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Published Papers(2016)

List of papers published by users January 1st, 2016 -- December 31st, 2016

Papers compiled at the end-of-year renewal in 2016

Supercomputer users in authors list (Japanese)Supercomputer users in authors listTitleJournal, Volume, Number, PagesPMIDDOI
1林 正康Masayasu HayashiChd5 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):780-92.26359639doi: 10.1002/jcb.25368.
2大柳 一Hajime OhyanagiOryzaGenome: Genome Diversity Database of Wild Oryza SpeciesPlant Cell Physiol. 2016 Jan;57(1):e1. 26578696doi: 10.1093/pcp/pcv171.
3石井 孝司Koji IshiiAn Outbreak of Acute Hepatitis Caused by Genotype IB Hepatitis A Viruses Contaminating the Water Supply in Thailand.ervirology. 2016;59(4):197-203.28208132doi: 10.1159/000455856.
4Rai Amit,高橋弘喜Amit Rai,Hiroki TakahashiRNA-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;7:481.27148308doi: 10.3389/fpls.2016.00481.
5斎藤 成也Naruya SaitouEmergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences.Genome Biol Evol. 2016 Jul 12;8(7):2076-92.27289096doi: 10.1093/gbe/evw132.
6Babarinde IA, 斎藤 成也Isaac Adeyemi Babarinde,Naruya SaitouGenomic Locations of Conserved Noncoding Sequences and Their Proximal Protein-Coding Genes in Mammalian Expression Dynamics.Mol Biol Evol. 2016 Jul;33(7):1807-17.27017584doi: 10.1093/molbev/msw058.
7Tsai Isheng Jason, 菊地 泰生Isheng J Tsai, Taisei KikuchiThe genomic basis of parasitism in the Strongyloides clade of nematodes.Nat Genet. 2016 Mar;48(3):299-307.26829753doi: 10.1038/ng.3495.
8菊地 泰生Taisei KikuchiTranscriptional 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):77-83.25831996doi: 10.1111/mpp.12261.
9菊地 泰生Taisei KikuchiGenome-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):e0005253.28033376doi: 10.1371/journal.pntd.0005253.
10菊地 泰生Taisei KikuchiComplete mitochondrial genomes of four entomopathogenic nematode species of the genus Steinernema.Parasit Vectors. 2016 Aug 5;9(1):430.27494995doi: 10.1186/s13071-016-1730-z.
11菊地 泰生Taisei KikuchiAn expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus.Sci Rep. 2016 Dec 22;6:39749.28004836doi: 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)NULLNULL
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)NULLNULL
14小林 和也Kazuya KobayashiCaste-Specific and Sex-Specific Expression of Chemoreceptor Genes in a Termite.PLoS One. 2016 Jan 13;11(1):e0146125.26760975doi: 10.1371/journal.pone.0146125.
15小林 和也Kazuya KobayashiA female-biased sex ratio reduces the twofold cost of sex.Sci Rep. 2016 Apr 1;6:23982.27035400doi: 10.1038/srep23982.
16小林 和也Kazuya KobayashiDifference in evolutionary patterns of strongly or weakly selected characters among ant populations.Sci Rep. 2016 Dec 20;6:39451.27995972doi: 10.1038/srep39451.
17高橋 佑磨Yuma TakahashiLack of genetic variation prevents adaptation at the geographic range margin in a damselfly.Mol Ecol. 2016 Sep;25(18):4450-60.27501054doi: 10.1111/mec.13782.
18土橋 映仁Akito DobashiFrequent BCOR aberrations in extranodal NK/T-Cell lymphoma, nasal type.Genes Chromosomes Cancer. 2016 May;55(5):460-71.26773734doi: 10.1002/gcc.22348.
19成相 直樹Naoki NariaiA Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes.BMC Genomics. 2016 Jan 11;17 Suppl 1(Suppl 1):2.26818838doi: 10.1186/s12864-015-2295-5.
20山田 洋一Yoichi YamadaMyeloid 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):253-63.26888865doi: 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):361-74.26956060doi: 10.1016/j.ijpara.2016.01.009.
22工藤 徹Toru KudoIdentification 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):111-125.27040147doi: 10.1266/ggs.15-00065.
23工藤 徹Toru KudoPleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae.Plant Cell Physiol. 2016 Jan;57(1):e6.26746174doi: 10.1093/pcp/pcv195.
