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Assistant Professor

    Md.Altaf-Ul-Amin Ph.D.    


Email : amin-m@is.naist.jp

Research Interests
In the post genomic era, we notice that network theory has substantially involved with biology for instance we can mention about protein-protein interaction networks (PPI network), protein-metabolite combined networks, gene regulatory networks etc. To understand a living organism as a system we first need to understand a cell as a system for which we need to comprehensively understand the functions of each gene/protein/metabolite and how they work as an individual or in a group. Conducting study on static and dynamic properties of the aforementioned networks will gather knowledge bit by bit towards this goal. In fact the concept of networks can be utilized in many ways to extract useful information from huge pile of biological data. My aim is to contribute in this area of science as much as possible by developing and finding out necessary algorithms and by applying them to real biological data.
Also, I am interested in developing network/graph related software especially visualizing software for large networks on the basis of clustering algorithms. Visualizing large graphs in a systematic way, I hope, will find applications in many branches of science. Furthermore, I am interested to explore the possibility of application of network theory in other areas of science especially in the area of VLSI design and testing on which subject I already conducted some research. Actually, graph theory and VLSI design are very closely related subjects because like any other circuits VLSI circuits can be easily represented as graphs. In fact, this is very often done, for example, to find optimum solutions in case of routing, partitioning, layout placement to meet constraints of area, delay, number of insulation layers etc. Graph algorithms are also useful to solving problems related to path delay fault testing.

Link to DPClus, a graph clustering software: http://kanaya.naist.jp/DPClus/




Short biography
I received B.Sc. degree in electrical and electronic engineering from Bangladesh University of Engineering and Technology (BUET), Dhaka, M.S. degree in electrical, electronic and systems engineering from Universiti Kebangsaan Malaysia (UKM) and PhD degree from Nara Institute of Science and Technology (NAIST), Japan. Currently I am working as an Assistant Professor in Comparative Genomics Lab of NAIST.



