Browse Active Research Projects
Undergraduates can participate in projects for credits by registering in CS 4974 or 4994. Consult the Faculty Advisor or Research Supervisor before you register for this course.
Participation on a VTURCS project could also lead to an honors thesis for CS majors interested in graduating with honors.
Can't find anything that piques your curiousity? Don't be afraid to check out the Computer Science faculty list for someone who has a research interest you'd like to know more about. They might just have something for you.
Algorithm Development for Molecular Dynamics
Faculty Advisor- Alexey Onufriev and Adrian Sandu
Research Supervisor- Alexey Onufriev and Adrian Sandu
Description of Work- To participate in development and testing of new algorithms that speed up molecular dynamics simulations. Here is the problem: a typical macromeolecule is made up of at least ~10,000 atoms, and so to describe its motion, 60,000 or more differential equations must be solved simultaneosly. One way to speed up the calculations is by using the so-called "multiple time-step" methods, in which the integration time-step is effectively increased with minimal impact on the accuracy of the solution. At this stage, we will be testing out different ideas to access their viability for further development. You will get hands-on experience with the software and methodology currently in high demand due to explosive development in the bio- and nano-technology areas.
Application Instructions- Please e-mail us.
Project URL- none
Area(s) of Research- Theory, Bioinformatics
Compensation- Negotiable
Contact- onufriev@cs.vt.edu
Bioinformatics in Genomics
- Faculty Advisor
- Liqing Zhang
- Research Supervisor
- Liqing Zhang
- Description of Work
- Ever wonder what do Bioformaticians do? Here is your opportunity to find out! The research question is: how genes with high sequence similarity diverge over time in both their function and expression? This is a fundamental question in biology, because most, if not all, genes in human and many other species' genomes are genes of this category. To answer this question, you need to know how to program in Perl and some knowledge on databases, both of which should be pretty easy to pick up. The benefit of doing this project is that not only will you get better at programming, but you will get to know some important questions in biology, especially to become aware what is going on in this exciting genomic era!
- Application Instructions
- Send e-mail.
- Project URL
- none
- Area(s) of Research
- Bioinformatics
- Compensation
- Negotiable
- Contact
- lqzhang@cs.vt.edu
Computational Biology and Bioinformatics
- Faculty Advisor
- Lenwood S. Heath
- Research Supervisor
- Various
- Description of Work
- The Department of Computer Science has a number of faculty members involved in computational biology and bioinformatics (CBB) research. Such research often employs CS skills involving Perl programming, relational data bases, web service development, and mathematical or statistical analysis of biological data. The field of bioinformatics changes rapidly and offers many opportunities, so it is not possible to list all specific projects in VTURCS. Basically, if you know Perl, database, web development, algorithmic, or have other relevant skills, consider CBB.
- Application Instructions
- See Dr. Heath's web site for his current office hours. Stop by during office hours for a chat. He can direct you to faculty members who might be able to use your skills.
- Project URL
- http://people.cs.vt.edu/~heath/
- Area(s) of Research
- Bioinformatics, Theory, Computational Biology
- Compensation
- Work for Credit
- Contact
- heath@vt.edu
Evolutionary mechanisms in bacterial diseases
- Faculty Advisor
- Boris A Vinatzer
- Research Supervisor
- Boris A Vinatzer
- Description of Work
- Apply bioinformatics to extract information on evolution of bacterial pathogens from public databases and to design experiments on bacterial plant pathogens isolated form the field. Data obtained in the lab will be analyzed using various bioinformatic tools to gain insieght into the evlution of bacterial plant pathogens. The long term goal is to understand how new genes evolve in bacteria. Your work will consist in using existing bioinformtaic tools to search databases, to compare DNA sequences, to design DNA "primers" for polymerase chain reaction, to analyze data produced in the lab, and possibly to develop scripts to grap outputs from one programm to use as input in other programs.
