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21st IEEE Conference on Computational Intelligence in bioinformatics and Computational Biology, CIBCB 2024

作者： Cavalcante, João Vitor F. De Souza, Iara Dantas Morais, Diego A. A. Dalmolin, Rodrigo J. S. Federal University of Rio Grande do Norte Bioinformatics Multidisciplinary Environment Natal Brazil Federal University of Rio Grande do Norte Department of Biochemistry Natal Brazil

ISBN: (纸本)9798350356632

EURYALE is a Nextflow pipeline designed for the sensitive taxonomic classification and flexible functional annotation of metagenomic shotgun sequences. It provides a comprehensive solution for preprocessing, assembly, alignment, taxonomic classification, and functional annotation of metagenomic data. EURYALE builds upon the Snakemake-based pipeline MEDUSA. EURYALE inherits the tools present in MEDUSA, selected based on rigorous benchmarks for performance, accuracy, and sensitivity. The new pipeline has been developed with the nf-core pipeline template, which focuses on modularity, allowing a high degree of parameterization. EURYALE provides easier resource management, enforcing strict memory and CPU requirements based on its Nextflow configuration. It has also become more versatile, as it can be executed using Docker and Singularity, which further extends its usability across various platforms. It can also natively take advantage of computational infrastructures such as SLURM and Amazon Web Services. EURYALE inherits the sensitivity in taxonomic classification and flexibility in functional annotation of its predecessor, combined with improved versatility. © 2024 IEEE.

关键词： Resource allocation

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

arXiv

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arXiv 2024年

作者： Imparato, Danilo Oliveira Cavalcante, João Vitor F. Dalmolin, Rodrigo J.S. Bioinformatics Multidisciplinary Environment Federal University of Rio Grande do Norte Natal Brazil

Motivation Network visualization is critical for effective communication in various fields of knowledge. Currently, a gap separates network manipulation from network visualization in programming environments. Users often export network data to be laid out in external interactive software, like Cytoscape and Gephi. We argue the current R package ecosystem lacks an interactive layout engine well integrated with common data analysis workflows. Results We present easylayout, an R package that bridges network manipulation and visualization by leveraging interactive force simulations within the IDE itself (e.g., RStudio, VSCode). It is not yet another visualization library, but instead aims to interconnect existing libraries and streamline their usage into the R ecosystem. easylayout takes an igraph object and serializes it into a web application integrated with the IDE’s interface through a Shiny server. The web application lays out the network by simulating attraction and repulsion forces. Simulation parameters can be adjusted in real-time. An editing mode allows moving and rotating nodes. The implementation aims for performance, so that even lower-end devices are able to work with relatively large networks. Once the user finishes tweaking the layout, it is sent back to the R session to be plotted through popular libraries like ggraph, igraph or even the base package itself. The current implementation focuses on the R ecosystem, but using web technologies makes it easily portable to similar environments, like Python/Jupyter Notebooks. We expect this tool to reduce the time spent searching for suitable network layouts, ultimately allowing researchers to generate more compelling figures. Availability and implementation easylayout is freely available under an MIT license on GitHub (https://***/dalmolingroup/easylayout). The package is implemented in R/Shiny and JavaScript/Svelte. © 2024, CC BY-NC-ND.

关键词： Data flow analysis

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A Closed-Loop Deep Brain Stimulation Biomedical Model of Parkinson's Disease 21

A Closed-Loop Deep Brain Stimulation Biomedical Model of Par...

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21st IEEE Conference on Computational Intelligence in bioinformatics and Computational Biology, CIBCB 2024

作者： Petitjean, Timothe Millet, Hugo Araújo, Mariana F. P. Moioli, Renan C. Vargas, Patricia A. Ranieri, Caetano M. Heriot-Watt University School of Mathematical And Computer Science Edinburgh United Kingdom Health Sciences Center Department of Physiological Sciences Vitoria Brazil Bioinformatics Multidisciplinary Environment Digital Metropolis Institute Natal Brazil Institute of Geosciences and Exact Sciences Rio Claro Brazil

ISBN: (纸本)9798350356632

In this paper, we introduce a new approach to the study of Parkinson's Disease (PD) through the implementation of a neurorobotics model via the integration of computational neuroscience with the latest robotic technology. Using the iCub as our robot platform, we adapted a computational model of the Basal Ganglia-Thalamo-Cortical (BG-T-C) circuit to investigate the efficiency of Deep Brain Stimulation (DBS) in mitigating PD's motor *** to our methodology is the use of closed-loop DBS, a technique that adjusts stimulation parameters in real time based on specific kinematic and neuronal biomarkers of PD severity, such as fluctuations in beta band activity and tremor movements. This dynamic approach allows for a more personalized and efficient treatment regimen compared to traditional, static open-loop systems, which cannot adapt to the patient's changing *** findings of our study corroborate the feasibility of using a neurorobotics model to simulate the motor symptoms of PD and provide evidence that closed-loop DBS can effectively modulate these symptoms. This was achieved by reducing the power spectral density at the beta-band frequency range (8-30 Hz) of the neural activity to below threshold levels and revealing a complex relationship between the severity of the disease and the effectiveness of the treatment. © 2024 IEEE.

