Publications
Below you can find the papers published by our group. Found something interesting, want to collaborate with us or can’t access a paper? Get in contact with us. In case you want to know more about our lines of research, check out the research page.
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2025
Unlocking the transcriptional profiles of an oily waste-degrading bacterial consortium
Rita de Cássia Barreto Silva-Portela, Carolina Fonseca Minnicelli, Júlia Firme Freitas, Marbella Maria Bernardes Fonseca, Douglas Felipe de Lima Silva, ..., Raul Maia Falcão, Thiago Bruce, João Vitor Ferreira Cavalcante, Rodrigo Juliani Siqueira Dalmolin, Lucymara Fassarella Agnez-Lima
Journal of Hazardous Materials
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01 Mar 2025
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doi:10.1016/J.JHAZMAT.2024.136866
easylayout: an R package for interactive force-directed layouts within RStudio
[no author info]
ArXiv
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06 Feb 2025
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wosuid:PPRN:100706260
Dysregulated autoantibodies targeting AGTR1 are associated with the accumulation of COVID-19 symptoms
Dennyson Leandro M. Fonseca, Maj Jäpel, Michael Adu Gyamfi, Igor Salerno Filgueiras, Gabriela Crispim Baiochi, ..., Yehuda Shoenfeld, Gabriela Riemekasten, Reza Akbarzadeh, Alexandre H. C. Marques, Otavio Cabral-Marques
npj Systems Biology and Applications
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13 Jan 2025
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doi:10.1038/S41540-025-00488-Z
2024
Sex-specific gene expression differences in the prefrontal cortex of major depressive disorder individuals
Iara D. de Souza, Vítor G. S. Fernandes, João Vitor F. Cavalcante, Ana Carolina M. F. Coelho, Diego A. A. Morais, Otavio Cabral-Marques, Matheus A. B. Pasquali, Rodrigo J. S. Dalmolin
Neuroscience
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01 Nov 2024
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doi:10.1016/J.NEUROSCIENCE.2024.09.012
Integrative systems neuroimmunology reveals leukocyte-expressing PAX6 as a critical predictor of major depressive disorder
Haroldo Dutra Dias, Anny Silva Adri, Adriel Leal Nóbile, Marilia Garcia de Oliveira, Elizabeth N. Chung, ..., Renato Bortoloti, Clement Hamani, Michael A. Wheeler, Rafael Machado Rezende, Otavio Cabral-Marques
Cold Spring Harbor Laboratory
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26 Sep 2024
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doi:10.1101/2024.09.25.614771
EURYALE: A versatile Nextflow pipeline for taxonomic classification and functional annotation of metagenomics data
João Vitor F. Cavalcante, Iara Dantas de Souza, Diego A. A. Morais, Rodrigo J. S. Dalmolin
2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)
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27 Aug 2024
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doi:10.1109/CIBCB58642.2024.10702116
A Prognostic Methylation-Driven Two-Gene Signature in Medulloblastoma
Gustavo Lovatto Michaelsen, Lívia dos Reis Edinger da Silva, Douglas Silva de Lima, Mariane da Cunha Jaeger, André Tesainer Brunetto, Rodrigo Juliani Siqueira Dalmolin, Marialva Sinigaglia
Journal of Molecular Neuroscience
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25 Apr 2024
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doi:10.1007/s12031-024-02203-9
Integrative Systems Immunology Analysis Reveals Elevated Anti-AGTR1 Levels with Accumulating COVID-19 Symptoms
Dennyson Leandro M Fonseca, Maj Jäpel, Igor Salerno Filgueiras, Gabriela Crispim Baiochi, Yuri Ostrinski, ..., Yehuda Shoenfeld, Gabriela Riemekasten, Reza Akbarzadeh, Alexandre H.C Marques, Otavio Cabral-Marques
Cold Spring Harbor Laboratory
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09 Apr 2024
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doi:10.1101/2024.04.05.24305287
What Powers Trastuzumab's Cardiotoxicity? Decoding Mitochondrial-Related Gene Expression Through Integrative Review and Meta-Analysis in Cardiomyocytes
Karoline dos Santos Rodrigues, Daniel Sturza Lucas Caetano, João Vitor Cavalcante, Rodrigo Dalmolin, Patrícia K. Ziegelmann, Michael Andrades
OMICS: A Journal of Integrative Biology
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01 Mar 2024
