List of Publications (English)

Nakai, K., Kidera, A., and Kanehisa, M., Cluster analysis of amino acid indices for prediction of protein structure and function, Protein Engineering 2, 93-100 (1988).
(PubMed)

Nakai, K. and Kanehisa, M., Prediction of in-vivo modification sites of proteins from their primary structures, J. Biochem. (Tokyo) 104, 693-699 (1988).
(PubMed)

Tomita, M., Nakai, K., Yamada, A., Taguchi, R., and Ikezawa, H., Secondary structure of sphingomyelinase from Bacillus cereus, J. Biochem. (Tokyo) 108, 811-815 (1990).
(PubMed)

Nakai, K. and Kanehisa, M., Expert system for predicting protein localization sites in Gram-negative bacteria, PROTEINS: Structure, Function, and Genetics 11, 95-110 (1991).
(PubMed)

Nakai, K., Predicting various targeting signals in amino acid sequences, Bull. Inst. Chem. Res., Kyoto Univ. 69, 269-291 (1991).
(Click here to get more information)

Nakai, K. and Kanehisa, M., A knowledge base for predicting protein localization sites in eukaryotic cells, Genomics 14, 897-911 (1992).
(PubMed)

Goffeau, A., Nakai, K., Slonimski, P., and Risler, J.-L., The membrane proteins encoded by yeast chromosome III genes, FEBS Lett. 325, 112-117 (1993).
(PubMed)

Goffeau, A., Slonimski, P., Nakai, K., and Risler, J.L., How many yeast genes code for membrane-spanning proteins?, Yeast 9, 691-702 (1993).
(PubMed)

Nakai, K. and Sakamoto, H., Construction of a novel database containing aberrant splicing mutations of mammalian genes, Gene 141, 171-177 (1994).
(PubMed)

Nakai, K., Tokimori, T., Ogiwara, A., Uchiyama, I., and Niiyama, T., Gnome -- an Internet-based sequence analysis tool, Comp. Appl. Biosci. 10, 547-550 (1994).
(PubMed)

Horton, P. and Nakai, K., A probabilistic classification system for predicting the cellular localization sites of proteins, Intellig. Syst. Mol. Biol. 4, 109-115 (1996).
(PubMed)

Nakai, K., Refinement of the prediction methods of signal peptides for the genome analyses of Saccharomyces cerevisiae and Bacillus subtilis, Genome Informatics Workshop GIW-96,72-81 (1996).
(Click here to get more information)

Horton, P. and Nakai, K., Better prediction of protein cellular localization sites with the k nearest neighbor classifier, Intellig. Syst. Mol. Biol. 5, 147-152 (1997).
(PubMed)

Yada, T., Totoki, Y., Ishii, T., and Nakai, K., Functional prediction of B. subtilis genes from their regulatory sequences Intellig. Syst. Mol. Biol. 5, 354-357 (1997).
(PubMed)

Fujiwara, Y., Asogawa, M., and Nakai, K., Prediction of mitochondrial targeting signals using hidden Markov models, Genome Informatics 1997, 53-60, (1997).
(PubMed)

Yoshioka, S., Kato, K., Nakai, K., Okayama, H., and Nojima, H., Identification of Open Reading Frames in Schizosaccharomyces pombe cDNAs, DNA Res., 4, 363-369 (1997).
(PubMed)

Yoshikawa, H., Fujiyama, A., Nakai, K., Inazawa, J., and Matsubara, K., Detection and isolation of a novel human gene located on Xp11.2-p11.4 that escapes X-inactivation using a two-dimensional DNA mapping method, Genomics, 49(2), 237-246 (1998).
(PubMed)

Hagiwara, K., Tomita, M., Nakai, K., Kobayashi, J., Miyajima, S., and Yoshimura, T., Determination of the nucleotide sequence of Bombyx mori cytoplasmic polyhedrosis virus segment 9 and its expression in BmN4 cells, J. Virol., 72(7) 5762-5768 (1998).
(PubMed)

Yada, T., Totoki, Y., Ishikawa, M., Asai, K., and Nakai, K., Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences, Bioinformatics, 14(4) 317-325 (1998).
(PubMed)

Miyajima, S., Mori, A., Hagiwara, K., Kobayashi, J., Yoshimura, T., Nakai, K., Suzuki, Y., and Tomita, M., Microheterogeneity in the polyhedrin gene of Bombyx mori, a cytoplasmic polyhedrosis virus, J. Seric. Sci. Jpn, 67(4) 287-294 (1998).

Nakai, K. and Horton, P., PSORT: a program for detecting the sorting signals of proteins and predicting their subcellular localization, Trends Biochem. Sci, 24(1) 34-35 (1999).
(PubMed)

Yada, T., Nakao, M., Totoki, Y., and Nakai, K., Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models, Bioinformatics, 15(12) 987-993 (1999).
(PubMed)

Nakai, K, Protein sorting signals and prediction of subcellular localization, Adv. Protein Chem., 54, 277-344 (2000).
(PubMed)

Stamm, S., Zhu, J., Nakai, K., Stoilov, P., Stoss, O. and Zhang, M.Q., An alternative exon database (AEDB) and its statistical analysis, DNA Cell Biol., 19(12), 739-756 (2000).
(PubMed)

Ishii, T., Yoshida, K., Terai, G., Fujita, Y., and Nakai, K., DBTBS: A database of Bacillus subtilis promoters and transcription factors, Nucleic Acids Res., 29, 278-280 (2001).
(PubMed)

Mizuno, H., Tanaka, Y., Nakai, K., and Sarai, A., ORI-GENE: gene classification based on the evolutionary tree, Bioinformatics, 17(2), 167-173 (2001).
(PubMed)

