Publication List


International Journal/Conference Papers
  1. Polina Yu Novikova, Nora Hohmann, Viktoria Nizhynska, Takashi Tsuchimatsu, Jamshaid Ali, Graham Muir, Alessia Guggisberg, Tim Paape, Karl Schmid, Olga M Fedorenko, Svante Holm, Torbjörn Säll, Christian Schlötterer, Karol Marhold, Alex Widmer, Jun Sese, Kentaro K Shimizu, Detlef Weigel, Ute Krämer, Marcus A Koch, Magnus Nordborg. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nature Genetics, in press.
  2. Tomoki Matsuzawa, Raissa Relator, Jun Sese, Tsuyoshi Kato. Stochastic Dykstra Algorithms for Metric Learning with Positive Definite Covariance Descriptors. To appear in The 14th European Conference on Computer Vision (ECCV 2016).[arXiv preprint]
  3. Aika Terada, Ryo Yamada, Koji Tsuda, Jun Sese. LAMPLINK: detection of statistically significant SNP combinations from GWAS data. Bioinformatics, in press
  4. Timothy Paape, Masaomi Hatakeyama, Rie Shimizu-Inatsugi, Teo Cereghetti, Yoshihiko Onda, Kenta Tanaka, Jun Sese, Kentaro Shimizu. Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploid Arabidopsis kamchatica. Molecular Biology and Evolution, in press.
  5. Song Liu, Suzuki Taiji, Raissa Relator, Jun Sese, Masashi Sugiyama, Kenji Fukumizu. Support Consistency of Direct Sparse-Change Learning in Markov Networks. The Annals of Statistics, in press.
  6. Rie Shimizu-Inatsugi, Aika Terada, Kyosuke Hirose, Hiroshi Kudoh, Jun Sese, Kentaro K. Shimizu. Plant adaptive radiation mediated by polyploid plasticity in transcriptomes. Molecular Ecology, in press.
  7. Koichi Yamagata, Ayako Yamanishi, Chikara Kokubu, Junji Takeda and Jun Sese. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples. Nucleic Acids Res.. 44 (8), e78, 2016
  8. Jun Sese, Aika Terada, Yuki Saito and Koji Tsuda. Statistically significant subgraphs for genome-wide association study. JMLR Workshop and Conference Proceedings. 47, 29-36, 2015.
  9. Aika Terada, Hanyoung Kim and Jun Sese. High-speed Westfall-Young permutation procedure for genome-wide association studies. In Proc. of the 6th ACM Conference on Bioinformatics and Computational Biology (ACM-BCB 2015), pp. 17-26, 2015.
  10. Andrew Tedder, Matthias Helling, John R. Pannell, Rie Shimizu-Inatsugi, Tetsuhiro Kawagoe, Julia van Campen, Jun Sese and Kentaro K. Shimizu. Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae) Annals of Botany. 115 (5), 763-776, 2015.
  11. Masahiro Tokunaga, Chikara Kokubu, Yusuke Maeda, Jun Sese, Kyoji Horie, Nakaba Sugimoto, Taroh Kinoshita, Kosuke Yusa and Junji Takeda Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells. BMC Genomics. 15: 1016, 2014.
  12. Makoto Yamada, Masashi Sugiyama, and Jun Sese. Least-squares independence regression for non-linear causal inference under non-gaussian noise. Machine Learning. Vol. 96 (3), pp. 249-267, 2014.
  13. Shingo Okuno, Tasuku Hiraishi, Hiroshi Nakashima, Masahiro Yasugi, and Jun Sese. Parallelization of extracting connected subgraphs with common itemsets. Information and Media Technologies. Vol. 9, No. 3, pp. 233-250, 2014.
  14. Satoru Akama(*), Rie Shimizu-Inatsugi(*), Kentaro K. Shimizu(+), and Jun Sese(+). Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis Nucleic Acids Research. 2014, 42 (6): e46. (* Joint first authors, + Joint correspondence authors) [Source Code].
  15. Shiori Setoguchi, Hisaki Takamori, Tadashi Aotsuka, Jun Sese, Yukio Ishikawa, Takashi Matsuo. Sexual dimorphism and courtship behavior in Drosophila prolongata. Journal of Ethology. Vol. 32, Issue 2, pp. 91-102. Map, 2014.
