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Items: 1 to 50 of 382

1.

Gene-by-gene or localized dosage compensation on the neo-X chromosome in Drosophila miranda.

Nozawa M, Ikeo K, Gojobori T.

Genome Biol Evol. 2018 Jul 7. doi: 10.1093/gbe/evy148. [Epub ahead of print]

PMID:
29986000
2.

Global Ramifications of Dust and Sandstorm Microbiota.

Behzad H, Mineta K, Gojobori T.

Genome Biol Evol. 2018 Jun 29. doi: 10.1093/gbe/evy134. [Epub ahead of print]

PMID:
29961874
3.

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters.

Othoum G, Bougouffa S, Razali R, Bokhari A, Alamoudi S, Antunes A, Gao X, Hoehndorf R, Arold ST, Gojobori T, Hirt H, Mijakovic I, Bajic VB, Lafi FF, Essack M.

BMC Genomics. 2018 May 22;19(1):382. doi: 10.1186/s12864-018-4796-5.

4.

Metagenome-based diversity analyses suggest a strong locality signal for bacterial communities associated with oyster aquaculture farms in Ofunato Bay.

Kobiyama A, Ikeo K, Reza MS, Rashid J, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Sato S, Ogata T, Jimbo M, Kudo T, Kaga S, Watanabe S, Naiki K, Kaga Y, Mineta K, Bajic V, Gojobori T, Watabe S.

Gene. 2018 Jul 30;665:149-154. doi: 10.1016/j.gene.2018.04.073. Epub 2018 Apr 30.

PMID:
29709640
5.

Seasonal changes in the communities of photosynthetic picoeukaryotes in Ofunato Bay as revealed by shotgun metagenomic sequencing.

Rashid J, Kobiyama A, Reza MS, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Kudo T, Kaga S, Watanabe S, Naiki K, Kaga Y, Mineta K, Bajic V, Gojobori T, Watabe S.

Gene. 2018 Jul 30;665:127-132. doi: 10.1016/j.gene.2018.04.071. Epub 2018 Apr 30.

PMID:
29709637
6.

Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis.

Kudo T, Kobiyama A, Rashid J, Reza MS, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Jimbo M, Kaga S, Watanabe S, Naiki K, Kaga Y, Segawa S, Mineta K, Bajic V, Gojobori T, Watabe S.

Gene. 2018 Jul 30;665:174-184. doi: 10.1016/j.gene.2018.04.072. Epub 2018 Apr 26.

PMID:
29705130
7.

Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay.

Reza MS, Kobiyama A, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Jimbo M, Kudo T, Kaga S, Watanabe S, Naiki K, Kaga Y, Mineta K, Bajic V, Gojobori T, Watabe S.

Gene. 2018 Jul 30;665:185-191. doi: 10.1016/j.gene.2018.04.074. Epub 2018 Apr 26.

PMID:
29705129
8.

Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay.

Reza MS, Kobiyama A, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Jimbo M, Kudo T, Kaga S, Watanabe S, Naiki K, Kaga Y, Mineta K, Bajic V, Gojobori T, Watabe S.

Gene. 2018 Jul 30;665:192-200. doi: 10.1016/j.gene.2018.04.075. Epub 2018 Apr 27.

PMID:
29705124
9.

Maser: one-stop platform for NGS big data from analysis to visualization.

Kinjo S, Monma N, Misu S, Kitamura N, Imoto J, Yoshitake K, Gojobori T, Ikeo K.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay027.

10.

Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms.

Pandit S, Ravikumar V, Abdel-Haleem AM, Derouiche A, Mokkapati VRSS, Sihlbom C, Mineta K, Gojobori T, Gao X, Westerlund F, Mijakovic I.

Front Microbiol. 2017 Dec 22;8:2599. doi: 10.3389/fmicb.2017.02599. eCollection 2017.

11.

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.

Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BO, Lewis NE, Jamshidi N.

PLoS Comput Biol. 2018 Jan 4;14(1):e1005895. doi: 10.1371/journal.pcbi.1005895. eCollection 2018 Jan.

12.

The Emerging Facets of Non-Cancerous Warburg Effect.

Abdel-Haleem AM, Lewis NE, Jamshidi N, Mineta K, Gao X, Gojobori T.

Front Endocrinol (Lausanne). 2017 Oct 23;8:279. doi: 10.3389/fendo.2017.00279. eCollection 2017.

13.

Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity.

Nielsen J, Archer J, Essack M, Bajic VB, Gojobori T, Mijakovic I.

Appl Microbiol Biotechnol. 2017 Jun;101(12):4837-4851. doi: 10.1007/s00253-017-8310-9. Epub 2017 May 20. Review.

