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Species Resource name RRC ID Author Title Journal Published Volume Pages Pubmed ID DOI
Wheat   KT3-5, KT1-1, RIL56   48835   Onishi K, Yamane M, Yamaji N, Tokui M, Kanamori H, Wu J, Komatsuda T, Sato K.   Sequence differences in the seed dormancy gene Qsd1 among various wheat genomes.   BMC Genomics   2017 -7 -1   18(1)   497   28662630   10.1186/s12864-017-3880-6  
Barley   Haruna Nijo, H602   47944   Hisano H, Sakamoto K, Takagi H, Terauchi R, Sato K.   Exome QTL-seq maps monogenic locus and QTLs in barley.   BMC Genomics   2017 -2 -6   18(1)   125   28148242   10.1186/s12864-017-3511-2  
Algae   NIES-39   47849   Motwalli O, Essack M, Jankovic BR, Ji B, Liu X, Ansari HR, Hoehndorf R, Gao X, Arold ST, Mineta K, Archer JA, Gojobori T, Mijakovic I, Bajic VB.   In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria.   BMC Genomics   2017 -1 -7   18(1)   33   28056772   10.1186/s12864-016-3389-4  
Barley   Haruna Nijo, H602   47245   Hisano H, Tsujimura M, Yoshida H, Terachi T, Sato K.   Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare).   BMC Genomics   2016 -10 -26   17(1)   824   27776481   10.1186/s12864-016-3159-3  
General Microbes   JCM 13438   48202   Massilamany C, Mohammed A, Loy JD, Purvis T, Krishnan B, Basavalingappa RH, Kelley CM, Guda C, Barletta RG, Moriyama EN, Smith TP, Reddy J.   Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe.   BMC Genomics   2016 -8 -25   17 Suppl 7   511   27557119   10.1186/s12864-016-2900-2  
Rats   WTC/Kyo (strainID=18), WTC-swh/Kyo (strainID=53...   40102   Yoshihara M, Saito D, Sato T, Ohara O, Kuramoto T, Suyama M.   Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat.   BMC Genomics   2016 -8 -11   17   593   27506932   10.1186/s12864-016-2975-9  
General Microbes   JCM 1330, JCM 12360, JCM 1332, JCM 16027   48201   Hiraoka S, Machiyama A, Ijichi M, Inoue K, Oshima K, Hattori M, Yoshizawa S, Kogure K, Iwasaki W.   Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami.   BMC Genomics   2016 -1 -15   17   53   26764021   10.1186/s12864-016-2380-4  
General Microbes   JCM 12225   41266   Endo A, Tanizawa Y, Tanaka N, Maeno S, Kumar H, Shiwa Y, Okada S, Yoshikawa H, Dicks L, Nakagawa J, Arita M.   Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp.   BMC Genomics   2015 -12 -31   16   1117   26715526   10.1186/s12864-015-2339-x  
Wheat     36380   Kobayashi F, Wu J, Kanamori H, Tanaka T, Katagiri S, Karasawa W, Kaneko S, Watanabe S, Sakaguchi T, Hanawa Y, Fujisawa H, Kurita K, Abe C, Iehisa JC, Ohno R, Šafář J, Šimková H, Mukai Y, Hamada M, Saito M, Ishikawa G, Katayose Y, Endo TR, Takumi S, Nakamura T, Sato K, Ogihara Y, Hayakawa K, Doležel J, Nasuda S, Matsumoto T, Handa H.   A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B.   BMC Genomics   2015 -8 -13   16   595   26265254   10.1186/s12864-015-1803-y  
Rice     35123   Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Maldonado L CE, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de Oliveira A, Han B, Henry R, Hsing YI, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA.   RiTE database: a resource database for genus-wide rice genomics and evolutionary biology.   BMC Genomics   2015 -7 -22   16   538   26194356   10.1186/s12864-015-1762-3  
Rice, Information   Oryzabase   34825   Zhang F, Huang LY, Zhang F, Ali J, Cruz CV, Zhuo DL, Du ZL, Li ZK, Zhou YL.   Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response.   BMC Genomics   2015 -3 -15   16   111   25765449   10.1186/s12864-015-1329-3  