  16. Aika Terada, Koji Tsuda, and Jun Sese. Fast Westfall-Young permutation procedure for combinatorial regulation discovery." IEEE Bioinformatics and Biomedicine (BIBM 2013). pp. 153-158. Shanghai, China. December 18-21, 2013.
  17. Aika Terada and Jun Sese. Bonferroni correction hides significant motif combinations. 13th IEEE Bioinformatics and Bioengineering (BIBE 2013), Chania, Greece. November 10-13, 2013.
  18. Aika Terada, Mariko Okada-Hatakeyama, Koji Tsuda(*), and Jun Sese(*). (* Joint correspondence authors).  Statistical significance of combinatorial regulationsProc. Natl. Acad. Sci. Vol. 110, No. 32, pp. 12996-13001, 2013.
  19. Akiko Izawa and Jun Sese. RECOT: A Tool for the Coordinate Transformation of Next-Generation Sequencing Reads between Related Species. Source Code for Biology and Medicine. 2013, 8:6.
  20. Atsushi Ogura, Konstantinos Sousounis, Takeya Moritaki, Yuki Okuda, Jun Sese, Kentaro Shimizu, Masa-aki Yoshida, Panagiotis A. Tsonis. Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus. Scientific Reports, 3, 1432, 2013.
  21. Chih-Chieh Yu, Mari Furukawa, Kazuhiro Kobayashi, Chizuru Shikishima, Pei-Chieng Cha, Jun Sese, Hiroko Sugawara, Kazuya Iwamoto, Tadafumi Kato, Juko Ando, Tatsushi Toda. Genome-wide DNA methylation and gene expression analyses of monozygotic twins discordant for intelligence levels. PLoS ONE 7(10): e47081, 2012.
  22. Mutsumi Fukuzaki, Masa-aki Yoshida, Atsushi Ogura and Jun Sese. Systematic Measurement of Missmatch Effect for Designing Inter-Species Microarray. IEEE Bioinformatics and Biomedicine 2012 (BIBM 2012), pp. 478-481. Philadelphia, Pennsylvania. Oct. 4-7, 2012.
  23. Jun Sese. Data Analysis of Large-Scale Glycan-Sample Interactions. Trends in Glycoscience and Glycotechnology. Vol. 24, No. 137, pp. 122-128, 2012.
  24. Rina Nakazawa, Takayuki Itoh, Jun Sese and Aika Terada. Integrated Visualization of Gene Network and Ontology Applying a Hierarchical Graph Visualization Technique. 16th International Conference on Information Visualization (IV2011), 2012.
  25. Terada and Jun Sese. Global Alignment of Protein-Protein Interaction Networks for Analyzing Evolutionary Changes of Network Frameworks. 4th International Conference on Bioinformatics and Computational Biology (BICoB-2012), pp. 196-201. Las Vegas, Nevada, USA. March 12 - 14, 2012.
  26. Masa-aki Yoshida, Yukiko Ishikura, Takeya Moritaki, Eiichi Shoguchi, Kentaro K. Shimizu, Jun Sese and Atsushi Ogura.Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation. Gene. Volume 483, Issues 1-2, Pages 63-71. 2011.
  27. Atsushi Ogura, Masaaki Yoshida, Mutsumi Fukuzaki, and Jun Sese. In vitro homology search array comprehensively reveals highly conserved genes and their functional characteristics in non-genome sequenced species. BMC Genomics. 11 (4), S9, 2010 (Presented in International Conference on Bioinformatics 2010 (InCoB 2010), Tokyo, Japan. Sept. 26-28, 2010).
  28. Jun Sese, Mio Seki, and Mutsumi Fukuzaki. Mining networks with shared items. The 19th ACM International Conference on Information and Knowledge Management (CIKM 2010), pp.1681–1684, Tronto, Canada. Oct. 26-30, 2010.
  29. Natsumi Abe and Jun Sese. Constructing a yeast phenotypic gene network using morphological inclusion relations. International Journal on Artificial Intelligence Tools, Vol. 19, No. 3, pp. 235-250, 2010.
  30. Mutsumi Fukuzaki, Mio Seki, Hisashi Kashima, and Jun Sese. Finding itemset-sharing patterns in a large itemset-associated graph. The 14th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2010), pp.147–159, Hyderabad, India, June. 21-24, 2010.
