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Published Papers(2022)

List of papers published by users January 1st, 2022 -- December 31st, 2022

Papers compiled at the end-of-year renewal in 2022

Supercomputer users in authors list(Japanese)Supercomputer users in authors listTitleJournal, Volume, Number, PagesPMIDDOI
1墨谷 暢子Nobuko SumiyaCoordination mechanism of cell and cyanelle division in the glaucophyte alga Cyanophora sudaeProtoplasma. 2022 Jul;259(4):855-867.34553240doi: 10.1007/s00709-021-01704-3
2佐藤 健吾Kengo SatoPrediction of RNA secondary structure including pseudoknots for long sequencesBriefings in bioinformatics. 2022 Jan 17;23(1):bbab395.34601552doi: 10.1093/bib/bbab395
3竹中 康浩Yasuhiro TakenakaProlonged disturbance of proteostasis induces cellular senescence via temporal mitochondrial dysfunction and subsequent mitochondrial accumulation in human fibroblastsThe FEBS journal. 2022 Mar;289(6):1650-1667.34689411doi: 10.1111/febs.16249
4Yassouf Mhd YousufMhd Yousuf YassoufBiphasic effect of mechanical stress on lymphocyte activationJournal of cellular physiology. 2022 Feb;237(2):1521-1531.34724217doi: 10.1002/jcp.30623
5イワサキ タケシTakeshi IwasakiMerkel cell polyomavirus-negative Merkel cell carcinoma is associated with JAK-STAT and MEK-ERK pathway activation.Cancer Sci. 2022 Jan; 113(1): 251-260.34724284doi: 1111/cas.15187
6小笠原 理Ogasawara OsamuDNA Data Bank of Japan (DDBJ) update report 2021.Nucleic Acids Res. 2022 Jan 07; 50(D1): D102-D105.34751405doi: 1093/nar/gkab995
7高田 豊行, 近藤 伸二Toyoyuki Takada, Shinji KondoMoG+: a database of genomic variations across three mouse subspecies for biomedical researchMammalian genome : official journal of the International Mammalian Genome Society. 2022 Mar;33(1):31-43.34782917doi: 10.1007/s00335-021-09933-w
8小野 肇Hajime OnoFunctional characterization of an olfactory receptor in the Oriental fruit fly, Bactrocera dorsalis, that responds to eugenol and isoeugenolComparative biochemistry and physiology. Part B, Biochemistry & molecular biology. 2022 Feb-Mar;258:110696.34800681doi: 10.1016/j.cbpb.2021.110696
9伊達 悠貴Yuki DateRunx3 is required for oncogenic Myc upregulation in p53-deficient osteosarcoma.Oncogene. 2022 Jan; 41(5): 683-691.34803166doi: 1038/s41388-021-02120-w
10市原 知哉kazuya ichiharaIdentification and characterization of novel proteins associated with CHD4.Genes Cells. 2022 Jan; 27(1): 61-71.34897913doi: 1111/gtc.12909
11加藤 裕之Hiroyuki KatoMNX1-HNF1B axis is ihttps://pubmed.ncbi.nlm.nih.gov/34953915/ndispensable for intraductal papillary mucinous neoplasm lineagesGastroenterology. 2022 Apr;162(4):1272-1287.e16.34953915doi: 10.1053/j.gastro.2021.12.254
12中川 草So NakagawaThe SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistanceCell reports. 2022 Jan 11;38(2):110218.34968415doi: 10.1016/j.celrep.2021.110218
13今野 直輝Naoki KonnoDeep distributed computing to reconstruct extremely large lineage trees.Nature biotechnology. 2022 Apr;40(4):566-575.34992246doi: 10.1038/s41587-021-01111-2
14阿部 陽Akira AbeRecombinant inbred lines and next-generation sequencing enable rapid identification of candidate genes involved in morphological and agronomic traits in foxtail millet.Sci Rep. 2022 Jan 07; 12(1): 218.34997038doi: 1038/s41598-021-04012-1
15川上 聖司Satoshi KawakamimTOR-AKT Signaling in Cellular Clock Resetting Triggered by Osmotic Stress.Antioxid Redox Signal. 2022 Oct; 37(10-12): 631-646.35018792doi: 1089/ars.2021.0059
16松波 雅俊Masatoshi MatsunamiGenomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: gene duplication facilitates social evolutionProceedings of the National Academy of Sciences of the United States of America. 2022 Jan 18;119(3):e2110361119.35042774doi: 10.1073/pnas.2110361119
17福永 津嵩Tsukasa FukunagaInverse Potts model improves accuracy of phylogenetic profilingBioinformatics (Oxford, England). 2022 Jan 21;38(7):1794-1800.35060594doi: 10.1093/bioinformatics/btac034
18鄒 兆南, 沖 真弥Zhaonan Zou, Shinya OkiEpigenetic landscape of drug responses revealed through large-scale ChIP-seq data analysesBMC bioinformatics. 2022 Jan 24;23(1):51.35073843doi: 10.1186/s12859-022-04571-8
19石井 悠, 丸山 真一朗Yuu Ishii, Shinichiro MaruyamaGene expression alterations from reversible to irreversible stages during coral metamorphosisZoological letters. 2022 Jan 25;8(1):4.35078542doi: 10.1186/s40851-022-00187-1
20前野 慎太朗Shintaro Maeno16S rRNA gene sequence diversity in Faecalibacterium prausnitzii-complex taxa has marked impacts on quantitative analysis.FEMS Microbiol Ecol. 2022 Feb 10; 98(1): fiac004.35090008doi: 1093/femsec/fiac004
21仮屋園 遼Ryo KariyazonoIdentification of genome-wide distribution of cyanobacterial group 2 sigma factor SigE accountable for its regulonThe Plant journal : for cell and molecular biology. 2022 Apr;110(2):548-561.35092706doi: 10.1111/tpj.15687