C.elegans   tm1200   45817   Ni JZ, Chen E, Gu SG.   Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans.   BMC Genomics   2014 -12 -24   15   1157   25534009   10.1186/1471-2164-15-1157  
Chicken / Quail     36216   Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O'Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK.   Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.   BMC Genomics   2014 -12 -17   15   1060   25496766   10.1186/1471-2164-15-1060  
Algae   NIES-252   32133   Lemieux C, Otis C, Turmel M.   Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species.   BMC Genomics   2014 -10 -5   15   857   25281016   10.1186/1471-2164-15-857  
C.elegans   tm4272   45725   Edmonds MJ, Morgan A.   A systematic analysis of protein palmitoylation in Caenorhabditis elegans.   BMC Genomics   2014 -10 -4   15   841   25277130   10.1186/1471-2164-15-841  
Pathogenic microorganisms   IFM 11049, IFM 10847, IFM 10152   46808   Komaki H, Ichikawa N, Hosoyama A, Takahashi-Nakaguchi A, Matsuzawa T, Suzuki K, Fujita N, Gonoi T.   Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species.   BMC Genomics   2014 -6 -3   15   323   24884595   10.1186/1471-2164-15-323  
C.elegans   tm538, tm539   45870   Vergara IA, Tarailo-Graovac M, Frech C, Wang J, Qin Z, Zhang T, She R, Chu JS, Wang K, Chen N.   Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans.   BMC Genomics   2014 -4 -4   15   255   24694239   10.1186/1471-2164-15-255  
Paramecium   P. bursaria, strains Yad1g1N (NBRP PB031010B) a...   29224   Kodama Y, Suzuki H, Dohra H, Sugii M, Kitazume T, Yamaguchi K, Shigenobu S, Fujishima M.   Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts.   BMC Genomics   2014 -3 -13   15   183   24612690   10.1186/1471-2164-15-183  
General Microbes   JCM 7686   34165   Dziewit L, Czarnecki J, Wibberg D, Radlinska M, Mrozek P, Szymczak M, Schlüter A, Pühler A, Bartosik D.   Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids.   BMC Genomics   2014 -2 -13   15   124   24517536   10.1186/1471-2164-15-124  
Drosophila   DGRC#112001   28868   Pendse J, Ramachandran PV, Na J, Narisu N, Fink JL, Cagan RL, Collins FS, Baranski TJ.   A Drosophila functional evaluation of candidates from human genome-wide association studies of type 2 diabetes and related metabolic traits identifies tissue-specific roles for dHHEX.   BMC Genomics   2013 -3 -1   14   136   23445342   10.1186/1471-2164-14-136  
C.intestinalis / (O.japonicus)   Wild C. int   19671   Satou Y, Shin-i T, Kohara Y, Satoh N, Chiba S.   A genomic overview of short genetic variations in a basal chordate, Ciona intestinalis.   BMC Genomics   2012 -6 -1   13   208   22646724   10.1186/1471-2164-13-208  
Silkworms   p50T   22756   Hara K, Fujii T, Suzuki Y, Sugano S, Shimada T, Katsuma S, Kawaoka S.   Altered expression of testis-specific genes, piRNAs, and transposons in the silkworm ovary masculinized by a W chromosome mutation.   BMC Genomics   2012 -3 -29   13   119   22452797   10.1186/1471-2164-13-119  
C.intestinalis / (O.japonicus)   Wild C. int   20942   Okamura K, Yamashita R, Takimoto N, Nishitsuji K, Suzuki Y, Kusakabe TG, Nakai K.   Profiling ascidian promoters as the primordial type of vertebrate promoter.   BMC Genomics   2012 -3 -6   12 Suppl 3   S7   22369359   10.1186/1471-2164-12-S3-S7  