14.

Corrigendum: The genome of Chenopodium quinoa.

Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B, Borm TJA, Ohyanagi H, Mineta K, Michell CT, Saber N, Kharbatia NM, Rupper RR, Sharp AR, Dally N, Boughton BA, Woo YH, Gao G, Schijlen EGWM, Guo X, Momin AA, Negrão S, Al-Babili S, Gehring C, Roessner U, Jung C, Murphy K, Arold ST, Gojobori T, van der Linden CG, van Loo EN, Jellen EN, Maughan PJ, Tester M.

Nature. 2017 May 25;545(7655):510. doi: 10.1038/nature22384. Epub 2017 May 10.

PMID:
28489823
15.

Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine-Dalgarno sequence in prokaryotes.

Nakagawa S, Niimura Y, Gojobori T.

Nucleic Acids Res. 2017 Apr 20;45(7):3922-3931. doi: 10.1093/nar/gkx124.

16.

The genome of Chenopodium quinoa.

Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B, Borm TJ, Ohyanagi H, Mineta K, Michell CT, Saber N, Kharbatia NM, Rupper RR, Sharp AR, Dally N, Boughton BA, Woo YH, Gao G, Schijlen EG, Guo X, Momin AA, Negrão S, Al-Babili S, Gehring C, Roessner U, Jung C, Murphy K, Arold ST, Gojobori T, Linden CG, van Loo EN, Jellen EN, Maughan PJ, Tester M.

Nature. 2017 Feb 16;542(7641):307-312. doi: 10.1038/nature21370. Epub 2017 Feb 8. Erratum in: Nature. 2017 May 25;545(7655):510.

PMID:
28178233
17.

In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria.

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.

BMC Genomics. 2017 Jan 5;18(1):33. doi: 10.1186/s12864-016-3389-4.

18.

VaProS: a database-integration approach for protein/genome information retrieval.

Gojobori T, Ikeo K, Katayama Y, Kawabata T, Kinjo AR, Kinoshita K, Kwon Y, Migita O, Mizutani H, Muraoka M, Nagata K, Omori S, Sugawara H, Yamada D, Yura K.

J Struct Funct Genomics. 2016 Dec;17(4):69-81. doi: 10.1007/s10969-016-9211-3. Epub 2016 Dec 23.

19.

FARNA: knowledgebase of inferred functions of non-coding RNA transcripts.

Alam T, Uludag M, Essack M, Salhi A, Ashoor H, Hanks JB, Kapfer C, Mineta K, Gojobori T, Bajic VB.

Nucleic Acids Res. 2017 Mar 17;45(5):2838-2848. doi: 10.1093/nar/gkw973.

20.

Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda.

Nozawa M, Onizuka K, Fujimi M, Ikeo K, Gojobori T.

Nat Commun. 2016 Nov 29;7:13659. doi: 10.1038/ncomms13659.

21.

Two-step evolution of endosymbiosis between hydra and algae.

Ishikawa M, Shimizu H, Nozawa M, Ikeo K, Gojobori T.

Mol Phylogenet Evol. 2016 Oct;103:19-25. doi: 10.1016/j.ympev.2016.07.010. Epub 2016 Jul 9.

PMID:
27404042
22.

Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis.

Ishikawa M, Yuyama I, Shimizu H, Nozawa M, Ikeo K, Gojobori T.

Genome Biol Evol. 2016 Aug 3;8(7):2155-63. doi: 10.1093/gbe/evw142.

23.

Selection pressure on human STR loci and its relevance in repeat expansion disease.

Shimada MK, Sanbonmatsu R, Yamaguchi-Kabata Y, Yamasaki C, Suzuki Y, Chakraborty R, Gojobori T, Imanishi T.

Mol Genet Genomics. 2016 Oct;291(5):1851-69. doi: 10.1007/s00438-016-1219-7. Epub 2016 Jun 11.

PMID:
27290643
24.

Evolutionary Transitions of MicroRNA-Target Pairs.

Nozawa M, Fujimi M, Iwamoto C, Onizuka K, Fukuda N, Ikeo K, Gojobori T.

Genome Biol Evol. 2016 Jun 4;8(5):1621-33. doi: 10.1093/gbe/evw092.

25.

Editorial.

Gojobori T, Wada T, Watabe S, Okamoto N, Bernardi G.

Gene. 2016 Feb 1;576(2 Pt 1):592. doi: 10.1016/j.gene.2015.11.017. No abstract available.

PMID:
26690055
26.

Comparative miRNAs analysis of Two contrasting broccoli inbred lines with divergent head-forming capacity under temperature stress.

