Papers - Kanai, Akio

Computational analysis of microRNA-mediated antiviral defense in Humans.

Watanabe, Y., Kishi, A., Yachie, N., Kanai, A. and Tomita, M.

FEBS Letters 581 ( 24 ) 4603-4610 2007.10

Research paper (scientific journal), Joint Work, Accepted

Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes.

Kochiwa, H., Tomita, M. and Kanai, A.

BMC Evolutionary Biology 7 ( 128 )  2007.07

Research paper (scientific journal), Joint Work, Accepted

Proteome-wide prediction of novel RNA/DNA-binding proteins using amino acid composition and periodicity in hyperthermophilic archeaon Pyrococcus furiosus.

Fujishima, K., Komasa, M., Kitamura, S., Suzuki, H., Tomita, M. and Kanai, A.

DNA Research 14   91-102 2007.06

Research paper (scientific journal), Joint Work

Comparative analysis of cis-encoded antisense RNAs in eukaryotes.

Numata, K., Okada, Y., Saito, R., Kiyosawa, H., Kanai, A., and Tomita, M.

Gene 392   134-141 2007.05

Research paper (scientific journal), Joint Work, Accepted

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., 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. and Tomita, M.

Science (AAAS)  316   593 - 597 2007.04

Research paper (scientific journal), Joint Work, Lead author, Accepted

　View Summary

Analysis of cellular components at multiple levels of biological information can provide valuable functional insights. We performed multiple high-throughput measurements to study the response of Escherichia coli cells to genetic and environmental perturbations. Analysis of metabolic enzyme gene disruptants revealed unexpectedly small changes in messenger RNA and proteins for most disruptants. Overall, metabolite levels were also stable, reflecting the rerouting of fluxes in the metabolic network. In contrast, E. coli actively regulated enzyme levels to maintain a stable metabolic state in response to changes in growth rate. E. coli thus seems to use complementary strategies that result in a metabolic network robust against perturbations.

• Access to Document (DOI)

Computational method for microRNA target prediction.

Watanabe, Y., Tomita, M. and Kanai, A.

Methods in Enzymology 427   65-86. 2007

Research paper (scientific journal), Joint Work

Importance of systematic identification of RNA-binding proteins in a hyperthermophilic archaeon

KANAI AKIO

Viva Origino 34   144-147. 2006.12

Research paper (scientific journal), Single Work, Accepted

1H, 13C and 15N resonance assignments of the 2’-5’ RNA ligase-like protein from Pyrococcus furiosus.

Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kanai, A. and Kawai, G.

Journal of Biomolecular NMR  2006.02

Research paper (scientific journal), Joint Work, Accepted

Computational analysis of micro RNA targets in Caenorhabditis elegans.

Watanabe, Y., Yachie, N., Numata, K., Saito, R., Kanai, A. and Tomita, M.

Gene 365   2-10 2006.01

Research paper (scientific journal), Joint Work, Accepted

Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein.

KANAI AKIO, Sato, A., Imoto, J. and Tomita, M.

Biochemical Journal 393   373-379 2006.01

Research paper (scientific journal), Joint Work, Accepted

Stage-specific expression of Caenorhabditis elegans ribonuclease H1 enzymes with different substrate specificity and bivalent cation requirements.

Kochiwa, H., Itaya, M., Tomita, M. and KANAI A.

FEBS Journal 273   420-429 2006.01

Research paper (scientific journal), Joint Work, Accepted

SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level.

Sugahara, J., Yachie, N., Sekine, Y., Soma, A., Matsui, M., Tomita, M. and Kanai, A.

In Silico Biology 6   411-418 2006

Research paper (scientific journal), Joint Work, Accepted

Prediction of non-coding and antisense RNA genes in the Escherichia coli with Gapped Markov Model.

Yachie, N., Numata, K., Saito, R., Kanai, A. and Tomita, M.

Gene 372   171-181 2006

Research paper (scientific journal), Joint Work, Accepted

Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus.

Okada, K., Takahashi, M., Sakamoto, T., Kawai, G., Nakamura, K. and Kanai, A.

Nucleosides, Nucleotides & Nucleic Acids 25   383-395 2006

Research paper (scientific journal), Joint Work, Accepted

Identification and expression analysis of mRNA-like non-coding RNAs in Drosophila.

Inagaki, S., Numata, K., Kondo, T., Tomita, M., Yasuda, K., Kanai, A. and Kageyama, Y.

Genes to Cells 10   1163-1173 2005.12

Research paper (scientific journal), Joint Work, Accepted

Toward large-scale modeling of the microbial cell for computer simulation

ISHII N, ROBERT M, NAKAYAMA Y, KANAI A, TOMITA M

Journal of Biotechnology 113 ( 1/3 ) 281-294 2004.09

Research paper (scientific journal), Joint Work,  ISSN  01681656

Cooperative regulation for Okazaki fragment processing by RNase HII and FEN-1 purified from a hyperthermophilic archaeon, Pyrococcus furiosus

Sato A, Kanai A, Itaya M, Tomita M

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 309 ( 1 ) 247-252 2003.09

Research paper (scientific journal), Joint Work,  ISSN  0006-291X

Computational analysis of stop codon readthrough in D-melanogaster

Sato M, Umeki H, Saito R, Kanai A, Tomita M

BIOINFORMATICS 19 ( 11 ) 1371-1380 2003.07

Research paper (scientific journal), Joint Work,  ISSN  1367-4803

Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection

Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming LG, Hume DA, Hayashizaki Y, Tomita M

GENOME RESEARCH 13 ( 6B ) 1301-1306 2003.06

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1088-9051

　View Summary

With the sequencing and annotation of genomes and transcriptomes of several eukaryotes, the importance of noncoding RNA (ncRNA)-RNA molecules that are not translated to protein products-has become more evident. A subclass of ncRNA transcripts are encoded by highly regulated, multi-exon, transcriptional units, are processed like typical protein-coding mRNAs and are increasingly implicated in regulation of many cellular functions in eukaryotes. This study describes the identification of candidate functional ncRNAs from among the RIKEN mouse full-length cDNA collection, which contains 60,770 sequences, by using a systematic computational filtering approach. We initially searched for previously reported ncRNAs and found nine murine ncRNAs and homologs of several previously described nonmouse ncRNAs. Through our computational approach to filter artifact-free clones that lack protein coding potential, we extracted 4280 transcripts as the largest-candidate set. Many clones in the set had EST hits, potential CpG islands surrounding the transcription start sites, and homologies with the human genome. This implies that many candidates are indeed transcribed in a regulated manner. Our results demonstrate that ncRNAs are a major functional subclass of processed transcripts in mammals.

• Access to Document (DOI)

Expression cloning and characterization of a novel gene that encodes the RNA-binding protein FAU-1 from Pyrococcus furiosus

Kanai A, Oida H, Matsuura N, Doi H

BIOCHEMICAL JOURNAL 372   253-261 2003.05

Research paper (scientific journal), Joint Work,  ISSN  0264-6021