 工藤 徹 Toru Kudo Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae. Plant Cell Physiol. 2016 Jan;57(1):e6. 26746174 doi: 10.1093/pcp/pcv195.
24 神沼 英里, 小笠原 理 Eli Kaminuma,Osamu Ogasawara DNA data bank of Japan (DDBJ) progress report. Nucleic Acids Res. 2016 Jan 4;44(D1):D51-7. 26578571 doi: 10.1093/nar/gkv1105.
25 今村 拓也 Takuya Imamura Bidirectional promoters link cAMP signaling with irreversible differentiation through promoter-associated non-coding RNA (pancRNA) expression in PC12 cells. Nucleic Acids Res. 2016 Jun 20;44(11):5105-22. 26945044 doi: 10.1093/nar/gkw113.
26 佐藤 健吾 Kengo Sato Prediction of Gene Structures from RNA-seq Data Using Dual Decomposition. IPSJ Transactions on Bioinformatics, vol 9(2016), p1-6 NULL doi.org/10.2197/ipsjtbio.9.1
27 松波 雅俊 Masatoshi Matsunami Population Structure and Evolution after Speciation of the Hokkaido Salamander (Hynobius retardatus). PLoS One. 2016 Jun 3;11(6):e0156815. 27257807 doi: 10.1371/journal.pone.0156815.
28 谷内江 望 Nozomu Yachie Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems Science. 2016 Sep 16;353(6305):aaf8729. 27492474 doi: 10.1126/science.aaf8729.
29 谷内江 望 Nozomu Yachie Pooled-matrix protein interaction screens using Barcode Fusion Genetics Mol Syst Biol. 2016 Apr 22;12(4):863. 27107012 doi: 10.15252/msb.20156660.
30 佐藤 和広 Kazuhiro Sato Improvement of barley genome annotations by deciphering the Haruna Nijo genome DNA Res. 2016 Feb;23(1):21-8. 26622062 doi: 10.1093/dnares/dsv033.
31 吉田 健太郎 Kentaro Yoshida Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements BMC Genomics. 2016 May 18;17:370. 27194050 doi: 10.1186/s12864-016-2690-6.
32 吉田 健太郎 Kentaro Yoshida Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions Mol Genet Genomics. 2016 Aug;291(4):1681-94. 27142109 doi: 10.1007/s00438-016-1211-2.
33 笠原 浩太 Kota Kasahara Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction. PLoS One. 2016 Mar 7;11(3):e0150716. 26950215 doi: 10.1371/journal.pone.0150716.
34 笠原 浩太, 中村 春木 Kota Kasahara,Haruki Nakamura myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme Biophys Physicobiol. 2016 Sep 7;13:209-216. 27924276 doi: 10.2142/biophysico.13.0_209.
35 笠原 浩太, 中村 春木 Kota Kasahara,Haruki Nakamura mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories. Bioinformatics. 2016 Aug 15;32(16):2531-3. 27153575 doi: 10.1093/bioinformatics/btw129.
36 青木 誠志郎 Seishiro Aoki Wide distribution range of rhizobial symbionts associated with pantropical sea-dispersed legumes Antonie Van Leeuwenhoek. 2016 Dec;109(12):1605-1614. 27664091 doi: 10.1007/s10482-016-0761-y.
37 高橋 鉄美 Tetsumi Takahashi A robust phylogeny among major lineages of the East African cichlids Mol Phylogenet Evol. 2016 Jul;100:234-242. 27068840 doi: 10.1016/j.ympev.2016.04.012.
38 山田 和範 Kazunori D Yamada Application of the MAFFT sequence alignment program to large data - reexamination of the usefulness of chained guide trees Bioinformatics. 2016 Nov 1;32(21):3246-3251. 27378296 doi: 10.1093/bioinformatics/btw412.
39 山田 和範 Kazunori D Yamada Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins Biophys Physicobiol. 2016 Jul 14;13:157-163. 27924270 doi: 10.2142/biophysico.13.0_157.
40 野澤 昌文 Masafumi Nozawa Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda Nat Commun. 2016 Nov 29;7:13659. 27897175 doi: 10.1038/ncomms13659.
41 野澤 昌文 Masafumi Nozawa Evolutionary Transitions of MicroRNA-Target Pairs Genome Biol Evol. 2016 Jun 4;8(5):1621-33. 27189995 doi: 10.1093/gbe/evw092.
42 内古閑 伸之 Nobuyuki Uchikoga Specificity of broad protein interaction surfaces for proteins with multiple binding partners. Biophys Physicobiol. 2016 Jul 14;13:105-115. 27924264 doi: 10.2142/biophysico.13.0_105.
43 黒田 真也 Shinya Kuroda Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin Sci Signal. 2016 Nov 22;9(455):ra112. 27879394 doi: 10.1126/scisignal.aaf3739.
44 吉武 和敏 Kazutoshi Yoshitake CCT2 Mutations Evoke Leber Congenital Amaurosis due to Chaperone Complex Instability. Sci Rep. 2016 Sep 20;6:33742. 27645772 doi: 10.1038/srep33742.
