A5007118532- Cancer Genomics and Diagnostics
- Hedgehog Signaling Pathway Studies
- RNA modifications and cancer
- Viral Infectious Diseases and Gene Expression in Insects
- Gene expression and cancer classification
- CAR-T cell therapy research
- Cancer Cells and Metastasis
- Epigenetics and DNA Methylation
- Metabolomics and Mass Spectrometry Studies
- Cell Image Analysis Techniques
- Advanced Proteomics Techniques and Applications
- Ferroptosis and cancer prognosis
- Cancer-related Molecular Pathways
- Nanotechnology research and applications
- Collagen: Extraction and Characterization
- Cell Adhesion Molecules Research
- vaccines and immunoinformatics approaches
- Contact Dermatitis and Allergies
- TGF-β signaling in diseases
- Concrete and Cement Materials Research
- Recycled Aggregate Concrete Performance
- T-cell and B-cell Immunology
- Glioma Diagnosis and Treatment
- Urinary and Genital Oncology Studies
- Microtubule and mitosis dynamics
University of Puerto Rico-Mayaguez
2017-2024
The University of Texas MD Anderson Cancer Center
2013-2015
Memorial Sloan Kettering Cancer Center
2014
Broad Institute
2014
Pitié-Salpêtrière Hospital
2013
Sorbonne Université
2013
Sri Sathya Sai Institute of Higher Medical Sciences
2013
Huashan Hospital
2013
Fudan University
2013
Bahçeşehir University
2013
Infiltrating stromal and immune cells form the major fraction of normal in tumour tissue not only perturb signal molecular studies but also have an important role cancer biology. Here we describe 'Estimation STromal Immune MAlignant Tumours using Expression data' (ESTIMATE)—a method that uses gene expression signatures to infer samples. ESTIMATE scores correlate with DNA copy number-based purity across samples from 11 different types, profiled on Agilent, Affymetrix platforms or based RNA...
Abstract Summary: Technological advances in high-throughput sequencing necessitate improved computational tools for processing and analyzing large-scale datasets a systematic automated manner. For that purpose, we have developed PRADA (Pipeline RNA-Sequencing Data Analysis), flexible, modular highly scalable software platform provides many different types of information available by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality metrics,...
With the advent of high-throughput sequencing technologies, much progress has been made in identification somatic structural rearrangements cancer genomes. However, characterization complex alterations and their associated mechanisms remains inadequate. Here, we report a comprehensive analysis whole-genome DNA copy number data sets from The Cancer Genome Atlas to relate chromosomal imbalances dosage describe landscape intragenic breakpoints glioblastoma multiforme (GBM). Gene length,...
Gene expression profiling technologies can generally produce mRNA abundance data for all genes in a genome. A dearth of proteomic persists because identification range and sensitivity measurements lag behind those transcriptomic measurements. Using partial data, it is likely that integrative analysis may introduce significant bias. Developing methodologies to accurately estimate missing will allow better integration datasets provide deeper insight into metabolic mechanisms underlying complex...
Large-scale, reproducible manufacturing of therapeutic cells with consistently high quality is vital for translation to clinically effective and widely accessible cell therapies. However, the biological logistical complexity a living product, including challenges associated their inherent variability uncertainties process parameters, currently make it difficult achieve predictable cell-product quality. Using degradable microscaffold-based T-cell process, we developed an artificial...
The fibril orientation of type I collagen has been shown to contribute tumor invasion and metabolic changes. Yet, there is limited information about its impact on cells' behavior in a restrictive growth environment. Restrictive environments are generated by the inhibition proliferation stimulus during therapy or as an inflammatory response suppress expansion. In this study, matrix fibrous architecture cell estrogen receptor (ER) were examined using estrogen-dependent breast cells (MCF-7...
Despite significant improvements in recent years, proteomic datasets currently available still suffer from large number of missing values. Integrative analyses based upon incomplete and transcriptomic could seriously bias the biological interpretation. In this study, we applied a non-linear data-driven stochastic gradient boosted trees (GBT) model to impute values using temporal dataset Shewanella oneidensis. dataset, genes' expression was measured after cells were exposed 1 mM potassium...
