Eddie Imada

Eddie Imada
Johns Hopkins Medicine | JHUSOM · Department of Oncology

MSc

About

33
Publications
4,761
Reads
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294
Citations
Additional affiliations
January 2013 - March 2015
Universidade Estadual de Londrina
Position
  • Master's Student

Publications

Publications (33)
Article
Prostate cancer (PCa) is associated with several genetic alterations which play an important role in the disease heterogeneity and clinical outcome. These alterations involve gene fusion between TMPRSS2 and members of the ETS family of transcription factors like ERG, ETV1, and ETV4 together with mutations or deletions in tumor suppressors like TP53...
Article
Mechanisms that control gene expression at the RNA level are often referred to as post-transcriptional regulation (PTR) mechanisms. Splicing and polyadenylation (PA) are well-known examples of PTR that can regulate not only gene expression but also their function. Alternative Polyadenylation (APA) has already been shown to be essential to many biol...
Preprint
Alternative polyadenylation (APA) is an important post-transcriptional mechanism that has major implications in biological processes and diseases. Although specialized sequencing methods for polyadenylation exist, their presence in public repositories is extremely limited when compared to traditional RNA-sequencing. To overcome this, we developed R...
Preprint
Full-text available
The increasing availability of high-quality genomic, annotation and phenotypic data for different species contrasts with the lack of general software for comparative genomics that integrates these data types in a statistically sound framework in order to produce biologically meaningful knowledge. In this work, we present CALANGO (Comparative AnaLys...
Article
Full-text available
Background PTEN is the most frequently lost tumor suppressor in primary prostate cancer (PCa) and its loss is associated with aggressive disease. However, the transcriptional changes associated with PTEN loss in PCa have not been described in detail. In this study, we highlight the transcriptional changes associated with PTEN loss in PCa. Methods...
Conference Paper
p>Although most commonly benign, neurofibromas (NFs) can have devastating functional and cosmetic effects in addition to the possibility of malignant transformation. Orbitofacial NFs in particular may cause progressive, disfiguring tumors of the lid, brow, temple, face and orbit, and anecdotal evidence suggest that they may have increased local agg...
Article
Full-text available
Although most commonly benign, neurofibromas (NFs) can have devastating functional and cosmetic effects in addition to the possibility of malignant transformation. Orbitofacial NFs, in particular, may cause progressive, disfiguring tumors of the lid, brow, temple, face, and orbit, and clinical evidence suggests that they may have increased local ag...
Preprint
Full-text available
Machine learning (ML) algorithms are used to build predictive models or classifiers for specific disease outcomes using transcriptomic data. However, some of these models show deteriorating performance when tested on unseen data which undermines their clinical utility. In this study, we show the importance of directly embedding prior biological kno...
Article
Full-text available
Since the beginning of the coronavirus disease-2019 (COVID-19) pandemic in 2020, there has been a tremendous accumulation of data capturing different statistics including the number of tests, confirmed cases and deaths. This data wealth offers a great opportunity for researchers to model the effect of certain variables on COVID-19 morbidity and mor...
Article
Full-text available
The COVID-19 mortality rate is higher in the elderly and in those with pre-existing chronic medical conditions. The elderly also suffer from increased morbidity and mortality from seasonal influenza infections; thus, an annual influenza vaccination is recommended for them. In this study, we explore a possible county-level association between influe...
Article
Full-text available
Black men die more often of prostate cancer yet, interestingly, may derive greater survival benefits from immune-based treatment with sipuleucel-T. Since no signatures of immune-responsiveness exist for prostate cancer, we explored race-based immune-profiles to identify vulnerabilities. Here we show in multiple independent cohorts comprised of over...
Preprint
Full-text available
PTEN is the most frequently lost tumor suppressor in primary prostate cancer (PCa) and its loss is associated with aggressive disease. However, the transcriptional changes associated with PTEN loss in PCa have not been described in detail. Here, we applied a meta-analysis approach, leveraging two large PCa cohorts with experimentally validated PTEN...
Article
Full-text available
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses u...
Preprint
Full-text available
