I am currently a
Ph.D. student in the department of
Computer Science, UC-Davis. I work
closely with Professor Nina
Bernd Hamann, Professor
Patrice Koehl from UCD
and scientist Inna Dubchak
from Ernest Orlando Lawrence Berkeley National Laboratory (LBNL). Before I
came to UCD, I received my B.S. degree for double majors in computer science
and economics from Rutgers University.
I am currently
interested in computer graphics, visualization and computational geometry.
||Molecular Docking. (Abstract) The structure determination
of protein-protein complexes remains a difficult
and lengthy process, both by NMR and X-ray crystallography. Several
computational methods based on docking have consequently been developed as
a support and even as a possible alternative to these experimental methods.
In this paper, we introduce a new protein-protein docking algorithm, shDock,
based on shape complementarity. We characterize the local geometry on each
protein surface with a new shape descriptor, the surface histogram. For checking
the complementarity between two surface histograms, one on each protein,
we use a modified Manhattan distance between their respective surface histograms.
When a match is found between two patches, a model is generated
for the protein complex which is then scored by checking for collision between
the two proteins. We have tested our algorithm on ZDOCK (version 3.0.1)
protein-protein docking benchmark. We found that for 110 out of the 124 test
cases of bound docking in the benchmark, our algorithm was able to generate a
model for the protein complex within a RMSD of 2.5 A from its native structure
in the top 3600 candidates. For unbound docking predictions, we find a similar
good model (within 2.5 A) within the top 3600 models in 54 out of 124 test cases. A
comparison with other shape-based docking algorithms demonstrates the good performance
of our approach.
(Left: 1AK4, a case from the benchmark, corresponds to the complex
formed by human cyclophilin A (magenta) with the N-terminal domain of HIV-1 capsid
1) Surface-Histogram for protein-protein docking (submitted)
2) Patricia Francis-Lyon, Shengyin Gu, Joel Hass, Nina Amenta and Patrice Koehl,
Sampling the conformation of protein surface residues for flexible protein
docking. BMC Bioinformatics 2010.
The ensembles can be found here.
|Image not available
||Web History Study (Project with Google Research):
Submitted a patent application ¡°Generating Action Trails from Web History¡±.
Paper: Elin Ronby Pedersen, Karl Gyllstrom, Shengyin Gu, Peter Jin Hong, Automatic
generation of research trails in web history. International Conference on Intelligent
User Interfaces, 2010.
||Geometric Representation of Proteins. (Abstract)
The amino acid sequence of a protein is the key to understanding its
structure and ultimately its function in the cell. This paper addresses
the fundamental issue of encoding amino acid in ways that the
visualization of protein sequences facilitate the decoding of its
information content. We show that a featured-based representation in a
three dimensional space provides an adequate representation from which
the folding class of a protein as well as its domain content can be
Gu, S., Poch, O., Hamann B., Koehl, P., A Geometric Representation of
of Protein Sequences, IEEE International Conference on Bioinformatics and
Biomedicine (BIBM), pp 135-142, 2007.
||TreeQ-Vista (Project with LBNL): An interactive Tree Visualization
Tool with Functional Annotation Query Capabilities. (Abstract) We
describe a general multiplatform exploratory tool called TreeQ-Vista,
designed for presenting functional annotations in a phylogenetic
context. Traits, such as phenotypic and genomic properties, are
interactively queried from a user-provided relational database with a
user-friendly interface which provides a set of tools for users with or
without SQL knowledge. The query results are projected onto a
phylogenetic tree and can be displayed in multiple color groups. A rich
set of browsing, grouping and query tools are provided to facilitate
trait exploration, comparison and analysis.
Gu, S., Anderson, I., Kunin, V., Cipriano, M.J., Minovitsky, S.,
Weber, G.H., Amenta, N., Hamann, B. and Dubchak, I.L. (2007),
TreeQ-VISTA: an interactive tree visualization tool with functional
annotation query capabilities, Bioinformatics 23(6), Oxford University
Press, pp. 764-766.
||Retro-deformation of fossils. (Abstract) We
consider a problem in which we want to restore the bilateral symmetry of
an object which has been deformed by compression. This problem arises in
paleontology, where symmetric fossils are deformed by the compression of
the rocks in which they are embedded. Our input is a user-selected set
of point-pairs on the deformed object, which are assumed to be
mirror-images on the original symmetric object, with some added noise.
We give a closed-form solution to one variant of the problem, and we
show examples using this solution.
Amenta, N., Gu, S., Wiley, D., Hamann, B., Symmetry Restoration
by stretching, Canadian Conference on Computational Geometry, CCCG 2009.
Retro-deformation is a part of a broader project called
Graphics and Visualization Class Projects:
||MemViz is a visualization tool of memory graph. A
memory graph is a footprint of memory for a program. Each node is
created for an allocated memory location and directed edges are created
for memory pointers. Memory graph evolves in different stages of a
running program. It can be helpful to debugging, code optimization,
security improvement etc. of a program.
||Multi-class segmentation of medical data using SVM.
In the world of medical image analysis, segmentation methods are
important and necessary. Automatic segmentation methods outperform
traditional segmentation methods which utilizes human judgment, in ways
that computer methods are more consistent, reliable and many times
faster; however they require human expertise at the refinement stage
after automatic procedure. I implemented a modified support vector
machine (SVM) and analyzed its performance for multi-class segmentation.
||First Person Shooter Game. A first person shooter (FPS)
game was created by using a simple game engine I wrote. The engine is organized
by scene graph. It supports quake 3 level maps, several 3D model formats, animations of characters,
user control key board events, sounds effects. It implements hierarchical transformation,
hierarchical bounding volumes, texturing, lighting, level of details (or LOD)
and view frustum culling.
||Volume Rending. I implemented several interpolation
methods in a volume render. The visual results were compared and