45 吉武 和敏 Kazutoshi Yoshitake Identification of Novel Mutations in the LRR-Cap Domain of C21orf2 in Japanese Patients With Retinitis Pigmentosa and Cone-Rod Dystrophy. Invest Ophthalmol Vis Sci. 2016 Aug 1;57(10):4255-63. 27548899 doi: 10.1167/iovs.16-19450.
46 水谷 紗弥佳 Sayaka Mizutani High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy. Gut. 2016 Sep;65(9):1574-5. 27340192 doi: 10.1136/gutjnl-2016-311937.
47 山形 浩一, 瀬々 潤 Koichi Yamagata, Jun Sese COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples. Nucleic Acids Res. 2016 May 5;44(8):e78. 26833260 doi: 10.1093/nar/gkw026.
48 城地 保昌 Yasumasa Joti Nucleosomal arrays self‐assemble into supramolecular globular structures lacking 30‐nm fibers EMBO J. 2016 May 17;35(10):1115-32. 27072995 doi: 10.15252/embj.201592660.
49 木村 敦 Atsushi P Kimura A genomic region transcribed into a long noncoding RNA interacts with the Prss42/Tessp-2 promoter in spermatocytes during mouse spermatogenesis, and its flanking sequences can function as enhancers Mol Reprod Dev. 2016 Jun;83(6):541-57. 27111572 doi: 10.1002/mrd.22650.
50 中川 草, 上田 真保子 So Nakagawa, Mahoko Ueda Takahashi gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes Database (Oxford). 2016 May 30;2016:baw087. 27242033 doi: 10.1093/database/baw087.
51 河田 雅圭 Masakado Kawata Differentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizards Mol Ecol. 2016 May;25(10):2273-85. 27027506 doi: 10.1111/mec.13625.
52 中尾 亮 Ryo Nakao Draft Genome Sequences of Three Strains of Ehrlichia ruminantium, a Tick-Borne Pathogen of Ruminants, Isolated from Zimbabwe, The Gambia, and Ghana. Genome Announc. 2016 Jun 16;4(3):e00453-16. 27313287 doi: 10.1128/genomeA.00453-16.
53 中井 亮佑 Ryosuke Nakai Complete Genome Sequence of Aurantimicrobium minutum Type Strain KNCT, a Planktonic Ultramicrobacterium Isolated from River Water Genome Announc. 2016 Jun 30;4(3):e00616-16. 27365350 doi: 10.1128/genomeA.00616-16.
54 石谷 隆一郎 Ryuichiro Ishitani Structural Insights into Divalent Cation Modulations of ATP-Gated P2X Receptor Channels Cell Rep. 2016 Feb 2;14(4):932-944. 26804916 doi: 10.1016/j.celrep.2015.12.087.
55 石谷 隆一郎 Ryuichiro Ishitani Structural basis for amino acid export by DMT superfamily transporter YddG Nature. 2016 Jun 16;534(7607):417-20. 27281193 doi: 10.1038/nature17991.
56 佐藤 賢二 Kenji Satou Application of Word Embedding to Drug Repositioning. J. Biomedical Science and Engineering, 2016, 9, 7-16 NULL doi: 10.4236/jbise.2016.91002.
57 佐藤 賢二 Kenji Satou DNA Sequence Classification by Convolutional Neural Networks. J. Biomedical Science and Engineering, 2016, 9, 280-286 NULL doi: 10.4236/jbise.2016.95021.
58 辻 敏之 Toshiyuki Tsuji Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease. Structure. 2016 Nov 1;24(11):1960-1971. 27773688 doi: 10.1016/j.str.2016.09.005.
59 榊原 康文 Yasubumi Sakakibara Genome sequence and analysis of the Japanese morning glory Ipomoea nil Nat Commun. 2016 Nov 8;7:13295. 27824041 doi: 10.1038/ncomms13295.
60 亀田 倫史 Tomoshi Kameda Origin of the Surfactant-Dependent Redox Chemistry of Single-Wall Carbon Nanotubes. ChemNanoMat 2016,Volume2, Issue9 Pages 911-920 NULL doi.org/10.1002/cnma.201600190
61 亀田 倫史 Tomoshi Kameda Detecting O2 binding sites in protein cavities. Sci Rep. 2016 Feb 2;6:20534. 26830762 doi: 10.1038/srep20534.
62 岩切 淳一, 亀田 倫史 Junichi Iwakiri, Tomoshi Kameda Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function J Chem Theory Comput. 2016 Sep 13;12(9):4688-97. 27494732 doi: 10.1021/acs.jctc.6b00254.
63 寺田 愛花, 瀬々 潤 Aika Terada,Jun Sese LAMPLINK: detection of statistically significant SNP combinations from GWAS data Bioinformatics. 2016 Nov 15;32(22):3513-3515. 27412093 doi: 10.1093/bioinformatics/btw418.
