Search Results - "Dalmolin, Rodrigo J S"

Metagenomic Analyses Reveal the Influence of Depth Layers on Marine Biodiversity on Tropical and Subtropical Regions by Santiago, Bianca C F, de Souza, Iara D, Cavalcante, João Vitor F, Morais, Diego A A, da Silva, Mikaelly B, Pasquali, Matheus Augusto de B, Dalmolin, Rodrigo J S

“…The emergence of open ocean global-scale studies provided important information about the genomics of oceanic microbial communities. Metagenomic analyses shed…”
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ViaComplex: software for landscape analysis of gene expression networks in genomic context by Castro, Mauro A. A., Filho, José L. Rybarczyk, Dalmolin, Rodrigo J. S., Sinigaglia, Marialva, Moreira, José C. F., Mombach, José C. M., de Almeida, Rita M. C.

“…ViaComplex is an open-source application that builds landscape maps of gene expression networks. The motivation for this software comes from two previous…”
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Sex-specific gene expression differences in the prefrontal cortex of major depressive disorder individuals by de Souza, Iara D., G. S. Fernandes, Vítor, Vitor F. Cavalcante, João, Carolina M. F. Coelho, Ana, A. A. Morais, Diego, Cabral-Marques, Otavio, A. B. Pasquali, Matheus, J. S. Dalmolin, Rodrigo

“…•Identified 1169 transcriptionally altered genes (TAGs) linked to major depressive disorder.•Nearly 50% of TAGs exhibited transcript-level alterations,…”
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Correction: preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks by Ferreira, Ricardo M, Rybarczyk-Filho, José Luiz, Dalmolin, Rodrigo J S, Castro, Mauro A A, Moreira, José C F, Brunnet, Leonardo G, de Almeida, Rita M C

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Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case by Rybarczyk-Filho, José Luiz, Castro, Mauro A A, Dalmolin, Rodrigo J S, Moreira, José C F, Brunnet, Leonardo G, de Almeida, Rita M C

“…Analysis of genome-wide expression data poses a challenge to extract relevant information. The usual approaches compare cellular expression levels relative to…”
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Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma by Hao, Yibin, Wu, Wei, Shi, Fachun, Dalmolin, Rodrigo J S, Yan, Ming, Tian, Fu, Chen, Xiaobing, Chen, Guoyong, Cao, Wei

“…Long non-coding RNAs (lncRNAs) are pervasively transcribed in the genome. They have important regulatory functions in chromatin remodeling and gene expression…”
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MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences by Morais, Diego A A, Cavalcante, João V F, Monteiro, Shênia S, Pasquali, Matheus A B, Dalmolin, Rodrigo J S

“…Metagenomic studies unravel details about the taxonomic composition and the functions performed by microbial communities. As a complete metagenomic analysis…”
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Evolutionary origins of human apoptosis and genome-stability gene networks by Castro, Mauro A.A, Dalmolin, Rodrigo J.S, Moreira, José C.F, Mombach, José C.M, de Almeida, Rita M.C

“…Apoptosis is essential for complex multicellular organisms and its failure is associated with genome instability and cancer. Interactions between apoptosis and…”
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Severe COVID-19 patients exhibit elevated levels of autoantibodies targeting cardiolipin and platelet glycoprotein with age: a systems biology approach by Fonseca, Dennyson Leandro M., Filgueiras, Igor Salerno, Marques, Alexandre H. C., Vojdani, Elroy, Halpert, Gilad, Ostrinski, Yuri, Baiocchi, Gabriela Crispim, Plaça, Desirée Rodrigues, Freire, Paula P., Pour, Shahab Zaki, Moll, Guido, Catar, Rusan, Lavi, Yael Bublil, Silverberg, Jonathan I., Zimmerman, Jason, Cabral-Miranda, Gustavo, Carvalho, Robson F., Khan, Taj Ali, Heidecke, Harald, Dalmolin, Rodrigo J. S., Luchessi, Andre Ducati, Ochs, Hans D., Schimke, Lena F., Amital, Howard, Riemekasten, Gabriela, Zyskind, Israel, Rosenberg, Avi Z., Vojdani, Aristo, Shoenfeld, Yehuda, Cabral-Marques, Otavio

“…Age is a significant risk factor for the coronavirus disease 2019 (COVID-19) severity due to immunosenescence and certain age-dependent medical conditions…”
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Systems Biology-Based Analysis Indicates Global Transcriptional Impairment in Lead-Treated Human Neural Progenitor Cells by Reis, Clovis F., de Souza, Iara D., Morais, Diego A. A., Oliveira, Raffael A. C., Imparato, Danilo O., de Almeida, Rita M. C., Dalmolin, Rodrigo J. S.