Hishigaki, H., Nakai, K., Ono, T., Tanigami, A., and Takagi, T., Assessment of prediction accuracy of protein function from protein-protein interaction data, Yeast, 18(6), 523-531 (2001).
(PubMed)

Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S., Views: fundamental building blocks in the process of knowledge discovery, Proc. 14th Int. FLAIRS Conf., 233-238, AAAI Press (2001).
(PDF)

Yada, T., Totoki, Y., Takagi, T., and Nakai, K., A novel bacterial gene-finding system with top-class accuracy in locating start codons, DNA Res., 8(3), 97-106 (2001).
(PDF)

Miura, F., Yada, T., Nakai, K., Sakaki, Y., and Ito, T., Differential display analysis of mutants for the transcription factor Pdr1p regulating multidrug resistance in the budding yeast, FEBS Lett., 505, 103-108 (2001).
(PubMed)

Nakai, K., Prediction of in vivo fates of proteins in the era of genomics and proteomics, J. Struct. Biol., 134(2/3), 103-116 (2001).
(PubMed)

Terai, G., Takagi, T., and Nakai, K., Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species, Genome Biology, 2(11), research0048.1-0048.12 (2001).
(full text / pdf)

Suzuki, Y., Yamashita, R., Nakai, K., and Sugano, S., DBTSS: database of human transcriptional start sites and full-length cDNAs, Nucl. Acids Res., 30(1), 328-331 (2002).
(abstract / pdf)

Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S., Extensive feature detection of N-terminal protein sorting signals, Bioinformatics, 18(2), 298-305 (2002).
(abstract)

Nakai, K. and Vert, J.-P., Genome informatics for data-driven biology: A report on the twelfth international conference on genome informatics, Tokyo, Japan, December 17-19, 2001, Genome Biology, 3(4), reports4010.1-4010.3 (2002).
(PubMed)

Nakai, K. Chapter 14: Signal peptides, in Ulo Langel (ed.), Cell-Penetrating Peptides: Processes and Applications, 295-324, CRC Press (2002).

Terashima, H., Fukuchi, S., Nakai, K., Arisawa, M., Hamada, K., Yabuki, N., and Kitada, K., Sequence-based approach for identification of cell wall proteins in Saccharomyces cerevisiae, Current Genetics, 40(5), 311-316 (2002).
(
abstract, pdf).

Koike, A., Nakai, K., and Takagi, T., The origin and evolution of eukaryotic protein kinases, Genome Lett., 1(2), 83-104 (2002).
(abstract).

Ott, S., Tamada, Y., Bannai, H., Nakai, K., and Miyano, S., Intrasplicing: analysis of long intron sequences, Pacific Symposium on Biocomputing, 8, 339-350 (2003).
(pdf).

Poluliakh, N., Takagi, T., and Nakai, K., MELINA: motif extraction from promoter regions of potentially co-regulated genes, Bioinformatics, 19(3), 423-424 (2003).
(PubMed)

Gardy, J. L., Spencer, C., Wang, K., Ester, M., Tusnady, G. E., Simon, I., Hua, S., deFays, K., Lambert, C., Nakai, K., and Brinkman, F. S. L., PSORT-B: Improving protein subcelular localization prediction for Gram-negative bacteria, Nucl. Acids Res., 31(13), 3613-3617 (2003).
(abstract)

Yamashita, R., Suzuki, Y., Nakai, K., and Sugano, S., Small open reading frames in 5' untranslated regions of mRNAs, C. R. Biol., 326(10-11), 987-991 (2003).
(abstract)

Makita, Y., Nakao, M., Ogasawara, N., and Nakai, K., DBTBS: Database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics, Nucl. Acids Res., 32, D75-D77 (2004)
(full text)

Suzuki, Y., Yamashita, R., Sugano, S., and Nakai, K., DBTSS (DataBase of Transcriptional Start Sites): Progress Report 2004, Nucl. Acids Res., 32, D78-D81 (2004).
(full text)

Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y, Nakamura Y, Nagahari K, Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M, Takahashi M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki M, Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Chiba Y, Ishida S, Ono Y, Takiguchi S, Watanabe S, Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii A, Hara H, Tanase TO, Nomura Y, Togiya S, Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, Matsunawa H, Ichihara T, Shiohata N, Sano S, Moriya S, Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Nakagawa S, Senoh A, Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Takemoto M, Kawakami B, Yamazaki M, Watanabe K, Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, Fujii Y, Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Kawakami T, Noguchi S, Itoh T, Shigeta K, Senba T, Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki M, Togashi T, Oyama M, Hata H, Watanabe M, Komatsu T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y, Yamashita R, Nakai K, Yada T, Nakamura Y, Ohara O, Isogai T, and Sugano S, Complete sequencing and characterization of 21,243 full-length human cDNAs, Nat. Genet., 36(1), 40-45 (2004).
(PubMed)

Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda JI, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Md M, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, R Gopinath G, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, and Sugano S., Integrative annotation of 21,037 human genes validated by full-length cDNA clones, PLoS Biol., 2(6), E162 (2004).
(full text)

Horton, P., Mukai, Y., and Nakai, K., Chapter 14: Protein subcellular localization prediction, in L. Wong (ed.), Practical Bioinformatician, World Scientific Publishing Co., pp.193-216, 2004.