24神沼 英里, 小笠原 理Eli Kaminuma,Osamu OgasawaraDNA data bank of Japan (DDBJ) progress report.Nucleic Acids Res. 2016 Jan 4;44(D1):D51-7.26578571doi: 10.1093/nar/gkv1105.
25今村 拓也Takuya ImamuraBidirectional 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):5105-22.26945044doi: 10.1093/nar/gkw113.
26佐藤 健吾Kengo SatoPrediction of Gene Structures from RNA-seq Data Using Dual Decomposition.IPSJ Transactions on Bioinformatics, vol 9(2016), p1-6NULLdoi.org/10.2197/ipsjtbio.9.1
27松波 雅俊Masatoshi MatsunamiPopulation Structure and Evolution after Speciation of the Hokkaido Salamander (Hynobius retardatus).PLoS One. 2016 Jun 3;11(6):e0156815.27257807doi: 10.1371/journal.pone.0156815.
28谷内江 望Nozomu YachieTargeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systemsScience. 2016 Sep 16;353(6305):aaf8729.27492474doi: 10.1126/science.aaf8729.
29谷内江 望Nozomu YachiePooled-matrix protein interaction screens using Barcode Fusion GeneticsMol Syst Biol. 2016 Apr 22;12(4):863.27107012doi: 10.15252/msb.20156660.
30佐藤 和広Kazuhiro SatoImprovement of barley genome annotations by deciphering the Haruna Nijo genomeDNA Res. 2016 Feb;23(1):21-8.26622062doi: 10.1093/dnares/dsv033.
31吉田 健太郎Kentaro YoshidaHost specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elementsBMC Genomics. 2016 May 18;17:370.27194050doi: 10.1186/s12864-016-2690-6.
32吉田 健太郎Kentaro YoshidaGenome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessionsMol Genet Genomics. 2016 Aug;291(4):1681-94.27142109doi: 10.1007/s00438-016-1211-2.
33笠原 浩太Kota KasaharaIon Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction.PLoS One. 2016 Mar 7;11(3):e0150716.26950215doi: 10.1371/journal.pone.0150716.
34笠原 浩太, 中村 春木Kota Kasahara,Haruki NakamuramyPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic schemeBiophys Physicobiol. 2016 Sep 7;13:209-216.27924276doi: 10.2142/biophysico.13.0_209.
35笠原 浩太, 中村 春木Kota Kasahara,Haruki NakamuramDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories.Bioinformatics. 2016 Aug 15;32(16):2531-3.27153575doi: 10.1093/bioinformatics/btw129.
36青木 誠志郎Seishiro AokiWide distribution range of rhizobial symbionts associated with pantropical sea-dispersed legumesAntonie Van Leeuwenhoek. 2016 Dec;109(12):1605-1614.27664091doi: 10.1007/s10482-016-0761-y.
37高橋 鉄美Tetsumi TakahashiA robust phylogeny among major lineages of the East African cichlidsMol Phylogenet Evol. 2016 Jul;100:234-242.27068840doi: 10.1016/j.ympev.2016.04.012.
38山田 和範Kazunori D YamadaApplication of the MAFFT sequence alignment program to large data - reexamination of the usefulness of chained guide treesBioinformatics. 2016 Nov 1;32(21):3246-3251.27378296doi: 10.1093/bioinformatics/btw412.
39山田 和範Kazunori D YamadaStructural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteinsBiophys Physicobiol. 2016 Jul 14;13:157-163.27924270doi: 10.2142/biophysico.13.0_157.
40野澤 昌文Masafumi NozawaAccelerated pseudogenization on the neo-X chromosome in Drosophila mirandaNat Commun. 2016 Nov 29;7:13659.27897175doi: 10.1038/ncomms13659.
41野澤 昌文Masafumi NozawaEvolutionary Transitions of MicroRNA-Target PairsGenome Biol Evol. 2016 Jun 4;8(5):1621-33.27189995doi: 10.1093/gbe/evw092.
42内古閑 伸之Nobuyuki UchikogaSpecificity of broad protein interaction surfaces for proteins with multiple binding partners.Biophys Physicobiol. 2016 Jul 14;13:105-115.27924264doi: 10.2142/biophysico.13.0_105.
43黒田 真也Shinya KurodaSelective control of up-regulated and down-regulated genes by temporal patterns and doses of insulinSci Signal. 2016 Nov 22;9(455):ra112.27879394doi: 10.1126/scisignal.aaf3739.