C.elegans   tm331, tm420   46042   Castro C, Sar F, Shaw WR, Mishima M, Miska EA, Griffin JL.   A metabolomic strategy defines the regulation of lipid content and global metabolism by Δ9 desaturases in Caenorhabditis elegans.   BMC Genomics   2012 -1 -24   13   36   22264337   10.1186/1471-2164-13-36  
Human and Animal Cells   COS-7 (RCB0539)   18245   Chimura T, Launey T, Ito M.   Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif.   BMC Genomics   2011 -6 -9   12   300   21649932   10.1186/1471-2164-12-300  
Barley   BAC clones   12002   Sato K, Motoi Y, Yamaji N, Yoshida H.   454 sequencing of pooled BAC clones on chromosome 3H of barley.   BMC Genomics   2011 -5 -20   12   246   21592415   10.1186/1471-2164-12-246  
Prokaryotes E. coli   W3110   6934   Horinouchi T, Tamaoka K, Furusawa C, Ono N, Suzuki S, Hirasawa T, Yomo T, Shimizu H.   Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress.   BMC Genomics   2010 -10 -20   11   579   20955615   10.1186/1471-2164-11-579  
Human and Animal Cells     38214   Kratz A, Arner E, Saito R, Kubosaki A, Kawai J, Suzuki H, Carninci P, Arakawa T, Tomita M, Hayashizaki Y, Daub CO.   Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns.   BMC Genomics   2010 -4 -23   11   257   20409305   10.1186/1471-2164-11-257  
Tomato   TOMJPF00001, full-length   6080   Aoki K, Yano K, Suzuki A, Kawamura S, Sakurai N, Suda K, Kurabayashi A, Suzuki T, Tsugane T, Watanabe M, Ooga K, Torii M, Narita T, Shin-I T, Kohara Y, Yamamoto N, Takahashi H, Watanabe Y, Egusa M, Kodama M, Ichinose Y, Kikuchi M, Fukushima S, Okabe A, Arie T, Sato Y, Yazawa K, Satoh S, Omura T, Ezura H, Shibata D.   Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics.   BMC Genomics   2010 -3 -31   11   210   20350329   10.1186/1471-2164-11-210  
Human and Animal Cells     6818   Ruike Y, Imanaka Y, Sato F, Shimizu K, Tsujimoto G.   Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing.   BMC Genomics   2010 -2 -26   11   137   20181289   10.1186/1471-2164-11-137  
Barley   ?   12014   Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R.   Development and implementation of high-throughput SNP genotyping in barley.   BMC Genomics   2009 -12 -8   10   582   19961604   10.1186/1471-2164-10-582  
Silkworms   p50   11331   Shimomura M, Minami H, Suetsugu Y, Ohyanagi H, Satoh C, Antonio B, Nagamura Y, Kadono-Okuda K, Kajiwara H, Sezutsu H, Nagaraju J, Goldsmith MR, Xia Q, Yamamoto K, Mita K.   KAIKObase: an integrated silkworm genome database and data mining tool.   BMC Genomics   2009 -10 -22   10   486   19843344   10.1186/1471-2164-10-486  
Zebrafish   Tol2 method   6331   Suster ML, Sumiyama K, Kawakami K.   Transposon-mediated BAC transgenesis in zebrafish and mice.   BMC Genomics   2009 -10 -17   10   477   19832998   10.1186/1471-2164-10-477  
Wheat   AK330135-AK336296   6458   Kawaura K, Mochida K, Enju A, Totoki Y, Toyoda A, Sakaki Y, Kai C, Kawai J, Hayashizaki Y, Seki M, Shinozaki K, Ogihara Y.   Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns.   BMC Genomics   2009 -6 -19   10   271   19534823   10.1186/1471-2164-10-271  
Prokaryotes E. coli   Keio collection   35233   Pérez-Mendoza D, de la Cruz F.   Escherichia coli genes affecting recipient ability in plasmid conjugation: are there any?   BMC Genomics   2009 -2 -11   10   71   19203375   10.1186/1471-2164-10-71  