关键词： Neurodegenerative diseases

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EURYALE: A versatile Nextflow pipeline for taxonomic classification and functional annotation of metagenomics data

EURYALE: A versatile Nextflow pipeline for taxonomic classif...

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IEEE Symposium on Computational Intelligence and bioinformatics and Computational Biology (CIBCB)

作者： João Vitor F. Cavalcante Iara Dantas de Souza Diego A. A. Morais Rodrigo J. S. Dalmolin Bioinformatics Multidisciplinary Environment Federal University of Rio Grande do Norte Natal Brazil Department of Biochemistry Federal University of Rio Grande do Norte Natal Brazil

ISBN: (数字)9798350356632

ISBN: (纸本)9798350356649

关键词： Metagenomics Schedules Sensitivity Data analysis Annotations Web services Pipelines Memory management Resource management Usability

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A Closed-Loop Deep Brain Stimulation Biomedical Model of Parkinson’s Disease

A Closed-Loop Deep Brain Stimulation Biomedical Model of Par...

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IEEE Symposium on Computational Intelligence and bioinformatics and Computational Biology (CIBCB)

作者： Timothe Petitjean Hugo Millet Mariana F. P. Araújo Renan C. Moioli Patricia A. Vargas Caetano M. Ranieri School of Mathematical And Computer Science Heriot-Watt University Edinburgh Scotland Department of Physiological Sciences Health Sciences Center Federal University of Espirito Santo (UFES) Vitoria Brazil Bioinformatics Multidisciplinary Environment Digital Metropolis Institute Federal University of Rio Grande do Norte (UFRN) Natal Brazil Institute of Geosciences and Exact Sciences Sao Paulo State University (UNESP) Rio Claro Brazil

ISBN: (数字)9798350356632

ISBN: (纸本)9798350356649

In this paper, we introduce a new approach to the study of Parkinson’s Disease (PD) through the implementation of a neurorobotics model via the integration of computational neuroscience with the latest robotic technology. Using the iCub as our robot platform, we adapted a computational model of the Basal Ganglia-Thalamo-Cortical (BG-T-C) circuit to investigate the efficiency of Deep Brain Stimulation (DBS) in mitigating PD’s motor *** to our methodology is the use of closed-loop DBS, a technique that adjusts stimulation parameters in real time based on specific kinematic and neuronal biomarkers of PD severity, such as fluctuations in beta band activity and tremor movements. This dynamic approach allows for a more personalized and efficient treatment regimen compared to traditional, static open-loop systems, which cannot adapt to the patient’s changing *** findings of our study corroborate the feasibility of using a neurorobotics model to simulate the motor symptoms of PD and provide evidence that closed-loop DBS can effectively modulate these symptoms. This was achieved by reducing the power spectral density at the beta-band frequency range (8-30 Hz) of the neural activity to below threshold levels and revealing a complex relationship between the severity of the disease and the effectiveness of the treatment.

关键词： Analytical models Adaptation models Computational modeling Biological system modeling Biomarkers Brain modeling Real-time systems Computational efficiency Robots Diseases

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The interplay between Kynurenine and Nociceptin/Orphanin FQ pathways can be related to depressive-like phenotype

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European journal of pharmacology 2025年 1001卷 177766页

作者： Alice Barros Câmara Igor Augusto Brandão School of Public Health University of São Paulo 715 Dr. Arnaldo Avenue São Paulo SP 01246-904 Brazil. Electronic address: alicecamara@usp.br. Bioinformatics Multidisciplinary Environment Federal University of Rio Grande do Norte Brazil.

