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Evolutionary plasticity determination by orthologous groups distribution

Rodrigo JS Dalmolin, Mauro AA Castro, José L Rybarczyk Filho, Luis HT Souza, Rita MC de Almeida, José CF Moreira
2011 Biology Direct  
Genetic plasticity may be understood as the ability of a functional gene network to tolerate alterations in its components or structure. Usually, the studies involving gene modifications in the course of the evolution are concerned to nucleotide sequence alterations in closely related species. However, the analysis of large scale data about the distribution of gene families in non-exclusively closely related species can provide insights on how plastic or how conserved a given gene family is.
more » ... e, we analyze the abundance and diversity of all Eukaryotic Clusters of Orthologous Groups (KOG) present in STRING database, resulting in a total of 4,850 KOGs. This dataset comprises 481,421 proteins distributed among 55 eukaryotes. Results: We propose an index to evaluate the evolutionary plasticity and conservation of an orthologous group based on its abundance and diversity across eukaryotes. To further KOG plasticity analysis, we estimate the evolutionary distance average among all proteins which take part in the same orthologous group. As a result, we found a strong correlation between the evolutionary distance average and the proposed evolutionary plasticity index. Additionally, we found low evolutionary plasticity in Saccharomyces cerevisiae genes associated with inviability and Mus musculus genes associated with early lethality. At last, we plot the evolutionary plasticity value in different gene networks from yeast and humans. As a result, it was possible to discriminate among higher and lower plastic areas of the gene networks analyzed. Conclusions: The distribution of gene families brings valuable information on evolutionary plasticity which might be related with genetic plasticity. Accordingly, it is possible to discriminate among conserved and plastic orthologous groups by evaluating their abundance and diversity across eukaryotes. Reviewers: This article was reviewed by Prof Manyuan Long, Hiroyuki Toh, and Sebastien Halary.
doi:10.1186/1745-6150-6-22 pmid:21586164 pmcid:PMC3117832 fatcat:5d5wtn7ppze2dbqfdnscofqoxa

ViaComplex: software for landscape analysis of gene expression networks in genomic context

Mauro A. A. Castro, José L. Rybarczyk Filho, Rodrigo J. S. Dalmolin, Marialva Sinigaglia, José C. F. Moreira, José C. M. Mombach, Rita M. C. de Almeida
2009 Computer applications in the biosciences : CABIOS  
ViaComplex is an open-source application that builds landscape maps of gene expression networks. The motivation for this software comes from two previous publications (Nucleic Acids Res., 35, 1859-1867 , 2007 Nucleic Acids Res., 36, 6269-6283, 2008). The first article presents a network-based model of genome stability pathways where we defined a set of genes that characterizes each genetic system. In the second article we analyzed this model by projecting functional information from several
more » ... riments onto the gene network topology. In order to systematize the methods developed in these articles, ViaComplex provides tools that may help potential users to assess different high-throughput experiments in the context of six core genome maintenance mechanisms. This model illustrates how different gene networks can be analyzed by the same algorithm.
doi:10.1093/bioinformatics/btp246 pmid:19369498 fatcat:une4knnwk5hbvcw2ljj7dplzhy

Analysis of EEG Sleep Spindle Parameters from Apnea Patients Using Massive Computing and Decision Tree

Gunther J. L. Gerhardt, Ney Lemke, Diego Z. Carvalho, Emerson L. de Santa-Helena, Suzana V. Schonwald, Guilherme Dellagustin, Jose L. Rybarczyk Filho
2014 Scientia cum Industria  
Francisco Getulio Vargas, 1130, Caxias do Sul-RS-Brazil, CEP95070-560; † Department of Physics and Biophysics, Institute of Biosciences, Universidade Estadual Paulista Julio de Mesquita Filho, Brazil;  ... 
doi:10.18226/23185279.v2iss1p15 fatcat:h5q2zb5bebdona7eijdp76xpxu

Gastrin-Releasing Peptide Receptor Antagonism Induces Protection from Lethal Sepsis: Involvement of Toll-like Receptor 4 Signaling

Fabricia Petronilho, Francieli Vuolo, Letícia Selinger Galant, Larissa Constantino, Cristiane Damiani Tomasi, Vinicius Renne Giombelli, Cláudio Teodoro de Souza, Sabrina da Silva, Denise Frediani Barbeiro, Francisco Garcia Soriano, Emílio Luiz Streck, Cristiane Ritter (+10 others)
2012 Molecular Medicine  
H O E T A L . | M O L M E D 1 8 : 1 2 0 9 -1 2 1 9 , 2 0 1 2L I N K B E T W E E N G R P R A N D T L R -4 A N D S E P S I S 2 1 2 | P E T R O N I L H O E T A L . | M O L M E D 1 8 : 1 2 0 9 -1 2 1  ...  R P R A N D T L R -4 A N D S E P S I S M O L M E D 1 8 : 1 2 0 9 -1 2 1 9 , 2 0 1 2 | P E T R O N I L H O E T A L . | 1 2 1 9  ... 
doi:10.2119/molmed.2012.00083 pmid:22735756 pmcid:PMC3510294 fatcat:zmvavc6vlnhr3agdfxatpufqz4