De Hoon, M.J.L., Makita, Y., Imoto, S., Kobayashi, K., Ogasawara, N., Nakai, K., and Miyano, S., Predicting gene regulation by sigma factors in Bacilllus subtilis from genome-wide data, Bioinformatics, 20(Supp. 1), I101-I108 (2004).
(PubMed)

Suzuki, Y., Yamashita, R., Shirota, M., Sakakibara, Y., Chiba, J., Mizushima-Sugano, J., Kel, A. E., Arakawa, T., Caminci, P., Kawai, J., Hayashizaki, Y., Takagi, T., Nakai, K., and Sugano, S., Large-scale collection and characterization of promoters of human and mouse genes, In silico Biol., 4, 0036 (2004).
(full text)

Suzuki, Y., Yamashita, R., Shirota, M., Sakakibara, Y., Chiba, J., Mizushima-Sugano, J., Nakai, K., and Sugano, S., Sequence comparison of human and mouse genes reveals a homolgous block structure in the promoter regions, Genome Res., 14, 1711-1718 (2004).
(abstract)

Bannai, H., Hyyro, H., Shinohara, A., Takeda, M., Nakai, K., and Miyano, S., Finding optimal pairs of patterns, Lecture Notes in Comp. Sci. (WABI 2004), 3240, 450-462 (2004).
(abstract)

Inenaga, S., Bannai, H., Hyyro, H., Shinohara, A., Takeda, M., Nakai, K., and Miyano, S., Finding optimal pairs of cooperative and competing patterns with bounded distance, Lecture Notes in Comp. Sci. (DS 2004),, 3245 32-46 (2004).
(abstract)

Bannai, H., Hyyro, H., Shinohara, A., Takeda, M., Nakai, K., and Miyano, S., An O(N^2) algorithm for discovering optimal boolean pattern pairs, IEEE/ACM Transactions on Computational Biology and Bioinformatics (special section on the Workshop on Algorithms in Bioinformatics), 1(4), 159-170 (2004).

Kato, K., Yamashita, R., Matoba, R., Monden, M., Noguchi, S., Takagi, T., and Nakai, K., Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues, Nucl. Acids Res., 33, D533-D536 (2005).
(full text)

Makita, Y., De Hoon, M.J.L., Ogasawara, N., Miyano, S., and Nakai, K., Bayesian joint prediction of associated transcription factors in Bacillus subtilis, Pacific Symposium on Biocomputing 2005 (Altman et al ed.), 507-518, World Scientific (2005).
(full paper)

Poluliakh, N., Konno, M., Horton, P., and Nakai, K., Parameter landscape analysis for common motif discovery programs, in Eskin, E. & Workman, C. (eds.), Regulatory Genomics, RECOMB 2004 International Workshop, RRG 2004, San Diego, CA, USA, March 26-27, 2004, Revised Selected Papers. Lecture Notes in Computer Science 3318, pp. 79-87, Springer (2005).
(abstract)

Yamashita, R., Suzuki, Y., Sugano, S., and Nakai, K., Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue-specificity, Gene, 350(2), 129-136 (2005); Mar 17, 2005 (Epub)
(abstract)

Nakao, M., Barrero, R.A., Mukai, Y., Motono, C., Suwa, M., and Nakai, K., Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals, Nucl. Acids Res., 33(8), 2355-2363, (2005); published online 28 April 2005
(full text)

De Hoon, M.J.L., Makita, Y., Nakai, K., and Miyano, S., Prediction of transcriptional terminators in Bacillus subtilis and related species, PLoS Comput. Biol., 1(3), e25 (2005).
(full text)

Horton, P., Park, K.-J., Obayashi, T., and Nakai, K., Protein subcellular localization prediction with WoLF PSORT, (Jiang, T. et al. eds) Proc. 4th Asia-Pacific BIOINFORMATICS Conference (APBC2006), 39-48, Imperial College Press (2006).

Kimura, K., Watanabe, A., Suzuki, Y., Ota, T., Nishikawa, T., Yamashita, R., Yamamoto, J., Sekine, M., Tsuritani, K., Ishii, S., Sugiyama, T., Saito, K., Isono, Y., Irie, R., Kushida, N., Yoneyama, T., Otsuka, R., Kanda, K., Yokoi, T., Kondo, H., Wagatsuma, M., Murakawa, K., Ishida, S., Ishibashi, T., Takahashi-Fujii, A., Tanase, T., Nagai, K., Kikuchi, H., Nakai, K., Isogai, T., and Sugano, S., Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes, Genome Res., 16, 55-65 (2006).
(abstract)

Sierro, N., Kusakabe, T., Park, K.-J., Yamashita, R., Kinoshita, K., and Nakai, K., DBTGR: a database of tunicate promoters and their regulatory elements, Nucl. Acids Res., 34, D552-D555 (2006)
(full text)

Yamashita, R., Suzuki, Y., Wakaguri, H., Tsuritani, K., Nakai, K., and Sugano, S., DBTSS: Database of Human Transcription Start Sites, Progress Report 2006, Nucl. Acids Res., 34, D86-D89 (2006).
(full text)

Cheong, J., Yamada, Y., Yamashita, R., Irie, T., Kanai, A., Wakaguri, H., Nakai, K., Ito, T., Saito, I., Sugano, S., and Suzuki, Y., Diverse DNA methylation status at alternative promoters of human genes in various normal tissues, DNA Res., 13(14), 155-167 (2006).
(full text)

Obayashi, T., Kinoshita, K., Nakai, K., Shibaoka, M., Hayashi, S., Saeki, M., Shibata, D., Saito, K., and Ohta, H., ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis, Nucl. Acids Res., 35, Database issue D863-D869 (2007); advance access published online on Nov. 27, 2006.
(full text)

Nakai, K. and Horton, P., Chapter 29: Computational prediction of subcellular localization (in M. van der Giezen ed., Protein Targeting Protocols (2nd ed.), Methods in Molecular Biology, vol. 390), pp.429-466, Humana Press, Totowa, 2007, (ISBN 13 978-1-58829-702-0)
(abstract)

Sakakibara, Y., Irie, T., Suzuki, Y., Yamashita, R., Wakaguri, H., Kanai, A., Chiba, J., Takagi, T., Mizushima-Sugano, J., Hashimoto, S., Nakai, K., and Sugano, S., Intrinsic promoter activities of primary DNA sequences in the human genome, DNA Res., 14(2), 71-77 (2007); advance access published online on May 23, 2007.
(full text)

Tsuritani, K., Irie, T., Yamashita, R., Wakaguri, H., Kanai, A., Mizushima-Sugano, J., Sugano, S., Nakai, K., and Suzuki, Y., Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes, Genome Res., 17(7), 1005-1014 (2007); published online before print June 13, 2007.
(abstract).