44吉武 和敏Kazutoshi YoshitakeCCT2 Mutations Evoke Leber Congenital Amaurosis due to Chaperone Complex Instability.Sci Rep. 2016 Sep 20;6:33742.27645772doi: 10.1038/srep33742.
45吉武 和敏Kazutoshi YoshitakeIdentification 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):4255-63.27548899doi: 10.1167/iovs.16-19450.
46水谷 紗弥佳Sayaka MizutaniHigh stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy.Gut. 2016 Sep;65(9):1574-5.27340192doi: 10.1136/gutjnl-2016-311937.
47山形 浩一, 瀬々 潤Koichi Yamagata, Jun SeseCOSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.Nucleic Acids Res. 2016 May 5;44(8):e78.26833260doi: 10.1093/nar/gkw026.
48城地 保昌Yasumasa JotiNucleosomal arrays self‐assemble into supramolecular globular structures lacking 30‐nm fibersEMBO J. 2016 May 17;35(10):1115-32.27072995doi: 10.15252/embj.201592660.
49木村 敦Atsushi P KimuraA 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 enhancersMol Reprod Dev. 2016 Jun;83(6):541-57.27111572doi: 10.1002/mrd.22650.
50中川 草, 上田 真保子So Nakagawa, Mahoko Ueda TakahashigEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomesDatabase (Oxford). 2016 May 30;2016:baw087.27242033doi: 10.1093/database/baw087.
51河田 雅圭Masakado KawataDifferentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizardsMol Ecol. 2016 May;25(10):2273-85.27027506doi: 10.1111/mec.13625.
52中尾 亮Ryo NakaoDraft 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):e00453-16.27313287doi: 10.1128/genomeA.00453-16.
53中井 亮佑Ryosuke NakaiComplete Genome Sequence of Aurantimicrobium minutum Type Strain KNCT, a Planktonic Ultramicrobacterium Isolated from River WaterGenome Announc. 2016 Jun 30;4(3):e00616-16.27365350doi: 10.1128/genomeA.00616-16.
54石谷 隆一郎Ryuichiro IshitaniStructural Insights into Divalent Cation Modulations of ATP-Gated P2X Receptor ChannelsCell Rep. 2016 Feb 2;14(4):932-944.26804916doi: 10.1016/j.celrep.2015.12.087.
55石谷 隆一郎Ryuichiro IshitaniStructural basis for amino acid export by DMT superfamily transporter YddGNature. 2016 Jun 16;534(7607):417-20.27281193doi: 10.1038/nature17991.
56佐藤 賢二Kenji SatouApplication of Word Embedding to Drug Repositioning. J. Biomedical Science and Engineering, 2016, 9, 7-16NULLdoi: 10.4236/jbise.2016.91002.
57佐藤 賢二Kenji SatouDNA Sequence Classification by Convolutional Neural Networks.J. Biomedical Science and Engineering, 2016, 9, 280-286NULLdoi: 10.4236/jbise.2016.95021.
58辻 敏之Toshiyuki TsujiStructure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease.Structure. 2016 Nov 1;24(11):1960-1971.27773688doi: 10.1016/j.str.2016.09.005.
59榊原 康文Yasubumi SakakibaraGenome sequence and analysis of the Japanese morning glory Ipomoea nilNat Commun. 2016 Nov 8;7:13295.27824041doi: 10.1038/ncomms13295.
60亀田 倫史Tomoshi KamedaOrigin of the Surfactant-Dependent Redox Chemistry of Single-Wall Carbon Nanotubes. ChemNanoMat 2016,Volume2, Issue9 Pages 911-920NULLdoi.org/10.1002/cnma.201600190
61亀田 倫史Tomoshi KamedaDetecting O2 binding sites in protein cavities.Sci Rep. 2016 Feb 2;6:20534.26830762doi: 10.1038/srep20534.
62岩切 淳一, 亀田 倫史Junichi Iwakiri, Tomoshi KamedaImproved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring FunctionJ Chem Theory Comput. 2016 Sep 13;12(9):4688-97.27494732doi: 10.1021/acs.jctc.6b00254.
63寺田 愛花, 瀬々 潤Aika Terada,Jun SeseLAMPLINK: detection of statistically significant SNP combinations from GWAS dataBioinformatics. 2016 Nov 15;32(22):3513-3515.27412093doi: 10.1093/bioinformatics/btw418.
64谷澤 靖洋Yasuhiro TanizawaDFAST and DAGA: web-based integrated genome annotation tools and resourcesBiosci Microbiota Food Health. 2016;35(4):173-184.27867804doi: 10.12938/bmfh.16-003.
