| Year |
Citation |
Score |
| 2019 |
Kono N, Nakamura H, Ohtoshi R, Moran DAP, Shinohara A, Yoshida Y, Fujiwara M, Mori M, Tomita M, Arakawa K. Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue. Scientific Reports. 9: 8380. PMID 31182776 DOI: 10.1038/S41598-019-44775-2 |
0.315 |
|
| 2019 |
Merino N, Zhang S, Tomita M, Suzuki H. Comparative genomics of Bacteria commonly identified in the built environment. Bmc Genomics. 20: 92. PMID 30691394 DOI: 10.1186/S12864-018-5389-Z |
0.303 |
|
| 2018 |
Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M, Yachie N. Fast and global detection of periodic sequence repeats in large genomic resources. Nucleic Acids Research. PMID 30304510 DOI: 10.1093/Nar/Gky890 |
0.322 |
|
| 2018 |
Yoshida Y, Konno S, Nishino R, Murai Y, Tomita M, Arakawa K. Ultralow Input Genome Sequencing Library Preparation from a Single Tardigrade Specimen. Journal of Visualized Experiments : Jove. PMID 30059025 DOI: 10.3791/57615 |
0.303 |
|
| 2018 |
Mariscal AM, Kakizawa S, Hsu JY, Tanaka K, González-González L, Broto A, Querol E, Lluch-Senar M, Piñero-Lambea C, Sun L, Weyman PD, Wise KS, Merryman C, Tse G, Moore AJ, ... ... Tomita M, et al. Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells. Acs Synthetic Biology. PMID 29786424 DOI: 10.1021/Acssynbio.8B00028 |
0.312 |
|
| 2017 |
Ikeda Y, Okada Y, Sato A, Kanai T, Tomita M, Atomi H, Kanai A. An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus. Scientific Reports. 7: 12674. PMID 28978920 DOI: 10.1038/S41598-017-13062-3 |
0.301 |
|
| 2017 |
Yoshida Y, Koutsovoulos G, Laetsch DR, Stevens L, Kumar S, Horikawa DD, Ishino K, Komine S, Kunieda T, Tomita M, Blaxter M, Arakawa K. Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. Plos Biology. 15: e2002266. PMID 28749982 DOI: 10.1371/Journal.Pbio.2002266 |
0.311 |
|
| 2016 |
Yoshida Y, Tomiyama T, Maruta T, Tomita M, Ishikawa T, Arakawa K. De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions. Bmc Genomics. 17: 182. PMID 26939900 DOI: 10.1186/S12864-016-2540-6 |
0.322 |
|
| 2016 |
Hamashima K, Tomita M, Kanai A. Expansion of Noncanonical V-Arm-Containing tRNAs in Eukaryotes. Molecular Biology and Evolution. 33: 530-40. PMID 26545920 DOI: 10.1093/Molbev/Msv253 |
0.301 |
|
| 2013 |
Matsui M, Tomita M, Kanai A. Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks. Genome Biology and Evolution. 5: 267-82. PMID 23315382 DOI: 10.1093/Gbe/Evt004 |
0.316 |
|
| 2013 |
Ohtani N, Tomita M, Itaya M. Identification of a replication initiation protein of the pVV8 plasmid from Thermus thermophilus HB8. Extremophiles : Life Under Extreme Conditions. 17: 15-28. PMID 23114983 DOI: 10.1007/S00792-012-0489-1 |
0.309 |
|
| 2012 |
Sugahara J, Fujishima K, Nunoura T, Takaki Y, Takami H, Takai K, Tomita M, Kanai A. Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption Plos One. 7. PMID 22403667 DOI: 10.1371/Journal.Pone.0032504 |
0.304 |
|
| 2012 |
Ohtani N, Tomita M, Itaya M. The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination. Extremophiles : Life Under Extreme Conditions. 16: 237-44. PMID 22212656 DOI: 10.1007/S00792-011-0424-X |
