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Dr Willian Da Silveira's Outputs (45)

Prominence of IL6, IGF, TLR, and Bioenergetics Pathway Perturbation in Lung Tissues of Scleroderma Patients With Pulmonary Fibrosis (2020)
Journal Article
Renaud, L., Abraham da Silveira, W., Takamura, N., Hardiman, G., & Feghali-Bostwick, C. (2020). Prominence of IL6, IGF, TLR, and Bioenergetics Pathway Perturbation in Lung Tissues of Scleroderma Patients With Pulmonary Fibrosis. Frontiers in Immunology, 11, Article 383. https://doi.org/10.3389/fimmu.2020.00383

Scleroderma-associated pulmonary fibrosis (SSc-PF) and idiopathic pulmonary fibrosis (IPF) are two of many chronic fibroproliferative diseases that are responsible for nearly 45% of all deaths in developed countries. While sharing several pathobiolog... Read More about Prominence of IL6, IGF, TLR, and Bioenergetics Pathway Perturbation in Lung Tissues of Scleroderma Patients With Pulmonary Fibrosis.

Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver (2019)
Journal Article

Spaceflight has several detrimental effects on the physiology of astronauts, many of which are recapitulated in rodent models. Mouse studies performed on the Space Shuttle showed disruption of lipid metabolism in liver. However, given that these anim... Read More about Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver.

The effects of rosiglitazone on the neonatal rat cardiomyocyte transcriptome: a temporal analysis (2019)
Journal Article
Abraham da Silveira, W., Vazquez-Hidalgo, E., Bartolotta, E., Renaud, L., Paolini, P., & Hardiman, G. (2019). The effects of rosiglitazone on the neonatal rat cardiomyocyte transcriptome: a temporal analysis. Pharmacogenomics, 20(16), 1125-1141. https://doi.org/10.2217/pgs-2019-0077

Aim: The objective was to determine via high-throughput RNA sequencing the temporal effects of rosiglitazone (Avandia®) on the neonatal rat ventricular myocyte transcriptome.

Materials & methods: Neonatal rat ventricular myocytes (NRVMs) were exp... Read More about The effects of rosiglitazone on the neonatal rat cardiomyocyte transcriptome: a temporal analysis.

Spaceflight influences gene expression, photoreceptor integrity, and oxidative stress-related damage in the murine retina (2019)
Journal Article

Extended spaceflight has been shown to adversely affect astronaut visual acuity. The purpose of this study was to determine whether spaceflight alters gene expression profiles and induces oxidative damage in the retina. Ten week old adult C57BL/6 mal... Read More about Spaceflight influences gene expression, photoreceptor integrity, and oxidative stress-related damage in the murine retina.

Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae (2019)
Journal Article

Spaceflight poses many challenges for humans. Ground-based analogs typically focus on single parameters of spaceflight and their associated acute effects. This study assesses the long-term transcriptional effects following single and combination spac... Read More about Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae.

Gene expression and immunohistochemical analyses identify SOX2 as major risk factor for overall survival and relapse in Ewing sarcoma patients (2019)
Journal Article

Background: Up to 30-40% of Ewing sarcoma (EwS) patients with non-metastatic disease develop local or metastatic relapse within a time span of 2-10 years. This is in part caused by the absence of prognostic biomarkers that can identify high-risk pati... Read More about Gene expression and immunohistochemical analyses identify SOX2 as major risk factor for overall survival and relapse in Ewing sarcoma patients.

GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature (2019)
Journal Article

In systems biology, inference of functional associations among genes is compelling because the construction of functional association networks facilitates biomarker discovery. Specifically, such gene associations in human can help identify putative b... Read More about GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature.

A Human Skin Model Recapitulates Systemic Sclerosis Dermal Fibrosis and Identifies COL22A1 as a TGFβ Early Response Gene that Mediates Fibroblast to Myofibroblast Transition (2019)
Journal Article
Watanabe, T., Baker Frost, D., Mlakar, L., Heywood, J., da Silveira, W. A., Hardiman, G., & Feghali-Bostwick, C. (2019). A Human Skin Model Recapitulates Systemic Sclerosis Dermal Fibrosis and Identifies COL22A1 as a TGFβ Early Response Gene that Mediates Fibroblast to Myofibroblast Transition. Genes, 10(2), Article 75. https://doi.org/10.3390/genes10020075

Systemic sclerosis (SSc) is a complex multi-system autoimmune disease characterized by immune dysregulation, vasculopathy, and organ fibrosis. Skin fibrosis causes high morbidity and impaired quality of life in affected individuals. Animal models do... Read More about A Human Skin Model Recapitulates Systemic Sclerosis Dermal Fibrosis and Identifies COL22A1 as a TGFβ Early Response Gene that Mediates Fibroblast to Myofibroblast Transition.

Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: From Raw Data to Systems Level Analyses (2019)
Journal Article
Abraham da Silveira, W., Hazard, E. S., Chung, D., & Hardiman, G. (2019). Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: From Raw Data to Systems Level Analyses. Methods in Molecular Biology, 185-204. https://doi.org/10.1007/978-1-4939-9004-7_13

RNAseq is a powerful technique enabling global profiles of transcriptomes in healthy and diseased states. In this chapter we review pipelines to analyze the data generated by sequencing RNA, from raw data to a system level analysis. We first give an... Read More about Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: From Raw Data to Systems Level Analyses.

Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: Overview of Library Preparation Methods (2019)
Book Chapter

RNA sequencing (RNA-seq) is revolutionizing the study of cancer by providing a highly sensitive and robust tool to interrogate the transcriptome. It leverages the power of deep sequencing technology and provides global and multidimensional views of t... Read More about Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: Overview of Library Preparation Methods.

Systems analysis of the liver transcriptome in adult male zebrafish exposed to the non-ionic surfactant nonylphenol (2018)
Journal Article
Huff, M., Abraham da Silveira, W., Starr Hazard, E., Courtney, S. M., Renaud, L., & Hardiman, G. (2019). Systems analysis of the liver transcriptome in adult male zebrafish exposed to the non-ionic surfactant nonylphenol. General and Comparative Endocrinology, 271, 1-14. https://doi.org/10.1016/j.ygcen.2018.10.016

Nonylphenol (NP) arises from the environmental degradation of nonylphenol ethoxylates. It is a ubiquitous environmental contaminant and has been detected at levels up to 167 nM in rivers in the United States. NP is an endocrine disruptor (ED) that ca... Read More about Systems analysis of the liver transcriptome in adult male zebrafish exposed to the non-ionic surfactant nonylphenol.

Identification of a Subtype of Poorly Differentiated Invasive Ductal Carcinoma of the Breast Based on Vimentin and E-cadherin Expression (2018)
Journal Article

Objective: The use of molecular markers can identify a subgroup of tumors with distinct recurrence patterns. The present study aimed to characterize the immunohistochemical expression of vimentin (VIM), of E-cadherin (CDH1), and of cytokeratin 5 (CK5... Read More about Identification of a Subtype of Poorly Differentiated Invasive Ductal Carcinoma of the Breast Based on Vimentin and E-cadherin Expression.

miRmapper: A Tool for Interpretation of miRNA–mRNA Interaction Networks (2018)
Journal Article
Da Silveira, W. A., Renaud, L., Simpson, J., Glen, W. B., Hazard, E. S., Chung, D., & Hardiman, G. (2018). miRmapper: A Tool for Interpretation of miRNA–mRNA Interaction Networks. Genes, 9(9), Article 458. https://doi.org/10.3390/genes9090458

It is estimated that 30% of all genes in the mammalian cells are regulated by microRNA (miRNAs). The most relevant miRNAs in a cellular context are not necessarily those with the greatest change in expression levels between healthy and diseased tissu... Read More about miRmapper: A Tool for Interpretation of miRNA–mRNA Interaction Networks.

Interplay Between MicroRNAs and Targeted Genes in Cellular Homeostasis of Adult Zebrafish (Danio rerio) (2018)
Journal Article
Renaud, L., da Silveira, W. A., Glen, W. B., Hazard, E. S., & Hardiman, G. (2018). Interplay Between MicroRNAs and Targeted Genes in Cellular Homeostasis of Adult Zebrafish (Danio rerio). Current Genomics, 19(7), 615-629. https://doi.org/10.2174/1389202919666180503124522

Background: Cellular homeostasis is regulated by the intricate interplay between a plethora of signaling pathways and "energetic sensors" in organs. In order to maintain energy balance, induction or repression of metabolic pathways must be regulated... Read More about Interplay Between MicroRNAs and Targeted Genes in Cellular Homeostasis of Adult Zebrafish (Danio rerio).

Systems Analysis of the Liver Transcriptome in Adult Male Zebrafish Exposed to the Plasticizer (2-Ethylhexyl) Phthalate (DEHP) (2018)
Journal Article
Huff, M., Carnevali, O., da Silveira, W. A., Renaud, L., & Hardiman, G. (2018). Systems Analysis of the Liver Transcriptome in Adult Male Zebrafish Exposed to the Plasticizer (2-Ethylhexyl) Phthalate (DEHP). Scientific reports, 8, Article 2118. https://doi.org/10.1038/s41598-018-20266-8

The organic compound diethylhexyl phthalate (DEHP) represents a high production volume chemical found in cosmetics, personal care products, laundry detergents, and household items. DEHP, along with other phthalates causes endocrine disruption in male... Read More about Systems Analysis of the Liver Transcriptome in Adult Male Zebrafish Exposed to the Plasticizer (2-Ethylhexyl) Phthalate (DEHP).

Semi-supervised identification of cancer subgroups using survival outcomes and overlapping grouping information (2018)
Journal Article

Identification of cancer patient subgroups using high throughput genomic data is of critical importance to clinicians and scientists because it can offer opportunities for more personalized treatment and overlapping treatments of cancers. In spite of... Read More about Semi-supervised identification of cancer subgroups using survival outcomes and overlapping grouping information.

Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype (2017)
Journal Article

Breast cancer is the most common cancer in women worldwide and metastatic dissemination is the principal factor related to death by this disease. Breast cancer stem cells (bCSC) are thought to be responsible for metastasis and chemoresistance. In thi... Read More about Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype.