Research

Research in modern biology relies on a host of experimental techniques which shed light into a variety of phenomena that come together to constitute this amazing thing we call “life”. These experiments generate massive amounts of data, most of which are in the form of strings or sequences. Making sense of these sequences requires, apart from a keen understanding of biology, the ability to employ a range of tools from the arsenal of computer and computational sciences. This includes techniques such as design of algorithms and data-structures, statistical modeling, mathematical optimization, machine learning, software programming, etc. Exploring this rapidly growing field of computational biology is what I love to do. Come, join me on this exciting ride !

My research activity:

Journal Articles

Software

  • I maintain a repository of repositories here.

Conference Presentations

  • Anish M.S. Shrestha, Martin C. Frith, Kiyoshi Asai, Hugues Richard: Jointly aligning a group of DNA reads improves accuracy of identifying large deletions, HiTSeq 2018, Chicago
  • Naruki Yoshikawa, Kiyoshi Asai, Anish M.S. Shrestha: Combining probabilistic alignments with read pair information improves accuracy of split-alignments, Poster at the 16th Asia Pacific Bioinformatics Conference, 2018, Kanagawa
  • Hideaki Noshiro, Kiyoshi Asai, Anish M.S. Shrestha: ZBDD-based representation and mining of RNA secondary structure ensemble, Poster at the 39th Annual Meeting of the Molecular Biology Society of Japan, 2016, Yokohama
  • Anish Man Singh Shrestha, Martin C. Frith, Kiyoshi Asai, Hugues Richard: A New Framework for Identifying Genomic Structural Variants Using Joint Alignment of Reads, Statistical Methods for Post Genomic Data Analysis 2016, Lille.
  • Anish Man Singh Shrestha, Martin C. Frith, Kiyoshi Asai, Hugues Richard: Identifying structural variations by jointly aligning a group of reads to a reference genome, GIW/ISCB-Asia 2014, Tokyo.
  • Anish Man Singh Shrestha and Martin C. Frith: An Approximate Bayesian Approach to Mapping Paired-End DNA Reads to a Reference Genome, ISCB-Asia/SCCG 2012, Shenzhen.
  • Satoshi Tayu, Anish Man Singh Shrestha, Shuichi Ueno: On the Complexity of Energy-Aware Mapping for NoCs, IEICE Technical Report, Niigata, Vol.111, No.465, pp.219-224, 2012
  • Anish Man Singh Shrestha, Satoshi Tayu, Shuichi Ueno: Bandwidth of Convex Bipartite Graphs and Related Graphs, 17th International Computing and Combinatorics Conference (COCOON, Dallas), Lecture Notes In Computer Science, vol. 6842, pp. 307 — 318, 2011. 

    *Extended abstract appears in the proceedings of the 7th Hungarian-Japanese Symposium on Discrete Mathematics and Its Applications, Kyoto, pp. 381 — 388, 2011.
  • Anish Man Singh Shrestha, Satoshi Tayu, Shuichi Ueno: A Necessary Condition for Orthogonal Ray Graphs, Proceedings of the 2010 IEICE General Conference, Sendai, A-1-29, 2010.
  • Anish Man Singh Shrestha, Satoshi Tayu and Shuichi Ueno. On Two-Directional Orthogonal Ray Graphs, Proceedings of the IEEE International Symposium on Circuits and Systems (ISCAS, Paris), pp.1807-1810, 2010. 

    *Extended abstract appears in the proceedings of the 7th Japan Conference on Computational Geometry and Graphs (JCCGG, Kanazawa), pp.93-94, 2009.
  • Anish Man Singh Shrestha, Satoshi Tayu, and Shuichi Ueno: Orthogonal Ray Graphs and Nano-PLA Design , Proceedings of the IEEE International Symposium on Circuits and Systems (ISCAS, Taipei), pp.2930-2933, 2009.
  • Anish Man Singh Shrestha, Satoshi Tayu, and Shuichi Ueno: On the Permutation Routing in All-Optical Caterpillar Networks; IEICE Technical Report, Niigata, Vol. 107, No. 361, pp. 23-27, 2007.[Original Manuscript contains some errors!]

Conference Organization

  • Program Committee Member, WABI 2016, 2017
  • Program Committee Member, 7th AYRCOB 2013 at CBRC, Tokyo
  • Program Committee Member, 6th AYRCOB 2012 at BGI, Shenzhen