Publications
Publications related to bioinformatics
    Journal & edited book
    1. Md. Altaf-Ul-Amin, Hisashi Tsuji, Ken Kurokawa, Hiroko Asahi, Yoko Shinbo, Shigehiko Kanaya, "DPClus: A Density-periphery Based Graph Clustering Software Mainly Focused on Detection of Protein Complexes in Interaction Networks", Journal of Computer Aided Chemistry , Vol.7, 150-156, 2006.
    2. Arifuzzaman M., Maeda M., Itoh A., Nishikata K., Takita C., Saito R., Ara T., Nakahigashi K., Huang, H.C., Hirai A., Tsuzuki K., Nakamura S., Altaf-Ul-Amin M., Oshima T., Baba T., Yamamoto N., Kawamura T., Ioka-Nakamichi T., Kitagawa M., Tomita M., Kanaya S., Wada C. and Mori H., "Large-scale identification of protein-protein interaction of Escherichia coli K-12", Genome Research 16: 686 - 691, May 2006.
    3. Md. Altaf-Ul-Amin, Yoko Shinbo, Kenji Mihara, Ken Kurokawa and Shigehiko Kanaya, "Development and implementation of an algorithm for detection of protein complexes in large interaction networks", BMC Bioinformatics 7:207, April 2006.
    4. Nevan J. Krogan, Gerard Cagney, Haiyuan Yu, Gouqing Zhong, Xinghua Guo, Alexandr Ignatchenko, Joyce Li, Shuye Pu, Nira Datta, Aaron P. Tikuisis, Thanuja Punna, Jos? M. Peregr?n-Alvarez, Michael Shales, Xin Zhang, Michael Davey, Mark D. Robinson, Alberto Paccanaro, James E. Bray, Anthony Sheung, Bryan Beattie, Dawn P. Richards, Veronica Canadien, Atanas Lalev, Frank Mena, Peter Wong, Andrei Starostine, Myra M. Canete, James Vlasblom, Samuel Wu, Chris Orsi, Sean R. Collins, Shamanta Chandran, Robin Haw, Jennifer J. Rilstone, Kiran Gandi, Natalie J. Thompson, Gabe Musso, Peter St Onge, Shaun Ghanny, Mandy H. Y. Lam, Gareth Butland, Amin M. Altaf-Ul, Shigehiko Kanaya, Ali Shilatifard, Erin O'Shea, Jonathan S. Weissman, C. James Ingles, Timothy R. Hughes, John Parkinson, Mark Gerstein, Shoshana J. Wodak, Andrew Emili and Jack F. Greenblatt, "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae", Nature 440, 637-643, March 2006
    5. Shinbo Y, Nakamura Y, Md. Altaf-Ul-Amin, Asahi H, Kurokawa K, Arita K, Saito K, Ohta D, Shibata D, Kanaya S, "KNApSAcK: A Comprehensive Species-Metabolite Relationship Database", Biotechnology in Agriculture and Forestry, Vol 57, Springer-Verlag Berlin Heidelberg 2006.
    6. Hirokazu Nishio, Md. Altaf-Ul-Amin, Ken Kurokawa, Shigehiko Kanaya, "Spherical SOM and arrangement of neurons using helix on sphere", IPSJ Transactions on Mathematical Modeling and its Applications, Vol.47, 56-60, 2006.
    Conference Proceedings (Reviewed)
    1. Md. Altaf-Ul-Amin, Toshihiro Koma, Ken Kurokawa, Shigehiko Kanaya, "Prediction of Protein Functions Based on Protein-Protein Interaction Networks: A Min-Cut Approach", Proceedings of the Workshop on Biomedical Data Engineering (BMDE), Tokyo, Japan, pp. 37-43, April 3-4, 2005.
    2. Yoko Shinbo, Toshihiro Koma, Md. Altaf-Ul-Amin, Ken Kurokawa, Hirotada Mori, Naotake Ogasawara, Yukiko Nakamura, Shigehiko Kanaya." Conserved Protein-Protein Interactions in Different Species", The 15th International Conference on Genome Informatics, December 13-15, 2004, Yokohama Japan
    3. Yoko Shinbo, Yukiko Nakamura, Hiroko Asahi, Md. Altaf-Ul-Amin, Ken Kurokawa, Shigehiko Kanaya. "Species -specific diversity of metabolites: A natural product database System", Proceedings of the Tenth International Congress for Culture Collections, Tsukuba, Japan, 10-15 October 2004
    4. Altaf-Ul-Amin and Shigehiko Kanaya, "Detection of Protein Complexes in Large Interaction Networks", Proceedings of The 8th World Multi-Conference on Systemics, Cybernetics and Informatics (Volume VII), Orlando, Florida, USA, July 18-21, 2004.
    5. Hirokazu Nishio, Md. Altaf-Ul-Amin, Yukiko Nakamura, Takashi Abe, Makoto Kinouchi, Toshimichi Ikemura, Kazuo Kobayashi, Naotake Ogasawara and Shigehiko Kanaya, "Gene Classification based on Expression Profile using BL-SOM: Suitability assessment of multivariate gene expression data to Spherical and plain SOM by N-measure", Proceedings of The 8th World Multi-Conference on Systemics, Cybernetics and Informatics (Volume VII), Orlando, Florida, USA, July 18-21, 2004.
    6. Hirokazu Nishio, Md. Altaf-Ul-Amin, Tetsuo Sato, Ken-nosuke Wada, Yoshiko Wada, Kotaro Minato, Kazuo Kobayashi, Ogasawara Naotake, Shigehiko Kanaya, "Visualization of Gene classification based on Expression Profile using BL-SOM", Workshop on Self Organizing Map (WSOM'03), Hibikino, Kitakyushu, September 11-14, 2003, Japan, pp. 101-106.
    7. Md. Altaf-Ul-Amin, Kensaku Nishikata, Toshihiro Koma, Teppei Miyasato, Yoko Shinbo, Md. Arifuzzaman, Chieko Wada, Maki Maeda, Taku Oshima, Hirotada Mori, Shigehiko Kanaya, "Prediction of Protein Functions Based on K-cores of Protein-Protein Interaction Networks and Amino Acid Sequences", The 14th International Conference on Genome Informatics December 14-17, 2003, Yokohama Japan.
Publications related to IC testing
    Journal
    1. Md. Altaf-Ul-Amin, Satoshi Ohtake and Hideo Fujiwara,"Design for hierarchical two-pattern testability of data paths", IEICE Trans. on Information and Systems, Vol. E85-D, No. 6, pp. 975-984, June 2002.
    2. Md. Altaf-Ul-Amin, Satoshi Ohtake and Hideo Fujiwara,"Design for two-pattern testability of controller-data path circuits", IEICE Trans. on Information and Systems, Vol. E86-D, No. 6, pp. 1042-1050, June 2003.
    Conference Proceedings (reviewed)
    1. Md. Altaf-Ul-Amin, S. Ohtake and H. Fujiwara, "Design for two-pattern testability of controller-data path circuits", Proceedings IEEE 11th Asian Test Symposium, November 18-20, 2002, Guam, USA, pp.73-79.
    2. Md. Altaf-Ul-Amin, Satoshi Ohtake and Hideo Fujiwara, gDesign for hierarchical two-pattern testability of data pathsh, Proceedings of IEEE 10th Asian Test Symposium, November 19-20, 2001, Kyoto, Japan, pp. 11-16.
    3. Md. Altaf-Ul-Amin and Zahari Mohamed Darus, gVHDL Design of a Test Processor Based on Mixed-Mode Test Generationh, Proceedings of IEEE Ninth Great Lakes Symposium on VLSI, March 4-6, 1999, Ann Arbor, Michigan, USA, pp. 244-245.
    4. Md. Altaf-Ul-Amin and Zahari Mohamed Darus, gAn Off-Chip Current Sensor for IDDQ Testing of CMOS ICsh, Proceedings of IEEE Seventh Asian Test Symposium (ATSf98), December 2-4, 1998, Singapore, pp. 318-322.
    5. Md. Altaf-Ul-Amin and Zahari Mohamed Darus, gCurrent Sensor and Test Processor Design for Integration of Logic and IDDQ Testing of CMOS ICsh, Proceedings of IEEE International Conference on Semiconductor Electronics, November 24-26, 1998, Bangi, Malaysia, pp. 162-167.
    6. Zahari Mohamed Darus, Md. Altaf-Ul-Amin and Huang Seow Ling gDetection of CMOS defects through power supply voltage pulsingh, Proceedings of IEEE National Symposium on Microelectronics, Nov. 24-25, 1997, Bangi, Malaysia, pp. 61-65.





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