Nucleic Acids Research Journal – Frost Institute for Data Science & Computing

piNET: A Versatile Web Platform for Downstream Analysis and…

May 29, 2020August 4, 2023

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” →

LINCS Data Portal 2.0: Next Generation Access Point for…

January 8, 2020August 8, 2025

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” →

LINCS Data Portal 2.0 Update with New Functionalities

November 6, 2019August 8, 2025

In this first major update of the LINCS Data Portal, 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” →