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knot.math.usf.edu

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Discrete and Topological Models for DNA Assembly. Summer research opportunities for graduates and undergraduates! In recent years it has become clear that mathematical tools from algebra, group theory, combinatorics, and topology play essential roles in understanding vital biological processes at the molecular scale. These include applications of. Polynomials over finite fields in systems biology;. Combinatorics, algebra and tiling theory in the modeling of viral capsid assembly; and. And the National In...

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knot | knot.math.usf.edu Reviews

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Discrete and Topological Models for DNA Assembly. Summer research opportunities for graduates and undergraduates! In recent years it has become clear that mathematical tools from algebra, group theory, combinatorics, and topology play essential roles in understanding vital biological processes at the molecular scale. These include applications of. Polynomials over finite fields in systems biology;. Combinatorics, algebra and tiling theory in the modeling of viral capsid assembly; and. And the National In...

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1 background

2 activities

3 data

4 software

5 multimedia

6 links

7 publications

8 members

9 or m saito

10 if interested

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knot | knot.math.usf.edu Reviews

https://knot.math.usf.edu

Discrete and Topological Models for DNA Assembly. Summer research opportunities for graduates and undergraduates! In recent years it has become clear that mathematical tools from algebra, group theory, combinatorics, and topology play essential roles in understanding vital biological processes at the molecular scale. These include applications of. Polynomials over finite fields in systems biology;. Combinatorics, algebra and tiling theory in the modeling of viral capsid assembly; and. And the National In...

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$knot.math.usf.edu$ knot.math.usf.edu

1

Background

http://knot.math.usf.edu/background/index.html

Background materials in PDF files. DNA recombination in ciliates and template theory. Assembly graphs and related concepts. Classification of assembly words and graphs. Assembly numbers and polynomials. Pathways of DNA recombination proceses via assembly graphs. Nesting of assembly words and reductions. Repeated pointer sequences in micronuclear genes. Macronuclear segments in assembly graphs. Genus ranges of assembly graphs. Linking and writhe of assembly graphs. Chirality of assembly graphs.

2

Members

http://knot.math.usf.edu/members

USF Math/Bio Research Group - Summer 2015. Works at Ionic Security. As of Summer 2016). Works for Google on Google Fiber. As of Spring 2016). As of Fall 2015). Works at Nascent Blue, Inc. as of Fall 2015). Graduate student at University of Washington. As of Fall 2014). Lecturer at University of Colorado Denver. As of Fall 2015). Maja Miloševi&cacute;. Undergraduate student at University of South Florida as of Fall 2014). Graduate student at the University of Denver. As of Fall 2013). As of Fall 2013).

3

Publications

http://knot.math.usf.edu/publications/index.html

Papers on DNA assembly. Recurring Patterns Among Scrambled Genes in the Encrypted Genome of the Ciliate Oxytricha trifallax. Laura F. Landweber. J Burns, D. Kukushkin, X. Chen, L. Landweber, M. Saito, N. Jonoska. Recurring Patterns Among Scrambled Genes in the Encrypted Genome of the Ciliate Oxytricha trifallax. Journal of Theoretical Biology. 2016) pp. 171-180. 101016/j.jtbi.2016.08.038. Mds ies db : A Database of Ciliate Genome Rearrangements. Laura F. Landweber. J Burns, D. Kukushkin, K. Lindb...X Che...

4

knot

http://knot.math.usf.edu/index.html

Discrete and Topological Models for DNA Assembly. Summer research opportunities for graduates and undergraduates! In recent years it has become clear that mathematical tools from algebra, group theory, combinatorics, and topology play essential roles in understanding vital biological processes at the molecular scale. These include applications of. Polynomials over finite fields in systems biology;. Combinatorics, algebra and tiling theory in the modeling of viral capsid assembly; and. And the National In...

5

links

http://knot.math.usf.edu/links

National Center for Biotechnology Information. Applied and Computational Algebraic Topology. Workshop on Discrete and Topological Models in Molecular Biology.

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jtburns.myweb.usf.edu

Jon The Burns - Math Research Homepage

http://jtburns.myweb.usf.edu/assembly/links.htm

DNA / Ciliates Links. USF's DNA Computing Research Group - Homepage. Princeton's Landweber Lab - Homepage. Ryan Arredondo - Homepage. Egor Dolzhenko - Homepage. Natasha Jonoska - Homepage. Maja Milosevic - Homepage. Tilahun Muche - Homepage. Masahico Saito - Homepage. Timothy Yeatman - Homepage. USF Bio/Math Research Group - Summer 2011.

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Discrete and Topological Models for DNA Assembly. Summer research opportunities for graduates and undergraduates! In recent years it has become clear that mathematical tools from algebra, group theory, combinatorics, and topology play essential roles in understanding vital biological processes at the molecular scale. These include applications of. Polynomials over finite fields in systems biology;. Combinatorics, algebra and tiling theory in the modeling of viral capsid assembly; and. And the National In...

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