Horton, P., Park, K.-J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C.J., and Nakai, K., WoLF PSORT: protein localization predictor, Nucl. Acids Res., 35, W585-W587, (2007); advanced access published online on May 21, 2007.
(full text)

Okumura, T., Makiguchi, H., Makita, Y., Yamashita, R., and Nakai, K., Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions, Nucl. Acids Res., 35, W227-W231 (2007); advanced access published online on May 30, 2007.
(full text)

Wakaguri, H., Yamashita, R., Suzuki, Y., Sugano, S., and Nakai, K., DBTSS: DataBase of Transcription Start Sites, progress report 2008, Nucl. Acids Res., 36(Database issue), D97-D101 (2008); advanced access published online on October 16, 2007.
(full text)

Sierro, N., Makita, Y., de Hoon, M., and Nakai, K., DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information, Nucl. Acids Res., 36(Database issue), D93-D96 (2008); advanced access published online on October 25, 2007.
(full text)

Genome Information Integration Project and H-invitational 2 Consortium, The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts, Nucl. Acids Res., 36(Database issue), D793-D799 (2008); advanced access published online on December 18, 2007.
(full text)

Izuho Hatada, Sumiyo Morita, Mika Kimura, Takuro Horii, Riu Yamashita, and Kenta Nakai, Genome-wide demethylation during neural differentiation of P19 embryonal carcinoma cells, J. Human Genet., 53(2), 185-191 (2008).
(full text)

Koshiro Miura, Hidehiro Toh, Hideki Hirakawa, Manabu Sugii, Masayuki Murata, Kenta Nakai, Kosuke Tashiro, Satoru Kuhara, Yoshinao Azuma, and Mutsunori Shirai, Genome-wide analysis of Chlamydophila pneumoniae gene expression at the late stage of infection, DNA Res., 15(2), 83-91 (2008); advance access published online on January 24, 2008.
(full text)

Alexis Vandenbon, Yuki Miyamoto, Noriko Takimoto, Takehiro Kusakabe, and Kenta Nakai, Markov chain-based promoter structure modeling for tissue-specific expression pattern prediction, DNA Res., 15(1), 3-11 (2008); advance access originally published online on February 7, 2008.
(full text)

Katsuhiko Murakami, Tadashi Imanishi, Takashi Gojobori, and Kenta Nakai, Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions, BMC Genomics, 9(1), 112 (2008).
(full text)

Kohji Okamura and Kenta Nakai, Retrotransposition as a source of new promoters, Mol. Biol. Evol., 25(6), 1231-1238 (2008); published online on March 25, 2008.
(full text)

Hirokazu Chiba, Riu Yamashita, Kengo Kinoshita, and Kenta Nakai, Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs, BMC Genomics, 9, 152 (2008).
(full text)

Riu Yamashita, Yutaka Suzuki, Nono Takeuchi, Hiroyuki Wakaguri, Takuya Ueda, Sumio Sugano, and Kenta Nakai, Comprehensive detection of human terminal oligo-pyrimidine (TOP) gene and analysis of their characteristics, Nucl. Acids Res., 36(11), 3707-3715 (2008); published online on May 14, 2008.
(full text)

Yosuke Hatanaka, Masao Nagasaki, Rui Yamaguchi, Takeshi Obayashi, Kazuyuki Numata, Andre Fujita, Teppei Shimomura, Yoshinoi Tamada, Seiya Imoto, Kengo Kinoshita, Kenta Nakai, and Satoru Miyano, A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human, Genome Informatics, 20, 212-221 (2008)
(pdf)

Alexis Vandenbon and Kenta Nakai, Using simple rules on presence and positioning of motifs for promoter structure modeling and tissue specific expression prediction, Genome Informatics (J. Arthur and S.-K. Ng ed.), vol. 21, pp. 188-199 (2008), Imperial College Press, London.
(pdf)

Nicolas Sierro, Shuang Li, Yutaka Suzuki, Riu Yamashita, and Kenta Nakai, Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis, Gene, 430, 44-49 (2009); available online on October 21, 2008
(PubMed)

Keishin Nishida, Martin Frith, and Kenta Nakai, Pseudocounts for transcription factor binding sites, Nucl. Acids Res., 37(3), 939-944 (2009); published online on December 23, 2008
(full text)

Katsuya Tsuchihara, Yutaka Suzuki, Hiroyuki Wakaguri, Takuma Irie, Kousuke Tanimoto, Shin-ichi Hashimoto, Kouji Matsushima, Junko Mizushima-Sugano, Riu Yamashita, Kenta Nakai, David Bentley, Hiroyasu Esumi, and Sumio Sugano, Massive transcriptional start site analysis of human genes in hypoxia cells, Nucl. Acids Res., 37, 2249-2263 (2009); published online on February 22, 2009.
(full text)

Hideaki Mizuno, Kunio Kitada, Kenta Nakai, and Akinori Sarai, PrognoScan: a new database for meta-analysis of the prognositic value of genes, BMC Med. Genomics, 2, 18 (2009); published online on April 24, 2009.
(full text)

