An algebraic view of bacterial genome evolution (Q476821): Difference between revisions

The paper describes the algebraic modelling of rearrangements of bacterial chromosomes at two levels: local (sequence level) and topological level. The author commences with an overview of evolutionary changes observed on bacterial genomes. Next, the underlying biological mechanisms are presented and the current approaches for modelling inversions are introduced. Following a description of the tangle algebra approach for describing topological evolution, the author discusses in detail the inversions and knotting in a common modelling framework, the Birman-Murakami-Wenzl algebra (BMW algebra), using features from braid groups and Coxeter groups. The algebraic connections with Iwahori-Hecke algebras and the Kauffman tangle algebra are also underlined.

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reviewed by

Irina Ioana Mohorianu

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zbMATH Keywords

bacteria

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genome rearrangement

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sequence level change

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topological level change

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inversion

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knotting

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Iwahori-Hecke algebra

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Birman-Murakami-Wenzl algebra

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BMW algebra

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tangle algebra

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Coxeter group

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braid group

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describes a project that uses

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MaRDI publication profile

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cites work

Q5449200

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Genome Rearrangements and Sorting by Reversals

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Q5471628

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Braids, Link Polynomials and a New Algebra

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On the Stable Equivalence of Plat Representations of Knots and Links

0 references

Affine reflection groups for tiling applications: Knot theory and DNA

0 references

The Magma algebra system. I: The user language

0 references

Q3637587

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BRAID SOLUTIONS TO THE ACTION OF THE GIN ENZYME

0 references

The Reversal Median Problem

0 references

Q5601331

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Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex

0 references

Q3840291

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Lectures on algebraic statistics

0 references

Reflection subgroups of Coxeter systems

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Group-theoretic models of the inversion process in bacterial genomes

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N-STRING TANGLES

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TANGLE EQUATIONS

0 references

Tangle Equations II

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A calculus for rational tangles: applications to DNA recombination

0 references

Solving tangle equations arising in a DNA recombination model

0 references

The minimum-length generator sequence problem is NP-hard

0 references

Q3393448

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A new polynomial invariant of knots and links

0 references

Q4679085

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Bounds for sorting by prefix reversal

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Rational tangles

0 references

Transforming cabbage into turnip

0 references

Q4414682

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On reflection length in reflection groups

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Topological analysis of enzymatic actions on DNA polyhedral links

0 references

Q3998721

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A polynomial invariant for knots via von Neumann algebras

0 references

Braid Groups

0 references

On the classification of rational tangles

0 references

Tangle analysis of Gin site-specific recombination

0 references

Q5760103

0 references

Q5457093

0 references

Comparative Genomics

0 references

The `Butterfly effect' in Cayley graphs with applications to genomics.

0 references

The Kauffman polynomial of links and representation theory

0 references

Knot theory and its applications. Transl. from the Japanese by Bohdan Kurpita

0 references

Q4699470

0 references

Combinatorial Pattern Matching

0 references

Q5442223

0 references

Algebraic Statistics for Computational Biology

0 references

Q4527384

0 references

Comparative Genomics

0 references

The Kazhdan-Lusztig cells in certain affine Weyl groups

0 references

Markov invariants, plethysms, and phylogenetics

0 references

Combinatorial Pattern Matching

0 references

A presentation for Hilden's subgroup of the braid group

0 references

Relations between the ‘percolation’ and ‘colouring’ problem and other graph-theoretical problems associated with regular planar lattices: some exact results for the ‘percolation’ problem

0 references

Quantum invariants of knots and 3-manifolds

0 references

On the cellularity of the cyclotomic Birman-Murakami-Wenzl algebras

0 references

Identifiers

zbMATH Open document ID

1302.92089

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Mathematics Subject Classification ID

