A5005968346- Lung Cancer Treatments and Mutations
- Synthesis and biological activity
- Quinazolinone synthesis and applications
- Cytokine Signaling Pathways and Interactions
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Colorectal Cancer Treatments and Studies
- PI3K/AKT/mTOR signaling in cancer
- Advanced Proteomics Techniques and Applications
- Semantic Web and Ontologies
- Computational Drug Discovery Methods
- HIV, Drug Use, Sexual Risk
- Opioid Use Disorder Treatment
- Genomics and Rare Diseases
- Substance Abuse Treatment and Outcomes
- Genomics and Phylogenetic Studies
- Microbial Natural Products and Biosynthesis
- Peptidase Inhibition and Analysis
- Cancer Cells and Metastasis
- Protein Structure and Dynamics
- Liver Disease Diagnosis and Treatment
- Biotin and Related Studies
- Cardiovascular Disease and Adiposity
- Extracellular vesicles in disease
- Tissue Engineering and Regenerative Medicine
University of Delaware
2013-2024
Nemours Children's Health System
2023
Christiana Care Health System
2023
Biotechnology Institute
2020
Georgetown University Medical Center
2013-2019
Georgetown University
2013-2019
Duke University
2013
Jackson Laboratory
2013
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach—combining text mining, data and ontological representation to capture rich information, including enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) conservation...
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific taxon-neutral protein-related entities in three major areas: proteins related by evolution; produced from a given gene; protein-containing complexes. PRO thus serves as tool for referencing protein at any level of specificity. To enhance this ability, to facilitate the comparison such described different resources, we developed standardized representation proteoforms using UniProtKB...
The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms interrelations. represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence modification metaclasses, there is a separate metaclass for complexes. All metaclasses also have organism-specific derivatives. complements established databases such as UniProtKB, interoperates with other biomedical...
Abstract Lung cancer is the leading cause of mortality worldwide. The treatment patients with lung harboring mutant EGFR orally administered tyrosine kinase inhibitors (TKI) has been a paradigm shift. Osimertinib and rociletinib are third-generation irreversible TKIs targeting T790M mutation. current standard care for mutations due to increased efficacy, lower side effects, enhanced brain penetrance. Unfortunately, all develop resistance. Genomic approaches have primarily used interrogate...
Oviductosomes (OVS) are nano-sized extracellular vesicles secreted in the oviductal luminal fluid by epithelial cells and known to be involved sperm capacitation fertility. Although they have been shown transfer encapsulated proteins sperm, cargo constituents other than not identified. Using next-generation sequencing, we demonstrate that OVS carriers of microRNAs (miRNAs), with 272 detected throughout estrous cycle. Of 50 most abundant, 6 (12%) 2 (4%) were expressed at significantly higher...
Abstract Summary The global response to the COVID-19 pandemic has led a rapid increase of scientific literature on this deadly disease. Extracting knowledge from biomedical and integrating it with relevant information curated biological databases is essential gain insight into etiology, diagnosis treatment. We used Semantic Web technology RDF integrate mined by iTextMine, PubTator SemRep formalized in standardized computable Knowledge Graph (KG). published KG via SPARQL endpoint support...
The extracellular matrix (ECM) is thought to play a critical role in the progression of breast cancer. In this work, we have designed photopolymerizable, biomimetic synthetic for controlled, 3D culture cancer cells and, combination with imaging and bioinformatics tools, utilized system investigate cell response different cues. Specifically, hydrogel-based matrices densities modified receptor-binding peptides derived from ECM proteins [fibronectin/vitronectin (RGDS), collagen (GFOGER),...
Abstract Late recurrences of breast cancer are hypothesized to originate from disseminated tumor cells that re‐activate after a long period dormancy, ≥5 years for estrogen‐receptor positive (ER+) tumors. An outstanding question remains as what the key microenvironment interactions regulate this complex process, and well‐defined human model systems needed probing this. Here, robust, bioinspired 3D ER+ dormancy culture is established utilized probe effects matrix properties common sites late...
Numerous efforts have been made for developing text-mining tools to extract information from biomedical text automatically. They assisted in many biological tasks, such as database curation and hypothesis generation. Text-mining are usually different each other terms of programming language, system dependency input/output format. There few previous works that concern the integration their results large-scale processing. In this paper, we describe iTextMine with an automated workflow run...
Abstract The Protein Ontology (PRO) provides an ontological representation of protein-related entities, ranging from protein families to proteoforms complexes. Linked Open Data (LOD) exposes, shares, and connects knowledge about entities on the Semantic Web using Resource Description Framework (RDF), thus enabling integration with other for biological discovery. For example, proteins (or variants thereof) can be retrieved basis specific disease associations. As a community resource, we...
In this work we present an approach to predict novel interaction partners for understudied kinases. Our involves constructing a biomedical knowledge graph and then using triple walking algorithm learn from graph.
Background: SARS-CoV2 infection has been associated with cardiovascular consequences, including myocarditis and cardiac arrhythmias. Myocarditis secondary to arrhythmias may often go unrecognized can present late nonspecific symptoms. Predicting those at risk allows for prompt treatment prevention of their potentially life-threatening consequences. Methods: The National COVID Cohort Collaborative (N3C) database was used identify patients aged 0-30 years COVID-19 index date between 1/1/2020...
Abstract Lung cancer is the leading cause of mortality worldwide. The treatment lung patients harboring mutant EGFR with orally administered TKIs has been a paradigm shift. Osimertinib and rociletinib are 3 rd generation irreversible targeting T790M mutation. current standard care for mutations due to increased efficacy, lower side effects, enhanced brain penetrance. Unfortunately, all develop resistance. Genomic approaches have primarily used interrogate resistance mechanisms. Here, we...
<div>Abstract<p>Lung cancer is the leading cause of mortality worldwide. The treatment patients with lung harboring mutant EGFR orally administered tyrosine kinase inhibitors (TKI) has been a paradigm shift. Osimertinib and rociletinib are third-generation irreversible TKIs targeting T790M mutation. current standard care for mutations due to increased efficacy, lower side effects, enhanced brain penetrance. Unfortunately, all develop resistance. Genomic approaches have primarily...
Background Aberrant protein kinase regulation leading to abnormal substrate phosphorylation is associated with several human diseases. Despite the promise of therapies targeting kinases, many kinases remain understudied. Most existing computational tools predicting cover less than 50% known kinases. They utilize local feature selection based on sequences, motifs, domains, structures, and/or functions, and do not consider heterogeneous relationships proteins. In this work, we present...
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<p>Table S5</p>
<p>Table S4</p>