Fumito Maruyama, Mitsuhiko Kobata, Ken Kurokawa, Keishin Nishida, Atsuo Sakurai, Kazuhiko Nakano, Ryota Nomura, Shigetada Kawabata, Takeshi Oshima, Kenta Nakai, Masahira Hattori, Shigeyuki Hamada, and Ichiro Nakagawa, Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content, BMC Genomics, 10, 358 (2009); published online on August 5, 2009.
(full text)

Yoshiaki Tanaka and Kenta Nakai, An assessment of prediction algorithms for nucleosome positioning, Genome Informatics, 23, 169-178 (2009); ISSN: 0919-9454.
(eProceedings)

Alexis Vandenbon and Kenta Nakai, Modeling tissue-specific structural patterns in human and mouse promoters, Nucl. Acids Res., 38(1), 17-25 (2010); published online on October 22, 2009.
(full text)

Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, and Kenta Nakai, DBTSS provides a tissue specific dynamic view of Transcription Start Sites, Nucl. Acids Res., 38, D98-D104 (2010); published online on November 13, 2009.
(full text)

Nuankanya Sathira, Riu Yamashita, Kousuke Tanimoto, Akinori Kanai, Takako Arauchi,Soutaro Kanematsu, Kenta Nakai, Yutaka Suzuki, and Sumio Sugano, Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer, DNA Res., 17(3), 169-183 (2010); published online on April 17, 2010.
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Yoshiaki Tanaka, Itsuki Yoshimura, and Kenta Nakai, Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin, Chromosoma, 119(4), 391-404 (2010); Epub on March 12, 2010
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Atsushi Kubo, Nobuhiro Suzuki, Xuyang Yuan, Kenta Nakai, Nori Satoh, Kaoru S. Imai, and Yutaka Satou, Genomic cis-regulatory networks in the Ciona intestinalis embryo, Development, 137(10), 1613-1623 (2010).
(PubMed)

Yoshiaki Tanaka, Riu Yamashita, Yutaka Suzuki, and Kenta Nakai, Effects of Alu elements on global nucleosome positioning in the human genome, BMC Genomics, 11, 309 (2010).
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Harumi Kawaki, Satoshi Kubota, Eriko Aoyama, Naoya Fujita, Hiroshi Hanagata, Akira Miyauchi, Kenta Nakai, and Masaharu Takigawa, Design and utility of CCN2 anchor peptide aptamers, Biochemie, 92(8), 1010-1015 (2010).
(PubMed)

Christian Schönbach, Kenta Nakai, Tin Wee Tan, and Shoba Ranganathan, InCoB2010 -- 9th Internatonal Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010, BMC Bioinformatics, 11(Suppl 7), S1 (15 October 2010).
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Kohji Okamura, Kazuaki A. Matsumoto, and Kenta Nakai, Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution, BMC Bioinformatics, 11(Suppl 7), S2 (15 October 2010).
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Takashi Satoh, Osamu Takeuchi, Alexis Vandenbon, Koubun Yasuda, Yoshiaki Tanaka, Yutaro Kumagai, Tohru Miyake, Kazufumi Matsushita, Toshihiko Okazaki, Tatsuya Saitoh, Kiri Honma, Toshifumi Matsuyama, Katsuyuki Yui, Tohru Tsujimura, Daron M. Standley, Kenji Nakanishi, Kenta Nakai and Shizuo Akira, The JMJD3-IRF4 axis regulates M2 macrophage polarization and host responses against helminth infection, Nature Immunol., 11(10), 936-944 (2010); published online: 22 Aug. 2010
(PubMed)

Kenichiro Imai and Kenta Nakai, Prediction of subcellular location of proteins: where to proceed?, Proteomics, 10(22), 3970-3983 (2010); first published online Nov. 2, 2010.
(abstract)

Shoba Ranganathan, Christian Schönbach, Kenta Nakai, Tin Wee Tan, Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010), BMC Genomics, 11(Suppl 4), S1 (2 December 2010).
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Ashwini Patil, Kenta Nakai, and Haruki Nakamura, HitPredict: a database of quality assessed protein-protein interactions in nine species, Nucl. Acids Res., 39, D744-D799 (2011); published online on October 14, 2010.
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Sung-Joon Park and Kenta Nakai, A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns, BMC Bioinformatics, 12(Suppl 1), S50 (Feb 15, 2011).
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Parul Khare, Sanra I. Mortimer, Cynthia L. Cleto, Kohji Okamura, Yutaka Suzuki, Takehiro Kusakabe, Kenta Nakai, Thomas H. Meedel, and Kenneth E. M. Hastings, Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene, Nucleic Acids Res., 39(7), 2638-2648 (2011); published online on November 24, 2010.
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Riu Yamashita, Nuankanya P Sathira, Akinori Kanai, Kousuke Tanimoto, Takako Arauchi, Yoshiaki Tanaka, Shin-ichi Hashimoto, Sumio Sugano, Kenta Nakai, and Yutaka Suzuki, Genome-wide characterization of transcription start sites in humans by integrative transcriptome analysis, Genome Res., 21(5), 775-789 (2011); published online on March 3, 2011.
(abstract)

Takuma Irie, Sung-Joon Park, Riu Yamashita, Masahide Seki, Tetsushi Yada, Sumio Sugano, Kenta Nakai, and Yutaka Suzuki, Predicting promoter activities of primary human DNA sequences, Nucl. Acids Res., 39(11), e75 (2011); published online on April 12, 2011.
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Daisuke Ohshima, Junwen Qin, Hiroyasu Konnno, Akihisa Hirosawa, Takuma Shiraishi, Hiromi Yanai, Yusuke Shimo, Nobuko Akiyama, Riu Yamashita, Kenta Nakai, and Jun-ichiro Inoue, RANK signaling induces interferon-stimulated genes in the fetal thymic stroma, Biochem. Biophys. Res. Comm., 408(4), 530-536 (2011).
(PubMed)

Kouichi Kimura, Asako Koike and Kenta Nakai, Seed-set construction by equi-entropy partitioning for efficient and sensitive short-read mapping, Algorithms in Bioinformatics in (T.M.Przytycka and M.-F. Sagot ed.) Lecture Notes in Computer Science, 6833, 151-162 (2011). (ISBN: 978-3-642-23037-0).

