Name
Abstract | ||
|---|---|---|
Motivated by an interest to understand how information is organized within genomes, and how genes communicate between each other in the transcription process, in this paper we propose a novel network based methodology for genomic sequence analysis, specifically applied to three organisms: Nanoarchaeum equitans, Escherichia coli, and Saccaromyces cerevisiae. A dictionary based approach previously introduced is here continued through a repeat analysis in genic and intergenic regions. Key results of this work have been found in a biological and computational analysis of novel parametrized gene networks, defined by means of motifs of fixed length occurring inside multiple genes. Cliques emerge as groups of genes sharing a long repeat with a clear biological interpretation, while a (complete, paralog) cluster analysis has outlined some unexpected regularity. Repeat sharing gene networks may be applied in contexts of comparative genomics, as an investigation methodology for a comprehension of evolutional and functional properties of genes. |
Year | DOI | Venue |
|---|---|---|
2015 | 10.1007/s11047-014-9437-6 | Natural Computing: an international journal |
Keywords | Field | DocType |
Genome analysis,Computational genomics,Comparative genomics,Infogenomics,Dictionaries,Word frequency,Repeat,k,-mer,Gene networks,Repeat-sharing gene networks,Paralog analysis,Cluster information theory,Text mining,Metagenomics,Nanoarchaeum equitans,Escherichia coli,Saccaromyces cerevisiae | Genome,Gene,Comparative genomics,Artificial intelligence,Computational biology,Nanoarchaeum equitans,Computational genomics,Gene regulatory network,Genetics,k-mer,Mathematics,Machine learning,Sequence analysis | Journal |
Volume | Issue | ISSN |
14 | 3 | 1567-7818 |
Citations | PageRank | References |
1 | 0.38 | 13 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Alberto Castellini | 1 | 60 | 14.16 |
| Giuditta Franco | 2 | 136 | 18.34 |
| alessio milanese | 3 | 1 | 0.38 |