65前野 慎太朗, 谷澤 靖洋, 遠藤 明仁Shintaro Maeno,Yasuhiro Tanizawa,Akihito EndoGenomic characterization of a fructophilic bee symbiont Lactobacillus kunkeei reveals its niche-specific adaptation.Syst Appl Microbiol. 2016 Dec;39(8):516-526. 27776911doi: 10.1016/j.syapm.2016.09.006.
66近藤 伸二Shinji KondoGenome-wide maps of nucleosomes of the trichostatin A treated and untreated archiascomycetous yeast Saitoella complicata. AIMS Microbiology 2016, Volume 2, Issue 1: 69-91.NULLdoi: 10.3934/microbiol.2016.1.69
67中村 祐哉Yuya NakamuraEstablishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communitiesAppl Microbiol Biotechnol. 2016 Aug;100(16):7263-79. 27102130doi: 10.1007/s00253-016-7532-6.
68熊谷 雄太郎Yutaro KumagaiGenome-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):1032.28155712doi: 10.1186/s12864-016-3325-7.
69木村 暁Akatsuki KimuraBayesian Inference of Forces Causing Cytoplasmic Streaming in Caenorhabditis elegans Embryos and Mouse Oocytes.PLoS One. 2016 Jul 29;11(7):e0159917. 27472658doi: 10.1371/journal.pone.0159917.
70川上 英良Eiryo KawakamiWeighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data.Nucleic Acids Res. 2016 Jun 20;44(11):5010-21.27131787doi: 10.1093/nar/gkw355.
71Mark RavinetMark RavinetA Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug Cimex lectularius.G3 (Bethesda). 2016 Dec 7;6(12):4059-4066.27733453doi: 10.1534/g3.116.033092.
72前原 一満Kazumitsu MaeharaChromatin-prebound Crm1 recruits Nup98-HoxA9 fusion to induce aberrant expression of Hox cluster genes.Elife. 2016 Jan 7;5:e09540. 26740045doi: 10.7554/eLife.09540.
73前原 一満Kazumitsu MaeharaExploration of nucleosome positioning patterns in transcription factor function.Sci Rep. 2016 Jan 21;6:19620.26790608doi: 10.1038/srep19620.
74前原 一満Kazumitsu MaeharaIdentification of Immunoglobulin Gene Sequences from a Small Read Number of mRNA-Seq Using HybridomasPLoS One. 2016 Oct 27;11(10):e0165473.27788226doi: 10.1371/journal.pone.0165473.
75浜田 道昭Michiaki HamadaComprehensive prediction of lncRNA-RNA interactions in human transcriptomeBMC Genomics. 2016 Jan 11;17 Suppl 1(Suppl 1):12.26818453doi: 10.1186/s12864-015-2307-5.
76安井 康夫Yasuo YasuiAssembly of the draft genome of buckwheat and its applications in identifying agronomically useful genesDNA Res. 2016 Jun;23(3):215-24.27037832doi: 10.1093/dnares/dsw012.
77岩崎 渉Wataru IwasakiGenomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake Tsunami.BMC Genomics. 2016 Jan 14;17:53.26764021doi: 10.1186/s12864-016-2380-4.
78尾崎 遼, 岩崎 渉Haruka Ozaki,Wataru IwasakiFlexible selection of diversified Na(+)/K(+)-ATPase α-subunit isoforms for osmoregulation in teleosts.Zoological Lett. 2016 Aug 3;2:15.27489726doi: 10.1186/s40851-016-0050-7.
79尾崎 遼Haruka OzakiMOCCS: clarifying DNA-binding motif ambiguity using ChIP-Seq data.Comput Biol Chem. 2016 Aug;63:62-72.26971251doi: 10.1016/j.compbiolchem.2016.01.014.
80清水 徳朗Tokurou ShimizuA 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. 23-32NULLdoi: 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)p68NULLNULL
82清水 徳朗, 神沼 英里Tokurou Shimizu,Eli KaminumaHybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes.PLoS One. 2016 Nov 30;11(11):e0166969.27902727doi: 10.1371/journal.pone.0166969.
83中井 亮佑, 藤澤 貴智Ryosuke Nakai,Takatomo FujisawaGenome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria.Stand Genomic Sci. 2016 Dec 13;11:90. 27999625doi: 10.1186/s40793-016-0210-6.