- Application Instructions
- Send e-mail to Boris Vinatzer at vinatzer@vt.edu
- Project URL
- http://
- Area(s) of Research
- Bioinformatics
- Compensation
- Work for Pay
- Contact
- vinatzer@vt.edu
Functional Annotation of Genes
- Faculty Advisor
- T. M. Murali and Brett Tyler
- Research Supervisor
- T. M. Murali and Brett Tyler
- Description of Work
- Genome sequencing projects have yielded thousands of genes whose biological function is currently not known. These genes may perform important functions in the cell. Some of these genes could be related to human diseases and could potentially serve as drug targets. The projects in this area will study and extend a novel technique for functional annotation that we have developed with collaborators at Boston University. In particular, we are interested in extending the technique to transfer functional information from one organism to another. More details on the technique are available in the following paper: http://people.cs.vt.edu/~murali/papers/pnas-yeast-ppi.pdf
- Application Instructions
- Please send us email with your resume, preferably in PDF format.
- Project URL
- none
- Area(s) of Research
- Bioinformatics
- Compensation
- Negotiable
- Contact
- murali@cs.vt.edu
High-Performance Biological Sequence Search
- Faculty Advisor
- Wu Feng
- Research Supervisor
- Jeremy Archuleta
- Description of Work
- Biological sequence searching has become a fundamental aspect of all bioinformatics. It can help in tasks such as sequencing the human genome, designing pathogen signatures for pathogen detection, identifying unknown viruses (e.g., the virus now known as SARS), and so on. In this project, you will be coding different modules of part of a much larger project (i.e., mpiBLAST at http://www.mpiblast.org) in order to improve functionality, maintainability, and performance.
- Application Instructions
- E-mail a resume to feng@cs.vt.edu. Optional, but preferred, materials include unofficial undergraduate transcript and a brief one-paragraph statement of what interests you about this project.
- Project URL
- http://www.mpiblast.org/
- Area(s) of Research
- Bioinformatics, Parallel Computation, Software Engineering, Systems, Theory, Computational Biology, Databases, Data Mining, Artificial Intelligence
- Compensation
- Negotiable
- Contact
- feng@cs.vt.edu
Interdiscplinary Projects in Computational Science/Bioinformatics
- Faculty Advisor
- Eunice Santos
- Research Supervisor
- Eunice Santos
- Description of Work
- Ever wondered how Computer Science interacts with other science and engineering disciplines? What does CS have to do with Protein Folding? If you're interested, we have projects that will give you insights into the interdisciplinary nature of CS. Projects span the combination of CS with problems in bioinformatics, computational biology/chemistry, and computational physics.
- Application Instructions
- see Dr. Santos
- Project URL
- http://www.cs.vt.edu/~santos
- Area(s) of Research
- Bioinformatics, Networking, Theory
- Compensation
- Negotiable
- Contact
- santos@cs.vt.edu
Mining Plant Biology Papers to Identify Gene Functions (MineFun)
- Faculty Advisor
- Lenwood S. Heath
- Research Supervisor
- Lenwood S. Heath, Naren Ramakrishnan
- Description of Work
- There are 26,000+ genes in the model plant Arabidopsis thaliana, each of which have some biological function. Biological databases such as TAIR (http://www.arabidopsis.org) catalog all the genes, including their DNA sequences and putative functions. In many cases, the functional annotation of a gene given in the database is inaccurate or simply unknown. However, an accurate annotation can often be extracted from the scientific literature. To avoid the laborious manual process of reading thousands of papers, it is desirable to partially automate the extraction of annotation from literature. There are databases of scientific literature, including public databases such as PubMed (http://www.ncbi.nim.nih.gov/sites/entrez?db=PubMed) and AGRICOLA (http://agricola.nal.usda.gov/), in which the abstracts of thousands of papers are indexed and searchable. Moreover, the process of extracting relationships from text has previously been automated in the Snowball system (http://snowball.cs.columbia.edu/). This tool is not particularly targeted toward the needs of Arabidopsis gene annotation, but their methods are an excellent starting point for the MineFun project. In this project, we are building tools to data mine gene function information from scientific extracts. The resulting improved annotations will be of great benefit to plant biology. The interested student must have proficiency in multiple languages: at least one high-level language such as C/C++/Java and especially important for this project, Perl. Experience in text processing is desirable.
- Application Instructions
- Please see Dr. Heath or Dr. Ramakrishnan during their office hours. Send email to set up an appointment, if necessary.
- Project URL
- http://
- Area(s) of Research
- Bioinformatics, Data Mining, Databases
- Compensation
- Negotiable
- Contact
- heath@vt.edu
Parallel Programming with Video Cards and More ...