22川島 武士, 吉田 真明, 濱田 麻友子Takeshi Kawashima, Masa-Aki Yoshida, Mayuko HamadaObserving Phylum-Level Metazoan Diversity by Environmental DNA Analysis at the Ushimado Area in the Seto Inland SeaZoological science. 2022 Feb;39(1):157-165.35107003doi: 10.2108/zs210073
23武藤 吉徳Yoshinori MutoComplete Genome Sequences of Three Phocaeicola vulgatus Strains Isolated from a Healthy Japanese IndividualMicrobiology resource announcements. 2022 Feb 17;11(2):e0112421.35112912doi: 10.1128/mra.01124-21
24伊達 悠貴Yuki DateOncogenic Runx1-Myc axis in p53-deficient thymic lymphoma.Gene. 2022 Apr 20; 819: 146234.35114276doi: 1016/j.gene.2022.146234
25松波 雅俊Masatoshi MatsunamiGene Structure Analysis of Chemokines and Their Receptors in Allotetraploid Frog, Xenopus laevisFrontiers in genetics. 2022 Jan 20;12:787979.35126458doi: 10.3389/fgene.2021.787979
26茂木 朋貴Tomoki MotegiAnti-CCR4 treatment depletes regulatory T cells and leads to clinical activity in a canine model of advanced prostate cancerJournal for immunotherapy of cancer. 2022 Feb;10(2):e003731.35131860doi: 10.1136/jitc-2021-003731
27佐久間 敦丈Atsuhiro SakumaA transcriptomic reevaluation of the accessory olfactory organ in Bichir (Polypterus senegalus)Zoological letters. 2022 Feb 8;8(1):5.35135614doi: 10.1186/s40851-022-00189-z
28茂木 朋貴Tomoki MotegiDystrophin-deficient muscular dystrophy in a Toy Poodle with a single base pair insertion in exon 45 of the Duchenne muscular dystrophy geneThe Journal of veterinary medical science. 2022 Apr 13;84(4):502-506.35135937doi: 10.1292/jvms.21-0504
29藤井 雅史Masashi FujiiFour features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humansNPJ systems biology and applications. 2022 Feb 8;8(1):6.35136093doi: 10.1038/s41540-022-00213-0
30五味 良太Ryota GomiEmergence of rare carbapenemases (FRI, GES-5, IMI, SFC and SFH-1) in Enterobacterales isolated from surface waters in JapanThe Journal of antimicrobial chemotherapy. 2022 Apr 27;77(5):1237-1246.35137119doi: 10.1093/jac/dkac029
31小木曽 映里Eri Ogiso-TanakaDe Novo Genome Assembly of Stinkhorn Mushroom Clathrus columnatus (Basidiomycota, Fungi) Using Illumina and Nanopore Sequencing DataMicrobiology resource announcements. 2022 Feb 17;11(2):e0102621.35142541doi: 10.1128/mra.01026-21
32坂山 英俊Hidetoshi SakayamaDiscovery of ultrafast myosin, its amino acid sequence, and structural featuresProceedings of the National Academy of Sciences of the United States of America. 2022 Feb 22;119(8):e2120962119.35173046doi: 10.1073/pnas.2120962119
33新里 宙也Chuya ShinzatoLarval transcriptomic responses of a stony coral, Acropora tenuis, during initial contact with the native symbiont, Symbiodinium microadriaticumSci Rep. 2022 Feb 21;12(1):2854.35190599doi: 10.1038/s41598-022-06822-3
34有泉 亨Tohru Ariizumiorf137 triggers cytoplasmic male sterility in tomato.Plant Physiol. 2022 Jun 01; 189(2): 465-468.35212743doi: 1093/plphys/kiac082
35黒田 真也Shinya KurodaMulti-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism.iScience. 2022 Feb 4;25(2):103787.35243212doi: 10.1016/j.isci.2022.103787
36小林 光智衣Michie KobayashiA jacalin-like lectin domain-containing protein of Sclerospora graminicola acts as an apoplastic virulence effector in plant-oomycete interactionsMolecular plant pathology. 2022 Jun;23(6):845-854.35257477doi: 10.1111/mpp.13197
37石下 聡, 郷 康広Satoshi Ishishita, Yasuhiro GoUterus-specific transcriptional regulation underlies eggshell pigment production in Japanese quailPloS one. 2022 Mar 10;17(3):e0265008.35271636doi: 10.1371/journal.pone.0265008
38茂木 朋貴Tomoki MotegimRNA sequencing analysis and growth inhibitory effects of palbociclib on cell lines from canine histiocytic proliferative disorders.Vet Comp Oncol. 2022 Sep; 20(3): 587-601.35278028doi: 1111/vco.12812
39高木 亙Wataru TakagiMolecular mechanism of nutrient uptake in developing embryos of oviparous cloudy catshark (Scyliorhinus torazame)PloS one. 2022 Mar 15;17(3):e0265428.35290397doi: 10.1371/journal.pone.0265428
40吉田 真明Masa-Aki YoshidaGut microbiota analysis of Blenniidae fishes including an algae-eating fish and clear boundary formation among isolated Vibrio strainsScientific reports. 2022 Mar 17;12(1):4642.35301363doi: 10.1038/s41598-022-08511-7
41笠井 淳司, 田沼 将人, 笠井 淳司, 奥野 浩行Atsushi Kasai, Masato Tanuma, Atsushi Kasai, Hiroyuki OkunoClaustrum mediates bidirectional and reversible control of stress-induced anxiety responsesScience advances. 2022 Mar 18;8(11):eabi6375.35302853doi: 10.1126/sciadv.abi6375
42比嘉 綱己Tsunaki HigaSpatiotemporal reprogramming of differentiated cells underlies regeneration and neoplasia in the intestinal epitheliumNature communications. 2022 Mar 21;13(1):1500.35314700doi: 10.1038/s41467-022-29165-z
