About: Generalized lattice graphs for 2D-visualization of biological information

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Generalized lattice graphs for 2D-visualization of biological information
Creator	Bolas-Fern Andez, F Costas, J Dea-Ayuela, M Dorado, J Duardo-Sanchez, A Gonz Alez-Díaz, H Munteanu, C P Erez-Montoto, L Paniagua, E Ubeira, F V Azquez-Prieto, S Vilas, R
topic	covid:192b2c4501ca099036a862f40bbc299aa3f86952#this
source	Elsevier; Medline; PMC
abstract	Abstract Several graph representations have been introduced for different data in theoretical biology. For instance, complex networks based on Graph theory are used to represent the structure and/or dynamics of different large biological systems such as protein–protein interaction networks. In addition, Randic, Liao, Nandy, Basak, and many others developed some special types of graph-based representations. This special type of graph includes geometrical constrains to node positioning in space and adopts final geometrical shapes that resemble lattice-like patterns. Lattice networks have been used to visually depict DNA and protein sequences but they are very flexible. However, despite the proved efficacy of new lattice-like graph/networks to represent diverse systems, most works focus on only one specific type of biological data. This work proposes a generalized type of lattice and illustrates how to use it in order to represent and compare biological data from different sources. We exemplify the following cases: protein sequence; mass spectra (MS) of protein peptide mass fingerprints (PMF); molecular dynamic trajectory (MDTs) from structural studies; mRNA microarray data; single nucleotide polymorphisms (SNPs); 1D or 2D-Electrophoresis study of protein polymorphisms and protein-research patent and/or copyright information. We used data available from public sources for some examples but for other, we used experimental results reported herein for the first time. This work may break new ground for the application of Graph theory in theoretical biology and other areas of biomedical sciences.
has issue date	2009-11-07(xsd:dateTime)
bibo:doi	10.1016/j.jtbi.2009.07.029
bibo:pmid	19646452
has license	els-covid
sha1sum (hex)	192b2c4501ca099036a862f40bbc299aa3f86952
schema:url	https://doi.org/10.1016/j.jtbi.2009.07.029
resource representing a document's title	Generalized lattice graphs for 2D-visualization of biological information
has PubMed Central identifier	PMC7094121
has PubMed identifier	19646452
schema:publication	Journal of Theoretical Biology
resource representing a document's body	covid:192b2c4501ca099036a862f40bbc299aa3f86952#body_text
is http://vocab.deri.ie/void#inDataset of	proxy:http/ns.inria.fr/covid19/192b2c4501ca099036a862f40bbc299aa3f86952
is schema:about of	named entity 'molecular dynamic' named entity 'patent' named entity 'Lattice networks' named entity 'Generalized' named entity 'SPECIFIC' named entity 'BASED' named entity 'STUDIES' named entity 'AREAS' named entity 'TIME' named entity 'MOLECULAR DYNAMIC' covid:arg/192b2c4501ca099036a862f40bbc299aa3f86952 named entity 'SHAPES' named entity 'PROTEIN SEQUENCE' named entity 'FINAL' named entity 'PEPTIDE' named entity 'COPYRIGHT' named entity 'DNA' named entity 'SOURCES' named entity 'GENERALIZED' named entity 'MASS SPECTRA' named entity 'FOLLOWING' named entity 'PROTEIN ' named entity 'BREAK' named entity 'EXPERIMENTAL RESULTS' named entity 'BIOLOGICAL INFORMATION' named entity 'PROTEIN-PROTEIN INTERACTION' named entity 'HAVE' named entity 'GENERALIZED' named entity 'VISUALIZATION' named entity 'LATTICE' named entity 'GRAPHS' named entity 'INFORMATION' named entity 'NODE' named entity 'STRUCTURAL' named entity 'DIFFERENT' named entity 'DATA' named entity 'STRUCTURE' named entity 'POSITIONING' named entity 'LATTICE' named entity 'BIOMEDICAL SCIENCES' named entity 'COMPARE' named entity 'REPRESENT' named entity 'WORKS' named entity 'SINGLE NUCLEOTIDE POLYMORPHISMS' named entity 'AVAILABLE' named entity 'NETWORKS' named entity 'LARGE' named entity 'INSTANCE' named entity 'ORDER' named entity 'PROTEIN SEQUENCES' named entity 'REPORTED' named entity 'FLEXIBLE' named entity 'TYPES' named entity 'SPECIAL' named entity 'SYSTEMS' named entity 'TRAJECTORY' named entity 'HOW' named entity 'GRAPH' named entity 'LIKE' named entity 'MASS' named entity 'BIOLOGICAL' named entity 'APPLICATION' named entity 'THEORETICAL BIOLOGY' named entity 'SPACE' named entity 'DYNAMICS' named entity 'USED' named entity 'FOCUS' named entity 'PATTERNS'

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