AIMS:This study aims to evaluate whether systemic administration of a nociceptin/orphanin FQ peptide (NOP) receptor agonist and exposure to the social defeat protocol are associated with upregulation of Kynurenine pathway. Additionally, we aim to investigate the potential association between NOP receptor-induced Kynurenine upregulation and markers of oxidative stress, neuroinflammation, and depressive-like behaviors. METHODS:Behavioral tests were applied to evaluate depressive behavior in male Swiss mice submitted to social defeat protocol and treated with Ro 65-6570 (1.5 or 2 mg/kg; IP). Biochemical analyses were performed in the animals' brains and blood using spectrophotometry and ELISA. The software SPSS v.29 and R programming language were used to analyze the data. RESULTS:High concentrations of Kynurenine were detected in the hippocampus, prefrontal cortex, and serum of animals treated with Ro 65-6570 and submitted to the social defeat protocol. In the prefrontal cortex, high doses of the agonist combined with the defeat protocol were associated with the Kynurenine upregulation. In the hippocampus, administration of the NOP agonist alone was associated with Kynurenine upregulation. Kynurenine levels were negatively correlated with the gain of weight, distance traveled, and interaction time of animals, as well as with IL-10 concentrations in the hippocampus, while Kynurenine levels were positively correlated with the immobility time of animals, IL-6 and carbonylated protein levels, as well as malondialdehyde in serum. CONCLUSION:Neuroinflammatory and oxidative effects related to the NOP receptor activation may contribute to the Kynurenine upregulation and this indirect interaction between Nociceptin and Kynurenine pathways can be related to sub-chronic depressive phenotype.

关键词： Animal model Depression Hippocampus Kynurenine Neuroinflammation Oxidative stress

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Gain of transcription factor binding sites is associated to changes in the expression signature of human brain and testis and is correlated to genes with higher expression breadth

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Science China(Life Sciences) 2019年第4期62卷 526-534页

作者： Vandeclécio Lira da Silva André Mauricio Ribeiro dos Santos Wilfredo Blanco Sandro José de Souza Bioinformatics Multidisciplinary Environment (BioME) Universidade Federal do Rio Grande do Norte (UFRN) Programa de Pós-Gradua??o em Genética e Biologia Molecular (PPGBM) Universidade Federal do Pará (UFPA) Department of Computer Science Universidade Estadual do Rio Grande do Norte (UERN) Brain Institute Universidade Federal do Rio Grande do Norte (UFRN)

The gain of transcription factor binding sites(TFBS) is believed to represent one of the major causes of biological *** we used strategies based on comparative genomics to identify 21,822 TFBS specific to the human lineage(TFBS-HS),when compared to chimpanzee and gorilla genomes. More than 40%(9,206) of these TFBS-HS are in the vicinity of 1,283 genes.A comparison of the expression pattern of these genes and the corresponding orthologs in chimpanzee and gorilla identified genes differentially expressed in human tissues. These genes show a more divergent expression pattern in the human testis and brain, suggesting a role for positive selection in the fixation of TFBS gains. Genes associated with TFBS-HS were enriched in gene ontology categories related to transcriptional regulation, signaling, differentiation/development and nervous ***, genes associated with TFBS-HS present a higher expression breadth when compared to genes in general. This biased distribution is due to a preferential gain of TFBS in genes with higher expression breadth rather than a shift in the expression pattern after the gain of TFBS.

关键词： TFBS transcript factor human evolution expression breadth

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Medulloblastoma’s master regulators and their association with patients’ risk

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Scientific Reports 2025年第1期15卷 1-11页

作者： Michaelsen, Gustavo Lovatto de Sousa Monteiro, Tayrone Imparato, Danilo Oliveira da Costa, João Vitor Almeida Silva, Daniel Rocha de Souza, Iara Dantas da Ribeiro-Dantas, Marcel Câmara Cabral-Marques, Otávio Sinigaglia, Marialva Dalmolin, Rodrigo Juliani Siqueira Bioinformatics Multidisciplinary Environment-BioME Digital Metropole Institute Federal University of Rio Grande do Norte RN Natal 59076-550 Brazil Children’s Cancer Institute RS Porto Alegre 90620-110 Brazil National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology – INCT BioOncoPed RS Porto Alegre 90035-003 Brazil Graduate Program of Biotechnology Universidade Potiguar RN Natal 59056-000 Brazil Department of Immunology Institute of Biomedical Sciences University of São Paulo Brazil São Paulo 05508-000 Brazil DO’R Institute for Research São Paulo 01401-002 Brazil Department of Biochemistry Federal University of Rio Grande do Norte RN Natal 59064-741 Brazil UFRN Central University Campus R. do Horto Lagoa Nova RN Natal 59078-900 Brazil

Medulloblastoma (MB) is the most common malignant pediatric brain tumor, accounting for approximately 20% of all childhood brain tumors. Despite recent advances, current treatments like surgery, radiation, and chemotherapy still lead to severe side effects and high morbidity. Limited knowledge exists regarding the regulatory mechanisms behind the MB transcriptional alterations in high-aggressive subgroups like Group 3 and Group 4, hindering the development of targeted therapies. Identifying key transcriptional regulators, known as master regulators (MRs), can elucidate the dysregulated pathways underlying MB progression and uncover potential treatment targets. In this study, we utilize primary MB gene expression samples to infer its regulatory network. Subsequently, we applied the Master Regulator Analysis identifying the transcription factors BHLHE41, RFX4, and NPAS3 as its main transcriptional regulators, showing tumor suppressor features. We also identified eight risk MRs highly associated with patient outcome: four regulators (MYC, REL, ZSCAN5 A, and ZFAT) with activities associated with poor prognosis, and four (PAX6, ARNT2, ZNF157, and HIVEP3) acting antagonistically, being associated with good outcome. Our results offer key insights into the molecular mechanisms driving these tumors and identify novel potential therapeutic targets, addressing the urgent need for more effective and less toxic treatments. © The Author(s) 2025.