Chen CC, Fu SF, Norikazu M, Yang YW, Liu YJ, Ikeo K, Gojobori T, Huang HJ.

BMC Genomics. 2015 Dec 1;16:1026. doi: 10.1186/s12864-015-2201-1.

27.

Marine Metagenome as A Resource for Novel Enzymes.

Alma'abadi AD, Gojobori T, Mineta K.

Genomics Proteomics Bioinformatics. 2015 Oct;13(5):290-5. doi: 10.1016/j.gpb.2015.10.001. Epub 2015 Nov 10. Review.

28.

DESM: portal for microbial knowledge exploration systems.

Salhi A, Essack M, Radovanovic A, Marchand B, Bougouffa S, Antunes A, Simoes MF, Lafi FF, Motwalli OA, Bokhari A, Malas T, Amoudi SA, Othum G, Allam I, Mineta K, Gao X, Hoehndorf R, C Archer JA, Gojobori T, Bajic VB.

Nucleic Acids Res. 2016 Jan 4;44(D1):D624-33. doi: 10.1093/nar/gkv1147. Epub 2015 Nov 5.

29.

Metagenomic studies of the Red Sea.

Behzad H, Ibarra MA, Mineta K, Gojobori T.

Gene. 2016 Feb 1;576(2 Pt 1):717-23. doi: 10.1016/j.gene.2015.10.034. Epub 2015 Oct 23. Review.

PMID:
26526132
30.

Databases of the marine metagenomics.

Mineta K, Gojobori T.

Gene. 2016 Feb 1;576(2 Pt 1):724-8. doi: 10.1016/j.gene.2015.10.035. Epub 2015 Oct 28. Review.

PMID:
26518717
31.

Speciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analyses.

Akihito, Akishinonomiya F, Ikeda Y, Aizawa M, Nakagawa S, Umehara Y, Yonezawa T, Mano S, Hasegawa M, Nakabo T, Gojobori T.

Gene. 2016 Feb 1;576(2 Pt 1):593-602. doi: 10.1016/j.gene.2015.10.014. Epub 2015 Oct 28.

PMID:
26475939
32.

Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique.

Nagai S, Hida K, Urushizaki S, Onitsuka G, Yasuike M, Nakamura Y, Fujiwara A, Tajimi S, Kimoto K, Kobayashi T, Gojobori T, Ototake M.

Gene. 2016 Feb 1;576(2 Pt 1):667-75. doi: 10.1016/j.gene.2015.10.025. Epub 2015 Oct 16.

PMID:
26475937
33.

V-GAP: Viral genome assembly pipeline.

Nakamura Y, Yasuike M, Nishiki I, Iwasaki Y, Fujiwara A, Kawato Y, Nakai T, Nagai S, Kobayashi T, Gojobori T, Ototake M.

Gene. 2016 Feb 1;576(2 Pt 1):676-80. doi: 10.1016/j.gene.2015.10.029. Epub 2015 Oct 22.

34.

Single-cell technologies in environmental omics.

Kodzius R, Gojobori T.

Gene. 2016 Feb 1;576(2 Pt 1):701-7. doi: 10.1016/j.gene.2015.10.031. Epub 2015 Oct 22. Review.

PMID:
26474748
35.

Marine metagenomics as a source for bioprospecting.

Kodzius R, Gojobori T.

Mar Genomics. 2015 Dec;24 Pt 1:21-30. doi: 10.1016/j.margen.2015.07.001. Epub 2015 Aug 12. Review.

36.

Eye-like ocelloids are built from different endosymbiotically acquired components.

Gavelis GS, Hayakawa S, White RA 3rd, Gojobori T, Suttle CA, Keeling PJ, Leander BS.

Nature. 2015 Jul 9;523(7559):204-7. doi: 10.1038/nature14593. Epub 2015 Jul 1.

PMID:
26131935
37.

Challenges and opportunities of airborne metagenomics.

Behzad H, Gojobori T, Mineta K.

Genome Biol Evol. 2015 May 6;7(5):1216-26. doi: 10.1093/gbe/evv064. Review.

38.

Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts.

Huang CL, Pu PH, Huang HJ, Sung HM, Liaw HJ, Chen YM, Chen CM, Huang MB, Osada N, Gojobori T, Pai TW, Chen YT, Hwang CC, Chiang TY.

BMC Genomics. 2015 Mar 15;16:188. doi: 10.1186/s12864-015-1369-8.

39.

Function and evolutionary origin of unicellular camera-type eye structure.

Hayakawa S, Takaku Y, Hwang JS, Horiguchi T, Suga H, Gehring W, Ikeo K, Gojobori T.