43村上 匠, 瀬川 高弘Takumi Murakami, Takahiro SegawaMetagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light harvesting mechanisms in glacier cryoconiteMicrobiome. 2022 Mar 23;10(1):50.35317857doi: 10.1186/s40168-022-01238-7
44阿部 陽Akira AbeHigh-performance pipeline for MutMap and QTL-seq.PeerJ. 2022; 10: e13170.35321412doi: 7717/peerj.13170
45森 宣仁Nobuhito MoriPotential Metabolite Markers for Pancreatic Cancer Identified by Metabolomic Analysis of Induced Cancer-Associated FibroblastsCancers. 2022 Mar 8;14(6):1375.35326527doi: 10.3390/cancers14061375
46田路 矩之, 郷 康広Noriyuki Toji, Yasuhiro GoNicotinic acetylcholine receptors in a songbird brain.J Comp Neurol. 2022 Aug; 530(11): 1966-1991.35344610doi: 1002/cne.25314
47市村 和也Kazuya IchimuraSimultaneous mutations in SMN1 and SUMM2 fully suppress the dwarf and autoimmune phenotypes of Arabidopsis mpk4 mutant.Plant Signal Behav. 2022 Dec 31; 17(1): 2046412.35350957doi: 1080/15592324.2022.2046412
48火原 日美子Himiko HibaraATTED-II v11: A Plant Gene Coexpression Database Using a Sample Balancing Technique by Subagging of Principal Components.Plant Cell Physiol. 2022 Jun 15; 63(6): 869-881.35353884doi: 1093/pcp/pcac041
49吉田 光範Mitsunori YoshidaComplete Genome Sequence of Mycobacterium fortuitum subsp. fortuitum JCM 6387, a Type Strain of Human-Pathogenic Mycobacteria Showing Inducible Macrolide ResistanceMicrobiology resource announcements. 2022 Apr 21;11(4):e0006022.35357161doi: 10.1128/mra.00060-22
50佐藤 行人Yukuto SatoAnalysis of human clinical and environmental Leptospira to elucidate the eco-epidemiology of leptospirosis in Yaeyama, subtropical Japan.PLoS Negl Trop Dis. 2022 Mar; 16(3): e0010234.35358181doi: 1371/journal.pntd.0010234
51笠原 雅弘Masahiro KasaharaLPMX: A pure rootless composable container systemBMC bioinformatics. 2022 Mar 31;23(1):112.35361130doi: 10.1186/s12859-022-04649-3
52瀧 雄介Yusuke TakiThe Association Between Onset of Staphylococcal Non-menstrual Toxic Shock Syndrome With Inducibility of Toxic Shock Syndrome Toxin-1 ProductionFrontiers in microbiology. 2022 Mar 14;13:765317.35369432doi: 10.3389/fmicb.2022.765317
53吉武 和敏Kazutoshi YoshitakeConstruction of a chromosome-level Japanese stickleback species genome using ultra-dense linkage analysis with single-cell sperm sequencing.NAR Genom Bioinform. 2022 Jun; 4(2): lqac026.35372836doi: 1093/nargab/lqac026
54西井 かなえkanae nishiiThe first genome for the Cape Primrose Streptocarpus rexii (Gesneriaceae), a model plant for studying meristem-driven shoot diversity.Plant Direct. 2022 Apr; 6(4): e388.35388373doi: 1002/pld3.388
55寺井 悟朗Goro TeraiQRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity.Nucleic Acids Res. 2022 Jul 22; 50(13): e73.35390152doi: 1093/nar/gkac220
56原 敏文Toshifumi HaraElevated METTL9 is associated with peritoneal dissemination in human scirrhous gastric cancers.Biochem Biophys Rep. 2022 Jul; 30: 101255.35402738doi: 1016/j.bbrep.2022.101255
57河口 真一Shinichi KawaguchiThe Tudor Domain-Containing Protein, Kotsubu (CG9925), Localizes to the Nuage and Functions in piRNA Biogenesis in D. melanogaster.Front Mol Biosci. 2022; 9: 818302.35425810doi: 3389/fmolb.2022.818302
58吉田 光範Mitsunori YoshidaMolecular Epidemiological Characteristics of Mycobacterium abscessus Complex Derived from Non-Cystic Fibrosis Patients in Japan and TaiwanMicrobiology spectrum. 2022 Jun 29;10(3):e0057122.35446117doi: 10.1128/spectrum.00571-22
59湯山 育子Ikuko YuyamaMetatranscriptomic Analysis of Corals Inoculated With Tolerant and Non-Tolerant Symbiont Exposed to High Temperature and Light Stress.Front Physiol. 2022; 13: 806171.35480050doi: 3389/fphys.2022.806171
60奥野 友介Yusuke OkunoEBV genome variations enhance clinicopathological features of nasopharyngeal carcinoma in a non-endemic region.Cancer Sci. 2022 Jul; 113(7): 2446-2456.35485636doi: 1111/cas.15381
61谷澤 靖洋Yasuhiro TanizawaGenome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida.Sci Adv. 2022 Apr 29; 8(17): eabi5075.35486731doi: 1126/sciadv.abi5075
62大槻 朝Hajime OhtsukiInvasions of an obligate asexual daphnid species support the nearly neutral theory.Sci Rep. 2022 May 04; 12(1): 7305.35508526doi: 1038/s41598-022-11218-4
63岡田 俊平Shunpei OkadasRegulation of A-to-I RNA editing and stop codon recoding to control selenoprotein expression during skeletal myogenesis.Nat Commun. 2022 May 06; 13(1): 2503.35523818doi: 1038/s41467-022-30181-2
64中岡 慎治Shinji NakaokaEvolving neural networks through bio-inspired parent selection in dynamic environments.Biosystems. 2022 Aug; 218: 104686.35525435doi: 1016/j.biosystems.2022.104686
65笠原 浩太Kota KasaharaInformation quantity for secondary structure propensities of protein subsequences in the Protein Data BankBiophysics and physicobiology. 2022 Feb 8;19:1-12.35532457doi: 10.2142/biophysico.bppb-v19.0002