0.335 |
|
| 2012 |
Murakami S, Fujishima K, Tomita M, Kanai A. Metatranscriptomic analysis of microbes in an Oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation. Applied and Environmental Microbiology. 78: 1015-22. PMID 22156430 DOI: 10.1128/Aem.06811-11 |
0.308 |
|
| 2011 |
Saito R, Kohno K, Okada Y, Osada Y, Numata K, Kohama C, Watanabe K, Nakaoka H, Yamamoto N, Kanai A, Yasue H, Murata S, Abe K, Tomita M, Ohkohchi N, et al. Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes. Bmc Medical Genomics. 4: 42. PMID 21575255 DOI: 10.1186/1755-8794-4-42 |
0.323 |
|
| 2011 |
Helmy M, Tomita M, Ishihama Y. OryzaPG-DB: rice proteome database based on shotgun proteogenomics. Bmc Plant Biology. 11: 63. PMID 21486466 DOI: 10.1186/1471-2229-11-63 |
0.314 |
|
| 2010 |
Tsuchiya M, Piras V, Giuliani A, Tomita M, Selvarajoo K. Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: The existence of genome vehicles revealed Plos One. 5. PMID 20725638 DOI: 10.1371/Journal.Pone.0012116 |
0.322 |
|
| 2010 |
Fujishima K, Sugahara J, Tomita M, Kanai A. Large-Scale tRNA Intron Transposition in the Archaeal Order Thermoproteales Represents a Novel Mechanism of Intron Gain Molecular Biology and Evolution. 27: 2233-2243. PMID 20430862 DOI: 10.1093/Molbev/Msq111 |
0.32 |
|
| 2010 |
Saito N, Ohashi Y, Soga T, Tomita M. Unveiling cellular biochemical reactions via metabolomics-driven approaches. Current Opinion in Microbiology. 13: 358-362. PMID 20430690 DOI: 10.1016/J.Mib.2010.04.006 |
0.307 |
|
| 2009 |
Suzuki H, Saito R, Tomita M. Measure of synonymous codon usage diversity among genes in bacteria Bmc Bioinformatics. 10: 167-167. PMID 19480720 DOI: 10.1186/1471-2105-10-167 |
0.302 |
|
| 2009 |
Saito N, Robert M, Kochi H, Matsuo G, Kakazu Y, Soga T, Tomita M. Metabolite Profiling Reveals YihU as a Novel Hydroxybutyrate Dehydrogenase for Alternative Succinic Semialdehyde Metabolism in Escherichia coli Journal of Biological Chemistry. 284: 16442-16451. PMID 19372223 DOI: 10.1074/Jbc.M109.002089 |
0.301 |
|
| 2009 |
Tsuchiya M, Piras V, Choi S, Akira S, Tomita M, Giuliani A, Selvarajoo K. Emergent Genome-Wide Control in Wildtype and Genetically Mutated Lipopolysaccarides-Stimulated Macrophages Plos One. 4. PMID 19300509 DOI: 10.1371/Journal.Pone.0004905 |
0.309 |
|
| 2009 |
Fujishima K, Sugahara J, Kikuta K, Hirano R, Sato A, Tomita M, Kanai A. Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea Proceedings of the National Academy of Sciences of the United States of America. 106: 2683-2687. PMID 19190180 DOI: 10.1073/Pnas.0808246106 |
0.319 |
|
| 2009 |
Yachie N, Saito R, Sugahara J, Tomita M, Ishihama Y. In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution. Molecular & Cellular Proteomics : McP. 8: 1061-71. PMID 19136663 DOI: 10.1074/Mcp.M800466-Mcp200 |
0.311 |
|
| 2008 |
Sugahara J, Kikuta K, Fujishima K, Yachie N, Tomita M, Kanai A. Comprehensive Analysis of Archaeal tRNA Genes Reveals Rapid Increase of tRNA Introns in the Order Thermoproteales Molecular Biology and Evolution. 25: 2709-2716. PMID 18832079 DOI: 10.1093/Molbev/Msn216 |