PLoS One. 2015 Mar 3;10(3):e0118415. doi: 10.1371/journal.pone.0118415. eCollection 2015.

40.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae).

Huang CL, Ho CW, Chiang YC, Shigemoto Y, Hsu TW, Hwang CC, Ge XJ, Chen C, Wu TH, Chou CH, Huang HJ, Gojobori T, Osada N, Chiang TY.

Plant J. 2014 Dec;80(5):834-47. doi: 10.1111/tpj.12676. Epub 2014 Nov 11.

41.

Dopamine receptor genes and evolutionary differentiation in the domestication of fighting cocks and long-crowing chickens.

Komiyama T, Iwama H, Osada N, Nakamura Y, Kobayashi H, Tateno Y, Gojobori T.

PLoS One. 2014 Jul 31;9(7):e101778. doi: 10.1371/journal.pone.0101778. eCollection 2014.

42.

Evolutionarily conserved transcription factor Apontic controls the G1/S progression by inducing cyclin E during eye development.

Liu QX, Wang XF, Ikeo K, Hirose S, Gehring WJ, Gojobori T.

Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9497-502. doi: 10.1073/pnas.1407145111. Epub 2014 Jun 16.

43.

Human genome network platform: a resource for TFRN analysis.

Monma N, Gojobori T, Ikeo K.

Methods Mol Biol. 2014;1164:147-62. doi: 10.1007/978-1-4939-0805-9_12.

PMID:
24927841
44.

Coevolution of axon guidance molecule Slit and its receptor Robo.

Yu Q, Li XT, Zhao X, Liu XL, Ikeo K, Gojobori T, Liu QX.

PLoS One. 2014 May 6;9(5):e94970. doi: 10.1371/journal.pone.0094970. eCollection 2014. Erratum in: PLoS One. 2014;9(10):e110582..

45.

Innexin gap junctions in nerve cells coordinate spontaneous contractile behavior in Hydra polyps.

Takaku Y, Hwang JS, Wolf A, Böttger A, Shimizu H, David CN, Gojobori T.

Sci Rep. 2014 Jan 7;4:3573. doi: 10.1038/srep03573. Erratum in: Sci Rep. 2014;4:4009.

46.

Tissue- and stage-dependent dosage compensation on the neo-X chromosome in Drosophila pseudoobscura.

Nozawa M, Fukuda N, Ikeo K, Gojobori T.

Mol Biol Evol. 2014 Mar;31(3):614-24. doi: 10.1093/molbev/mst239. Epub 2013 Dec 3.

PMID:
24307686
47.

Computational analysis and functional expression of ancestral copepod luciferase.

Takenaka Y, Noda-Ogura A, Imanishi T, Yamaguchi A, Gojobori T, Shigeri Y.

Gene. 2013 Oct 10;528(2):201-5. doi: 10.1016/j.gene.2013.07.011. Epub 2013 Jul 23.

PMID:
23886588
48.

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.

Nakamura Y, Mori K, Saitoh K, Oshima K, Mekuchi M, Sugaya T, Shigenobu Y, Ojima N, Muta S, Fujiwara A, Yasuike M, Oohara I, Hirakawa H, Chowdhury VS, Kobayashi T, Nakajima K, Sano M, Wada T, Tashiro K, Ikeo K, Hattori M, Kuhara S, Gojobori T, Inouye K.

Proc Natl Acad Sci U S A. 2013 Jul 2;110(27):11061-6. doi: 10.1073/pnas.1302051110. Epub 2013 Jun 18.

49.

The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis).

Nakamura Y, Sasaki N, Kobayashi M, Ojima N, Yasuike M, Shigenobu Y, Satomi M, Fukuma Y, Shiwaku K, Tsujimoto A, Kobayashi T, Nakayama I, Ito F, Nakajima K, Sano M, Wada T, Kuhara S, Inouye K, Gojobori T, Ikeo K.

PLoS One. 2013;8(3):e57122. doi: 10.1371/journal.pone.0057122. Epub 2013 Mar 11.

50.

Comparison of gene expression profile of epiretinal membranes obtained from eyes with proliferative vitreoretinopathy to that of secondary epiretinal membranes.

Asato R, Yoshida S, Ogura A, Nakama T, Ishikawa K, Nakao S, Sassa Y, Enaida H, Oshima Y, Ikeo K, Gojobori T, Kono T, Ishibashi T.

PLoS One. 2013;8(1):e54191. doi: 10.1371/journal.pone.0054191. Epub 2013 Jan 23. Erratum in: PLoS One. 2013;8(4). doi:10.1371/annotation/6032dd20-65b4-4d4d-bef6-7ba2ef6d3591.

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