Vasileios Stathias – Frost Institute for Data Science & Computing

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” →

Publications

Machine and Deep Learning Approaches for Cancer Drug Repurposing

In past years, medical oncology has witnessed an unprecedented explosion in the understanding of cancer pathophysiology and pathogenesis. With the advancement of next-generation sequencing technologies such as single-cell RNA sequencing, we are better equipped to explore and model complex phenomena such as cancer heterogeneity, resistance, and etiologies at a granular level. Read more “Machine and Deep Learning Approaches for Cancer Drug Repurposing” →

Publications

Gene 36. Integrating Transcriptomics and Kinomics Identifies Synergistic Drug…

Glioblastoma (GBM) is the most common and malignant adult brain tumor. Despite years of research, few advancements have been made in its management. One promising avenue of research has been treatment with BRD4 inhibitors, which decrease oncogene expression in GBM cells. Read more “Gene 36. Integrating Transcriptomics and Kinomics Identifies Synergistic Drug Combinations for Glioblastoma Treatment” →

News

Comp-16. Comprehensive Transcriptomic Analysis of Single Cells From Recurrent…

Glioblastoma (GBM) remains the most common adult brain tumor, with poor survival expectations, and no new therapeutic modalities approved in the last decade. Our laboratories have recently demonstrated that the integration of a transcriptional disease signature obtained from Read more “Comp-16. Comprehensive Transcriptomic Analysis of Single Cells From Recurrent and Primary Glioblastoma to Predict Cell-Type-Specific Therapeutics” →

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

Abstract 5103: The Dark Cancer Kinome—Untapped Opportunities for the…

Kinases are firmly established drug targets in cancer. There are currently 44 FDA-approved kinase drugs and hundreds of compounds are in clinical development. However, less than 10% of the Kinome is currently targeted and a large proportion is considered understudied by the NIH Illuminating the Druggable Genome Program (https://druggablegenome.net/). Read more “Abstract 5103: The Dark Cancer Kinome—Untapped Opportunities for the Development of Novel Drugs” →

Publications

DrugCentral 2018: An Update in Nucleic Acids Research

DrugCentral is a drug information resource (http://drugcentral.org) open to the public since 2016 and previously described in the 2017 Nucleic Acids Research Database issue. Since the 2016 release, 103 new approved drugs were updated. The following new data sources have been included: Read more “DrugCentral 2018: An Update in Nucleic Acids Research” →

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

CARM1 Is Essential for Myeloid Leukemogenesis but Dispensable for…

Chromatin-modifying enzymes, and specifically the protein arginine methyltransferases (PRMTs), have emerged as important targets in cancer. Here, we investigated the role of CARM1 in normal and malignant hematopoiesis. Read more “CARM1 Is Essential for Myeloid Leukemogenesis but Dispensable for Normal Hematopoiesis” →

n>Vasileios Stathias