- Faculty Advisor
- Wu Feng
- Research Supervisor
- Description of Work
- The world of computing is now irrevocably parallel. CPUs have "topped" out roughly 3.0 GHz. So, while performance in the past has doubled roughly every 2 years due to increases in clock frequency, future performance increases will be due to the doubling of the number of cores in a system every 2 years. As such, we are looking at programming models, environments, and applications on multicore and manycore architectures. Of particular relevance and accessibility for VTURCS students are mapping applications onto traditional multicore (Intel and AMD), hybrid multicore (Cell and PlayStation3), manycore (video cards), and reconfigurable multicore (Tilera TILE64) architectures.
- Application Instructions
- E-mail a resume to feng@cs.vt.edu. Optional, but preferred, materials include unofficial undergraduate transcript and a brief one-paragraph statement of what interests you about this project.
- Project URL
- http://synergy.cs.vt.edu/
- Area(s) of Research
- Bioinformatics, Computational Biology, Data Mining, Human-Computer Interaction, Parallel Computation, Systems, Theory
- Compensation
- Negotiable
- Contact
- feng@cs.vt.edu
Protein Completion (A Structural Biology Web Server)
- Faculty Advisor
- Alexey Onufriev, Lenwood Heath
- Research Supervisor
- Jon Myers, Alexey Onufriev
- Description of Work
- Structure of a biological molecule is a key determinant of its biological function. However, experimentally available structures (from X-ray crystallography) are missing the hydrogen atoms. Without them, structures are seriously incomplete. We have developed a (first in the world) prototype web application that uses theoretical methods to add the missing hydrogens. Lots of work is still to be done, and we need help in virtually every aspect of the project: PHP, web design, C++/PERL programming, core algorithm development, testing. We are also planning to use the server to address some important biological questions. This is an "instant gratification" project, as your contribution becomes immediately accessible to researchers world-wide + you get your name on the project's credits page (good for your resume...)
- Application Instructions
- Contact Alexey Onufriev alexey@cs.vt.edu
- Project URL
- http://chekhov.cs.vt.edu/completion
- Area(s) of Research
- Bioinformatics, Human-Computer Interaction, Software Engineering, Computational Biology
- Compensation
- Negotiable
- Contact
- alexey@cs.vt.edu
Protein folding on a PC.
- Faculty Advisor
- Alexey Onufriev
- Research Supervisor
- Alexey Onufriev and grad. students
- Description of Work
- Have you heard of the famous "protein folding" problem? What people call the "grand challenge of computational science"? We are working on an algorithm that has the potential to solve the problem on a --single PC--. If you want to be a part of the team and have a chance to publish in prestigious journals, join us. No prior knowledge of biology or physics is required, only enthusiasm for solving hard problems. However, excellent programming skills and solid math background are a must.
- Application Instructions
- email me.
- Project URL
- http://
- Area(s) of Research
- Bioinformatics, Software Engineering, Theory, Computational Biology
- Compensation
- Negotiable
- Contact
- alexey@cs.vt.edu
Revealing the mystery of the evolution of overlapping genes
- Faculty Advisor
- Liqing Zhang
- Research Supervisor
- Liqing Zhang
- Description of Work
- Increasing studies have shown that overlapping genes are an important phenomenon in many eukaryotic genomes such as human, mouse, flies, and plants. These genes play an important role in regulation of gene expression at the levels of transcription, mRNA processing, splicing, or translation. However, functional studies of these genes are still in its infancy. Little is known about the exact functional role of these genes and their evolutionary dynamics in the genome. In this project, we will perform a large scale analysis of these genes in several animal and plant genomes and analyse the birth and death of these genes using bioinformatics approaches.
- Application Instructions
- Send an email to me.
- Project URL
- http://
- Area(s) of Research
- Bioinformatics, Computational Biology
- Compensation
- Work for Credit or Volunteer
- Contact
- lqzhang@v.tedu
Supercomputing on Video Gaming Consoles
- Faculty Advisor
- W. Feng
- Research Supervisor
- Ashwin Aji
- Description of Work
- Given the extreme needs of today's sophisticated video games, game consoles and video graphics cards in their own right have become supercomputers. The goal of this project is to program *and* optimize a bioinformatics application (or perhaps something else, if reasonable) on the Sony PlayStation 3 and/or the NVIDIA Tesla video graphics card using the CUDA programming environment. (For those interested in human-computer interaction, a nice interface to the above bioinformatics application would serve as a nice project as well, or an interface to our existing codes.)