  31. Seiji Saito, Kazuki Ohno, Kanako Sugawara, Jun Sese, and Hitoshi Sakuraba. Prediction of the clinical phenotype of Fabry disease based on protein sequential and structural information. Journal of Human Genetics, Vol.55, pp.175–178, 2010.
  32. Masashi Sugiyama, Tsuyoshi Idé, Shinichi Nakajima, and Jun Sese. Semi-supervised local Fisher discriminant analysis for dimensionality reduction. Machine Learning, Vol. 78, No. 1–2, pp. 35–62, 2010.
  33. Aika Terada and Jun Sese. Discovering large network motifs from a complex biological network. Journal of Physics: Conference Series. 012011, vol. 197, 2009.
  34. Mutsumi Fukuzaki, Mio Seki, Hisashi Kashima, and Jun Sese. Side effect prediction using cooperative pathways. IEEE International Conference on Bioinformatics and Biomedicine 2009 (IEEE BIBM 2009), pp.142–147, Washington D.C., USA, Nov. 1-4, 2009.
  35. Masashi Sugiyama, Takafumi Kanamori, Taiji Suguki, Shohei Hido, Jun Sese, Ichiro Takeuchi, and Liewi Wang. A density-ratio framework for statistical data processing. IPSJ Transactions on Computer Vision and Applications, pages 183–208, Vol. 1, 2009.
  36. Natsumi Abe and Jun Sese. Uncovering an Yeast Phenotypic Gene Network Using Morphological Inclusion Relations. 9th IEEE International Conference on BioInformatics and BioEngineering (BIBE2009), pp.30–37, Taichung, Taiwan, June. 22-24, 2009.
  37. Takayuki Itoh, Chris Muelder, Kwan-Liu Ma, and Jun Sese. A Hybrid Space-Filling and Force-Directed Layout Method for Visualizing Multiple-Category Graphs. IEEE Pacific Visualization Symposium 2009, pp.121–128, Beijing, China, Apr. 20-23, 2009
  38. Taiji Suzuki, Masashi Sugiyama, Takafumi Kanamori, and Jun Sese. Mutual information estimation reveals global associations between stimuli and biological process. BMC Bioinformatics 2009, 10(Suppl 1):S52 (The Seventh Asia Pacific Bioinformatics Conference (APBC 2009), pp. 297-309, Beijing, China, Jan. 13-16, 2009).
  39. Mio Seki and Jun Sese. Identification of active biological networks and common expression conditions. 8th IEEE International Conference on BioInformatics and BioEngineering (BIBE2008), Athens, Greece, Oct. 8-10, 2008.
  40. Eriko Muzutani and Jun Sese. GOMA: Web utility for direct finding of enriched gene ontology terms from gene expression profile. 8th IEEE International Conference on BioInformatics and BioEngineering (BIBE2008), Athens, Greece, Oct. 8-10, 2008.
  41. Taiji Suzuki, Masashi Sugiyama, Jun Sese, and Takafumi Kanamori. Approximating mutual information by maximum likelihood density ratio estimation. In Proceedings of the 3rd workshop on new challenges for feature selection in data mining and knowledge discovery (FSDM2008), JMLR workshop and conference proceedings, Vol. 4, pp.5–20, 2008.
  42. Taiji Suzuki, Masashi Sugiyama, Jun Sese, and Takafumi Kanamori. A least-squares approach to mutual information estimation with application in variable selection. Workshop on New Challenges for Feature Selection in Data Mining and Knowledge Discoverty 2008 (FSDM2008), Antwerp, Belgium, Sep. 15, 2008.