Kohji Okamura, Riu Yamashita, Noriko Takimoto, Koki Nishitsuji, Yutaka Suzuki, Takehiro G. Kusakabe, and Kenta Nakai, Profiling ascidian promoters as the primordial type of vertebrate promoter, BMC Genomics 12(Suppl. 3), S7 (2011).BEST PAPER AWARD in InCoB211
(full text)

Ashwini Patil, Kenta Nakai, and Kengo Kinoshita, Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks, BMC Genomics 12(Suppl. 3), S19 (2011).
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Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, and Daron M. Standley, Functional annotation of intrinsically disordered domains by their amino acid content using IDD Navigator, Pacific Symposium on Biocomputing 17, 164-175 (2012)
(pdf)

Riu Yamashita, Sumio Sugano, Yutaka Suzuki, and Kenta Nakai, DBTSS: database of transcriptional start sites progress report in 2012, Nucl. Acids Res., 40(Database Issue), D150-154 (2012); published online on Nov. 15, 2011.
(full text)

Kouichi Kimura, Asako Koike, and Kenta Nakai, A Bit-parallel dynamic programming algorithm suitable for DNA sequence alignment, J. Bioinformatics and Computational Biology, 10(4), 1250002 (2012); published online on Feb. 2, 2012.
(abstract)

Daniel Kraut, Eitan Israeli, Erin Schrade, Ashwini Patil, Kenta Nakai, Dhaval Nanavati, Tomonao Inobe, and Andreas Matouschek, Sequence- and species-dependence of proteasomal processivity, ACS Chemical Biology,7(8), 1444-1453 (2012); epub 2012 Jun. 22.
(abstract)

Sumiyo Morita, Ryou-u Takahashi, Riu Yamashita, Atsushi Toyoda, Takuro Horii, Mika Kimura, Asao Fujiyama, Kenta Nakai, Shoji Tajima, Ryo Matoba, Takahiro Ochiya and Izuho Hatada, Genome-wide analysis of DNA methylation and expression of microRNAs in breast cancer cells, Int. J. Mol. Sci., 13(7), 8259-8272 (2012).
(abstract)

Harry Amri Moesa, Shunichi Wakabayashi, Kenta Nakai, and Ashwini Patil, Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification. Mol. Biosystems, 8(12), 3262-3273 (2012); published online on 18 Oct 2012
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Naganari Ohkura, Masahide Hamaguchi, Hiromasa Morikawa, Kyoko Sugimura, Atsushi Tanaka, Yoshinaga Ito, Motonao Osaki, Yoshiaki Tanaka, Riu Yamashita, Naoko Nakano, Jochen Huehn, Hans-Joerg Fehling, Tim Sparwasser, Kenta Nakai, and Shimon Sakaguchi, T cell receptor stimulation-induced epigenetic changes and Foxp3 expression are independent and complementary events required for Treg cell development, Immunity, 37(5), 785-799 (2012).
(PubMed)

Manabu Ozawa, Miki Sakatani, JiQiang Yao, Savita Shanker, Fahong Yu, Riu Yamashita, Shuichi Wakabayashi, Kenta Nakai, Kyle B Dobbs, Mateus J. Sudano, William G. Farmerie, and Peter J. Hensen, Global gene expression of the inner cell mass and trophectoderm of the bovine blastcyst, BMC Dev. Biol., 12, 33 (2012)
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Rie Kusakabe, Saori Tani, Koki Nishitsuji, Miyuki Shindo, Kohji Okamura, Yuki Miyamoto, Kenta Nakai, Yutaka Suzuki, Takehiro G. Kusakabe, and Kunio Inoue, Characterization of the compact bicistronic microRNA precursor, miR-1/miR-133, expressed specifically in Ciona muscle tissues, Gene Expression Patterns, 13(1-2), 43-50.(2013)
(PubMed)

Yuko Makita and Kenta Nakai, Chapter 8: Bacillus subtilis transcriptional network, in (M. Madan Babu ed.) Bacterial Gene Regulation and Transcriptional Networks, pp.155-165, Caister Academic Press (ISBN: 978-1-908230-14-0) (2013)

Yasunori Sasakura, Nicolas Sierro, Kenta Nakai, Kazuo Inaba, and Takehiro G. Kusakabe, Chapter 4: Genome structures, functional genomics, and proteomics in ascidians, in (Denny, P. & Kole, C. eds.) Genome mapping and genomics in laboratory animals, pp.87-132, Springer (2013).

