The Peccoud Lab specializes in rationally designing and testing genetic constructs in high throughput. We employ a state-of-the-art data management infrastructure in order to develop and test models of complex gene networks.
DEVELOPING SOFTWARE TO WRITE AND READ SELF-DOCUMENTING PLASMIDS
Abstract: Life scientists rely heavily on engineered DNA molecules in basic research and the development of new biotechnology products. Proper documentation of these molecules is critical to ensure the reproducibility and safety of the processes in which they are used. Documentation generally comes in the form of standard computer files. However, there is no direct linkage between the DNA molecules and the files that describe them. Keeping track of the association between a DNA molecule and the computer file describing it proves surprisingly challenging because DNA molecules can mutate on their own or be modified at the molecular level…
AUTOMATED PRIORITIZATION AND DESIGN OF EXPERIMENTS
Abstract: Complex networks of interacting molecules control all the physiological processes that occur in a living cell. It is impossible to deduce the functions of these networks using intuitive reasoning alone. Therefore, scientists construct mathematical models of cellular processes that can be simulated in the computer. Unfortunately, it takes many years of careful study of the scientific literature and steady, incremental progress to construct detailed, comprehensive, and accurate mathematical models. This project will create an integrated computational – experimental framework that will significantly accelerate the process of mathematical…
MODELING DNA MANUFACTURING
Abstract: This EArly-concept Grant for Exploratory Research (EAGER) project supports the NSF mission of advancing the national health, prosperity and welfare by increasing the capabilities, accessibility and affordability of manufacturing services in support of America’s leadership in the life sciences. The execution of many complex DNA manufacturing projects essential for life sciences research requires the combination of existing DNA fragments derived from biological samples with new DNA fragments chemically synthesized by commercial operators. Most life science laboratories lack the essential computational resources needed to plan and
STOCHASTIC MODELS OF CELL CYCLE REGULATION IN EUKARYOTES
Abstract:The cell cycle is the process by which a growing cell replicates its genome and partitions the two copies of each chromosome to two daughter cells at division. It is of utmost importance to the perpetuation of life that these processes of replication (DNA synthesis) and partitioning (mitosis) be carried out with great fidelity. In eukaryotic cells, DNA synthesis (S phase) and mitosis (M phase) are separated in time by two gaps (G1 and G2). Proper alternation of S phase and M phase is enforced by `checkpoints’ that block progression through the cell cycle if the genomic integrity of the cell is compromised in any way…
Previous research projects of the Peccoud Lab.
MODELING AND OPTIMIZATION OF DNA MANUFACTURING
Abstract: This INSPIRE award is partially funded by the Advances in Biological Informatics Program in the Division of Biological Infrastructure in the Directorate for Biological Sciences, the Manufacturing Enterprise Systems Program in the Division of Civil, Mechanical and Manufacturing Innovation in the Directorate for Engineering and the Networks and Regulation Cluster in the Division of Molecular Cellular Biology in the Directorate for Biological Sciences. Virginia Polytechnic University is awarded a grant to evaluate the feasibility and benefits of analyzing DNA fabrication processes by using techniques…
TOP-DOWN AND BOTTOM-UP CELL CYCLE
Abstract: Project Summary Two distinct approaches are being used to study complex cellular systems. The first approach automatically searches large datasets for correlations between genes and proteins and represents these as a graph with nodes and edges. The second approach painstakingly crafts detailed models that can be simulated by computer. These approaches have largely been developed separately until now. This project will meld these two approaches into a single framework, thereby allowing fast database searches to augment models that can be simulated. Specifically, the project will 1. Develop fast algorithms to search databases…