  43. Masashi Sugiyama, Tsuyoshi Idé, Shinichi Nakajima, and Jun Sese. Semi-supervised local Fisher discriminant analysis for dimensionality reduction. the 12th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD2008)
  44. Fumihito Miura, Noriko Kawaguchi, Jun Sese, Atsushi Toyoda , Masahira Hattori, Shinichi Morishita, and Takashi Ito. A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc. Nat. Acad. Sci., Vol. 103. No.47. pp 17846–17851, November 21, 2006
  45. Mariko Taniguchi, Hiroki Kurahashi, Satoru Noguchi, Jun Sese, Takeshi Okinaga, Toshifumi Tsukahara, Pascale Guicheney, Keiichi Ozono, Ichizo Nishino, ShinichiMorishita and Tatsushi Toda. Expression profiling of muscles from Fukuyama-type congenital muscular dystrophy and laminin-deficient congenital muscular dystrophy; is congenital muscular dystrophy a primary fibrotic disease? BBRC(Biochemical and Biophysical Research Communications), 2006 Apr. 7; 342(2): 489-502
  46. Genjiro Suzuki, Hiroshi Sawai, Miwaka Ohtani, Satoru Nogami, Fumi Sano-Kumagai, Ayaka Saka, Masashi Yukawa, Taro L. Saito, Jun Sese, Dai Hirata, Shinichi Morishita and Yoshikazu Ohya. Evaluation of image processing programs for accurate measurement of budding and fission yeast morphology. Current Genetics. 2006 Jan 6
  47. Yoshikazu Ohya, Jun Sese, Masashi Yukawa, Fumi Sano, Yoichiro Nakatani, Taro L. Saito, Ayaka Saka, Tomoyuki Fukuda, Satoru Ishihara, Satomi Oka, Genjiro Suzuki, Machika Watanabe, Aiko Hirata, Miwaka Ohtani, Hiroshi Sawai, Nicolas Fraysse, Jean-Paul Latge, Jean M. Francois, Markus Aebi, Seiji Tanaka, Sachiko Muramatsu, Hiroyuki Araki, Kintake Sonoike, Satoru Nogami, and Shinichi Morishita. High-dimensional and large-scale phenotyping of yeast mutants. Proc. Natl. Acad. Sci. Vol. 102. No. 52. 19015-19020. 2005
  48. Taro Saito, Jun Sese, Yoichiro Nakatani, Fumi Sano, Masashi Yukawa, Yoshikazu Ohya, Shinichi Morishita. Data Mining Tools for Saccharomyces Cerevisiae Morphological Database. Nucleic Acids Res. Web Server Issue 2005. 33: W753-W757.
  49. Yasuhiko Kasai, Sihn-ichi Hashimoto, Tomoyuki Yamada, Jun Sese, Sumio Sugano, Kouji Matsushima, Shinichi Morishita. 5′SAGE: 5′-end Serial Analysis of Gene Expression database. Nucleic Acids Res. Vol 33. D550-D552, 2005.
  50. Shin-ichi Hashimoto, Yutaka Suzuki, Yasuhiro Kasai, Kei Morohoshi, Tomoyuki Yamada, Jun Sese, Shinichi Morishita, Sumio Sugano, Kouji Matsushima. 5′-end SAGE for the analysis of transcriptional start sites. Nature Biotechnology, Vol. 22, 1146 – 1149, 2004.
  51. Jun Sese, Yukinori Kurokawa, Morito Monden, Kikuya Kato and Shinichi Morishita. Constrained Clusters of Gene Expression Profiles with Pathological Features. Bioinformatics, Vol20, pp 3137-3145, Nov. 2004.
  52. Jun Sese and Shinichi Morishita. Itemset Classified Clustering. Proc of 8th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD’04), pp. 398-409
  53. Shin-ichi Hashimoto, Shigenori Nagai, Jun Sese, Takuji Suzuki, Aya Obata, Taku Sato, Nobuaki Toyoda, Hong-Yan Dong, Makoto Kurachi, Tomoyuki Nagahata, Ken-ichi Shizuno, Shinichi Morishita, and Kouji Matsushima; Gene expression profile in human leukocytes. Blood, May 2003; 101: 3509 – 3513.
  54. Suzuki Y, Taira H, Tsunoda T, Mizushima-Sugano J, Sese J, Hata H, Ota T, Isogai T, Tanaka T, Morishita S, Okubo K, Sakaki Y, Nakamura Y, Suyama A, Sugano S. Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep. 2001 May;2(5):388-93.
  55. Yutaka Suzuki, Tatsuhiko Tsunoda, Jun Sese, Hirotoshi Taira, Junko Mizushima-Sugano, Hiroko Hata, Toshio Ota, Takao Isogai, Toshihiro Tanaka, Yusuke Nakamura, Akira Suyama, Yoshiyuki Sakaki, Shinichi Morishita, Kousaku Okubo, and Sumio Sugano. Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes. Genome Research, 2001, 11: 677-684.