Yosvany López, Ashwini Patil, and Kenta Nakai, Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana, BMC Systems Biol., 7(Suppl 3): S10 (2013).
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Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, and Kenta Nakai, Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response, PLoS Comput. Biol., 9(11), e1003323 (2013); Epub Nov.7, 2013
(full text)

Sung-Joon Park, Makiko Komata, Fukashi Inoue, Kaori Yamada, Kenta Nakai, Miho Ohsugi and Katsuhiko Shirahige, Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis, Genes Dev., 27(24), 2736-2748 (2013).
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Kuo-ching Liang, Yutaka Suzuki, Yutaro Kumagai, and Kenta Nakai, Analysis of changes in transcription start site distribution by a classification approach, Gene, 537(1), 29-40 (2014); published online 31 December 2013
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Asmaa Elzawahry, Ashwini Patil, Yutaro Kumagai, Yutaka Suzuki, and Kenta Nakai, Innate immunity interactome dynamics, Gene Regulation and Systems Biology, 8, 1-15 (2014)
(abstract & pdf)

Alok Sharma, Abdollah Dehzangi, James Lyons, Seiya Imoto, Satoru Miyano, Kenta Nakai, and Ashwini Patil, Evaluation of sequence features from intrinsically disordered regions for the estimation of protein function, PLoS One, 9(2), e89890 (2014).
(full text)

Sung-Joon Park, Terumasa Umemoto, Mihoko Saito-Adachi, Yoshiko Shiratsuchi, Masayuki Yamato, and Kenta Nakai, Computational promoter modeling identifies the modes of transcriptional regulation in hematopoietic stem cells, PLoS One, 9(4), e93853 (2014).
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Kyungtaek Lim, Ichizo Kobayashi, and Kenta Nakai, Alterations in rRNA-mRNA interaction during plastid evolution, Mol. Biol, Evol., 31(7), 1728-1740 (2014).
(PubMed)

Kenta Nakai, Overview of Bioinformatics Research in Japan, Asia Pacific Biotech, 18(9), 35-37 (2014).

Sanaz Firouzi, Yosvany López, Yutaka Suzuki, Kenta Nakai, Sumio Sugano, Tadanori Yamochi and Toshiki Watanabe, Development and validation of a new high-throughput method to investigate the clonality of HTLV-1-infected cells based on provirus integration sites, Genone Medicine, 6, 46 (2014).
(full text)

Yosvany López, Alexis Vandenbon, and Kenta Nakai, A Set of Structural Features Defines the Cis-Regulatory Modules of Antenna-Expressed Genes in Drosophila melanogaster, PLoS One 9(8), e104342 (2014).
(full text)

Ashwini Patil and Kenta Nakai, TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles, BMC Syst. Biol., 8(Suppl.4), S2 (2014).
(full text).

Lucky R. Runtuwene, Kaori Noguchi, Akinori Tokunaga, Takashi Kobayashi, Kenta Nakai, and Yuki Eshita, Vector competence of Aedes aegypti to dengue virus. Urban Pest Management, 4(1), 1-14 (2014),

Sung-Joon Park, Katsuhiko Shirahige, Miho Ohsugi and Kenta Nakai, DBTMEE: a database of transcriptome in mouse early embryos. Nucl. Acids Res., 43, D771-D776 (2015).
(full text).

Ayako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, and Kenta Nakai, DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. Nucl. Acids Res., 43, D87-D91 (2015).
(full text).

Josep Basha Gutierrez, Martin Frith, and Kenta Nakai, A genetic algorithm for motif finding based on statistical significance. Bioinformatics and Biomedical Engineering (Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015, Proceedings, Part I), Springer, LNCS 9043, pp.438-449 (2015).

Jong-Hun Lee, Sung-Joon Park, and Kenta Nakai, An integrative approach for efficient analysis of whole genome bisulfite sequencing data. BMC Genomics 16(Suppl 12), S14 (2015)
(full text).

Kuo-ching Liang, Ashwini Patil, and Kenta Nakai, Discovery of intermediary genes between pathways using sparse regression. PLoS One, 10(9), e0137222 (2015).
(full text).

Yosvany López, Kenta Nakai, and Ashwini Patil, HitPredict version 4 - comprehensive reliablity scoring of physical protein-protein interactions from more than 100 species, DATABASE, 2015, bav117 (2015).
(full text).

Sung-Joon Park, Yusuke Komiyama, Hirofumi Suemori, Akihiro Umezawa, and Kenta Nakai, OpenTein: a database of digital whole-slide images of stem cell-derived teratomas. Nucl. Acids Res., 44(D1), D1000-D1004 (2016).
(full text)

Rui Yokomori, Kotaro Shimai, Koki Nishitsuji, Yutaka Suzuki, Takehiro G. Kusakabe, and Kenta Nakai, Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis. Genome Res., 26, 140-150 (2016).
(abstract)

Sung-Joon Park, Mihoko Saito-Adachi, Yusuke Komiyama, and Kenta Nakai, Advances, practice, and clinical perspectives in high-throughput sequencing, Oral Diseases, 22(5), 353-364 (2016).
(PubMed)

Yuzuru Sasamoto, Ryuhei Hayashi, Sung-Joon Park, Mihoko Saito-Adachi, Yutaka Suzuki, Satoshi Kawasaki, Andrew Quantock, Kenta Nakai, Motokazu Tsujikawa, and Kohji Nishida, PAX6 isoforms, along with reprogramming factors, differentially regulate the induction of cornea-specific genes. Sci. Rep., 6, 20807 (2016).
(abstract)

Sung-Joon Park and Kenta Nakai, Chapter 7: Computational inference of gene regulation from whole-transcriptome analysis of early embryos. in (Ivan V. Ivanov, Xiaoning Qian, and Ranadip Pal eds.) Emerging Research in the Analysis and Modeling of Gene Regulatory Networks, pp.241-279, IGI Global, ISBN: 9781522503538 (2016).

