[Japanese / English]
 

Papers

  1. Yohei Shimura, Yuu Hirose, Naomi Miasawa, Yasunori Osana, Hiroshi Katoh, Haruyo Yamaguchi and Masanobu Kawachi: "Comparison of the terrestrial cyanobacterium Leptolyngbya sp. NIES-2104 and the freshwater Leptolyngbya boryana PCC 6306 genomes." DNA Research, Oct. 2015.
  2. Takayuki Akamine, Mohamad Sofian Abu Talip, Yasunori Osana, Naoyuki Fujita, Hideharu Amano: "Reconfigurable Out-of-order System for Fluid Dynamics Computation Using Unstructured Mesh.", IEICE Transaction on Information and Systems, Vol.E97-D, No.5, pp.1225-1234, May.2014.
  3. Mohamad Sofian Abu Talip, Takayuki Akamine, Mao Hatto, Yasunori Osana, Naoyuki Fujita and Hideharu Amano: "Adaptive Flux Calculation Scheme in Advection Term Computation Using Partial Reconfiguration.", International Journal of Networking and Computing, Vol.3 No.2, July 2013, pp.289-306.
  4. Mohamad Sofian Abu Talip, Takayuki Akamine, Yasunori Osana, Naoyuki Fujita and Hideharu Amano: "Partial Reconfiguration of Flux Limiter Functions in MUSCL Scheme Using FPGA.", IEICE Transaction on Information and Systems, Vol.E95-D, No.10, pp.2369-2376, Oct. 2012.
  5. Kris Popendorf, Tsuyoshi Hachiya, Yasunori Osana and Yasubumi Sakakibara: "Murasaki: A Fast, Parallelizable Algorithm to Find Anchors from Multiple Genomes.", PLoS ONE 5(9): e12651. doi:10.1371/journal.pone.0012651, Sep.2010.
  6. Hideki Yamada, Yui Ogawa, Tomonori Ooya, Tomoya Ishimori, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata and Kiyoshi Oguri: "Automatic Pipeline Construction Focused on Similarity of Rate Law Functions for an FPGA-based Biochemical Simulator.", IPSJ Transactions on System LSI Design Methodology, Vol.3, pp.244-256, 2010.
  7. Yukari Nishito, Yasunori Osana, Tsuyoshi Hachiya, Kris Popendorf, Atsushi Toyoda, Asao Fujiyama, Mitsuhiro Itaya and Yasubumi Sakakibara: "Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data.", BMC Genomics 2010, Vol.11(243), Apr.2010.
  8. Takeshi Akama, Koichi Suzuki, Kazunari Tanigawa, Akira Kawashima, Huhehasi Wu, Noboru Nakata, Yasunori Osana, Yasubumi Sakakibara, and Norihisa Ishii: "Whole genome tiling array analysis of Mycobacterium leprae RNA reveals high expression of pseudogenes and non-coding regions.", Journal of Bacteriology, Vol.191(10). pp.3321-3327. Mar.2009.
  9. Tsuyoshi Hachiya, Yasunori Osana, Kris Popendorf, and Yasubumi Sakakibara: "Accurate identification of orthologous segments among multiple genomes.", Bioinformatics, Vol.25(7). pp.853-860. Feb.2009.
  10. Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano: "ReCSiP: An FPGA-based general-purpose biochemical simulator.", Electronics and Communications in Japan (Part II: Electronics). Vol.90(7). Jul.2007. pp.1-10.
  11. Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, and Hideharu Amano: "An FPGA-Based Acceleration Method for Metabolic Simulation.", IEICE Trans. on Information and Systems, E87-D(8). Aug.2004. pp.2029-2037.

