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1,228 results
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In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs.
Sugahara J, Yachie N, Arakawa K, Tomita M. Sugahara J, et al. Among authors: arakawa k. RNA. 2007 May;13(5):671-81. doi: 10.1261/rna.309507. Epub 2007 Mar 16. RNA. 2007. PMID: 17369313 Free PMC article.
A comprehensive software suite for the analysis of cDNAs.
Arakawa K, Suzuki H, Fujishima K, Fujimoto K, Ueda S, Matsui M, Tomita M. Arakawa K, et al. Genomics Proteomics Bioinformatics. 2005 Aug;3(3):179-88. doi: 10.1016/s1672-0229(05)03023-8. Genomics Proteomics Bioinformatics. 2005. PMID: 16487083 Free PMC article.
Noise-reduction filtering for accurate detection of replication termini in bacterial genomes.
Arakawa K, Saito R, Tomita M. Arakawa K, et al. FEBS Lett. 2007 Jan 23;581(2):253-8. doi: 10.1016/j.febslet.2006.12.021. Epub 2006 Dec 18. FEBS Lett. 2007. PMID: 17188685
Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli.
Arakawa K, Uno R, Nakayama Y, Tomita M. Arakawa K, et al. Gene. 2007 May 1;392(1-2):239-46. doi: 10.1016/j.gene.2006.12.022. Epub 2007 Jan 12. Gene. 2007. PMID: 17270364
Multiple high-throughput analyses monitor the response of E. coli to perturbations.
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, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M. Ishii N, et al. Among authors: arakawa k. Science. 2007 Apr 27;316(5824):593-7. doi: 10.1126/science.1132067. Epub 2007 Mar 22. Science. 2007. PMID: 17379776
Restauro-G: a rapid genome re-annotation system for comparative genomics.
Tamaki S, Arakawa K, Kono N, Tomita M. Tamaki S, et al. Among authors: arakawa k. Genomics Proteomics Bioinformatics. 2007 Feb;5(1):53-8. doi: 10.1016/S1672-0229(07)60014-X. Genomics Proteomics Bioinformatics. 2007. PMID: 17572364 Free PMC article.
Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes.
Arakawa K, Tomita M. Arakawa K, et al. Evol Bioinform Online. 2007 Oct 9;3:279-86. Evol Bioinform Online. 2007. PMID: 19461975 Free PMC article.
Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index.
Arakawa K, Suzuki H, Tomita M. Arakawa K, et al. BMC Genomics. 2009 Dec 30;10:640. doi: 10.1186/1471-2164-10-640. BMC Genomics. 2009. PMID: 20042086 Free PMC article.
Validation of bacterial replication termination models using simulation of genomic mutations.
Kono N, Arakawa K, Tomita M. Kono N, et al. Among authors: arakawa k. PLoS One. 2012;7(4):e34526. doi: 10.1371/journal.pone.0034526. Epub 2012 Apr 3. PLoS One. 2012. PMID: 22509315 Free PMC article.
Merging multiple omics datasets in silico: statistical analyses and data interpretation.
Arakawa K, Tomita M. Arakawa K, et al. Methods Mol Biol. 2013;985:459-70. doi: 10.1007/978-1-62703-299-5_23. Methods Mol Biol. 2013. PMID: 23417818
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