Duke University | Howard Hughes Undergraduate Program
Vertically Integrated Partners (VIP) Program
May 27-August 1, 2008
The Vertical Integration Partners (VIP) Program is a 10 week program that provides ten Duke undergraduates with support for a summer of research in Systems Biology. Application (pdf)
The Vertical Integration Partners (VIP) Program is a new addition to Hughes-funded initiatives at Duke. The program provides advanced opportunities for systems-level summer research for rising Duke juniors and seniors. In this annual 10-week program, undergraduate partners from different disciplines (biology, mathematics, computer science and engineering) join interdisciplinary teams with two graduate students and together, they are guided by two faculty members.
There will be five VIP research teams in summer 2008:
• Cell Systems,
• Cell Signaling,
• Information Signaling and Processing,
• Modeling Biological Systems,
• Models for Genetics and Evolution of Complex Systems
Each team will accept two undergraduates, one majoring in a biological science (biology, biomedical engineering, etc.) and one majoring in a quantitative discipline (mathematics, computer science or engineering). Students whose majors are not in these areas, but who have a substantial background in one, e.g., multiple upper level courses and research experience, will also be considered. Priority will be given to rising juniors and seniors; students may not participate in this program after graduation.
Application to the VIP Program for undergraduate students requires one copy of each of the following:
• Application cover sheet (see p4).
• A personal statement, not to exceed three pages (double spaced), addressing (1) the VIP project for which you wish be considered;
(2) your background in science and what additional abilities you will bring to this interdisciplinary project in systems biology;
(3) your previous research experience, if any;
(4) your career goals.
• Two letters of recommendation from Duke faculty who can address your abilities in the life sciences and/or in the quantitative sciences. One letter must be from a course instructor; the second may be from an instructor or research supervisor.
• An official Duke transcript.
VIP applications will be considered on a rolling basis beginning February 1; interviews may be required. All materials should be mailed, faxed or emailed to the URS Office:
Howard Hughes VIP Program
Office of Undergraduate Research Support
011 Allen Building (Box 90051)
Phone 684-6536, Fax 660-0488; ursoffice@duke.edu
Nijhout-Reed VIP Team 2007
2008 VIP Program Projects
1. Cell Systems
As of March 7, both undergraduate positions in this team have been filled.
In this VIP project, Dr. Steven Haase (Biology) and Dr. Alex Hartemink (Computer Science) will engage team members in how yeast cells regulate the many steps required for the replication cycle. Understanding the transcription regulatory processes will provide insights into such questions as how the loss of regulation at these steps leads to diseases of under- or over-proliferation. Experimental approaches include developing the appropriate methods for inducing and maintaining synchrony within populations of cells; measuring distributions of DNA content; and determining protocols for mRNA extraction, purification, and quantification on oligonucleotide arrays. Computational issues include modeling synchrony under different protocols; deconvolution of both flow cytometric measurements and mRNA expression profiles; and modeling the transcriptional regulatory networks governing the cell cycle.
Related publication:
David A. Orlando, Charles Y. Lin, Allister Bernard, Edwin S. Iversen, Alexander J. Hartemink and Steven B. Haase. 2006. A Probabilistic Model for Cell Cycle Distributions in Synchrony Experiments. Molecular and Cellular Biology Vol 26, No. 6. p. 2456-2466. Mar. (2006)
2. Cell Signaling
As of March 4, both undergraduate positions in this team have been filled.
The long-term goal of this project, directed by Dr. Linchong You (Biomedical Engineering and IGSP) and Dr. Joseph Nevins (Molecular Genetics and Microbiology and IGSP), is to establish a computational and experimental framework for an in-depth view of signaling pathways central to mammalian cell cycle entry and, building on this foundation, to engineer synthetic gene circuits for therapeutic applications by reprogramming the cell cycle. Specifically, we use both mathematical modeling and cell biology experiments to investigate the major dynamics involved in mammalian cell cycle entry, focusing on regulation of the restriction point (R-point), which represents a threshold for commitment to entry into the cell cycle. Underscoring its critical importance, the R-point is deregulated in virtually all human tumors that confer cancer cells growth advantages.