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10.1007/S00285-013-0747-6

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Sitelinks

Mathematics(1 entry)

mardi Publication:476821

@@ Property / DOI @@
-.1007/s00285-013-0747-6
@@ Property / DOI: 10.1007/s00285-013-0747-6 / rank @@
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+The paper describes the algebraic modelling of rearrangements of bacterial chromosomes at two levels: local (sequence level) and topological level. The author commences with an overview of evolutionary changes observed on bacterial genomes. Next, the underlying biological mechanisms are presented and the current approaches for modelling inversions are introduced. Following a description of the tangle algebra approach for describing topological evolution, the author discusses in detail the inversions and knotting in a common modelling framework, the Birman-Murakami-Wenzl algebra (BMW algebra), using features from braid groups and Coxeter groups. The algebraic connections with Iwahori-Hecke algebras and the Kauffman tangle algebra are also underlined.
+Normal rank
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+Irina Ioana Mohorianu
@@ Property / reviewed by: Irina Ioana Mohorianu / rank @@
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+genome rearrangement
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+sequence level change
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+topological level change
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+inversion
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+Iwahori-Hecke algebra
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+Birman-Murakami-Wenzl algebra
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+BMW algebra
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+tangle algebra
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+Coxeter group
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+Genome Rearrangements and Sorting by Reversals
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+Q5471628
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+Braids, Link Polynomials and a New Algebra
@@ Property / cites work: Braids, Link Polynomials and a New Algebra / rank @@
+Normal rank
@@ Property / cites work @@
+On the Stable Equivalence of Plat Representations of Knots and Links
+Normal rank
@@ Property / cites work @@
+Affine reflection groups for tiling applications: Knot theory and DNA
+Normal rank
@@ Property / cites work @@
+The Magma algebra system. I: The user language
@@ Property / cites work: The Magma algebra system. I: The user language / rank @@
+Normal rank
@@ Property / cites work @@
+Q3637587
@@ Property / cites work: Q3637587 / rank @@
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+BRAID SOLUTIONS TO THE ACTION OF THE GIN ENZYME
@@ Property / cites work: BRAID SOLUTIONS TO THE ACTION OF THE GIN ENZYME / rank @@
+Normal rank
@@ Property / cites work @@
+The Reversal Median Problem
@@ Property / cites work: The Reversal Median Problem / rank @@
+Normal rank
@@ Property / cites work @@
+Q5601331
@@ Property / cites work: Q5601331 / rank @@
+Normal rank
@@ Property / cites work @@
+Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex
+Normal rank
@@ Property / cites work @@
+Q3840291
@@ Property / cites work: Q3840291 / rank @@
+Normal rank
@@ Property / cites work @@
+Lectures on algebraic statistics
@@ Property / cites work: Lectures on algebraic statistics / rank @@
+Normal rank
@@ Property / cites work @@
+Reflection subgroups of Coxeter systems
@@ Property / cites work: Reflection subgroups of Coxeter systems / rank @@
+Normal rank
@@ Property / cites work @@
+Group-theoretic models of the inversion process in bacterial genomes
+Normal rank
@@ Property / cites work @@
+N-STRING TANGLES
@@ Property / cites work: N-STRING TANGLES / rank @@
+Normal rank
@@ Property / cites work @@
+TANGLE EQUATIONS
@@ Property / cites work: TANGLE EQUATIONS / rank @@
+Normal rank
@@ Property / cites work @@
+Tangle Equations II
@@ Property / cites work: Tangle Equations II / rank @@
+Normal rank
@@ Property / cites work @@
+A calculus for rational tangles: applications to DNA recombination
+Normal rank
@@ Property / cites work @@
+Solving tangle equations arising in a DNA recombination model
+Normal rank
@@ Property / cites work @@
