Publications

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 · 01 Mar 2025 · doi:10.1016/J.JHAZMAT.2024.136866

easylayout: an R package for interactive force-directed layouts within RStudio

[no author info]

ArXiv · 06 Feb 2025 · 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 · 13 Jan 2025 · doi:10.1038/S41540-025-00488-Z

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 · 01 Nov 2024 · 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 · 26 Sep 2024 · 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) · 27 Aug 2024 · 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 · 25 Apr 2024 · 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 · 09 Apr 2024 · 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 · 01 Mar 2024 · doi:10.1089/omi.2024.0004

<i>Bridge</i>: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analyses

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 · 01 Feb 2024 · doi:10.1093/molbev/msae019

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 · 01 Dec 2023 · doi:10.1089/omi.2023.0232

Revealing metastatic castration‐resistant prostate cancer master regulator through <scp>lncRNAs</scp>‐centered regulatory network

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 · 29 Aug 2023 · 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 · 27 Jun 2023 · doi:10.3390/microorganisms11071668

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 · 05 Dec 2022 · 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 · 18 Oct 2022 · doi:10.1101/2022.10.18.512769

A survey of transcriptomic datasets identifies ABA-responsive factors as regulators of photomorphogenesis in<i>Arabidopsis</i>

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 · 24 Jul 2022 · 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 · 07 Mar 2022 · 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 · 01 Jan 2022 · doi:10.1016/j.isci.2021.103610

<i>TreeAndLeaf</i>: an R/Bioconductor package for graphs and trees with focus on the leaves

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 · 02 Dec 2021 · 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 · 23 Sep 2021 · 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 · 01 Jul 2021 · 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 · 13 Apr 2021 · doi:10.3390/cancers13081860

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 · 28 Sep 2020 · 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 · 01 Aug 2020 · 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 · 30 Jun 2020 · 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 · 01 Jun 2020 · doi:10.1016/j.bbagrm.2019.194472

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 · 31 Oct 2019 · 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 · 10 Sep 2019 · 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 · 08 Jan 2019 · doi:10.1093/bioinformatics/btz007

Sunlight Incidence, Vitamin D Deficiency, and Alzheimer's Disease

Alice Barros Câmara, Iara Dantas de Souza, Rodrigo Juliani Siqueira Dalmolin

Journal of Medicinal Food · 01 Sep 2018 · 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 · 12 Feb 2018 · doi:10.1080/10408444.2018.1429387

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 · 16 Jan 2017 · doi:10.1093/mutage/gew068

Antioxidant and Anti‐Inflammatory Properties of <i>Anacardium occidentale</i> Leaf Extract

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 · 01 Jan 2017 · doi:10.1155/2017/2787308

<i>Turnera subulata</i>Anti-Inflammatory Properties in Lipopolysaccharide-Stimulated RAW 264.7 Macrophages

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 · 01 Oct 2016 · 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 · 01 Sep 2016 · doi:http://dx.doi.org/10.1016/j.toxlet.2016.06.2026

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 · 24 Mar 2015 · 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 · 13 Mar 2015 · doi:10.1371/journal.pone.0118425

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 · 03 Dec 2014 · 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 · 01 Jan 2014 · 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. · 01 Jan 2014 · doi:10.1039/c3mb70590k

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 · 05 Dec 2013 · 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 · 26 Feb 2013 · doi:10.1371/journal.pone.0056579

Transcriptomic analysis reveals pH-responsive antioxidant gene networks

Rodrigo Juliani Siqueira Dalmolin

Frontiers in Bioscience · 01 Jan 2012 · doi:10.2741/s352

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 · 01 Feb 2011 · 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 · 01 Jan 2011 · doi:10.1186/1745-6150-6-22

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 · 15 Dec 2010 · doi:10.1093/nar/gkq1269

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 · 15 Apr 2009 · doi:10.1093/bioinformatics/btp246

A systematic review of human antioxidant genes

Daniel, P. Gelain

Frontiers in Bioscience · 01 Jan 2009 · doi:10.2741/3541

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 · 02 Oct 2008 · 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 · 01 Aug 2008 · 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 · 01 Jan 2008 · doi:10.1016/j.cellbi.2007.08.018

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 · 03 Jan 2007 · 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 · 01 Jan 2007 · doi:10.1080/10715760701717427

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 · 01 Aug 2003 · doi:10.1016/S1383-5718(03)00155-4

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 · 01 Jan 2001 · doi:10.1080/10715760100301251