关键词： Medulloblastoma Regulome Systems biology Transcription factor

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Cyclic alternation of quiet and active sleep states in the octopus

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iScience 2021年第4期24卷 102223页

作者： Medeiros, Sylvia Lima de Souza Paiva, Mizziara Marlen Matias de Lopes, Paulo Henrique Blanco, Wilfredo Lima, Françoise Dantas de Oliveira, Jaime Bruno Cirne de Medeiros, Inácio Gomes Sequerra, Eduardo Bouth de Souza, Sandro Leite, Tatiana Silva Ribeiro, Sidarta Brain Institute Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Graduate Program in Psychobiology Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Graduate Program in Neuroscience Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Computer Science Department State University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Bioinformatics Multidisciplinary Environment Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Department of Ecology and Zoology Federal University of Santa Catarina Florianópolis Santa Catarina Brazil Graduate Program in Bioinformatics Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil

Previous observations suggest the existence of ‘Active sleep’ in cephalopods. To investigate in detail the behavioral structure of cephalopod sleep, we video-recorded four adult specimens of Octopus insularis and quantified their distinct states and transitions. Changes in skin color and texture and movements of eyes and mantle were assessed using automated image processing tools, and arousal threshold was measured using sensory stimulation. Two distinct states unresponsive to stimulation occurred in tandem. The first was a ‘Quiet sleep’ state with uniformly pale skin, closed pupils, and long episode durations (median 415.2 s). The second was an ‘Active sleep’ state with dynamic skin patterns of color and texture, rapid eye movements, and short episode durations (median 40.8 s). ‘Active sleep’ was periodic (60% of recurrences between 26 and 39 min) and occurred mostly after ‘Quiet sleep’ (82% of transitions). These results suggest that cephalopods have an ultradian sleep cycle analogous to that of amniotes. © 2021 The Authors

关键词： Biological Sciences Ethology Zoology

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Differential transcript usage unravels transcriptional alterations in Alzheimer's disease human brains

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Alzheimer's & Dementia 2020年第S2期16卷

作者： Diego Marques-Coelho Lukas Iohan Jean-Charles Lambert Marcos Romualdo Costa Brain Institute Natal Brazil Bioinformatics Multidisciplinary Environment (BioME) Natal Brazil University of Lille Inserm CHU Lille Institut Pasteur de Lille U1167 Lille France Institut Pasteur de Lille Lille France

Background Alzheimer’s disease (AD) is the leading cause of dementia in aging individuals. Several studies have shown that 60-80% of late-onset AD attributable risk has an important genetic component. However, a comprehensive overview of gene expression alterations in the diseased brain remains elusive. Method In this work, we compared the differential expression of genes in different regions (temporal and frontal lobes) of the brain of healthy and AD adult subjects from three large datasets: MAYO Clinic; Mount Sinai Brain Bank (MSBB) and ROSMAP. We also used isoform switch analysis to identify genes with altered transcript usage. Finally, we assigned altered genes to specific cell types of the adult brain and evaluate the expression of AD risk genes previously identified in pan-genomic association studies. Result We show that gene expression is dramatically altered in the temporal lobe (TL), but not in the frontal lobe (FL), suggesting regional specificities in transcriptional alterations. Moreover, we show that a large set of genes without alteration in the classical differential expression (DEG) analysis do have alterations in the transcript usage ratio in AD. Ontology analysis for genes with differential transcript usage (gDTUs) show enrichment for key biological processes associated with AD pathology, which are not observed for DEGs only. Using single-cell RNAseq data, we are able to assign DEGs and gDTUs to individual cell types of the adult brain and show that genes associated with synaptic transmission are mostly affected in GABAergic neurons. Lastly, we show that 52 out of 116 putative AD risk factors expressed in neural cells, microglia or endothelial cells of the adult human brain are differentially expressed in the TL, whereas only 13 are altered in the FL of AD patients. Among those altered genes, we detect an increased expression of APP isoforms containing the Kunitz protease inhibitor (KPI) domain, which is associated with plaque deposition. Conclusio

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