  56. Jun Sese and Shinichi Morishita. Answering the Most Correlated N Association Rules Efficiently. Proc. of 6th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD’02), Helsinki, Finland, August 19-23, 2002, pp. 410-422.
  57. Jie Cheng, Christos Hatzis, Hisashi Hayashi, Mark-A. Krogel, Shinichi Morishita , David Page, and Jun Sese. KDD Cup 2001 Report. ACM SIGKDD Explorations, Volume 3, Issue 2, Janurary 2002, pp. 47-64.
  58. Junichi Akita, Jun Sese. Fast Homology Search Architecture for Recognizing Genome Function. Proceedings of 5th World Multiconference on Systemics, Cybernetics and Informatics(SCI2001), Vol.VI, Part I, pp.6–9, 2001.7.
  59. Shinichi Morishita and Jun Sese. Traversing Itemset Lattices with Statistical Metric Pruning. Proc. of ACM SIGACT-SIGMOD-SIGART Symp. on Database Systems (PODS), pp.226-236, May 2000.
  60. Jun Sese, Hitoshi Nikaidou, Shoko Kawamoto, Yuichi Minesaki, Shinichi Morishita, and Kousaku Okubo. BodyMap incorporated PCR-based expression profiling data and a gene ranking system. Nucleic Acids Res. 2001 29: 156-158.
  61. Shoko Kawamoto, Junji Yoshii, Katsuya Mizuno, Kouichi Ito, Yasuhide Miyamoto, Tadashi Ohnishi, Ryo Matoba, Naohiro Hori, Yuhiko Matsumoto, Toshiyuki Okumura, Yuko Nakao, Hisae Yoshii, Junko Arimoto, Hiroko Ohashi, Hiroko Nakanishi, Ikko Ohno, Jun Hashimoto, Kota Shimizu, Kazuhisa Maeda, Hiroshi Kuriyama, Koji Nishida, Akiyo Shimizu-Matsumoto, Wakako Adachi, Reiko Ito, Satoshi Kawasaki, K.S. Chae, Katsuji Murakawa, Masahiro Yokoyama, Atsushi Fukushima, Teruyoshi Hishiki, Akihiko Nakaya, Jun Sese, Norikazu Monma, Hitoshi Nikaido, Shinichi Morishita, Kenichi Matsubara, and Kousaku Okubo. BodyMap: A Collection of 3′ ESTs for Analysis of Human Gene Expression Information. Genome Research, 2000, 10: 1817-1827.
Domestic book, journal and conference papers (selected)
  1. 瀬々 潤, 浜田 道昭. 生命情報処理における機械学習 - 多重検定と推定量統計. 講談社サイエンティフィック. 192ページ. 2015年12月
  2. 瀬々 潤, 寺田 愛花, 津田 宏治. 網羅的トランスオミクスにおけるビッグデータの解析. 実験医学. Vol.32 No.8. 2014年5月号 
  3. 瀬々 潤. 生命情報解析で活躍する機械学習. オペレーションズ・リサーチ. Vol. 57, No. 7. 2012年 7月.
  4. 伊藤真和吏, 寺井はるな, 瀬々潤. クラスタリングによる糖鎖認識パターン解析. 日本データベース学会論文誌(DBSJ Journal). 9(1), 56-63, 2010.
  5. Masashi Sugiyama, Takafumi Kanamori, Taiji Suzuki, Shohei Hido, Jun Sese, Ichiro Takeuchi and Liwei Wang. Direct Importance Estimation — A New Versatile Tool for Statistical Pattern Recognition. MIRU2008 (第11回 画像の認識・理解シンポジウム), 軽井沢, 2008. [優秀論文賞]
  6. 瀬々 潤.非階層型クラスタリング—k-平均法、自己組織化マップ(マイクロアレイデータ統計解析プロトコール, 藤淵航, 堀本勝久編. pp 159–167, 2008/5)
  7. 瀬々 潤,池村 淑道. ライフサイエンスにおけるデータベース構築のための人材育成.蛋白質 核酸 酵素. 2008年1月号.pp 87–93.
  8. 瀬々 潤. 遺伝子間の関連を洗い出すバイオデータマイニング. 月刊DBマガジン.2007年7月号. pp 122–123