“…Lead poisoning effects are wide and include nervous system impairment, peculiarly during development, leading to neural damage. Lead interaction with calcium…”
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Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks by Ferreira, Ricardo M, Rybarczyk-Filho, José Luiz, Dalmolin, Rodrigo J S, Castro, Mauro A A, Moreira, José C F, Brunnet, Leonardo G, de Almeida, Rita M C

“…Whole genome protein-protein association networks are not random and their topological properties stem from genome evolution mechanisms. In fact, more…”
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Evolutionary plasticity determination by orthologous groups distribution by Dalmolin, Rodrigo J S, Castro, Mauro A A, Rybarczyk Filho, José L, Souza, Luis H T, de Almeida, Rita M C, Moreira, José C F

“…Genetic plasticity may be understood as the ability of a functional gene network to tolerate alterations in its components or structure. Usually, the studies…”
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Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analyses by Campos, Leonardo R S, Trefflich, Sheyla, Morais, Diego A A, Imparato, Danilo O, Chagas, Vinicius S, Albanus, Ricardo D'Oliveira, Dalmolin, Rodrigo J S, Castro, Mauro A A

“…Orthology information has been used for searching patterns in high-dimensional data, allowing transferring functional information between species. The key…”
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TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves by Cardoso, Milena A, Rizzardi, Luis E A, Kume, Leonardo W, Groeneveld, Clarice S, Trefflich, Sheyla, Morais, Diego A A, Dalmolin, Rodrigo J S, Ponder, Bruce A J, Meyer, Kerstin B, Castro, Mauro A A

“…Abstract Motivation Dendrogram is a classical diagram for visualizing binary trees. Although efficient to represent hierarchical relations, it provides limited…”
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Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein-protein interaction by Morais, Diego A A, Almeida, Rita M C, Dalmolin, Rodrigo J S

“…Several freely available tools perform analysis using algorithms developed to identify significant variation of gene expression individually. The…”
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Which came first, the transcriptional regulator or its target genes? An evolutionary perspective into the construction of eukaryotic regulons by Trefflich, Sheyla, Dalmolin, Rodrigo J.S., Ortega, José Miguel, Castro, Mauro A.A.

“…Eukaryotic regulons are regulatory units formed by a set of genes under the control of the same transcription factor (TF). Despite the functional plasticity,…”
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NFκB inhibitors induce cell death in glioblastomas by Zanotto-Filho, Alfeu, Braganhol, Elizandra, Schröder, Rafael, de Souza, Luís Henrique T., Dalmolin, Rodrigo J.S., Pasquali, Matheus A. Bittencourt, Gelain, Daniel Pens, Battastini, Ana Maria Oliveira, Moreira, José Cláudio Fonseca

“…Identification of novel target pathways in glioblastoma (GBM) remains critical due to poor prognosis, inefficient therapies and recurrence associated with…”
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Ancestry analysis indicates two different sets of essential genes in eukaryotic model species by de Souza, Iara D., Reis, Clovis F., Morais, Diego A. A., Fernandes, Vítor G. S., Cavalcante, João Vitor F., Dalmolin, Rodrigo J. S.

“…Essential genes are so-called because they are crucial for organism perpetuation. Those genes are usually related to essential functions to cellular metabolism…”
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A systematic review of human antioxidant genes by Gelain, Daniel P, Dalmolin, Rodrigo J S, Belau, Vanessa L, Moreira, Jose C F, Klamt, Fabio, Castro, Mauro A A

“…The balance between production and clearance of reactive species is essential for cell survival. Antioxidant cellular systems evolved to maintain a redox…”
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Retinol and retinoic acid increase MMP-2 activity by different pathways in cultured Sertoli cells by Dalmolin, Rodrigo J S, Zanotto-Filho, Alfeu, De Oliveira, Ramatis B, Duarte, Roxane F, Pasquali, Matheus A B, Moreira, José C F

“…Diseases such as atherosclerosis, arthritis and cancer have been related with imbalance in ROS production and failures in regulation of the MMPs. Authors…”
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