Poster: Quantification of correlations between sleep spindles in EEG for patients with sleep apnea

Rafael Toledo F. de Souza, Jose Luiz Rybarczyk Filho, Ney Lemke, Suzana V. Schonwald, Emerson L. de Santa-Helena, Gunther J. L. Gerhardt
2013 2013 IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS)  
doi:10.1109/iccabs.2013.6629210 dblp:conf/iccabs/SouzaFLSSG13 fatcat:4grcsbam6bfv3nwywbcqdpufvm

Ferramenta em R para comparar padrões de expressão de vias metabólicas e proteínas associadas ao glioblastoma

Heleno Carmo Borges Cabral, Bruna Garcia Pedrolo, Josiane Fontoura Anjos, Michele Rorato Sagrillo, Evamberto Garcia Góes, José Luiz Rybarczyk Filho, Éder Maiquel Simão
2020 Brazilian Journal of Development  
L.; OLTVAI, Z. Network biology: Under standing the cell's functional organization. s.l.: Nature Reviews Genetics, 2004. pp. 101-113, 2004. BAÚ, C. E. G.  ... 
doi:10.34117/bjdv6n1-244 fatcat:aqiykk6warewzgyt63ehlisolu

Acknowledgement to Reviewers of Sensors in 2019

Sensors Editorial Office
2020 Sensors  
Rybakowska, Iwona Rybarczyk, Yves Rydosz, Artur Ryndin, Eugeny A.  ...  Rotter, Pawel Rotunno Filho, Otto Corrêa Rouco, José Rouillard, José Roupioz, Yoann Rousakis, Theodoros Roussey, Catherine Rout, Bhimsen Rouzbahani, Hamid Karimi Roveri, Marco Rovini, Erika Rovira-Garcia  ... 
doi:10.3390/s20020576 fatcat:yjjvds6ndvdx5dp6gfcsvyfar4

Preferential Duplication of Intermodular Hub Genes: An Evolutionary Signature in Eukaryotes Genome Networks

Ricardo M. Ferreira, José Luiz Rybarczyk-Filho, Rodrigo J. S. Dalmolin, Mauro A. A. Castro, José C. F. Moreira, Leonardo G. Brunnet, Rita M. C. de Almeida, Ying Xu
2013 PLoS ONE  
Minimization of this function, by changing the genes localization on the list, implies approximating mutually interacting genes, as discussed by Rybarczyk-Filho et al. [32] .  ...  The experimental points indicate that the number of links is proportional to the number of nodes, that is, N L *N 1 .  ... 
doi:10.1371/journal.pone.0056579 pmid:23468868 pmcid:PMC3582557 fatcat:m6ltmnathnczro77vlumtjeigy

Manejo aversivo em bovinos leiteiros e efeitos no bem-estar, comportamento e aspectos produtivos

M.D.P. Peters, I.D. Barbosa Silveira, L.C. Pinheiro Machado Filho, A.A. Machado, L.M.R. Pereira
2010 Archivos de Zootecnia  
Ao meu co-orientador Luiz Carlos Pinheiro Machado Filho pela orientação e conhecimentos transmitidos.  ...  Maria José Hötzel pelas ótimas aulas. Aos amigos Angela, Queliz e Luana pela acolhida, amizade e alegria de ter conhecido vocês.  ...  vaca/dia vs 18,78 l/vaca/dia, respectivamente).  ... 
doi:10.4321/s0004-05922010000300011 fatcat:fy6sk7geufa3ppdkrxeoi5ugmq

Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case

José Luiz Rybarczyk-Filho, Mauro A. A. Castro, Rodrigo J. S. Dalmolin, José C. F. Moreira, Leonardo G. Brunnet, Rita M. C. de Almeida
2010 Nucleic Acids Research  
On Figure 1d -l window modularity is represented as gray landscapes. There we have chosen w = 251.  ...  (d-l) Projection of diverse terms of the Gene Ontology: Biological Process, as indicated in the right hand frame of each row. Gray landscape backgrounds: window modularity for the orderings.  ... 
doi:10.1093/nar/gkq1269 pmid:21169199 pmcid:PMC3082889 fatcat:xdfup7ggq5gkfhapnejd6vqdma


Claudia Petry, Elisabeth Maria Foschiera, Lísia Rodigheri Godinho, Rodrigo Marciano da Luz, Isabel Cristina Lourenço da Silva, Maddalena Bruna Capello Fusaro, Tarik Ian Reinehr, Fabiane Bernardini Favaretto, Bruno de Oliveira Jacques, Solange Maria Longhi
2020 Meio Ambiente: Impacto do Convívio entre Vegetação, Animais e Homens 2  
À VREAC-UPF e a Coonalter pela implementação da Feira Ecológica na REFERÊNCIAS São José: ICEP, 2017, p. 311-318. PETRY, C.; BORTOLUZZI, E. C. ; FOSCHIERA, E. M. ; FOSCHIERA, L. A. ; LONGHI, S.  ...  L.; VIEIRA, S. R.  ... 
doi:10.22533/at.ed.8252013102 fatcat:gwvxxkjeuzemro6yewosxza37q