A5032771078- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- Cell Image Analysis Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Computational Drug Discovery Methods
- Gene expression and cancer classification
- Scientific Computing and Data Management
- Epigenetics and DNA Methylation
- Metabolomics and Mass Spectrometry Studies
- Advanced Fluorescence Microscopy Techniques
- RNA Research and Splicing
- Random lasers and scattering media
- vaccines and immunoinformatics approaches
- Genetic Associations and Epidemiology
- Electronic Health Records Systems
- RNA modifications and cancer
- Semantic Web and Ontologies
- Photoacoustic and Ultrasonic Imaging
- Radiomics and Machine Learning in Medical Imaging
- AI in cancer detection
- MicroRNA in disease regulation
- Network Traffic and Congestion Control
- Distributed and Parallel Computing Systems
- RNA and protein synthesis mechanisms
University of Michigan–Ann Arbor
2015-2025
Health Technomics (United States)
2020
Michigan Medicine
2018
Novem (Netherlands)
2017
Washtenaw Community College
2015
University of California, San Diego
2014
Michigan United
2000-2012
University of Verona
2011
Michigan Center for Translational Pathology
2009-2010
The University of Texas Health Science Center at Houston
2009
Genome-wide expression profiling is a powerful tool for implicating novel gene ensembles in cellular mechanisms of health and disease. The most popular platform genome-wide the Affymetrix GeneChip. However, its selection probes relied on earlier genome transcriptome annotation which significantly different from current knowledge. resultant informatics problems have profound impact analysis interpretation data. Here, we address these critical issues offer solution. We identified several...
MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3′-UTR, which interacts mainly with 5′-end of miRNA in animals. Here we identify many endogenous motifs within human 5′-UTRs specific 3′-ends miRNAs. The 3′-end conserved miRNAs particular has significant interaction sites human-enriched, less 5′-UTR motifs, while human-specific have only implying both and actively evolving response each other. Additionally, their turn out simultaneously contain 3′-UTRs....
Metabolomics is a rapidly evolving field that holds promise to provide insights into genotype-phenotype relationships in cancers, diabetes and other complex diseases. One of the major informatics challenges providing tools link metabolite data with types high-throughput molecular (e.g. transcriptomics, proteomics), incorporate prior knowledge pathways interactions.We describe new, substantially redesigned version our tool Metscape allows users enter experimental for metabolites, genes...
Extensive simulations of PAMAM dendrimer generation 2 were performed at several pH conditions with explicit water molecules, to obtain proper and validity for additional without water. Within the range validity, simulation greatly extends size duration practical simulations. We investigated effects long-range interaction parameters such as distance dielectric constant molecular dynamics water, concluding that charged distance-dependent but cutoff best mimics results. Structural variations...
This paper examines the effects of using parallel TCP flows to improve end-to-end network performance for distributed data intensive applications. A series transmission experiments were conducted over a wide-area assess how throughput, and understand number necessary throughput while avoiding congestion. An empirical expression based on experimental is presented, guidelines use are discussed.
Abstract Summary: Metscape is a plug-in for Cytoscape, used to visualize and interpret metabolomic data in the context of human metabolic networks. We have developed metabolite database by extracting integrating information from several public sources. By querying this database, allows users trace connections between metabolites genes, compound networks display structures as well reactions, enzymes, genes pathways. Applying pathway filter, can create subnetworks that consist compounds...
Abstract Motivation: The elucidation of biological concepts enriched with differentially expressed genes has become an integral part the analysis and interpretation genomic data. Of additional importance is ability to explore networks relationships among previously defined from diverse information sources, results visually multiple perspectives. Accomplishing these tasks requires a unified framework for agglomeration data various resources, novel visualizations, user functionality. Results:...
Cell lines have been widely used in biomedical research. The community-based Line Ontology (CLO) is a member of the OBO Foundry library that covers domain cell lines. Since its publication two years ago, significant updates made, including new groups joining CLO consortium, line cells, upper level alignment with (CL) and for Biomedical Investigation, logical extensions. Collaboration among CLO, CL, OBI has established consensus definitions line-specific terms such as ‘cell line’, cell’,...
The Coronavirus Infectious Disease Ontology (CIDO) is a community-based ontology that supports coronavirus disease knowledge and data standardization, integration, sharing, analysis.
Blood monocytes are the principal reservoir for tissue macro- phages in rheumatoid synovitis.Receptor-mediated adhesive interactions between circulating cells and synovial venules initiate recruitment.These have been studied pri- marily cultured endothelial cells.Thus functional activi- ties of specific adhesion receptors, such as se- lectins leukocytic integrins, not evaluated directly diseased tissues.We therefore examined monocyte- microvascular synovitis by modify- ing Stamper-Woodruff...
Protein interaction data exists in a number of repositories. Each repository has its own format, molecule identifier and supplementary information. Michigan Molecular Interactions (MiMI) assists scientists searching through this overwhelming amount protein data. MiMI gathers from well-known databases deep-merges the Utilizing an identity function, molecules that may have different identifiers but represent same real-world object are merged. Thus, allows users to retrieve information many at...
Molecular interaction data exists in a number of repositories, each with its own format, molecule identifier and information coverage. Michigan molecular interactions (MiMI) assists scientists searching through this profusion data. The original release MiMI gathered from well-known protein databases, deep merged while keeping track provenance. Based on the feedback received users, has been completely redesigned. This article describes resulting Release 2 (MiMIr2). New functionality includes...
Significant interest exists in establishing synergistic research bioinformatics, systems biology and intelligent computing. Supported by the United States National Science Foundation (NSF), International Society of Intelligent Biological Medicine (http://www.ISIBM.org), Journal Computational Biology Drug Design (IJCBDD) Functional Informatics Personalized Medicine, ISIBM Joint Conferences on Bioinformatics, Systems Computing (ISIBM IJCBS 2009) attracted more than 300 papers 400 researchers...
The bilateral imaging approach known from confocal applications operating in the line mode was used to realize real‐time two‐photon imaging. It is shown that sectioning inherent could be improved by introduction of a aperture path. Using high‐power, low‐repetition‐rate amplified Ti:sapphire system, various biological objects were visualized including live boar sperm.
MicroRNAs (miRNA) are endogenous tissue-specific short RNAs that regulate gene expression. Discriminating each let-7 family member expression is especially important due to let-7' s abundance and connection with development cancer. However, lengths (22 nt) similarities between multiple sequences have prevented identification of individual members. Here, we present ProDeG, a computational algorithm which designs imperfectly matched (previously yielding only noise levels in microarray...
<title>Abstract</title> Neuroimaging is a ubiquitous tool for evaluating patients with neurological diseases. The global demand magnetic resonance imaging (MRI) studies has risen steadily, placing significant strain on health systems, prolonging turnaround times, and intensifying physician burnout. These challenges disproportionately impact in low-resource rural settings. Here, we utilized large academic system as data engine to develop Prima, the first vision-language model (VLM) serving an...
Applications that require good network performance often use parallel TCP streams and modifications to improve the effectiveness of TCP. If bottleneck is fully utilized, this approach boosts throughput by unfairly stealing bandwidth from competing streams. Improving easy, but improving while maintaining fairness difficult. In paper, we describe an implemented uses a long virtual round trip time in combination with on underutilized networks. Our prioritizes at expense when utilized. We...
Abstract Motivation: Finding the potential functional significance of SNPs is a major bottleneck in understanding genome-wide SNP scanning results, as related data are distributed across many different databases. The Function Portal designed to be clearing house for all public domain annotation data, well in-house annotations derived from sources. It currently contains six categories including genomic elements, transcription regulation, protein function, pathway, disease and population...