Dusica Vidovic – Frost Institute for Data Science & Computing

piNET: A Versatile Web Platform for Downstream Analysis and…

Rapid progress in proteomics and large-scale profiling of biological systems at the protein level necessitates the continued development of efficient computational tools for the analysis and interpretation of proteomics data. Here, we present the piNET server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with the LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Read more “piNET: A Versatile Web Platform for Downstream Analysis and Visualization of Proteomics Data” →

Publications

Protemic Cellular Signatures of Kinase Inhibitor-Induced Cardiotoxicity: Mount Sinai…

Abstract The Drug Toxicity Signature Generation Center (DToxS) at the Icahn School of Medicine at Mount Sinai is one of the centers of the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. A key aim of DToxS is to generate both proteomic and transcriptomic signatures that can predict adverse effects, especially cardiotoxicity, of kinase inhibitors approved by the Food and Drug Administration. Read more “Protemic Cellular Signatures of Kinase Inhibitor-Induced Cardiotoxicity: Mount Sinai DToxS LINCS Center Dataset” →

Publications

LINCS Data Portal 2.0: Next Generation Access Point for…

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program with the goal of generating a large-scale and comprehensive catalog of perturbation-response signatures by utilizing a diverse collection of perturbations across many model systems and assay types. The LINCS Data Portal (LDP) has been the primary access point for the compendium of LINCS data and has been widely utilized. Read more “LINCS Data Portal 2.0: Next Generation Access Point for Perturbation-Response Signatures” →

News

LINCS Data Portal 2.0 Update with New Functionalities

In this first major update of the portal (available at http://lincsportal.ccs.miami.edu/signatures), substantial changes in both the data architecture, and the user interface, are being introduced to enable a deeper exploration of the LINCS data, and to support new integrative and analytical capabilities for both computational and non-computational researchers. The cornerstone of this update has been the decision to reprocess all high-level LINCS datasets and make them accessible at the data-point level enabling users to directly access and download any subset of signatures across the entire library independent from the originating source, project or assay. Access to the individual signatures also enables the newly implemented signature search functionality, which utilizes the iLINCS platform to identify conditions that mimic or reverse gene set queries, and a newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures. Read more “LINCS Data Portal 2.0 Update with New Functionalities” →

News

Connecting Omics Signatures of Diseases, Drugs, and Mechanisms of…

iLINCS (http://ilincs.org) is an integrative web-based platform for analysis of omics data and signatures of cellular perturbations. The portal facilitates analysis of user-submitted omics signatures of diseases and cellular perturbations in the context of a large compendium of pre-computed signatures (>200,000), Read more “Connecting Omics Signatures of Diseases, Drugs, and Mechanisms of Actions with iLINCS” →

Publications

Sustainable Data and Metadata Management at the BD2K-LINCS DCIC

The NIH-funded LINCS Consortium is creating an extensive reference library of cell-based perturbation response signatures and sophisticated informatics tools incorporating a large number of perturbagens, model systems, and assays. To date, more than 350 datasets have been generated including transcriptomics, proteomics, epigenomics, cell phenotype and competitive binding profiling assays. Read more “Sustainable Data and Metadata Management at the BD2K-LINCS DCIC” →

Publications

Anti-Diabetic Actions of a Non-Agonist PPARγ Ligand Blocking Cdk5-Mediated…

PPARγ is the functioning receptor for the thiazolidinedione (TZD) class of anti-diabetes drugs including rosiglitazone and pioglitazone. These drugs are full classical agonists for this nuclear receptor, but recent data have shown that many PPARγ-based drugs have a separate biochemical activity, blocking the obesity-linked phosphorylation of PPARγ by Cdk5. Read more “Anti-Diabetic Actions of a Non-Agonist PPARγ Ligand Blocking Cdk5-Mediated Phosphorylation” →

News

Featured Scientist Dusica Vidovic, PhD

Dr. Dušica Vidović joined the Chemoinformatics team at CCS in September 2008. Before she joined, she was a Research Associate at The Scripps Research Institute and The Computer-Chemistry Centrum in the field of chemoinformatics.

Publications

Suppression of TH17 Differentiation and Autoimmunity by a Synthetic…

T-helper cells that produce interleukin-17 (TH17 cells) are a recently identified CD4+ T-cell subset with characterized pathological roles in autoimmune diseases1,2,3. The nuclear receptors retinoic-acid-receptor-related orphan receptors α and γt (RORα and RORγt, respectively) have indispensable roles in the development of this cell type4,5,6,7. Here we present SR1001, a high-affinity synthetic ligand—the first in a new class of compound—that is specific to both RORα and RORγt and which inhibits TH17 cell differentiation and function. Read more “Suppression of TH17 Differentiation and Autoimmunity by a Synthetic ROR Ligand” →

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