eBriefing

By the Numbers

By the Numbers
Reported by
Don Monroe

Posted March 13, 2010

Overview

Systems biologists often strive simply to identify interactions in the cell: which molecules affect which others? The resulting maps of interactions among genes, RNA, and proteins are humbling in their complexity. The Systems Biology Discussion Group at the New York Academy of Sciences is a forum for researchers who use various techniques to explore these interactions. Learning how molecules influence each other can improve basic understanding and suggest strategies for intervention with drugs.

A complete description of cellular processes, however, requires more than a list of influences: it requires that the dynamic effects of these influences be described quantitatively. A symposium at the Academy on May 19, 2005 brought together three speakers who are trying in different ways to accomplish this goal. They are learning that quantitative changes in the parameters that describe a network or the shape of the cell can radically change the way the network behaves.

Use the tabs above to view the meeting report and multimedia presentations.

Web Sites

Center for Cell Analysis and Modeling
A collaborative effort at the at the University of Connecticut Health Center involving research faculty involved in diagnostic and cell biological imaging, optoelectronic design, and computer imaging science.

Computational Cell Biology Lab
John Tyson's lab at the Virginia Polytechnic Institute and State University is devoted primarily to building mathematical models of biological cells.

Virtual Cell Modeling and Simulation Framework
Based at the National Resource for Cell Analysis and Modeling (NRCAM), this national resource center is supported by the National Center for Research Resources (NCRR), National Institutes of Health, and hosted at the University of Connecticut Health Center. The Virtual Cell program is available here.


Books

Fall, C., E. Marland, J. Wagner & J. Tyson, Eds. 2002. Computational Cell Biology. Springer, New York.

Keener, J. & J. Sneyd. 1998. Mathematical Physiology. Springer, New York.

Murray, J. D. 2002. Mathematical Biology: An Introduction. Volume I. Springer, New York.


Journal Articles

The Virtual Cell Project

Csete, M. E. & J. C. Doyle. 2002. Reverse engineering of biological complexity. Science 295: 1664-9166.

Fink, C. C., B. Slepchenko, I. I. Moraru et al. 1999. Morphological control of inositol-1,4,5-trisphosphate-dependent signals. J. Cell Biol. 147: 929-936. Full Text

Fink, C.C., B. Slepchenko, I. I. Moraru et al. 2000. An image-based model of calcium waves in differentiated neuroblastoma cells. Biophys J. 79:163-183. Full Text

Slepchenko, B. M., Schaff, J. C., I Macara & L. M. Loew. 2003. Quantitative cell biology with the Virtual Cell. Trends Cell Biol. 13: 570-576.

Smith, A. E., B. M. Slepchenko, J. C. Schaff et al. 2002. Systems analysis of Ran transport. Science 295: 488-491.

Mathematical Models of Cell-Cycle Regulation in Yeasts and Bacteria

Chen, K. C., L. Calzone, A. Csikasz-Nagy et al. 2004. Integrative analysis of cell cycle control in budding yeast. Mol. Biol. Cell 15: 3841-3862. Full Text

Dolan, J. W., C. Kirkman & S. Fields. 1989. The yeast STE12 protein binds to the DNA sequence mediating pheromone induction. Proc. Natl. Acad. Sci. USA 86: 5703-5707. Full Text

Errede, B. & G. Ammerer. 1989. STE12, a protein involved in cell-type-specific transcription and signal transduction in yeast, is part of protein-DNA complexes. Genes Dev. 3: 1349-1361.

Tyson, J. J., K. C. Chen & B. Novak. 2003. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15: 221-231.

Tyson, J. J., K. Chen & B. Novak. 2001. Network dynamics and cell physiology. Nat. Rev. Molec. Cell Biol. 2: 908-916.

Oscillations and Switches in Cell Signaling: A Quantitative Analysis

Aulehla, A. & B. G. Herrmann. 2004. Segmentation in vertebrates: clock and gradient finally joined. Genes Dev. 18: 2060-2067. Full Text

Barken, D., C. J. Wang, J. Kearns et al. 2005. Comment on "Oscillations in NF-κB signaling control the dynamics of gene expression." Science 308: 52. Full Text

Cooke, J. & E. C. Zeeman 1976. A clock and wavefront model for control of the number of repeated structures during animal morphogenesis. J. Theor. Biol. 58: 455-476.

Hoffman, A., A. Levchenko, M. L. Scott & D. Baltimore. 2002. The IκB-NF-κB signaling module: temporal control and selective gene activation. Science 298: 1241-1245.

Nelson, D. E., A. E. Ihekwaba, M. Elliott et al. 2004. Oscillations in NF-κB signaling control the dynamics of gene expression. Science 306: 704-708.

Nelson, D. E., C. A. Horton, V. See et al. 2005. Response to 'Comment on "Oscillations in NF-κB signaling control the dynamics of gene expression."' Science 308: 52. Full Text

Pourquie, O. 2003. The segmentation clock: converting embryonic time into spatial pattern. Science 301: 328-330.

Roberts, C. J., B. Nelson, M. J. Marton et al. 2000. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287: 873-880.

Speakers

Leslie Loew, PhD

University of Connecticut Health Center
e-mail | web site | publications

Leslie Loew is the director of the Center for Cell Analysis and Modeling at the University of Connecticut Health Center, where he is a professor of both cell biology and of computer science and engineering. He earned a PhD in chemistry from Cornell University in 1974 and did a postdoc at Harvard before joining the faculty of the State University of New York at Binghamton. He has been with the University of Connecticut Health Center since 1984.

John Tyson, PhD

Virginia Polytechnic Institute and State University
e-mail | web site | publications

John Tyson is University Distinguished Professor in the department of biological sciences at Virginia Polytechnic Institute and State University. In 1989, he received the Bellman Prize in Mathematical Biosciences, and in 2004 he was named one of three Outstanding Scientists in Virginia. He served as co-chief editor of the Journal of Theoretical Biology for ten years, and was president of the Society for Mathematical Biology from 1993 to 1995.

Trained in chemistry and physics at the University of Chicago, John Tyson was drawn to problems in mathematical and computational cell biology in the 1970s. Since then he has made many pioneering contributions to the theoretical understanding of spatial and temporal organization in the molecular mechanisms that underlie important aspects of cell physiology (cell cycle, circadian rhythms, and cell signaling).

Andre Levchenko, PhD

Johns Hopkins University
e-mail | web site | publications

Andre Levchenko is an assistant professor of biomedical engineering at the Johns Hopkins University. After earning a PhD from Columbia University and working at Memorial Sloan-Kettering Cancer Center on cancer cell drug resistance, he was a postdoc at CalTech working on problems in computer science and cell biology. He joined Johns Hopkins in 2001.


Don Monroe

web site

Don Monroe is a science writer based in Murray Hill, New Jersey. After getting a PhD in physics from MIT, he spent more than fifteen years doing research in physics and electronics technology at Bell Labs. He writes on physics, technology, and biology.

Presented by the Systems Biology Discussion Group