Search Results - "Darcy, Isabel K"

Applications of Topological Data Analysis in Oncology by Bukkuri, Anuraag, Andor, Noemi, Darcy, Isabel K

“…The emergence of the information age in the last few decades brought with it an explosion of biomedical data. But with great power comes great responsibility:…”
Get full text

Determining the topology of stable protein-DNA complexes by Darcy, Isabel K, Vazquez, Mariel

“…Difference topology is an experimental technique that can be used to unveil the topological structure adopted by two or more DNA segments in a stable…”
Get more information

Tracing patterns and shapes in remittance and migration networks via persistent homology by Ignacio, Paul Samuel P., Darcy, Isabel K.

“…Pattern detection in network models provides insights to both global structure and local node interactions. In particular, studying patterns embedded within…”
Get full text

A topological analysis of difference topology experiments of condensin with topoisomerase II by Kim, Soojeong, Darcy, Isabel K

“…An experimental technique called difference topology combined with the mathematics of tangle analysis has been used to unveil the structure of DNA bound by the…”
Get full text

TopoICE-R: 3D visualization modeling the topology of DNA recombination by Darcy, Isabel K., Scharein, Robert G.

“…TopoICE-R is a three-dimensional visualization and manipulation software for solving 2-string tangle equations and can be used to model the topology of DNA…”
Get full text

DNA Topology and Geometry in Flp and Cre Recombination by Vetcher, Alexandre A., Lushnikov, Alexander Y., Navarra-Madsen, Junalyn, Scharein, Robert G., Lyubchenko, Yuri L., Darcy, Isabel K., Levene, Stephen D.

“…The Flp recombinase of yeast and the Cre recombinase of bacteriophage P1 both belong to the λ-integrase (Int) family of site-specific recombinases. These…”
Get full text

Rational tangle surgery and Xer recombination on catenanes by Darcy, Isabel K, Ishihara, Kai, Medikonduri, Ram K, Shimokawa, Koya

Get full text

Coloring the Mu transpososome by Darcy, Isabel K, Chang, Jeff, Druivenga, Nathan, McKinney, Colin, Medikonduri, Ram K, Mills, Stacy, Navarra-Madsen, Junalyn, Ponnusamy, Arun, Sweet, Jesse, Thompson, Travis

“…Tangle analysis has been applied successfully to study proteins which bind two segments of DNA and can knot and link circular DNA. We show how tangle analysis…”
Get full text

Modeling protein–DNA complexes with tangles by Darcy, Isabel K.

“…The mathematics of tangles has been applied to model protein–DNA binding. A tangle consists of strings properly embedded in a 3-dimensional ball. The protein…”
Get full text

TopolCE-R : 3D visualization modeling the topology of DNA recombination by DARCY, Isabel K, SCHAREIN, Robert G

Get full text

A topological analysis of difference topology experiments of condensin with Topoisomerase II by Kim, Soojeong, Darcy, Isabel K

“…An experimental technique called difference topology combined with the mathematics of tangle analysis has been used to unveil the structure of DNA bound by the…”
Get full text

Modeling knotted proteins with tangles by Darcy, Isabel K, Jones, Garrett, Pongtanapaisan, Puttipong

“…Although rare, an increasing number of proteins have been observed to contain entanglements in their native structures. To gain more insight into the…”
Get full text

Tangle analysis of difference topology experiments: Applications to a Mu protein-DNA complex by Darcy, Isabel, Luecke, John, Vazquez, Mariel

Get full text

Biological metrics on DNA knots and catenanes by Darcy, Isabel K

“…Molecular biologists use circular DNA to probe the action of enzymes which are important in cellular metabolism. Ordinary cellular processes such as…”
Get full text

Rational tangle surgery and Xer recombination on catenanes by Darcy, Isabel K, Ishihara, Kai, Medikonduri, Ram K, Shimokawa, Koya

“…Algebr. Geom. Topol. 12 (2012) 1183-1210 The protein recombinase can change the knot type of circular DNA. The action of a recombinase converting one knot into…”
Get full text

Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex by Darcy, Isabel K, Luecke, John, Vazquez, Mariel

“…Algebr. Geom. Topol. 9 (2009) 2247-2309 We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference…”
Get full text

Biological metrics on DNA knots and catenanes by Darcy, Isabel K

“…Molecular biologists use circular DNA to probe the action of enzymes which are important in cellular metabolism. Ordinary cellular processes such as…”
Get full text

Coloring $n$-String Tangles by Darcy, Isabel K, Navarra-Madsen, Junalyn

“…This expository paper describes how the knot invariant Fox coloring can be applied to tangles…”
Get full text