- Application Instructions
- E-mail a resume to feng@cs.vt.edu. Optional, but preferred, materials include unofficial undergraduate transcript and a brief one-paragraph statement of what interests you about this project.
- Project URL
- http://
- Area(s) of Research
- Bioinformatics, Human-Computer Interaction, Parallel Computation, Problem Solving Environments, Software Engineering, Systems, Theory, Databases, Data Mining, Knowledge
- Compensation
- Negotiable
- Contact
- feng@cs.vt.edu
Veterinary Experiment Analysis - Force Plate Lab
- Faculty Advisor
- Edward A. Fox
- Research Supervisor
- Edward A. Fox, along with Peter K. Shires (BVSc, MS, Diplomate ACVS, shirespk@vt.edu) and H. Marie Suthers-McCabe (D.V.M., msuthers@vt.edu)
- Description of Work
- The Virginia-Maryland Regional College of Veterinary Medicine has a force plate laboratory. Animals are walked across a plate with sensors, with video recorded as well, to help assess their gait, which can be used to determine effectiveness of treatments and therapies on lameness, hip dysplasia, and other problems. Analysis of the computerized sensor data and video records from experiments is needed, along with development and deployment of tools to help.
- Application Instructions
- Please contact Professor Fox or Shires.
- Project URL
- http://fox.cs.vt.edu
- Area(s) of Research
- Bioinformatics, Digital Libraries, Software Engineering
- Compensation
- Work for Credit
- Contact
- fox@vt.edu
XcisClique
- Faculty Advisor
- Lenwood S. Heath
- Research Supervisor
- Lenwood S. Heath
- Description of Work
- The genome of an organism consists of DNA molecules (chromosomes) in every
cell that encode information for the functioning of the cell. The genome
is typically thought of as sequences over the chemical alphabet {A,C,G,T}.
These sequences encode, among other things, the genes of the organism.
In turn, genes carry the genetic codes for proteins. For a genetic code
to result in a protein, the gene must be transcribed (copied) to a
messenger RNA (mRNA) molecule, which later forms the template to translate
into a protein. The transcription step is controlled by regulatory
sequences embedded in the genomic sequence. If the gene is actually
transcribed into mRNA, then the gene is said to be expressed.
XcisClique is a system that combines the analysis of genomic sequence, known regulatory sequences, and experimental data on gene expression to analyze the statistical significance of combinations (bicliques) of regulatory sequences and gene expression. It consists of local data resources in a relational database together with tools for analyzing sequences and bicliques. Currently, it only has the genome of a small model plant called Arabidopsis thaliana. Amrita Pati completed the current version in 2005, and she is still part of the research group.
Opportunities for Enhancements
(1) A very important genome that recently became available is that of rice. In addition, other organisms will become available over time that can benefit from the capabilities of XcisClique. Every organism has unique challenges related to putting it into a relational database. In other words, there are no standards for what must be included in a genome and in what format. The rice genome will be highly valuable to add to XcisClique, but it will take some effort.
(2) There are some time-consuming analyses that take too long to be done through the web interface. Instead, they are precomputed for a limited set of parameters and stored in a database. A research task is to develop and implement methods that eliminate precomputation and to enhance the web interface to support greater user capabilities.
(3) Certain functionalities of the XcisClique system could be made more efficient with appropriate enhancements to the code. Improving the running time for an analysis in the current system is another research task.
(4) The computational biology and bioinformatics (CBB) group is acquiring a database server so we can expand the size of the databases that are available through our web services. The rice genome is much larger than the Arabidopsis genome. And there is more gene expression data available on the web that could be integrated with the rest of the data.
(5) With enough data, one can imagine mining the database for biologically meaningful patterns. Tools available from Amrita and others can be used, or new mining tools based on specific needs can be developed.
Background Required
Knowledge of Perl and MATLAB is required. Knowledge of C++ is desirable but not essential. The current database is built on the Postgres platform, so knowledge of SQL will be helpful. The existing web-interface has been built using PHP and Perl.
- Application Instructions
- Visit Dr. Heath during his office hours to discuss your interest.
- Project URL
- https://bioinformatics.cs.vt.edu/xcisclique/
- Area(s) of Research
- Bioinformatics, Computational Biology, Databases
- Compensation
- Work for Credit
- Contact
- heath@vt.edu