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doi:10.1089/omi.2024.0004
Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analyses
Leonardo R S Campos, Sheyla Trefflich, Diego A A Morais, Danilo O Imparato, Vinicius S Chagas, Ricardo D’Oliveira Albanus, Rodrigo J S Dalmolin, Mauro A A Castro
Molecular Biology and Evolution
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01 Feb 2024
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doi:10.1093/molbev/msae019
2023
Bridging the Gaps in Meta-Omic Analysis: Workflows and Reproducibility
João Vitor Ferreira Cavalcante, Iara Dantas de Souza, Diego Arthur de Azevedo Morais, Rodrigo Juliani Siqueira Dalmolin
OMICS: A Journal of Integrative Biology
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01 Dec 2023
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doi:10.1089/omi.2023.0232
Revealing metastatic castration‐resistant prostate cancer master regulator through lncRNAs ‐centered regulatory network
Rafaella Sousa Ferraz, João Vitor Ferreira Cavalcante, Leandro Magalhães, Ândrea Ribeiro‐dos‐Santos, Rodrigo Juliani Siqueira Dalmolin
Cancer Medicine
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29 Aug 2023
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doi:10.1002/cam4.6481
Metagenomic Analyses Reveal the Influence of Depth Layers on Marine Biodiversity on Tropical and Subtropical Regions
Bianca C. F. Santiago, Iara D. de Souza, João Vitor F. Cavalcante, Diego A. A. Morais, Mikaelly B. da Silva, Matheus Augusto de B. Pasquali, Rodrigo J. S. Dalmolin
Microorganisms
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27 Jun 2023
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doi:10.3390/microorganisms11071668
2022
SARS-CoV-2 infection induces the production of autoantibodies in severe COVID-19 patients in an age-dependent manner
Dennyson Leandro M Fonseca, Igor Salerno Filgueiras, Alexandre HC Marques, Elroy Vojdani, Gilad Halpert, ..., Israel Zyskind, Avi Z Rosenberg, Aristo Vojdani, Yehuda Shoenfeld, Otavio Cabral-Marques
Cold Spring Harbor Laboratory
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05 Dec 2022
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doi:10.1101/2022.12.04.22282902
Metagenomic analyses reveal the influence of depth layers on marine biodiversity in tropical and subtropical regions
Bianca C. F. Santiago, Iara D. de Souza, João Vitor F. Cavalcante, Diego A. A. Morais, Rodrigo J. S. Dalmolin
Cold Spring Harbor Laboratory
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18 Oct 2022
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doi:10.1101/2022.10.18.512769
A survey of transcriptomic datasets identifies ABA-responsive factors as regulators of photomorphogenesis inArabidopsis
Cássia Fernanda Stafen, Iara Souza, Ben Hur de Oliveira, Luísa Abruzzi de Oliveira-Busatto, Rodrigo Juliani Siqueira Dalmolin, Oscar Lorenzo Sánchez, Felipe dos Santos Maraschin
Cold Spring Harbor Laboratory
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24 Jul 2022
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doi:10.1101/2022.07.24.501316
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences
Diego A. A. Morais, João V. F. Cavalcante, Shênia S. Monteiro, Matheus A. B. Pasquali, Rodrigo J. S. Dalmolin
Frontiers in Genetics
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07 Mar 2022
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doi:10.3389/fgene.2022.814437
The evolution of knowledge on genes associated with human diseases
Thomaz Lüscher-Dias, Rodrigo Juliani Siqueira Dalmolin, Paulo de Paiva Amaral, Tiago Lubiana Alves, Viviane Schuch, Glória Regina Franco, Helder I. Nakaya
iScience
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01 Jan 2022
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doi:10.1016/j.isci.2021.103610
2021
TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves
Milena A Cardoso, Luis E A Rizzardi, Leonardo W Kume, Clarice S Groeneveld, Sheyla Trefflich, Diego A A Morais, Rodrigo J S Dalmolin, Bruce A J Ponder, Kerstin B Meyer, Mauro A A Castro
Bioinformatics
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02 Dec 2021
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doi:10.1093/bioinformatics/btab819
Reverse Engineering of the Pediatric Sepsis Regulatory Network and Identification of Master Regulators
