Predicting the evolution of syntenies—an algorithmic review
N El-Mabrouk - Algorithms, 2021 - mdpi.com
Syntenies are genomic segments of consecutive genes identified by a certain conservation
in gene content and order. The notion of conservation may vary from one definition to …
in gene content and order. The notion of conservation may vary from one definition to …
Ancestral genome organization: an alignment approach
We present a comparative genomics approach for inferring ancestral genome organization
and evolutionary scenarios, based on present-day genomes represented as ordered gene …
and evolutionary scenarios, based on present-day genomes represented as ordered gene …
Evolution of tRNA Repertoires in Bacillus Inferred with OrthoAlign
O Tremblay-Savard, B Benzaid, BF Lang… - Molecular biology …, 2015 - academic.oup.com
OrthoAlign, an algorithm for the gene order alignment problem (alignment of orthologs),
accounting for most genome-wide evolutionary events such as duplications, losses …
accounting for most genome-wide evolutionary events such as duplications, losses …
The SCJ small parsimony problem for weighted gene adjacencies
Reconstructing ancestral gene orders in a given phylogeny is a classical problem in
comparative genomics. Most existing methods compare conserved features in extant …
comparative genomics. Most existing methods compare conserved features in extant …
Evolution of genome organization by duplication and loss: An alignment approach
We present a comparative genomics approach for inferring ancestral genome organization
and evolutionary scenarios, based on a model accounting for content-modifying operations …
and evolutionary scenarios, based on a model accounting for content-modifying operations …
The duplication-loss small phylogeny problem: from cherries to trees
The reconstruction of the history of evolutionary genome-wide events among a set of related
organisms is of great biological interest since it can help to reveal the genomic basis of …
organisms is of great biological interest since it can help to reveal the genomic basis of …
The SCJ small parsimony problem for weighted gene adjacencies
N Luhmann, A Thévenin, A Ouangraoua… - … and Applications: 12th …, 2016 - Springer
Reconstructing ancestral gene orders in a given phylogeny is a classical problem in
comparative genomics. Most existing methods compare conserved features in extant …
comparative genomics. Most existing methods compare conserved features in extant …
Linearization of median genomes under DCJ
S Jiang, MA Alekseyev - … , WABI 2014, Wroclaw, Poland, September 8-10 …, 2014 - Springer
Reconstruction of the median genome consisting of linear chromosomes from three given
genomes is known to be intractable. There exist efficient methods for solving a relaxed …
genomes is known to be intractable. There exist efficient methods for solving a relaxed …
Gene order alignment on trees with multiorthoalign
B Benzaid, N El-Mabrouk - BMC genomics, 2014 - Springer
We relate the comparison of gene orders to an alignment problem. Our evolutionary model
accounts for both rearrangement and content-modifying events. We present a heuristic …
accounts for both rearrangement and content-modifying events. We present a heuristic …
Fast median computation for symmetric, orthogonal matrices under the rank distance
J Meidanis, L Chindelevitch - Linear algebra and its applications, 2021 - Elsevier
Biological genomes can be represented as square, symmetric, orthogonal, 0-1 matrices. It
turns out that the rank distance applied to two genome matrices has a biological …
turns out that the rank distance applied to two genome matrices has a biological …