International Conferences

  1. Mohamad Sofian Abu Talip, Takayuki Akamine, Mao Hatto, Yasunori Osana, Naoyuki Fujita and Hideharu Amano: "Partially reconfigurable flux calculation scheme in advection term computation.", The 2013 International Conference on Field-Programmable Technology, Kyoto, Japan, Dec.2013.
  2. Takayuki Akamine, Kenta Inakagata, Yasunori Osana, Naoyuki Fujita and Hideharu Amano: "Reconfigurable Out-of-Order Mechanism Generator for Unstructured Grid Computation in Computational Fluid Dynamics.", The 2012 Internal Conference on Field Programmable Logic and Applications, Oslo, Norway, Aug.2012.
  3. Mohamad Sofian Abu Talip, Takayuki Akamine, Yasunori Osana, Naoyuki Fujita and Hideharu Amano: "Cost Effective Implementation of Flux Limiter Functions using Partial Reconfiguration.", The 8th International Symposium on Applied Reconfigurable Computing, Hong Kong, Mar.2012.
  4. Takayuki Akamine, Kenta Inakagata, Yasunori Osana, Naoyuki Fujita and Hideharu Amano: "An implementation of out-of-order execution system for acceleration of computational fluid dynamics on FPGAs.", The 2011 International Workshop on Highly-Efficient Accelerator and Reconfigurable Technologies. London, UK. Jun.2011. (also accepted on ACM SIGARCH Computer Architecture News, 39(4), pp.50-55. Sep.2011.)
  5. Yui Ogawa, Tomonori Ooya, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata and Kiyoshi Oguri: "A datapath classification method for FPGA-based scientific application accelerator systems." The 2010 International Conference on Field Programmable Technology, Beijing, China, Dec.2010.
  6. Hirokazu Morishita, Kenta Inakagata, Yasunori Osana, Naoyuki Fujita and Hideharu Amano: "Implementation and Evaluation of an Arithmetic Pipeline on FLOPS-2D: Multi-FPGA System.", The 2010 International Workshop on Highly-Efficient Accelerator and Reconfigurable Technologies. Tsukuba, Japan. Jun.2010. (also accepted on ACM SIGARCH Computer Architecture News, 38(4), pp.8-13. Sep.2010.)
  7. Hideki Yamada, Yasunori Osana, Tomoya Ishimori, Tomonori Ooya, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata and Kiyoshi Oguri: "A Modular Approach to Heterogeneous Biochemical Model Simulation on an FPGA.", The 2009 International Conference on ReConFigurable Computing and FPGAs. Cancun, Mexico. Dec.2009.
  8. Kenta Inakagata, Hirokazu Morishita, Yasunori Osana, Naoyuki Fujita and Hideharu Amano: "Modularizing Flux Limiter Functions for a Computational Fluid Dynamics Accelerator on FPGAs.", The 19th International Conference on Field Programmable Logic and Applications. Prague, Czech. pp.654-657. Sep.2009.
  9. Tomonori Ooya, Hideki Yamada, Tomoya Ishimori, Yuichihiro Shibata, Yasunori Osana, Yuichiro Shibata, Kiyoshi Oguri, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi and Hideharu Amano: "Configuring Area and Performance: Empirical Evaluation on an FPGA-based Biochemical Simulator.", the 19th International Conference on Field Programmable Logic and Applications. Prague, Czech. pp.679-682. Sep.2009.
  10. Tomoya Ishimori, Hideki Yamada, Yuichiro Shibata, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Hideharu Amano, Akira Funahashi, Hiroi Noriko, Kiyoshi Oguri: "Pipeline Scheduling with Input Port Constraints for an FPGA-based Biochemical Simulator", The 5th International Workshop on Applied Reconfigurable Computing. Karlsruhe, Germany. May.2009.
  11. Hirokazu Morishita, Yasunori Osana, Naoyuki Fujita and Hideharu Amano: "Exploiting memory hierarchy for a Computational Fluid Dynamics accelerator on FPGAs", International Conference on Field-Programmable Technology 2008. Taipei, Taiwan. pp.193-200. Dec.2008.
  12. Masato Yoshimi, Yuri Nishikawa, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Hideki Yamada, Hiroaki Kitano and Hideharu Amano: "Practical Implementation of a Network-based Stochastic Biochemical Simulation System on an FPGA", 2008 International Conference on Field Programmable Logic and Applications. pp.663-666. Heidelberg, Germany. Sep.2009.
  13. Masato Yoshimi, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Hideki Yamada, Hiroaki Kitano, and Hideharu Amano: "A Framework for Implementing a Network-Based Stochastic Biochemical Simulator on an FPGA.", International Conference on Field-Programmable Technology 2007, Kitakyushu, Fukuoka, Japan. Nov.2007. pp.193-200.
  14. Hideki Yamada, Naoki Iwanaga, Yuichiro Shibata, Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Hiroaki Kitano, and Kiyoshi Oguri: "A Combining Technique of Rate Law Functions for a Cost-effective Reconfigurable Biological Simulator (poster)", The 17th International Conference on Field Programmable Logic and Applications. Amsterdam, Holland. Aug.2007. pp.808-811.
  15. Masato Yoshimi, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hideki Iwanaga, Hiroaki Kitano, and Hideharu Amano: "FPGA Implementation of a Data-Driven Stochastic Biochemical Simulator with the Next Reaction Method", The 17th International Conference on Field Programmable Logic and Applications. Amsterdam, Holland. Aug.2007. pp.254-259.
