Mahesh Visvanathan

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OBJECTIVES:Risk stratification of Barrett's esophagus (BE) using biomarkers remains an important goal. We evaluated feasibility and clinical accuracy of novel microRNA (miRNA) biomarkers for prediction of BE dysplasia.METHODS:Paired fresh-frozen and hematoxylin/eosin specimens from a prospective tissue repository where only biopsies with the lesion of(More)
LipidomeDB Data Calculation Environment (DCE) is a web application to quantify complex lipids by processing data acquired after direct infusion of a lipid-containing biological extract, to which a cocktail of internal standards has been added, into an electrospray source of a triple quadrupole mass spectrometer. LipidomeDB DCE is located on the public(More)
OBJECTIVE Barrett's esophagus (BE) is transition from squamous to columnar mucosa as a result of gastroesophageal reflux disease (GERD). The role of microRNA during this transition has not been systematically studied. DESIGN For initial screening, total RNA from 5 GERD and 6 BE patients was size fractionated. RNA <70 nucleotides was subjected to SOLiD 3(More)
Lung cancer is the leading cause of death from cancer in the world and its treatment is dependant on the type and stage of cancer detected in the patient. Molecular biomarkers that can characterize the cancer phenotype are thus a key tool in planning a therapeutic response. A common protocol for identifying such biomarkers is to employ genomic microarray(More)
OBJECTIVES Presently, the protein interaction information concerning different signaling pathways is available in a qualitative manner in different online protein interaction databases. The challenge here is to derive a quantitative way of modeling signaling pathways from qualitative way of modeling signaling pathways from a qualitative level. To address(More)
INTRODUCTION Understanding the biological processes of signaling pathways as a whole system requires an integrative software environment that has comprehensive capabilities. The environment should include tools for pathway design, visualization, simulation and a knowledge base concerning signaling pathways as one. In this paper we introduce a new(More)
Lung cancer accounts for the most cancer-related deaths. The identification of cancer-associated genes and the related pathways are essential to prevent many types of cancer. In this paper, a more systematic approach is considered. First, we did pathway analysis using Hyper Geometric Distribution (HGD) and significantly overrepresented sets of reactions(More)
Plant phospholipids and glycolipids can be analyzed by direct infusion electrospray ionization triple-quadrupole mass spectrometry. A biological extract is introduced in solvent by continuous infusion into the mass spectrometer's electrospray ionization source, where ions are produced from the lipids. For analysis of membrane lipids, a series of precursor(More)
We investigated different mathematical models concerning signaling pathways and built a new pathway model for TNF -NF B signaling using an integrative analytical approach. This integrative approach consists of a knowledgebase, model designing/visualization and simulation environments. In particular, our new TNF -NF B signaling pathway model was developed(More)
Glycomics is a discipline of biology that deals with the structure and function of glycans (or carbohydrates). Analytical techniques such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) are having a significant impact on the field of glycomics. However, effective progress in glycomics research requires collaboration between laboratories to(More)