Kazuhiro Fukumura, Shunichi Wakabayashi, Naoyuki Kataoka, Hiroshi Sakamoto, Yutaka Suzuki, Kenta Nakai, Akila Mayeda, and Kunio Inoue, The exon junction complex controls the efficient and faithful splicing of a subset of transcripts involved in miotic cell-cycle progression. Int. J. Mol. Sci., 17(8), 1153 (2016).
(full text)

Satoru Onizuka, Takanori Iwata, Sung-Joon Park, Kenta Nakai, Masayuki Yamato, Teruo Okano, and Yuichi Izumi, ZBTB16, a downstream target gene of Osterix, regulates osteoblastogenesis of human multipotent mesenchymal stromal cells. J. Cell. Biochem., 117(10), 2423-2434 (2016).
(PubMed)

Myungjin Moon and Kenta Nakai, Stable feature selection based on the ensemble L1-norm support vector machine for biomarker discovery. BMC Genomics 17(Suppl. 13), 3320 (2016).
(full text)

Josep Basha Gutierrez and Kenta Nakai, A study on the application of topic models to motif finding algorithms. BMC Bioinformatics 17(Suppl. 19), 1364 (2016).
(full text)

Yasunori Sasakura, Yosuke Ogura, Nicholas Treen, Rui Yokomori, Sung-Joon Park, Kenta Nakai, Hidetoshi Saiga, Tetsushi Sakuma, Takashi Yamamoto, Shigeki Fujiwara, and Keita Yoshida, Transcriptional regulation of a horizontally transferred gene from bacterium to chordate. Proc. Royal Soc. B. 283(1845), pii: 20161712 (2016).
(PubMed)

Yosvany López, Alexis Vandenbon, Akinao Nose, and Kenta Nakai, Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster, PeerJ, 5, e3389 (2017).
(full text)

Jong-Hun Lee, Sung-Joon Park, Kenta Nakai, Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s, Sci. Rep. 7, 11295 (2017).
(full text)

Motohiko Kadoki, Ashwini Patil, Cornelius C. Thaiss, Donald J. Brooks, Surya Pandey, Deeksha Deep, David Alvarez, Ulrich H. von Andrian, Amy J. Wagers, Kenta Nakai, Tarjei S. Mikkelsen, Magali Soumillon, and Nicolas Chevrier, Organism-level analysis of vaccination reveals networks of protection across tissues. Cell 171(2), 398-413.e21 (2017),, published September 21, 2017.
(abstract)

Ayako Suzuki, Shin Kawano, Toutai Mitsuyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, and Yutaka Suzuki, DBTSS/DBKERO for integrated analysis of transcriptional regulation. Nucl. Acids Res., 46(D1), D229-D238 (2018); published online on Nov. 8, 2017.
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Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, Mathieu Gineste, Alexandra Louis, Kazuhiro Nitta, Magali Naville, Jacques Piette, Céline Scornavacca, Paul Simion, Renaud Vincentelli, Maelle Bellec, Sameh Ben Aicha, Marie Fagotto, Marion Guéroult-Bellone, Maximilian Haeussler, Edwin Jacox, Elijah Lowe, Mickael Mendez, Wendy Reeves, Alexis Roberge, Alberto Stolfi, Rui Yokomori, C. Titus Brown, Christian Cambillau, Lionel Christiaen, Frédéric Delsuc, Emmanuel Douzery, Rémi Dumollard, Takehiro Kusakabe, Kenta Nakai, Hiroki Nishida, Yutaka Satou, Billie Swalla, Michael Veeman, Jean-Nicolas Volff, and Patrick Lemaire, ANISEED 2017 : Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucl. Acids Res., 46(D1), D718-D725 (2018); published on 15 Nov. 2017.
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Masashi Fujita, Nagahide Matsubara, Ikuo Matsuda, Kazuhiro Maejima, Ayako Ohsawa, Tomoki Yamano,, Akihiro Fujimoto, Mayuko Furuta, Kaoru Nakano, Aya Oku-Sasaki, Hiroko Tanaka, Yuichi Shiraishi, Raúl Mateos, Kenta Nakai, Satoru Miyano, Naohiro Tomita, Seiichi Hirota, Hiroki Ikeuchi, Hidewaki Nakagawa, Genomic landscape of colitis-associated cancer indicates the impact of chronic inflammation and its stratification by mutations in the Wnt signaling. Oncotarget 9, 969-981 (2018).
(full text)

Myungjin Moon and Kenta Nakai, Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers. J. Bioinf. Comput. Biol., 16(2), 1850006 (2018).
(abstract)

Yasuo Ouchi, Ashwini Patil, Yusuke Tamura, Hiroshi Nishimasu, Aina Negishi, Sudip Kumar Paul, Naoki Takemura, Takeshi Satoh, Yasumasa Kimura, Makoto Kurachi, Osamu Nureki, Kenta Nakai, Hiroshi Kiyono, Satoshi Uematsu. Generation of tumor antigen-specific murine CD8+ T cells with enhanced anti-tumor activity via highly efficient CRISPR/Cas9 genome editing. Int. Immunol., 30(4) 141-154 (2018).
(full text) Editor's choice

Phit Ling Tan, Yosvany López, Kenta Nakai, and Ashwini Patil, TimeXNet Web: Identifying cellular response networks from diverse omics time-course data. Bioinformatics 34(21), 3764-3765 (2018)..
(PubMed)

Naoya Fujita, Shinji Mizuarai, Katsuhiko Murakami, and Kenta Nakai. Biomarker discovery by integrated joint non-negative matrix factorization and pathway signature analyses. Sci. Rep. 8, 9743 (2018).
(full text)

Alexis Vandenbon, Yutaro Kumagai, Mengjie Lin, Yutaka Suzuki, and Kenta Nakai. Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation. Genome Biol., 19, 138 (2018).
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Luis A. E. Nagai, Sung-Joon Park, and Kenta Nakai. Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma. BMC Medical Genomics, in press.

Last update: November 22, 2018