Raffael Azevedo de Carvalho Oliveira, Danilo Oliveira Imparato, Vítor Gabriel Saldanha Fernandes, João Vitor Ferreira Cavalcante, Ricardo D’Oliveira Albanus, Rodrigo Juliani Siqueira Dalmolin
Biomedicines
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23 Sep 2021
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doi:10.3390/biomedicines9101297
Ancestry analysis indicates two different sets of essential genes in eukaryotic model species
Iara D. de Souza, Clovis F. Reis, Diego A. A. Morais, Vítor G. S. Fernandes, João Vitor F. Cavalcante, Rodrigo J. S. Dalmolin
Functional & Integrative Genomics
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01 Jul 2021
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doi:10.1007/s10142-021-00794-9
Reverse Engineering of Ewing Sarcoma Regulatory Network Uncovers PAX7 and RUNX3 as Master Regulators Associated with Good Prognosis
Marcel da Câmara Ribeiro-Dantas, Danilo Oliveira Oliveira Imparato, Matheus Gibeke Siqueira Dalmolin, Caroline Brunetto de Farias, André Tesainer Brunetto, Mariane da Cunha Jaeger, Rafael Roesler, Marialva Sinigaglia, Rodrigo Juliani Siqueira Dalmolin
Cancers
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13 Apr 2021
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doi:10.3390/cancers13081860
2020
Ionotropic Receptors as a Driving Force behind Human Synapse Establishment
Lucas Henriques Viscardi, Danilo Oliveira Imparato, Maria Cátira Bortolini, Rodrigo Juliani Siqueira Dalmolin
Molecular Biology and Evolution
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28 Sep 2020
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doi:10.1093/molbev/msaa252
Anti-inflammatory and antixidant properties of blend formulated with compounds of Malpighia emarginata D.C (acerola) and Camellia sinensis L. (green tea) in lipopolysaccharide-stimulated RAW 264.7 macrophages
Natália Cabral Souza, Eduardo Natan de Oliveira Nascimento, Iara Bezerra de Oliveira, Hugo Miguel Lisboa Oliveira, Eudeson Gustavo Paiva Santos, Mário Eduardo Rangel Moreira Cavalcanti Mata, Daniel Pens Gelain, José Cláudio Fonseca Moreira, Rodrigo Juliani Siqueira Dalmolin, Matheus Augusto de Bittencourt Pasquali
Biomedicine & Pharmacotherapy
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01 Aug 2020
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doi:10.1016/j.biopha.2020.110277
CoRINs: A tool to compare residue interaction networks from homologous proteins and conformers
Felipe V. da Fonseca, Romildo O. Souza Júnior, Marília V. A. de Almeida, Thiago D. Soares, Diego A. A. Morais, Rodrigo J. S. Dalmolin, João Paulo M. S. Lima
Cold Spring Harbor Laboratory
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30 Jun 2020
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doi:10.1101/2020.06.29.178541
Which came first, the transcriptional regulator or its target genes? An evolutionary perspective into the construction of eukaryotic regulons
Sheyla Trefflich, Rodrigo J.S. Dalmolin, José Miguel Ortega, Mauro A.A. Castro
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
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01 Jun 2020
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doi:10.1016/j.bbagrm.2019.194472
2019
Analysis of Arabidopsis thaliana Redox Gene Network Indicates Evolutionary Expansion of Class III Peroxidase in Plants
Raffael Azevedo de Carvalho Oliveira, Abraão Silveira de Andrade, Danilo Oliveira Imparato, Juliana Gabriela Silva de Lima, Ricardo Victor Machado de Almeida, João Paulo Matos Santos Lima, Matheus Augusto de Bittencourt Pasquali, Rodrigo Juliani Siqueira Dalmolin
Scientific Reports
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31 Oct 2019
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doi:10.1038/s41598-019-52299-y
Systems Biology-Based Analysis Indicates Global Transcriptional Impairment in Lead-Treated Human Neural Progenitor Cells
Clovis F. Reis, Iara D. de Souza, Diego A. A. Morais, Raffael A. C. Oliveira, Danilo O. Imparato, Rita M. C. de Almeida, Rodrigo J. S. Dalmolin
Frontiers in Genetics
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10 Sep 2019
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doi:10.3389/fgene.2019.00791
Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein–protein interaction
Diego A A Morais, Rita M C Almeida, Rodrigo J S Dalmolin
Bioinformatics
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08 Jan 2019
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doi:10.1093/bioinformatics/btz007