66水口 洋平, 豊田 敦Yohei Minakuchi, Atsushi ToyodaEarly embryonic mutations reveal dynamics of somatic and germ cell lineages in mice.Genome Res. 2022 May; 32(5): 945-955.35534232doi: 1101/gr.276363.121
67遠藤 明仁Akihito EndoExtracellular fructooligosaccharide degradation in Anaerostipes hadrus for co-metabolism with non-fructooligosaccharide utilizers.Biochem Biophys Res Commun. 2022 Jul 12; 613: 81-86.35537289doi: 1016/j.bbrc.2022.04.134
68森 宙史, 西原 秀典Hiroshi Mori, Hidenori NishiharaPaleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan.Curr Biol. 2022 Jun 06; 32(11): 2494-2504.e5.35537455doi: 1016/j.cub.2022.04.034
69井関 洸太朗kohtaro isekiVariability of Flowering Sex and Its Effect on Agronomic Trait Expression in White Guinea Yam.Front Plant Sci. 2022; 13: 837951.35548274doi: 3389/fpls.2022.837951
70秋山 泰身Taishin AkiyamaIntegrative analysis of scRNA-seq and scATAC-seq revealed transit-amplifying thymic epithelial cells expressing autoimmune regulator.Elife. 2022 May 17; 11: e73998.35578835doi: 7554/eLife.73998
71加藤 大明Hiroaki KatoRecognition of pathogen-derived sphingolipids in Arabidopsis.Science. 2022 May 20; 376(6595): 857-860.35587979doi: 1126/science.abn0650
72齋藤 裕Yutaka SaitoAI and computational chemistry-accelerated development of an alotaketal analogue with conventional PKC selectivity.Chem Commun (Camb). 2022 Jun 09; 58(47): 6693-6696.35608215doi: 1039/d2cc01759h
73新里 宙也Chuya ShinzatoComparative genomics highlight the importance of lineage-specific gene families in evolutionary divergence of the coral genus, Montipora.BMC Ecol Evol. 2022 May 27; 22(1): 71.35624412doi: 1186/s12862-022-02023-8
74張 再軍Zaijun ZhangTemporal and Locational Values of Images Affecting the Deep Learning of Cancer Stem Cell Morphology.Biomedicines. 2022 Apr 19; 10(5): 941.35625678doi: 3390/biomedicines10050941
75石川 麻乃Asano IshikawaConvergent copy number increase of genes associated with freshwater colonization in fishesPhilosophical transactions of the Royal Society of London. Series B, Biological sciences. 2022 Jul 18;377(1855):20200509.35634928doi: 10.1098/rstb.2020.0509
76川瀬 雅貴, 一柳 健司Masaki Kawase, Kenji IchiyanagiThe Expression Dynamics of piRNAs Derived From Male Germline piRNA Clusters and Retrotransposons.Front Cell Dev Biol. 2022; 10: 868746.35646920doi: 3389/fcell.2022.868746
77山本 泰智Yamamoto YasunoriOnline tools for efficient paper writing.Hum Genome Var. 2022 Jun 06; 9(1): 20.35668068doi: 1038/s41439-022-00195-9
78押木 守mamoru oshikiGrowth of nitrite-oxidizing Nitrospira and ammonia-oxidizing Nitrosomonas in marine recirculating trickling biofilter reactors.Environ Microbiol. 2022 Aug; 24(8): 3735-3750.35672869doi: 1111/1462-2920.16085
79山本 容正Yoshimasa YamamotoFusion plasmid carrying the colistin resistance gene mcr of Escherichia coli isolated from healthy residents.J Glob Antimicrob Resist. 2022 Sep; 30: 152-154.35705132doi: 1016/j.jgar.2022.06.007
80鴻巣 明日香Asuka KounosupiRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode.Sci Rep. 2022 Jun 16; 12(1): 10156.35710810doi: 1038/s41598-022-14247-1
81佐藤 賢二Kenji SatouProtTrans-Glutar: Incorporating Features From Pre-trained Transformer-Based Models for Predicting Glutarylation Sites.Front Genet. 2022; 13: 885929.35711929doi: 3389/fgene.2022.885929
82近藤 伸二Shinji KondoNintedanib induces gene expression changes in the lung of induced-rheumatoid arthritis-associated interstitial lung disease mice.PLoS One. 2022; 17(6): e0270056.35714115doi: 1371/journal.pone.0270056
83藤井 雅史, 菊池 裕Masashi Fujii, Yutaka KikuchiIdentification of aberrant transcription termination at specific gene loci with DNA hypomethylated transcription termination sites caused by DNA methyltransferase deficiency.Genes Genet Syst. 2022 Oct 18; 97(3): 139-152.35718462doi: 1266/ggs.21-00092
84塚本 雄也Yuta TsukamotoMineralogical and Genomic Constraints on the Origin of Microbial Mn Oxide Formation in Complexed Microbial Community at the Terrestrial Hot Spring.Life (Basel). 2022 May 30; 12(6): 816.35743847doi: 3390/life12060816
85川崎 純菜Junna KawasakiConvergent evolution of antiviral machinery derived from endogenous retrovirus truncated envelope genes in multiple species.Proc Natl Acad Sci U S A. 2022 Jun 28; 119(26): e2114441119.35749360doi: 1073/pnas.2114441119
86藤井 雅史Masashi FujiiMathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast.Biophys Physicobiol. 2022; 19: 1-12.35749629doi: 2142/biophysico.bppb-v19.0012
87吉田 圭佑Keisuke YoshidaPriority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides.ISME J. 2022 Sep; 16(9): 2265-2279.35768643doi: 1038/s41396-022-01270-3
88福永 津嵩, 岩崎 渉Tsukasa Fukunaga, Wataru IwasakiMirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families.Bioinformatics. 2022 Aug 10; 38(16): 4039-4041.35771653doi: 1093/bioinformatics/btac433