0.314 |
|
| 2008 |
Kosugi S, Hasebe M, Tomita M, Yanagawa H. Nuclear Export Signal Consensus Sequences Defined Using a Localization-Based Yeast Selection System Traffic. 9: 2053-2062. PMID 18817528 DOI: 10.1111/J.1600-0854.2008.00825.X |
0.3 |
|
| 2008 |
Fujishima K, Sugahara J, Tomita M, Kanai A. Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves Plos One. 3. PMID 18286179 DOI: 10.1371/Journal.Pone.0001622 |
0.306 |
|
| 2008 |
Okada Y, Tashiro C, Numata K, Watanabe K, Nakaoka H, Yamamoto N, Okubo K, Ikeda R, Saito R, Kanai A, Abe K, Tomita M, Kiyosawa H. Comparative expression analysis uncovers novel features of endogenous antisense transcription. Human Molecular Genetics. 17: 1631-40. PMID 18283053 DOI: 10.1093/Hmg/Ddn051 |
0.304 |
|
| 2007 |
Soma A, Onodera A, Sugahara J, Kanai A, Yachie N, Tomita M, Kawamura F, Sekine Y. Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae Science. 318: 450-453. PMID 17947580 DOI: 10.1126/Science.1145718 |
0.301 |
|
| 2007 |
Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, ... ... Tomita M, et al. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science (New York, N.Y.). 316: 593-7. PMID 17379776 DOI: 10.1126/Science.1132067 |
0.308 |
|
| 2007 |
Sugahara J, Yachie N, Arakawa K, Tomita M. In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs Rna. 13: 671-681. PMID 17369313 DOI: 10.1261/Rna.309507 |
0.306 |
|
| 2007 |
Arakawa K, Uno R, Nakayama Y, Tomita M. Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli. Gene. 392: 239-46. PMID 17270364 DOI: 10.1016/J.Gene.2006.12.022 |
0.309 |
|
| 2007 |
Numata K, Okada Y, Saito R, Kiyosawa H, Kanai A, Tomita M. Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene. 392: 134-41. PMID 17250976 DOI: 10.1016/J.Gene.2006.12.005 |
0.317 |
|
| 2007 |
Mori K, Saito R, Kikuchi S, Tomita M. Inferring rules of Escherichia coli translational efficiency using an artificial neural network. Biosystems. 90: 414-420. PMID 17150301 DOI: 10.1016/J.Biosystems.2006.10.005 |
0.317 |
|
| 2006 |
Yachie N, Arakawa K, Tomita M. On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli Febs Letters. 580: 6909-6914. PMID 17156778 DOI: 10.1016/J.Febslet.2006.11.053 |
0.301 |
|
| 2006 |
Fujita H, Samejima H, Kitagawa N, Mitsuhashi T, Washio T, Yonemoto J, Tomita M, Takahashi T, Kosaki K. Genome-wide screening of dioxin-responsive genes in fetal brain: bioinformatic and experimental approaches. Congenital Anomalies. 46: 135-143. PMID 16922920 DOI: 10.1111/J.1741-4520.2006.00116.X |
0.305 |
|
| 2006 |
Uno R, Nakayama Y, Tomita M. Over-representation of Chi sequences caused by di-codon increase in Escherichia coli K-12. Gene. 380: 30-7. PMID 16854534 DOI: 10.1016/J.Gene.2006.05.013 |
0.309 |
|
| 2006 |
Yachie N, Numata K, Saito R, Kanai A, Tomita M. Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model. Gene. 372: 171-81. PMID 16564143 DOI: 10.1016/J.Gene.2005.12.034 |
0.32 |
|
| 2006 |