General Microbes   JCM 13490   15627   Rodrigues DF, Ivanova N, He Z, Huebner M, Zhou J, Tiedje JM.   Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach.   BMC Genomics   2008 -11 -21   9   547   19019206   10.1186/1471-2164-9-547  
Silkworms   EST database   4716   Okamoto S, Futahashi R, Kojima T, Mita K, Fujiwara H.   Catalogue of epidermal genes: genes expressed in the epidermis during larval molt of the silkworm Bombyx mori.   BMC Genomics   2008 -8 -30   9   396   18721459   10.1186/1471-2164-9-396  
Silkworms   Samia cynthia ricini   4718   Arunkumar KP, Tomar A, Daimon T, Shimada T, Nagaraju J.   WildSilkbase: an EST database of wild silkmoths.   BMC Genomics   2008 -7 -19   9   338   18637161   10.1186/1471-2164-9-338  
Cellular slime molds   G02859, G02848, G03169, G02092, G00214   6747   Sillo A, Bloomfield G, Balest A, Balbo A, Pergolizzi B, Peracino B, Skelton J, Ivens A, Bozzaro S.   Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium.   BMC Genomics   2008 -6 -19   9   291   18559084   10.1186/1471-2164-9-291  
Algae   NIES-293   20777   Cattolico RA, Jacobs MA, Zhou Y, Chang J, Duplessis M, Lybrand T, McKay J, Ong HC, Sims E, Rocap G.   Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains.   BMC Genomics   2008 -5 -9   9   211   18462506   10.1186/1471-2164-9-211  
Information   Oryzabase   12488   Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK, Kapoor S.   MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress.   BMC Genomics   2007 -7 -21   8   242   17640358   10.1186/1471-2164-8-242  
DNA material, Tropical clawed frog, Medaka   pCS111-XtFas (Xenopus Fas) (RDB08077); mtgd021e23...   28640   Sakamaki K, Nozaki M, Kominami K, Satou Y.   The evolutionary conservation of the core components necessary for the extrinsic apoptotic signaling pathway, in Medaka fish.   BMC Genomics   2007 -6 -2   8   141   17540041   10.1186/1471-2164-8-141  
Human and Animal Cells     42886   Anisimov SV, Christophersen NS, Correia AS, Li JY, Brundin P.   "NeuroStem Chip": a novel highly specialized tool to study neural differentiation pathways in human stem cells.   BMC Genomics   2007 -2 -10   8   46   17288595   10.1186/1471-2164-8-46  
C.elegans   tm1866, tm2188   3426   Gilchrist EJ, O'Neil NJ, Rose AM, Zetka MC, Haughn GW.   TILLING is an effective reverse genetics technique for Caenorhabditis elegans.   BMC Genomics   2006 -10 -20   7   262   17049087   10.1186/1471-2164-7-262  
Information   E.coli   1757   Peng J, Zhang X, Yang J, Wang J, Yang E, Bin W, Wei C, Sun M, Jin Q.   The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella.   BMC Genomics   2006 -8 -31   7   218   16939645   10.1186/1471-2164-7-218  
Rice   W0106   28425   Hass-Jacobus BL, Futrell-Griggs M, Abernathy B, Westerman R, Goicoechea JL, Stein J, Klein P, Hurwitz B, Zhou B, Rakhshan F, Sanyal A, Gill N, Lin JY, Walling JG, Luo MZ, Ammiraju JS, Kudrna D, Kim HR, Ware D, Wing RA, San Miguel P, Jackson SA.   Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum.   BMC Genomics   2006 -8 -10   7   199   16895597   10.1186/1471-2164-7-199  
Cellular slime molds   S00041, S00044   29067   Rivero F, Muramoto T, Meyer AK, Urushihara H, Uyeda TQ, Kitayama C.   A comparative sequence analysis reveals a common GBD/FH3-FH1-FH2-DAD architecture in formins from Dictyostelium, fungi and metazoa.   BMC Genomics   2005 -3 -3   6   28   15740615   10.1186/1471-2164-6-28  
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