89清水 元樹motoki shimizuA genetically linked pair of NLR immune receptors shows contrasting patterns of evolution.Proc Natl Acad Sci U S A. 2022 Jul 05; 119(27): e2116896119.35771942doi: 1073/pnas.2116896119
90深井 英吾Eigo FukaiWidespread and transgenerational retrotransposon activation in inter- and intraspecies recombinant inbred populations of Lotus japonicus.Plant J. 2022 Sep; 111(5): 1397-14doi:35792830doi: 1111/tpj.15896
91藤井 雅史Masashi FujiiEpigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells.Biophys Physicobiol. 2022; 19: 1-14.35797402doi: 2142/biophysico.bppb-v19.0018
92池田 秀也, 川島 秀一Shuya Ikeda, Shuichi KawashimaTogoID: an exploratory ID converter to bridge biological datasets.Bioinformatics. 2022 Sep 02; 38(17): 4194-4199.35801937doi: 1093/bioinformatics/btac491
93宮路 直実Naomi MiyajiWhole-Genome DNA Methylation Analysis in Brassica rapa subsp. perviridis in Response to Albugo candida Infection.Front Plant Sci. 2022; 13: 849358.35812966doi: 3389/fpls.2022.849358
94久保 貴彦Takahiko KuboWhole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells.Rice (N Y). 2022 Jul 16; 15(1): 38.35841399doi: 1186/s12284-022-00585-1
95越水 静Shizuka KoshimizuPhylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis.New Phytol. 2022 Nov; 236(3): 1182-1196.35842793doi: 1111/nph.18385
96大野 翔Sho OhnoA novel aldo-keto reductase gene is involved in 6'-deoxychalcone biosynthesis in dahlia (Dahlia variabilis).Planta. 2022 Jul 24; 256(3): 47.35871668doi: 1007/s00425-022-03958-4
97夏目 俊, 杉原 優, 工藤 葵, 阿部 陽Satoshi Natsume, Yu Sugihara, Aoi Kudoh, Akira AbeGenome Analysis Revives a Forgotten Hybrid Crop Edo-dokoro in the Genus Dioscorea.Plant Cell Physiol. 2022 Nov 22; 63(11): 1667-1678.35876055doi: 1093/pcp/pcac109
98藤原 奈央子naoko fujiwaraMPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus.Nucleic Acids Res. 2022 Aug 26; 50(15): 8779-8806.35902094doi: 1093/nar/gkac559
99木村 朋紀Tomoki KimuraCadmium inhibits forskolin-induced differentiation of human placental BeWo cells.J Toxicol Sci. 2022; 47(8): 309-315.35908931doi: 2131/jts.47.309
100五味 良太Ryota GomiChromosomal integration of bla CTX-M genes in diverse Escherichia coli isolates recovered from river water in Japan.Curr Res Microb Sci. 2022; 3: 100144.35909619doi: 1016/j.crmicr.2022.100144
101川久保 修佑Shusuke KawakuboLeek Yellow Stripe Virus Can Adjust for Host Adaptation by Trimming the N-Terminal Domain to Allow the P1 Protein to Function as an RNA Silencing Suppressor.Plant Pathol J. 2022 Aug; 38(4): 383-394.35953058doi: 5423/PPJ.FT.06.2022.0077
102角谷 徹仁tetsuji kakutaniTranscription-coupled and epigenome-encoded mechanisms direct H3K4 methylation.Nat Commun. 2022 Aug 11; 13(1): 4521.35953471doi: 1038/s41467-022-32165-8
103藤井 雅史, 黒田 真也Masashi Fujii, Shinya KurodaIn vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states.Sci Rep. 2022 Aug 12; 12(1): 13719.35962137doi: 1038/s41598-022-17964-9
104佐藤 大気Daiki SatoHumanized substitutions of Vmat1 in mice alter amygdala-dependent behaviors associated with the evolution of anxiety.iScience. 2022 Aug 19; 25(8): 104800.35992083doi: 10.1016/j.isci.2022.104800
105川上 聖司Satoshi KawakamiRhythmic transcription of Bmal1 stabilizes the circadian timekeeping system in mammals.Nat Commun. 2022 Aug 23; 13(1): 4652.35999195doi: 1038/s41467-022-32326-9
106中川 草So NakagawaNeoRdRp: A Comprehensive Dataset for Identifying RNA-dependent RNA Polymerases of Various RNA Viruses from Metatranscriptomic Data.Microbes Environ. 2022; 37(3): ME22001.36002304doi: 1264/jsme2.ME22001
107木村 敦Atsushi KimuraEvidence for a functional role of Start, a long noncoding RNA, in mouse spermatocytes.PLoS One. 2022; 17(8): e0273279.36006924doi: 1371/journal.pone.0273279
108高木 亙Wataru TakagiMolecular and morphological investigations on the renal mechanisms enabling euryhalinity of red stingray Hemitrygon akajei.Front Physiol. 2022; 13: 953665.36017340doi: 3389/fphys.2022.953665
109藤井 雅史Masashi FujiiMethylome data derived from maternal-zygotic DNA methyltransferase 3aa-/- zebrafish.Data Brief. 2022 Oct; 44: 108514.36034642doi: 1016/j.dib.2022.108514
110田村 啓太Keita TamuraGenome Sequence of the Edible Green Alga Ulva prolifera, Originating from the Yoshinogawa River in Japan.Microbiol Resour Announc. 2022 Oct 20; 11(10): e0043022.36036606doi: 1128/mra.00430-22
111前田 雪Yuki MaedaMolecular characterization of Vasa homolog in the pen shell Atrina pectinata: cDNA cloning and expression analysis during gonadal development.Comp Biochem Physiol B Biochem Mol Biol. 2022 Sep 03; 263: 110798.36064136doi: 1016/j.cbpb.2022.110798
112矢原 耕史Koji YaharaWhole blood transcriptome profiling identifies gene expression subnetworks and a key gene characteristic of the rare type of osteomyelitis.Biochem Biophys Rep. 2022 Dec; 32: 101328.36065290doi: 1016/j.bbrep.2022.101328