  16. Yow Iwaoka, Yasunori Osana, Masato Yoshimi, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano: "An Acceleration of a Biochemical Simulator on Programmable Hardware (Poster)", The Seventh International Conference on Systems Biology (ICSB2006). Yokohama, Japan. 2006. PosterID: FI67.
  17. Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano: "A Hardware Accelerator for Biochemical Simulations", The 2006 Winter Simulation Conference. Monterey, CA, USA. Dec.2006.
  18. Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano: "Performance Evaluation of an FPGA-based Biochemical Simulator ReCSiP", Proceedings of 2006 International Conference on Field Programmable Logic and Applications. Madrid, Spain. Aug.2006. 845-850.
  19. Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Akira Funahashi, Noriko Hiroi, Yuichiro Shiabta, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano: "An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems", Proceedings of 2006 International Conference on Field Programmable Logic and Applications. Madrid, Spain. Aug.2006. 227-232.
  20. Yuri Nishikawa, Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano: "An Evaluation and Investigation of Dual-Thread Numerical Integration Mechanism for FPGA-based Biochemical Simulator ReCSiP.", Proceedings of CoolChips IX. Yokohama, Japan. Apr.2006. 195-197.
  21. Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano: "The Design of Scalable Stochastic Biochemical Simulator on FPGA.", Proceedings of 2005 IEEE International Conference on Field Programmable Technology, Signapore, Dec.2005, pp.339-340.
  22. Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Masato Yoshimi, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano: "A Framework for ODE-Based Multimodel Biochemical Simulations on an FPGA.", Proceedings of the 15th Field Programmable Logic and its applications(FPL) 2005, Tampere, Finland. August~2005. pp.574-577.
  23. Naoki Iwanaga, Yuichiro Shibata, Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Hiroaki Kitano, and Kiyoshi Oguri: "Efficient Scheduling of Rate Law Functions for ODE-based Multimodel Biochemical Simulation on an FPGA.", Proceedings of the 15th Field Programmable Logic and its applications(FPL) 2005, Tampere, Finland. Aug.2005. pp.666-669.
  24. Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Hiroaki Kitano, and Hideharu Amano: "An FPGA-Based, Multi-model Simulation Method for Biochemical Systems.", Proccedings of the 19th International Parallel and Distributed Processing Symposium / Reconfigurable Architecture Workshop, Denver, Colorado, USA. Apr.2005.
  25. Masato Yoshimi, Yasunori Osana, Tomonori Fukushima, and Hideharu Amano: "Stochastic Simulation for Biochemical Reactions on FPGA.", Proceedings of the 14th International Conference on Field Programmable Logic and Applications, Aug.2004. pp.105-114.
  26. Yasunori Osana, Tomonori Fukushima, and Hideharu Amano: "ReCSiP: a ReConfigurable Cell SImulation Platform - Accelerating Biological Applications with FPGA -.", Proceedings of the 9th Asia South Pacific Design Automation Conference, Jan.2004. pp.731-733.
  27. Yasunori Osana, Tomonori Fukushima, and Hideharu Amano: "Implementation of ReCSiP: a Reconfigurable Cell SImulation Platform.", Proceedings of the 13th International Conference on Field Programmable Logic and Applications, Sep.2003. pp.766-775.
  28. Yasunori Osana, Hironori Nakajo, Noriaki Suzuki, Tomonori Tam ura, and Hideharu Amano: "Performance Evaluation of a Parallel I/O Mechanism on a Massively Parallel Processing System JUMP-1.", Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, Jun.2001. pp.1179-1185.

Workshops and others (abstract submission)

  1. Kris Popendorf, Yasunori Osana, Hacchiya Tsuyoshi, and Yasubumi Sakakibara: "Murasaki: Homology Detection Across Multiple Large-Scale Genomes (poster)", Fifth Annual RECOMB Satellite Workshop on Comparative Genomics. San Diego CA, USA. Sep.2007.
  2. Yasunori Osana, Kris Popendorf, and Yasubumi Sakakibara: "GMV: a multi-platform comparative genome browser for Murasaki (poster)", Fifth Annual RECOMB Satellite Workshop on Comparative Genomics. San Diego CA, USA. Sep.2007.
  3. Yasunori Osana,: "CellDesigner-SBML Layout Extension Annotation Converter.", The 10th Workshop on Software Platforms for Systems Biology, Harvard Medical School, Boston, MA, Oct.2005.
  4. Yow Iwaoka, Yasunori Osana, Masato Yoshimi, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano,: "A System Design of Accelerating Biochemical Simulations on Programmable Hardware.", The 10th Workshop on Software Platforms for Systems Biology, Harvard Medical School, Boston, MA, Oct.2005.

More publication in Japanese is listed in Japanese page.