Abstract Sarcomatoid transformation, wherein an epithelioid carcinomatous tumour component coexists with a sarcomatoid histology, is predictor of poor prognosis in clear cell renal carcinoma. Our understanding change has been hindered by the lack molecular examination. Thus, we sought to characterize molecularly biphasic and components carcinoma compare them non‐sarcomatoid We examined transcriptome advanced stage ( n =43) =37) from independent discovery validation cohorts using cDNA...
The paracrine interaction between tumor cells and adjacent stroma has been associated with the oncogenic activity of Hedgehog (Hh) pathway in triple-negative breast tumors. present study developed a model Hh signaling examined impact mesenchymal cell sources culture modalities oncogenicity cells. Studies consisted monocultures co-cultures cancer-associated normal fibroblasts, that undergo epithelial–mesenchymal transition (EMT), or adipose-derived stem (ADMSCs). ligand inhibitors, GANT61...
Poly(methyl methacrylate) (PMMA) is considered an attractive substrate material for fabricating wearable skin sensors such as fitness bands and microfluidic devices. Despite its widespread use, inflammatory allergic responses have been attributed to the use of this material. Therefore, main objective study was obtain a comprehensive understanding potential biological effects triggered by PMMA at non-cytotoxic concentrations using in vitro models NIH3T3 fibroblasts reconstructed human...
In this work, we show that a 15-gene Hh-mesenchyme signature identifies potential bimodal prognosis among basal and luminal A subgroups.
Phenotypic characterization of individual cells provides crucial insights into intercellular heterogeneity and enables access to information that is unavailable from ensemble averaged, bulk cell analyses. Single-cell studies have attracted significant interest in recent years spurred the development a variety commercially available research-grade technologies. To quantify cell-to-cell variability populations, we developed an experimental platform for real-time measurements oxygen consumption...
Abstract A significant subset (30-40%) of triple-negative breast cancer (TNBC) cases exhibit hyperactivation the sonic hedgehog (SHH) pathway, correlating with poor clinical outcomes. However, therapeutic efficacy SHH inhibitors in TNBC has yielded inconsistent results, showcasing biphasic tumor responses going from complete remission some patients to faster disease progression others. Such response discrepancies underscore need for more relevant culture models elucidate how stromal cells...
Abstract Preclinical models of Sonic Hedgehog (SHH)-driven tumors support the therapeutic benefit pharmacological inhibitors, yet clinical outcomes are conflicted due to biphasic tumor responses that include complete remission or faster disease progression. In such studies, activity SHH pathway in tumor-adjacent stroma supported restrained Our prior studies show altered ligand levels can lead growth during inhibition suggesting a role for strength triple-negative breast cancer (TNBC) model....
Abstract Large-scale, reproducible manufacturing of therapeutic cells with consistently high quality is vital for translation to clinically effective and widely accessible cell therapies. However, the biological logistical complexity a living product, including challenges associated their inherent variability uncertainties process parameters, currently make it difficult achieve predictable cell-product quality. Using degradable microscaffold-based T as an example, we developed Artificial...
Abstract Gene fusions are an important class of cancer-contributing somatic alteration, and have significance as a tumor-initiating event molecular therapeutic target for specific tumors. We analyzed RNA sequencing, DNA copy number gene mutation data from 4,366 primary tumor samples to comprehensively detect fusion events in 13 types. To reduce the false-positive predictions, we developed strict quality criteria on basis homology, transcript allele fraction (TAF), partner variety. In...
To assist GK-12 teachers in their effort to improve science and math instruction, the STARS (Students, Teachers Resources Sciences) program from University of South Florida has developed a training plan for 3-5 band. is National Science Foundation project, which aims promote systemic change primary grade levels by enriching courses encouraging long-term professional development teachers. This paper discusses tools employed facilitate integration advanced concepts, such as materials...
Gene interactions play a fundamental role in the proneness to cancer. However, detect- ing and ranking these is complex problem due high dimensionality of genomic data. Hence, we aim find patterns composed multiple features molecularly characterize breast cancer subtypes from integration different omics datasets using data mining approach. To retrieve biological understanding computational results, developed IBIF-RF (Importance Between Interactive Features Random Forest), new metric capable...