Research

 

 

Research Areas

  • Bioinformatics
  • Geometric Computing
  • Biological/Geometric Modeling
  • Design and Analysis of Algorithms
  • Combinatorial Optimization
  • Sensor Networks

 

 

 

My primary research interests are bioinformatics and computational biology, geometric computing, biological modeling, design and analysis of algorithms

and combinatorial optimization. For example, my previous research includes solving geometric problems in secondary memory, map labeling, etc.,

which all come from GIS and spatial databases; and 3D weak visibility computation, which comes from computer graphics (more specifically,

3D image rendering), etc. I've also worked on intelligent web searching (information retrieval). For all these research areas I am interested in both the

theoretical and practicalaspects of research. Since early 2004, my interests have been shifted to bioinformatics and computational biology.

One of my current research interest is in computational biology, especially in biological modeling, there are many problems related to 3D geometry.

One of such examples is to approximate a polyhedron (modeling a neuron) with a set of cylindrical segments with different radii, which has applications in neural

maps. Another research area that I have worked on are problems related to protein folding and protein (common) structure identification and simplification.

Since 2004 I have also been working on many problems related to computational genomics; for instance on computing the translocation distance

between signed genomes, phylogenetic reconstruction and RNA multiple structural alignment, etc.

 

Some Software Which Uses My Algorithm

Some Recent and Past Research Grants

  • Collaborative Research:FET:Small: De Novo Protein Scaffold Filling by Combinatorial Algorithms and Deep Learning Models, NSF grant CCF-2307572, $99,384+$19,876 (suppl.) = $119,260, from July, 2023 to June, 2026.
  • REU Site: Algorithms and Optimization for Sustainability and Biology, NSF grant CNS-2243010, $323,949 + $16,000 (suppl.) = $339,949, from Feb, 2023 to Feb, 2026 (co-I, Dr. Yaw is the PI).
  • Building a Montana Computing Consortium, NSF grant DUE-2221684, $99,836 from July, 2022 to June, 2026 (co-PI, Dr. Fasy is the PI).
  • 61628207: Approximation Algorithms, Paramerized Algorithms and Their Applications in Computational Genomics, NSF of China, 180,000 RMB, from Jan, 2017 to Dec, 2018.
  • NeTS:EAGER: Intelligent Information Dissemination in Vehicular Networks based on Social Computing, NSF grant CNS-1644348, $179,988, from Oct, 2016 to Sep, 2018 (co-PI, Dr. Qing Yang is the PI).
  • Conference on Models and Algorithms for Genome Evolution, NSF grant IIS-1340180, $16,475, from Sep, 2013 to Jan, 2014.
  • 60928006: Approximation Algorithms, Parametric Search, Discrete Frechet Distance and Applications, NSF of China, 200,000 RMB, from Jan, 2010 to Dec, 2011.
  • Discrete Frechet Distance and its Biological Applications, NSF grant DMS-0918034, $106,556, from Sep, 2009 to Aug, 2012.
  • CARGO: Approximation and Simulation of Neurons, NSF CARGO grant DMS-0138065, $100,000, from May, 2002 to Apr, 2005.
  • Approximations for Geometric Optimization Problems, HK government RGC CERG [Competitive Earmarked Research Grant] grant, 596K HK$ [roughly 77K US$], from 1999 to 2001.

Some Web Pages Related to My Research