64 谷澤 靖洋 Yasuhiro Tanizawa DFAST and DAGA: web-based integrated genome annotation tools and resources Biosci Microbiota Food Health. 2016;35(4):173-184. 27867804 doi: 10.12938/bmfh.16-003.
65 前野 慎太朗, 谷澤 靖洋, 遠藤 明仁 Shintaro Maeno,Yasuhiro Tanizawa,Akihito Endo Genomic characterization of a fructophilic bee symbiont Lactobacillus kunkeei reveals its niche-specific adaptation. Syst Appl Microbiol. 2016 Dec;39(8):516-526. 27776911 doi: 10.1016/j.syapm.2016.09.006.
66 近藤 伸二 Shinji Kondo Genome-wide maps of nucleosomes of the trichostatin A treated and untreated archiascomycetous yeast Saitoella complicata. AIMS Microbiology 2016, Volume 2, Issue 1: 69-91. NULL doi: 10.3934/microbiol.2016.1.69
67 中村 祐哉 Yuya Nakamura Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities Appl Microbiol Biotechnol. 2016 Aug;100(16):7263-79. 27102130 doi: 10.1007/s00253-016-7532-6.
68 熊谷 雄太郎 Yutaro Kumagai Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs. BMC Genomics. 2016 Dec 22;17(Suppl 13):1032. 28155712 doi: 10.1186/s12864-016-3325-7.
69 木村 暁 Akatsuki Kimura Bayesian Inference of Forces Causing Cytoplasmic Streaming in Caenorhabditis elegans Embryos and Mouse Oocytes. PLoS One. 2016 Jul 29;11(7):e0159917. 27472658 doi: 10.1371/journal.pone.0159917.
70 川上 英良 Eiryo Kawakami Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data. Nucleic Acids Res. 2016 Jun 20;44(11):5010-21. 27131787 doi: 10.1093/nar/gkw355.
71 Mark Ravinet Mark Ravinet A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug Cimex lectularius. G3 (Bethesda). 2016 Dec 7;6(12):4059-4066. 27733453 doi: 10.1534/g3.116.033092.
72 前原 一満 Kazumitsu Maehara Chromatin-prebound Crm1 recruits Nup98-HoxA9 fusion to induce aberrant expression of Hox cluster genes. Elife. 2016 Jan 7;5:e09540. 26740045 doi: 10.7554/eLife.09540.
73 前原 一満 Kazumitsu Maehara Exploration of nucleosome positioning patterns in transcription factor function. Sci Rep. 2016 Jan 21;6:19620. 26790608 doi: 10.1038/srep19620.
74 前原 一満 Kazumitsu Maehara Identification of Immunoglobulin Gene Sequences from a Small Read Number of mRNA-Seq Using Hybridomas PLoS One. 2016 Oct 27;11(10):e0165473. 27788226 doi: 10.1371/journal.pone.0165473.
75 浜田 道昭 Michiaki Hamada Comprehensive prediction of lncRNA-RNA interactions in human transcriptome BMC Genomics. 2016 Jan 11;17 Suppl 1(Suppl 1):12. 26818453 doi: 10.1186/s12864-015-2307-5.
76 安井 康夫 Yasuo Yasui Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes DNA Res. 2016 Jun;23(3):215-24. 27037832 doi: 10.1093/dnares/dsw012.
77 岩崎 渉 Wataru Iwasaki Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake Tsunami. BMC Genomics. 2016 Jan 14;17:53. 26764021 doi: 10.1186/s12864-016-2380-4.
78 尾崎 遼, 岩崎 渉 Haruka Ozaki,Wataru Iwasaki Flexible selection of diversified Na(+)/K(+)-ATPase α-subunit isoforms for osmoregulation in teleosts. Zoological Lett. 2016 Aug 3;2:15. 27489726 doi: 10.1186/s40851-016-0050-7.
79 尾崎 遼 Haruka Ozaki MOCCS: clarifying DNA-binding motif ambiguity using ChIP-Seq data. Comput Biol Chem. 2016 Aug;63:62-72. 26971251 doi: 10.1016/j.compbiolchem.2016.01.014.
80 清水 徳朗 Tokurou Shimizu A genomic approach to selecting robust and versatile SNP sets from next-generation sequencing data for genome-wide association study in citrus cultivars. Acta horticulturae 2016 v. no.1135 pp. 23-32 NULL doi: 10.17660/ActaHortic.2016.1135.4
81 清水 徳朗 Tokurou Shimizu カンキツの高密度連鎖地図の構築と参照ゲノム配列との比較 Acta Horticulturae, 2016, 育種学研究 18（別1）p68 NULL NULL
82 清水 徳朗, 神沼 英里 Tokurou Shimizu,Eli Kaminuma Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes. PLoS One. 2016 Nov 30;11(11):e0166969. 27902727 doi: 10.1371/journal.pone.0166969.
83 中井 亮佑, 藤澤 貴智 Ryosuke Nakai,Takatomo Fujisawa Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria. Stand Genomic Sci. 2016 Dec 13;11:90. 27999625 doi: 10.1186/s40793-016-0210-6.