2018
Sunlight Incidence, Vitamin D Deficiency, and Alzheimer's Disease
Alice Barros Câmara, Iara Dantas de Souza, Rodrigo Juliani Siqueira Dalmolin
Journal of Medicinal Food
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01 Sep 2018
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doi:10.1089/jmf.2017.0130
Lead-interacting proteins and their implication in lead poisoning
Iara Dantas de Souza, Abraão Silveira de Andrade, Rodrigo Juliani Siqueira Dalmolin
Critical Reviews in Toxicology
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12 Feb 2018
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doi:10.1080/10408444.2018.1429387
2017
Analysis of genome instability biomarkers in children with non-syndromic orofacial clefts
Luíza Araújo da Costa Xavier, João Felipe Bezerra, Adriana Augusto de Rezende, Raffael Azevedo de Carvalho Oliveira, Rodrigo Juliani Siqueira Dalmolin, Viviane Souza do Amaral
Mutagenesis
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16 Jan 2017
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doi:10.1093/mutage/gew068
Antioxidant and Anti‐Inflammatory Properties of Anacardium occidentale Leaf Extract
Natália Cabral Souza, Juliana Medeiros de Oliveira, Maurílio da Silva Morrone, Ricardo D’Oliveira Albanus, Maria do Socorro Medeiros Amarante, ..., Silvana Maria Zucolotto Langassner, Daniel Pens Gelain, José Cláudio Fonseca Moreira, Rodrigo Juliani Siqueira Dalmolin, Matheus Augusto de Bittencourt Pasquali
Evidence-Based Complementary and Alternative Medicine
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01 Jan 2017
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doi:10.1155/2017/2787308
2016
Turnera subulataAnti-Inflammatory Properties in Lipopolysaccharide-Stimulated RAW 264.7 Macrophages
Natália Cabral Souza, Juliana Medeiros de Oliveira, Maurílio da Silva Morrone, Ricardo D'Oliveira Albanus, Maria do Socorro Medeiros Amarante, ..., Silvana Maria Zucolotto Langassner, Daniel Pens Gelain, José Cláudio Fonseca Moreira, Rodrigo Juliani Siqueira Dalmolin, Matheus Augusto de Bittencourt Pasquali
Journal of Medicinal Food
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01 Oct 2016
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doi:10.1089/jmf.2016.0047
Genome instability biomarkers in children with non-syndromic orofacial clefts
V.S. Amaral, L.A. Xavier, J.F. Bezerra, A.A. Rezende, R. Azevedo, R.J. Dalmolin
Toxicology Letters
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01 Sep 2016
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doi:http://dx.doi.org/10.1016/j.toxlet.2016.06.2026
2015
Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma
Yibin Hao, Wei Wu, Fachun Shi, Rodrigo JS Dalmolin, Ming Yan, Fu Tian, Xiaobing Chen, Guoyong Chen, Wei Cao
BMC Cancer
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24 Mar 2015
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doi:10.1186/s12885-015-1179-z
Correction: 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
PLOS ONE
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13 Mar 2015
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doi:10.1371/journal.pone.0118425
2014
Gene Expression Profile of NF-κB, Nrf2, Glycolytic, and p53 Pathways During the SH-SY5Y Neuronal Differentiation Mediated by Retinoic Acid
Matheus Augusto de Bittencourt Pasquali, Vitor Miranda de Ramos, Ricardo D′Oliveira Albanus, Alice Kunzler, Luis Henrinque Trentin de Souza, Rodrigo Juliani Siqueira Dalmolin, Daniel Pens Gelain, Leila Ribeiro, Luigi Carro, José Cláudio Fonseca Moreira
Molecular Neurobiology
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03 Dec 2014
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doi:10.1007/s12035-014-8998-9
Differential Evolutionary Constraints in the Evolution of Chemoreceptors: A Murine and Human Case Study
Ricardo D’Oliveira Albanus, Rodrigo Juliani Siqueira Dalmolin, José Luiz Rybarczyk-Filho, Mauro Antônio Alves Castro, José Cláudio Fonseca Moreira
The Scientific World Journal
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01 Jan 2014
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doi:10.1155/2014/696485
Computational analyses reveal a prognostic impact of TULP3 as a transcriptional master regulator in pancreatic ductal adenocarcinoma
I. T. S. Sartor, F. Zeidán-Chuliá, R. D. Albanus, R. J. S. Dalmolin, J. C. F. Moreira
Mol. BioSyst.