113國枝 武和Takekazu KuniedaStress-dependent cell stiffening by tardigrade tolerance proteins that reversibly form a filamentous network and gel.PLoS Biol. 2022 Sep; 20(9): e3001780.36067153doi: 1371/journal.pbio.3001780
114新里 宙也Chuya ShinzatoGenomic analysis of a reef-building coral, Acropora digitifera, reveals complex population structure and a migration network in the Nansei Islands, Japan.Mol Ecol. 2022 Oct; 31(20): 5270-5284.36082782doi: 1111/mec.16665
115松井 求Motomu MatsuiLifestyle Evolution Analysis by Binary-State Speciation and Extinction (BiSSE) Model.Methods Mol Biol. 2022; 2569: 327-342.36083456doi: 1007/978-1-0716-2691-7_16
116川村 昇吾, 矢倉 勝Shogo Kawamura, Masaru YaguraMarpolBase Expression: A Web-Based, Comprehensive Platform for Visualization and Analysis of Transcriptomes in the Liverwort Marchantia polymorpha.Plant Cell Physiol. 2022 Nov 22; 63(11): 1745-1755.36083565doi: 1093/pcp/pcac129
117草間 和哉Kazuya KusamaToll-like receptor signaling pathway triggered by inhibition of serpin A1 stimulates production of inflammatory cytokines by endometrial stromal cells.Front Endocrinol (Lausanne). 2022; 13: 966455.36093086doi: 3389/fendo.2022.966455
118瀬川 高弘takahiro segawaApplication of a high-throughput quantitative PCR system for simultaneous monitoring of SARS-CoV-2 variants and other pathogenic viruses in wastewater.Sci Total Environ. 2022 Dec 20; 853: 158659.36096223doi: 1016/j.scitotenv.2022.158659
119渡邊 美穂Miho WatanabeSulfuricystis multivorans gen. nov., sp. nov. and Sulfuricystis thermophila sp. nov., facultatively autotropic sulfur-oxidizing bacteria isolated from a hot spring, and emended description of the genus Rugosibacter.Arch Microbiol. 2022 Sep 02; 204(9): 595.36102984doi: 1007/s00203-022-03186-0
120林 俊宏Toshihiro HayashiIdiopathic rapid eye movement sleep behavior disorder in Japan: An observational study.Parkinsonism Relat Disord. 2022 Oct; 103: 129-135.36113390doi: 1016/j.parkreldis.2022.08.011
121Cronin AdamCronin AdamDifferential Gene Expression Correlates with Behavioural Polymorphism during Collective Behaviour in Cockroaches.Animals (Basel). 2022 Sep 08; 12(18): 2354.36139214doi: 3390/ani12182354
122渡邊 美穂Miho WatanabeDesulfofustis limnaeus sp. nov., a freshwater sulfate-reducing bacterium isolated from marsh soil.Arch Microbiol. 2022 Sep 27; 204(10): 647.36166176doi: 1007/s00203-022-03261-6
123岡田 愛Ai OkadaSystematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data.Nat Commun. 2022 Sep 29; 13(1): 5357.36175409doi: 1038/s41467-022-32887-9
124中川 草So NakagawaMonotreme-specific conserved putative proteins derived from retroviral reverse transcriptase.Virus Evol. 2022; 8(2): veac084.36176487doi: 1093/ve/veac084
125河村 理輝Riki Kawamurac-fos expression in the olfactory epithelium of the East African cichlid (Haplochromis chilotes) in response to odorant exposure.J Exp Biol. 2022 Oct 15; 225(20): jeb244737.36189492doi: 1242/jeb.244737
126郷 康広Yasuhiro GoCognitive genomics of learning delay and low level of social performance monitoring in macaque.Sci Rep. 2022 Oct 03; 12(1): 16539.36192455doi: 1038/s41598-022-20948-4
127一柳 健司Kenji IchiyanagiSequence divergence and retrotransposon insertion underlie interspecific epigenetic differences in primates.Mol Biol Evol. 2022 Oct 11; 39(10): msac208.36219870doi: 1093/molbev/msac208
128岩切 淳一Junichi IwakiriDDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells.Leukemia. 2022 Nov; 36(11): 2605-2620.36229594doi: 1038/s41375-022-01708-9
129加藤 有己Yuki KatoAlignment of single-cell trajectory trees with CAPITAL.Nat Commun. 2022 Oct 14; 13(1): 5972.36241645doi: 1038/s41467-022-33681-3
130飯塚 康介kosuke iizukaReal time monitoring of cold Ca2+ dependent transcription and its modulation by NCX inhibitors.Sci Rep. 2022 Oct 15; 12(1): 17325.36243739doi: 1038/s41598-022-22166-4
131布施 直之Naoyuki FuseTranscriptome features of innate immune memory in Drosophila.PLoS Genet. 2022 Oct; 18(10): e1010005.36252180doi: 1371/journal.pgen.1010005
132久保 顕登Kento KuboStructure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation.Nucleic Acids Res. 2022 Oct 28; 50(19): 11229-11242.36259651doi: 1093/nar/gkac825
133矢倉 勝, 工樂 樹洋Masaru Yagura, Shigehiro KurakuSqualomix: shark and ray genome analysis consortium and its data sharing platform.F1000Res. 2022; 11: 1077.36262334doi: 12688/f1000research.123591.1
134遠野 雅徳, 谷澤 靖洋masanori tohno, Yasuhiro TanizawaA novel species of lactic acid bacteria, Ligilactobacillus pabuli sp. nov., isolated from alfalfa silage.Int J Syst Evol Microbiol. 2022 Oct; 72(10):36269574doi: 1099/ijsem.0.005587
135吉田 真明, 廣田 主樹Masa-Aki Yoshida, Kazuki HirotaGene Recruitments and Dismissals in the Argonaut Genome Provide Insights into Pelagic Lifestyle Adaptation and Shell-like Eggcase Reacquisition.Genome Biol Evol. 2022 Nov 04; 14(11): evac140.36283693doi: 1093/gbe/evac140