Arakawa K, Yamada Y, Shinoda K, Nakayama Y, Tomita M. GEM system: Automatic prototyping of cell-wide metabolic pathway models from genomes Bmc Bioinformatics. 7: 168-168. PMID 16553966 DOI: 10.1186/1471-2105-7-168 |
0.304 |
|
| 2006 |
Ishii K, Washio T, Uechi T, Yoshihama M, Kenmochi N, Tomita M. Characteristics and clustering of human ribosomal protein genes Bmc Genomics. 7: 37-37. PMID 16504170 DOI: 10.1186/1471-2164-7-37 |
0.309 |
|
| 2006 |
Arakawa K, Tomita M. G-language System as a platform for large-scale analysis of high-throughput omics data Journal of Pesticide Science. 31: 282-288. DOI: 10.1584/Jpestics.31.282 |
0.313 |
|
| 2005 |
Arakawa K, Suzuki H, Fujishima K, Fujimoto K, Ueda S, Matsui M, Tomita M. A comprehensive software suite for the analysis of cDNAs. Genomics, Proteomics & Bioinformatics. 3: 179-188. PMID 16487083 DOI: 10.1016/S1672-0229(05)03023-8 |
0.31 |
|
| 2005 |
Arita M, Robert M, Tomita M. All systems go: launching cell simulation fueled by integrated experimental biology data. Current Opinion in Biotechnology. 16: 344-349. PMID 15961035 DOI: 10.1016/J.Copbio.2005.04.004 |
0.313 |
|
| 2004 |
Ishii N, Robert M, Nakayama Y, Kanai A, Tomita M. Toward large-scale modeling of the microbial cell for computer simulation. Journal of Biotechnology. 113: 281-294. PMID 15380661 DOI: 10.1016/J.Jbiotec.2004.04.038 |
0.317 |
|
| 2004 |
Ohtani N, Yanagawa H, Tomita M, Itaya M. Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA-DNA junction. The Biochemical Journal. 381: 795-802. PMID 15115438 DOI: 10.1042/Bj20040153 |
0.302 |
|
| 2004 |
Wang E, Nakayama Y, Tomita M. Chapter seven Integrating genome and metabolome toward whole cell modeling with the E-cell system Recent Advances in Phytochemistry. 38: 139-151. DOI: 10.1016/S0079-9920(04)80008-X |
0.312 |
|
| 2003 |
Sato M, Umeki H, Saito R, Kanai A, Tomita M. Computational analysis of stop codon readthrough in D.melanogaster Bioinformatics. 19: 1371-1380. PMID 12874049 DOI: 10.1093/Bioinformatics/Btg183 |
0.331 |
|
| 2003 |
Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming LG, Hume DA, Hayashizaki Y, Tomita M. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Research. 13: 1301-6. PMID 12819127 DOI: 10.1101/Gr.1011603 |
0.311 |
|
| 2003 |
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, ... ... Tomita M, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (Oxford, England). 19: 524-31. PMID 12611808 DOI: 10.1093/Bioinformatics/Btg015 |
0.522 |
|
| 2003 |
Arakawa K, Yamada Y, Komai H, Shinoda K, Nakayama Y, Tomita M. Automatic Generation of Cell-Wide Pathway Model from Complete Genome Genome Informatics. 14: 639-640. DOI: 10.11234/Gi1990.14.639 |
0.341 |
|
| 2003 |
Itoh H, Washio T, Tomita M. Identifying Potential Regulatory Sequences of Alternative Splicing Genome Informatics. 14: 428-429. DOI: 10.11234/Gi1990.14.428 |
0.329 |
|
| 2002 |
Sakurai A, Fujimori S, Kochiwa H, Kitamura-Abe S, Washio T, Saito R, Carninci P, Hayashizaki Y, Tomita M. On biased distribution of introns in various eukaryotes. Gene. 300: 89-95. PMID 12468090 DOI: 10.1016/S0378-1119(02)01035-1 |
0.325 |
|
| 2002 |
Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, ... ... Tomita M, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 420: 563-73. PMID 12466851 DOI: 10.1038/Nature01266 |
0.305 |
|
| 2002 |
Kochiwa H, Suzuki R, Washio T, Saito R, Bono H, Carninci P, Okazaki Y, Miki R, Hayashizaki Y, Tomita M. Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. Genome Research. 12: 1286-93. PMID 12176936 DOI: 10.1101/Gr.220302 |
0.303 |
|
| 2002 |
Kosaki K, Kosaki R, Suzuki T, Yoshihashi H, Takahashi T, Sasaki K, Tomita M, McGinnis W, Matsuo N. Complete mutation analysis panel of the 39 human HOX genes. Teratology. 65: 50-62. PMID 11857506 DOI: 10.1002/Tera.10009 |
0.316 |
|
| 2002 |
Kyuma D, Arakawa K, Uno R, Nakayama Y, Tomita M. Development of Chi Sequence Analysis System on the G-Language Genome Analysis Environment Genome Informatics. 13: 533-534. DOI: 10.11234/Gi1990.13.533 |
0.307 |
|
| 2002 |
Nakamura S, Matsuzaki T, Arakawa K, Mori K, Nakayama Y, Tomita M. Development of Comparative Genome Analysis System (COMGA) on the G-Language Genome Analysis Environment Genome Informatics. 13: 531-532. DOI: 10.11234/Gi1990.13.531 |
0.301 |
|
| 2002 |
Takahashi K, Yugi K, Hashimoto K, Yamada Y, Pickett CJF, Tomita M. Computational challenges in cell simulation: a software engineering approach Ieee Intelligent Systems. 17: 64-71. DOI: 10.1109/Mis.2002.1039834 |
0.303 |
|
| 2001 |
Ohno H, Sakai H, Washio T, Tomita M. Preferential usage of some minor codons in bacteria. Gene. 276: 107-115. PMID 11591477 DOI: 10.1016/S0378-1119(01)00670-9 |
0.302 |
|
| 2001 |
Sakai H, Imamura C, Osada Y, Saito R, Washio T, Tomita M. Correlation between Shine--Dalgarno sequence conservation and codon usage of bacterial genes. Journal of Molecular Evolution. 52: 164-170. PMID 11231896 DOI: 10.1007/S002390010145 |
0.315 |
|
| 2001 |
Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, ... ... Tomita M, et al. Functional annotation of a full-length mouse cDNA collection. Nature. 409: 685-90. PMID 11217851 DOI: 10.1038/35055500 |
0.311 |
|
| 2000 |
Arakawa K, Uno R, Nakayama Y, Tomita M. Computational Analysis of the Strand Bias of the Chi Sequences and Other Oligonucleotides in Bacterial Genomes Genome Informatics. 11: 311-312. DOI: 10.11234/Gi1990.11.311 |
0.309 |
|
| 2000 |
Tomita M, Hashimoto K, Takahashi K, Matsuzaki Y, Matsushima R, Saito K, Yugi K, Miyoshi F, Nakano H, Tanida S, Saito Y, Kawase A, Watanabe N, Simizu TS, Nakayama Y. The E-CELL project: Towards integrative simulation of cellular processes New Generation Computing. 18: 1-12. DOI: 10.1007/Bf03037563 |
0.306 |
|
| 1999 |
Saito R, Tomita M. Computer analyses of complete genomes suggest that some archaebacteria employ both eukaryotic and eubacterial mechanisms in translation initiation. Gene. 238: 79-83. PMID 10570986 DOI: 10.1016/S0378-1119(99)00254-1 |
0.302 |
|
| 1999 |
Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA. E-CELL: software environment for whole-cell simulation. Bioinformatics (Oxford, England). 15: 72-84. PMID 10068694 DOI: 10.1093/Bioinformatics/15.1.72 |
0.35 |
|
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