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01 Jan 2014
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doi:10.1039/c3mb70590k
2013
Reverse Engineering the Neuroblastoma Regulatory Network Uncovers MAX as One of the Master Regulators of Tumor Progression
Ricardo D’Oliveira Albanus, Rodrigo Juliani Siqueira Dalmolin, Mauro Antônio Alves Castro, Matheus Augusto de Bittencourt Pasquali, Vitor de Miranda Ramos, Daniel Pens Gelain, José Cláudio Fonseca Moreira
PLoS ONE
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05 Dec 2013
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doi:10.1371/journal.pone.0082457
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
PLoS ONE
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26 Feb 2013
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doi:10.1371/journal.pone.0056579
2012
Transcriptomic analysis reveals pH-responsive antioxidant gene networks
Rodrigo Juliani Siqueira Dalmolin
Frontiers in Bioscience
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01 Jan 2012
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doi:10.2741/s352
2011
NFκB inhibitors induce cell death in glioblastomas
Alfeu Zanotto-Filho, Elizandra Braganhol, Rafael Schröder, Luís Henrique T. de Souza, Rodrigo J.S. Dalmolin, Matheus A. Bittencourt Pasquali, Daniel Pens Gelain, Ana Maria Oliveira Battastini, José Cláudio Fonseca Moreira
Biochemical Pharmacology
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01 Feb 2011
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doi:10.1016/j.bcp.2010.10.014
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
Biology Direct
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01 Jan 2011
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doi:10.1186/1745-6150-6-22
2010
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
Nucleic Acids Research
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15 Dec 2010
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doi:10.1093/nar/gkq1269
2009
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
Bioinformatics
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15 Apr 2009
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doi:10.1093/bioinformatics/btp246
A systematic review of human antioxidant genes
Daniel, P. Gelain
Frontiers in Bioscience
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01 Jan 2009
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doi:10.2741/3541
2008
Evolutionary origins of human apoptosis and genome-stability gene networks
Mauro A. A. Castro, Rodrigo J. S. Dalmolin, José C. F. Moreira, José C. M. Mombach, Rita M. C. de Almeida
Nucleic Acids Research
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02 Oct 2008
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doi:10.1093/nar/gkn636
Retinoic acid induces apoptosis by a non-classical mechanism of ERK1/2 activation
Alfeu Zanotto-Filho, Martin Cammarota, Daniel P. Gelain, Ramatis B. Oliveira, Andres Delgado-Cañedo, Rodrigo J.S. Dalmolin, Matheus A.B. Pasquali, José Cláudio F. Moreira
Toxicology in Vitro
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01 Aug 2008
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doi:10.1016/j.tiv.2008.04.001
Vitamin A treatment induces apoptosis through an oxidant‐dependent activation of the mitochondrial pathway
Fábio Klamt, Felipe Dal‐Pizzol, Daniel Pens Gelain, Rodrigo Siqueira Dalmolin, Birnfeld Ramatis de Oliveira, Michele Bastiani, Fabiana Horn, José Cláudio Fonseca Moreira
Cell Biology International
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01 Jan 2008
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doi:10.1016/j.cellbi.2007.08.018
2007
Can electrons travel through actin microfilaments and generate oxidative stress in retinol treated Sertoli cell?
Ramatis Birnfeld de Oliveira, Matheus Augusto de Bittencourt Pasquali, Alfeu Zanotto Filho, Rodrigo Juliani Siqueira Dalmolin, Daniel Pens Gelain, Carmem Gottfried, José Luiz Rodrigues, Fábio Klamt, José Cláudio Fonseca Moreira
Molecular and Cellular Biochemistry
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03 Jan 2007
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doi:10.1007/s11010-006-9394-1
Retinol and retinoic acid increase MMP-2 activity by different pathways in cultured Sertoli cells
Rodrigo J. S. Dalmolin, Alfeu Zanotto-filho, Ramatis B. De oliveira, Roxane F. Duarte, Matheus A. B. Pasquali, José C. F. Moreira
Free Radical Research
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01 Jan 2007
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doi:10.1080/10715760701717427
2003
Genotoxicity, recombinogenicity and cellular preneoplasic transformation induced by Vitamin a supplementation
Fábio Klamt, Felipe Dal-Pizzol, Rafael Roehrs, Ramatis Birnfeld de Oliveira, Rodrigo Dalmolin, João A.P Henriques, Heloisa Helena Rodrigues de Andrades, Ana Lı́gia Lia de Paula Ramos, Jenifer Saffi, José Cláudio Fonseca Moreira
Mutation Research/Genetic Toxicology and Environmental Mutagenesis
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01 Aug 2003
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doi:10.1016/S1383-5718(03)00155-4
2001
Mitogenic signaling mediated by oxidants in retinol treated sertoli cells
Felipe Dal-Pizzol, Fábio Klamt, Rodrigo J.S. Dalmolin, Elena A. Bernard, José Cláudio F. Moreira
Free Radical Research
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01 Jan 2001
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doi:10.1080/10715760100301251