136今井 裕季子yukiko imaiTherapeutic Potential of Adipose Stem Cell-Derived Conditioned Medium on Scar Contraction Model.Biomedicines. 2022 Sep 24; 10(10): 2388.36289649doi: 3390/biomedicines10102388
137瀬川 高弘takahiro segawaAstrocytic dysfunction induced by ABCA1 deficiency causes optic neuropathy.Sci Adv. 2022 Nov 04; 8(44): eabq1081.36332025doi: 1126/sciadv.abq1081
138金森 駿介, 河田 雅圭shunsuke kanamori, Masakado KawataDraft genome of six Cuban Anolis lizards and insights into genetic changes during their diversification.BMC Ecol Evol. 2022 Nov 04; 22(1): 129.36333669doi: 1186/s12862-022-02086-7
139沖 真弥Shinya OkiThe Histone Methyltransferase SETD8 Regulates the Expression of Tumor Suppressor Genes via H4K20 Methylation and the p53 Signaling Pathway in Endometrial Cancer Cells.Cancers (Basel). 2022 Oct 31; 14(21): 5367.36358786doi: 3390/cancers14215367
140坂本 卓磨Takuma SakamotoNutritional and metabolic process of the dung beetle Phelotrupes auratus depends on the plant ingredients that the herbivores eat.BMC Genomics. 2022 Nov 12; 23(1): 751.36371160doi: 1186/s12864-022-08982-y
141松井 求Motomu MatsuiNondestructive microbial discrimination using single-cell Raman spectra and random forest machine learning algorithm.STAR Protoc. 2022 Dec 16; 3(4): 101812.36386892doi: 1016/j.xpro.2022.101812
142田中 龍聖,菊地 泰生Ryusei Tanaka,Taisei KikuchiThe compact genome of Caenorhabditis niphades n. sp., isolated from a wood-boring weevil, Niphades variegatus.BMC Genomics. 2022 Nov 22; 23(1): 765.36418933doi: 1186/s12864-022-09011-8
143武藤 吉徳Yoshinori MutoIdentification of Key Genes and Pathways Associated with Preeclampsia by a WGCNA and an Evolutionary Approach.Genes (Basel). 2022 Nov 17; 13(11): 2134.36421809doi: 3390/genes13112134
144佐藤 健吾Kengo SatoDirect Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots.Genes (Basel). 2022 Nov 18; 13(11): 2155.36421829doi: 3390/genes13112155
145奥野 聖也Seiya OkunoCommunity phylogeny and spatial scale affect phylogenetic diversity metrics in a species-rich rainforest in Borneo.Ecol Evol. 2022 Nov; 12(11): e9536.36440315doi: 1002/ece3.9536
146小野 幸輝yukiteru onoPBSIM3: a simulator for all types of PacBio and ONT long reads.NAR Genom Bioinform. 2022 Dec; 4(4): lqac092.36465498doi: 1093/nargab/lqac092
147片山 俊明Toshiaki KatayamaTogoVar: A comprehensive Japanese genetic variation database.Hum Genome Var. 2022 Dec 12; 9(1): 44.36509753doi: 1038/s41439-022-00222-9
148小笠原 理Ogasawara OsamuBuilding cloud computing environments for genome analysis in Japan.Hum Genome Var. 2022 Dec 14; 9(1): 46.36517473doi: 1038/s41439-022-00223-8
149八谷 剛史Tsuyoshi HachiyaThe NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan.Hum Genome Var. 2022 Dec 20; 9(1): 48.36539398doi: 1038/s41439-022-00225-6
150三科 興平Kohei MishinaGenome-Wide Analysis of Snf2 Gene Family Reveals Potential Role in Regulation of Spike Development in Barley.Int J Mol Sci. 2022 Dec 27; 24(1): 457.36613901doi: 3390/ijms24010457
151山田 啓介Keisuke YamadaPrediction of RNA-protein interactions using a nucleotide language model.Bioinform Adv. 2022; 2(1): vbac023.36699410doi: 1093/bioadv/vbac023
152福永 津嵩Tsukasa FukunagaLinAliFold and CentroidLinAliFold: fast RNA consensus secondary structure prediction for aligned sequences using beam search methods.Bioinform Adv. 2022; 2(1): vbac078.36699418doi: 1093/bioadv/vbac078
153尾崎 遼Haruka OzakiCCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells.Bioinformatics. 2022 Oct 31; 38(21): 4868-4877.36795083doi: 1093/bioinformatics/btac599
154大田 達郎Tazro OhtaWorkflow sharing with automated metadata validation and test execution to improve the reusability of published workflows.Gigascience. 2022 Dec 28; 12: giad006.36810800doi: 1093/gigascience/giad006
155矢原 耕史Koji YaharaRepeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations.Nat Commun. 2022 Nov 11; 13(1): 6842.36941300doi: 1038/s41467-022-34475-3
156筒井 直昭Naoaki TsutsuMultiple insulin-like peptides in the gonads of the kuruma prawn Marsupenaeus japonicusFisheries Science. 2022; 88:387-396NULLdoi: 10.1007/s12562-022-01596-z
157林 方州Fangzhou LinCosmos Propagation Network: Deep learning model for point cloud completionNeurocomputing. 2022 October 1; 507: 221-234NULLdoi: 10.1016/j.neucom.2022.08.007
158近藤 文哉Fumiya KondoRNA sequencing in parthenocarpic chili pepper (Capsicum annuum) fruit reveals genes involved in transcriptional regulation of capsaicinoid biosynthesis genes responsible for the fluctuation of pungencyScientia Horticulturae. 2022 December; 306: 111456NULLdoi: 10.1016/j.scienta.2022.111456
159稲葉 皓子Hiroko InabaGenerative aptamer discovery using RaptGenNat Comput Sci. 2022 Jun; 2:378-386NULLdoi: 10.1038/s43588-022-00249-6