+The minimum-length generator sequence problem is NP-hard
+Normal rank
@@ Property / cites work @@
+Q3393448
@@ Property / cites work: Q3393448 / rank @@
+Normal rank
@@ Property / cites work @@
+A new polynomial invariant of knots and links
@@ Property / cites work: A new polynomial invariant of knots and links / rank @@
+Normal rank
@@ Property / cites work @@
+Q4679085
@@ Property / cites work: Q4679085 / rank @@
+Normal rank
@@ Property / cites work @@
+Bounds for sorting by prefix reversal
@@ Property / cites work: Bounds for sorting by prefix reversal / rank @@
+Normal rank
@@ Property / cites work @@
+Rational tangles
@@ Property / cites work: Rational tangles / rank @@
+Normal rank
@@ Property / cites work @@
+Transforming cabbage into turnip
@@ Property / cites work: Transforming cabbage into turnip / rank @@
+Normal rank
@@ Property / cites work @@
+Q4414682
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+Normal rank
@@ Property / cites work @@
+On reflection length in reflection groups
@@ Property / cites work: On reflection length in reflection groups / rank @@
+Normal rank
@@ Property / cites work @@
+Topological analysis of enzymatic actions on DNA polyhedral links
+Normal rank
@@ Property / cites work @@
+Q3998721
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+Normal rank
@@ Property / cites work @@
+A polynomial invariant for knots via von Neumann algebras
+Normal rank
@@ Property / cites work @@
+Braid Groups
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+Normal rank
@@ Property / cites work @@
+On the classification of rational tangles
@@ Property / cites work: On the classification of rational tangles / rank @@
+Normal rank
@@ Property / cites work @@
+Tangle analysis of Gin site-specific recombination
+Normal rank
@@ Property / cites work @@
+Q5760103
@@ Property / cites work: Q5760103 / rank @@
+Normal rank
@@ Property / cites work @@
+Q5457093
@@ Property / cites work: Q5457093 / rank @@
+Normal rank
@@ Property / cites work @@
+Comparative Genomics
@@ Property / cites work: Comparative Genomics / rank @@
+Normal rank
@@ Property / cites work @@
+The `Butterfly effect' in Cayley graphs with applications to genomics.
+Normal rank
@@ Property / cites work @@
+The Kauffman polynomial of links and representation theory
+Normal rank
@@ Property / cites work @@
+Knot theory and its applications. Transl. from the Japanese by Bohdan Kurpita
+Normal rank
@@ Property / cites work @@
+Q4699470
@@ Property / cites work: Q4699470 / rank @@
+Normal rank
@@ Property / cites work @@
+Combinatorial Pattern Matching
@@ Property / cites work: Combinatorial Pattern Matching / rank @@
+Normal rank
@@ Property / cites work @@
+Q5442223
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+Normal rank
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+Algebraic Statistics for Computational Biology
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+Normal rank
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+Q4527384
@@ Property / cites work: Q4527384 / rank @@
+Normal rank
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+Comparative Genomics
@@ Property / cites work: Comparative Genomics / rank @@
+Normal rank
@@ Property / cites work @@
+The Kazhdan-Lusztig cells in certain affine Weyl groups
+Normal rank
@@ Property / cites work @@
+Markov invariants, plethysms, and phylogenetics
@@ Property / cites work: Markov invariants, plethysms, and phylogenetics / rank @@
+Normal rank
@@ Property / cites work @@
+Combinatorial Pattern Matching
@@ Property / cites work: Combinatorial Pattern Matching / rank @@
+Normal rank
@@ Property / cites work @@
+A presentation for Hilden's subgroup of the braid group
+Normal rank
@@ Property / cites work @@
+Relations between the ‘percolation’ and ‘colouring’ problem and other graph-theoretical problems associated with regular planar lattices: some exact results for the ‘percolation’ problem
+Normal rank
@@ Property / cites work @@
+Quantum invariants of knots and 3-manifolds
@@ Property / cites work: Quantum invariants of knots and 3-manifolds / rank @@
+Normal rank
@@ Property / cites work @@
+On the cellularity of the cyclotomic Birman-Murakami-Wenzl algebras
+Normal rank
@@ Property / DOI @@
+.1007/S00285-013-0747-6
@@ Property / DOI: 10.1007/S00285-013-0747-6 / rank @@
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+Publication:476821