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.
2024
Sex-specific gene expression differences in the prefrontal cortex of major depressive disorder individuals
Neuroscience
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01 Nov 2024
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doi:10.1016/j.neuroscience.2024.09.012
Sex-specific gene expression differences in the prefrontal cortex of major depressive disorder individuals
Neuroscience
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01 Nov 2024
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doi:10.1016/J.NEUROSCIENCE.2024.09.012
A Prognostic Methylation-Driven Two-Gene Signature in Medulloblastoma
Journal of Molecular Neuroscience
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25 Apr 2024
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doi:10.1007/s12031-024-02203-9
What Powers Trastuzumab's Cardiotoxicity? Decoding Mitochondrial-Related Gene Expression Through Integrative Review and Meta-Analysis in Cardiomyocytes
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Bioinformatics
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15 Apr 2009
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doi:10.1093/bioinformatics/btp246
A systematic review of human antioxidant genes
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
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
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
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?
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
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
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
Free Radical Research
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01 Jan 2001
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doi:10.1080/10715760100301251