Note: Currently only Jun's publication is available.
  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, 48, 1077-1082, 2016..
  2. Tomoki Matsuzawa, Raissa Relator, Jun Sese, Tsuyoshi Kato. Stochastic Dykstra Algorithms for Metric Learning with Positive Definite Covariance Descriptors. In Proc. of the 14th European Conference on Computer Vision (ECCV 2016), 786-799. [arXiv preprint]
  3. Aika Terada, Ryo Yamada, Koji Tsuda, Jun Sese. LAMPLINK: detection of statistically significant SNP combinations from GWAS data. Bioinformatics, 32 (22), 3513-3515, 2016.
  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, 33 (11), 2781-2800, 2016.
  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. (Also presented as highlight paper in ISMB 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. Shin-ichi Minato, Takeaki Uno, Koji Tsuda, Aika Terada and Jun Sese. A fast method of statistical assessment for combinatorial hypotheses based on frequent itemset enumeration. Machine Learning and Knowledge Discovery in Databases (ECML/PKDD 2014). LNCS 8725, pp. 422-436, 2014.
  14. 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.
  15. 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. 42 (6), e46, 2014. (* Joint first authors, + Joint correspondence authors) [Source Code].
  16. 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. May, 2014.
  17. 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.
  18. Aika Terada and Jun Sese. Bonferroni correction hides significant motif combinations. 13th IEEE Bioinformatics and Bioengineering (BIBE 2013), Chania, Greece. November 10-13, 2013.
  19. Aika Terada, Mariko Okada-Hatakeyama, Koji Tsuda(*), and Jun Sese(*). Statistical significance of combinatorial regulations. Proc. Natl. Acad. Sci., Vol. 110, No. 32, pp. 12996-13001, 2013. (* Joint correspondence authors) [Source Code]
  20. Akiko Izawa and Jun Sese. RECOT: A Tool for the Coordinate Transformation of Next-Generation Sequencing Reads for comparative genomics and transcriptomics. Source Code for Biology and Medicine, 2013, 8:6. [Source Code]
  21. 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.
  22. 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
  23. Tetsuo Shibuya, Hisashi Kashima, Shandar Ahmad, and Jun Sese (eds). Pattern Recognition in Bioinformatics. Springer, 2012.
  24. 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.
  25. Jun Sese. Data Analysis of Large-Scale Glycan-Sample Interactions. Trends in Glycoscience and Glycotechnology, Vol. 24, No. 137, pp. 122-128, 2012.
  26. Rina Nakazawa, Takayuki Itoh, Jun Sese, and Aika Terada. Integrated visualization of gene network on ontology applying hierarchical graph visualization technique. 16th Int. Conf. on Information Visualization (IV) 2012, pp. 81-86, July 11-13, 2012.
  27. Aika 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.
  28. 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.
  29. 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.
  30. 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).
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. Aika Terada and Jun Sese. Discovering large network motifs from a complex biological network. Journal of Physics: Conference Series. 012011, vol. 197, 2009.
  36. 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.
  37. 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.
  38. Natsumi Abe and Jun Sese. Constructing an Yeast Phenotypic Gene Network Using Morphological Inclusion Relations. 9th IEEE International Conference on BioInformatics and BioEngineering (BIBE2009), pages 30–37, Taichung, Taiwan, June. 22-24, 2009.
  39. 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, Beijing, China, Apr. 20-23, 2009.
  40. Taiji Suzuki, Masashi Sugiyama, Takafumi Kanamori, and Jun Sese. Mutual Information Estimation Reveals Global Associations between Stimuli and Biological Process. BMC Bioinformatics, 10(Suppl 1):S52, 2009. (Presented at The Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, Jan. 13-16, 2009).
  41. 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.
  42. 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.
  43. 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.
  44. Masashi Sugiyama, Tsuyoshi Ide, Shinichi Nakajima, and Jun Sese. Semi-Supervised Local Fisher Discriminant Analysis for Dimensionality Reduction. PAKDD 2008, Osaka, Japan. May 2008.

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