3. Information Signaling and Processing
As of March 26, both undergraduate position in this team have been filled.
This VIP project, directed by Dr. Leslie Collins (Electrical and Computer Engineering) and Dr. Debara Tucci (Surgery, Duke Medical Center), will enable students to apply signal processing concepts to address biological system challenges. These system challenges drive enabling technology research to develop and optimize sensor systems, which in turn requires new computational algorithms for sensor optimization. This team will address the challenge posed in the development of cochlear implants and, specifically, how sensing and processing can be integrated in a neural prosthetic system to optimally stimulate the implant that is designed to provide speech information. Students will build implants and, in the process, pursue research on the physiology and the mechanisms of electrical stimulation of the cochlea; develop computational models and evaluate how well the algorithms are extracting data; and investigate the theoretical, experimental, and ethical issues associated with the design of an implantable electrode array system.
Related publications:
Remus, J. J., Throckmorton, C. S., and Collins, L. M., Expediting the identification of impaired channels in cochlear implants via analysis of speech-based confusion matrices, in press, IEEE Trans. Biomedical Engineering, March, 2007.
Throckmorton, C. S., Kucukoglu, M. S., Remus, J. J., and Collins, L. M., Encoding fine frequency structure for improved speech recognition in cochlear implant subjects: a multiple carrier frequency algorithm, Hearing Research, 218, August, 2006, 30-42.
4. Modeling Biological Systems
As of March 26, one undergraduate position on this team is open.
The ultimate goal of this VIP research team, directed by Dr. Philip Benfey (Biology) and Dr. Uwe Ohler (Biology), is to identify the gene regulatory networks controlling development and the response to environmental stimuli in the plant model system, Arabidopsis. To infer gene regulatory networks, we will explore different quantitative methods for identifying links between genes which are specific for particular cell types or stages, and which support interactions of positive or negative regulators with their target genes. Experimental research will focus on generating reporter lines to validate inferred relationships.
Related publications:
Brady et al. 2007. A High-Resolution Root Spatiotemporal Map Reveals Dominant Expression Patterns. Science 318: 801-806
Lee JY, Colinas J, Wang JY, Mace D, Ohler U and Benfey PN (2006) Transcriptional and post-transcriptional regulation of transcription factor expression in Arabidopsis roots. PNAS 103:6055-6
Mace DL, Lee JY, Twigg RW, Colinas J, Benfey PN and Ohler U. (2006) Quantification of transcription factor expression from Arabidopsis images. Bioinformatics. 22:e323-31.
5. Models for Genetics and Evolution of Complex Systems
As of March 4, both undergraduate positions for this team have been filled.
This VIP project, directed by Dr. Frederik Nijhout (Biology) and Dr. Michael Reed (Mathematics), will focus on how real genes, biochemical systems and physiological systems interact to produce observed properties of living systems. The team will develop mathematical models to describe the details of specific complex systems (e.g., folic acid metabolism) in which all components are known and in which the dynamics and kinetics have been studied experimentally. The challenges are to evaluate and combine data obtained from such fields as genetics, biochemistry, physiology, and clinical medicine into a single model system that can be used by experimenters and clinicians to test specific experimental or therapeutic interventions. The mathematical models developed are also used to deduce plausible scenarios for the evolution of the system, since complex systems do not come into existence fully formed; a mathematical model makes it possible to study scenarios for the piecewise addition and modification of components.
Related publications:
Reed, M.C., Nijhout, H.F., Neuhouser, M.L., Gregory J.F. III., Shane, B., James, S.J., Boynton, A. and Ulrich, C.M. 2006. A mathematical model gives insights into nutritional and genetic aspects of folate-mediated one-carbon metabolism. J. Nutr. 136: 2653-2661.
Nijhout HF, Reed M.C., Lam S-L, Shane B, Gregory J.F., and Ulrich CM. 2006. In silico experimentation with a model of hepatic mitochondrial folate metabolism. Theoretical Biology and Medical Modelling 3: 40ff.