160美世 一守, 岩崎 渉Kazumori Mise, Wataru IwasakiUnexpected absence of ribosomal protein genes from metagenome-assembled genomesISME Communications. 2022; 2: 118NULLdoi: 10.1038/s43705-022-00204-6
161栗田 隆気Takaki KuritaComparison of morphological identification and DNA metabarcoding for dietary analysis of faeces from a subtropical lizardWildlife Research. 2022 September; 50(3): 224-236NULLdoi: 10.1071/WR22054
162坂山 英俊Hidetoshi SakayamaMorphology, taxonomy and phylogenetic positions of two Spirogyra species (Zygnematophyceae, Streptophyta) with replicate and semi-replicate transverse walls from JapanPhycologia. 2022; 61: 425-435NULLdoi: 10.1080/00318884.2022.2068299
163山田 啓介Keisuke YamadaPrediction of RNA-protein interactions using a nucleotide language modelBioinformatics Advances, 2022. ; 2(1): 1-9NULLdoi: 10.1093/bioadv/vbac023
164晝間 敬Kei HirumaGenome Resource of Colletotrichum spaethianum, the Causal Agent of Leaf Anthracnose in Polygonatum falcatumPhytoFrontiers. 2022; 2(2): 152-155NULLdoi: 10.1094/PHYTOFR-12-21-0082-A
165田原 沙絵子Saeko TaharaMOCCS profile analysis clarifies the cell type dependency of transcription factor-binding sequences and cis-regulatory SNPs in humansbioRxiv. 2022 Apr 10;NULLdoi: 10.1101/2022.04.08.487641
166岸田 拓士Takushi KishidaGenetic diversity and population history of the Japanese black bear (Ursus thibetanus japonicus) based on the genome-wide analyses.Ecological Research. 2022; 27(5): 647-657NULLdoi: 10.1111/1440-1703.12335
167岩切 淳一Junichi Iwakiri大規模配列データにより加速するノンコーディングRNA研究JSBi Bioinformatics Review. 2022; 3(1): 1-10NULLdoi: 10.11234/jsbibr.2022.primer1
168北野 誉Takashi KitanoComplete mitochondrial genomes of three fairy shrimps from snowmelt pools in JapanBMC Zoology. 2022; 7(11)NULLdoi: 10.1186/s40850-022-00111-2
169末竹 裕貴Hirotaka SuetakeSapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformaticsF1000Research. 2022 AugNULLdoi: 10.12688/f1000research.122924.1
170出口 亜由美Ayumi DeguxhiLocalized Repression of Two bHLH Genes is Involved in the Formation of White Margins and White Abaxial Surfaces in Carnation Petals by Inducing the Absence of Anthocyanin SynthesisThe Horticulture Journal. 2022; 91(1): 68-84NULLdoi: 10.2503/hortj.utd-313
171横溝 匠, 高橋 佑磨Takumi Yokomizo, Yuma TakahashiEndogenous rhythm variation and adaptation to the tidal environment in the freshwater snail, Semisulcospira reinianaFrontiers in Ecology and Evolution. 2022 December; 10NULLdoi: 10.3389/fevo.2022.1078234
172松波 雅俊Masatoshi MatsunamiTranscriptomics on Social Interactions in Termites: Effects of Soldier PresenceFrontiers in Ecology and Evolution. 2022 June 27; 10NULLdoi: 10.3389/fevo.2022.924151/
173安田 仁奈Nina YasudaIntegrated Population Genomic Analysis and Numerical Simulation to Estimate Larval Dispersal of Acanthaster cf. solaris Between Ogasawara and Other Japanese RegionsFrontiers in Marine Science. 2022 Jan; 8(688139)NULLdoi: 10.3389/fmars.2021.688139
174齋藤 裕Yutaka Saito深層学習によるタンパク質の機能予測と設計生物工学会誌. 2022 Nov; 100(11): 589-592NULLdoi: 10.34565/seibutsukogaku.100.11_589
175藤井 雅史, 粟津 暁紀Masashi Fujii, Akinori AwazuSelf-Organization of Diverse Directional Hierarchical Networks in Simple Coupled Maps with Connection ChangesJournal of the Physical Society of Japan. 2022; 91(023801)NULLdoi: 10.7566/JPSJ.91.023801
176粟津 暁紀Akinori AwazuFormation of Small-World Network Containing Module Networks in Globally and Locally Coupled Map System with Changes in Global Connection with Time Delay EffectsJ. Phys. Soc. Jpn. 2022 February; 9NULLdoi: 10.7566/JPSJ.92.034801
177齋藤 裕Yutaka SaitoEvoOpt: an MSA-guided, fully unsupervised sequence optimization pipeline for protein designMachine Learning in Structural Biology Workshop, The 36th Conference on Neural Information Processing Systems (NeurIPS 2022)NULLNULL

Additional papers submitted after the end-of-year renewal in 2020

Supercomputer users in authors list(Japanese)Supercomputer users in authors listTitleJournal, Volume, Number, PagesPMIDDOI
1石崎 公庸Kimitsune IshizakiMigration of prospindle before the first asymmetric division in germinating spore of Marchantia polymorpha.Plant Biotechnol (Tokyo). 2022 Mar 25; 39(1): 5-12.35800969doi: 10.5511/plantbiotechnology.21.1217b
2付 希Xi FuCircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes.F1000Res. 2022; 11: 1221.38686041doi: 10.12688/f1000research.127348.1
3古村 祥也, 吉田 健太郎Shoya Komura, Kentaro YoshidaGenome sequencing-based coverage analyses facilitate high-resolution detection of deletions linked to phenotypes of gamma-irradiated wheat mutants.BMC Genomics. 2022 Feb 09; 23(1): 111.35139819doi: 10.1186/s12864-022-08344-8
4森 隆弘Takahiro MoriA single-nucleotide-polymorphism in the 5'-flanking region of MSX1 gene as a predictive marker candidate for platinum-based therapy of esophageal carcinoma.Ther Adv Med Oncol. 2022; 14: 17588359221080580.35251318doi: 10.1177/17588359221080580