COVID-19 mortality rate is higher in the elderly and in those with preexisting chronic medical conditions. The elderly also suffer from increased morbidity and mortality from seasonal influenza infection, and thus annual influenza vaccination is recommended for them. In this study, we explore a possible area-level association between influenza vacc...
Article
Aims Neurofibromatosis 1 (NF1) is an autosomal dominant cancer predisposition syndrome caused by loss of function alterations involving the NF1 locus on chromosome 17. The most common brain tumours encountered in affected patients are low‐grade gliomas (pilocytic astrocytomas), although high‐grade gliomas are also observed at increased frequency. W...
Article
Full-text available
Although most commonly benign, neurofibromas (NFs) can have devastating functional and cosmetic effects in addition to the possibility of malignant transformation. In orbitofacial neurofibromatosis type 1, NFs may cause progressive, disfiguring tumors of the lid, brow, temple, face and orbit. The purpose of this study was to identify biological dif...
Article
Full-text available
Long noncoding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression across cells and tissues is key to understanding their role in determining phenotypes including human diseases. We present here FC-R2, a comprehensive expression atlas across a broadly defined human transcriptome, in...
Article
Background and objective: Echinacea angustifolia DC. and Zingiber officinale Roscoe are two natural products with documented immunomodulatory activity, both able to modulate the expression of important immune-related genes. Thus, their use in combination seems to be particularly promising. In this context, we have considered the oral supplementati...
Preprint
Long non-coding RNAs (lncRNAs) constitute the majority of transcripts in mammalian genomes and yet, their functions remain largely unknown. We systematically suppressed 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). The resu...
Conference Paper
The three-prime untranslated region (3'-UTR) of a mRNA influences its biological behavior, from stability, post-transcriptional control through miRNAs, and availability for translation. Alternative polyadenylation (APA) can modulate 3' end site selection, and approximately 50% of coding genes are subject to it. Global transcript shortening has been...
Preprint
Full-text available
Long non-coding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression across cells and tissues is key to understanding their role in determining phenotypes including disease. We present hereFC-R2, a comprehensive expression atlas across a broadly-defined human transcriptome, inclusive...
Article
Full-text available
Inactivating CDK12 alterations have been reported in ovarian and prostate cancers and may have therapeutic implications; however, the prevalence of these mutations across other cancer types is unknown. We searched the cBioPortal and GENIE Project (public release v4.1) databases for cancer types with > 200 sequenced cases, that included patients wit...
Article
In recent years, in depth exploration of genomes structure and function has revealed a central role for non-coding RNAs (ncRNAs) in orchestrating key biological and cellular processes through the fine tuning of gene expression regulation. Most importantly a role for ncRNAs has also started to emerge in human disease pathogenesis. This further speak...
Article
Full-text available
Like many rhizobia, Rhizobium tropici produces indole-3-acetic acid (IAA), an important signal molecule required for root hair infection in rhizobia-legume symbioses. However, the IAA biosynthesis pathway and its regulation by R. tropici are still poorly understood. In this study, IAA synthesis and the effects of mineral N in IAA production by R. t...
Article
Full-text available
Gluconacetobacter diazotrophicus is a beneficial nitrogen-fixing endophyte found in association with sugarcane plants and other important crops. Beneficial effects of G. diazotrophicus on sugarcane growth and productivity have been attributed to biological nitrogen fixation process and production of phytohormones especially indole-3-acetic acid (IA...

Questions

Question (1)
Question
I'm trying to predict some sRNA's (small rna's) which are non-coding rna's in bacteria. I'm following an approach that i have seen in a paper, that uses MAUVE and RNAz to predict them. But the paper is not clear on protocols and i have no idea how to do this. Can someone with expertise on ncRNA's help me?
I'm trying the following: I have aligned 6 Genomes of closely related bacteria with MAUVE, and converted the output to MAF as it's the input for RNAz. Tried to run RNAz directly on this alignment but it resulted in an strange output (did not make sense to me).
My question is, what do I have to do after aligning with MAUVE? I have read things like make a set of intergenic regions in BED format e and use it and the MAF alignment to create alignments of intergenic regions, but i have no idea how to this. Do someone know?
ps: any aproach to predict sRNA's is more than welcome, i'm only citing MAUVE because of the papers that i have read.
Thanks in advance.