A5012592479- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- SARS-CoV-2 and COVID-19 Research
- Scientific Computing and Data Management
- Cell Image Analysis Techniques
- Data Quality and Management
- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Genetics, Bioinformatics, and Biomedical Research
- CRISPR and Genetic Engineering
- Pharmacogenetics and Drug Metabolism
- Single-cell and spatial transcriptomics
- Microbial Natural Products and Biosynthesis
- Receptor Mechanisms and Signaling
- RNA Research and Splicing
- Pain Mechanisms and Treatments
- Advanced Biosensing Techniques and Applications
- Genomics and Chromatin Dynamics
- Gene expression and cancer classification
Icahn School of Medicine at Mount Sinai
2019-2022
Mount Sinai Medical Center
2021
Illumina (United States)
2021
Mount Sinai Health System
2020
Profiling samples from patients, tissues, and cells with genomics, transcriptomics, epigenomics, proteomics, metabolomics ultimately produces lists of genes proteins that need to be further analyzed integrated in the context known biology. Enrichr (Chen et al., 2013; Kuleshov 2016) is a gene set search engine enables querying hundreds thousands annotated sets. uniquely integrates knowledge many high-profile projects provide synthesized information about mammalian The platform provides...
Identifying the transcription factors (TFs) responsible for observed changes in gene expression is an important step understanding regulatory networks. ChIP-X Enrichment Analysis 3 (ChEA3) a factor enrichment analysis tool that ranks TFs associated with user-submitted sets. The ChEA3 background database contains collection of set libraries generated from multiple sources including TF-gene co-expression RNA-seq studies, TF-target associations ChIP-seq experiments, and co-occurrence computed...
PubMed contains millions of abstracts that co-mention terms describe drugs with other biomedical such as genes or diseases. Unique opportunities exist for leveraging these co-mentions by integrating them drug-drug similarity resources the Library Integrated Network-based Cellular Signatures (LINCS) L1000 signatures to develop novel hypotheses.DrugShot is a web-based server application and an Appyter enables users enter any search term into simple input form receive ranked lists small...
Jupyter Notebooks have transformed the communication of data analysis pipelines by facilitating a modular structure that brings together code, markdown text, and interactive visualizations. Here, we extended to broaden their accessibility with Appyters. Appyters turn into fully functional standalone web-based bioinformatics applications. present users an entry form enabling them upload set various parameters for multitude workflows. Once is filled, Appyter executes corresponding notebook in...
In a short period, many research publications that report sets of experimentally validated drugs as potential COVID-19 therapies have emerged. To organize this accumulating knowledge, we developed the Drug and Gene Set Library (https://amp.pharm.mssm.edu/covid19/), collection drug gene related to from multiple sources. The platform enables users view, download, analyze, visualize, contribute research. evaluate content library, compared results six in vitro screens for repurposing candidates....
The Library of Integrated Network-based Cellular Signatures (LINCS) was an NIH Common Fund program that aimed to expand our knowledge about human cellular responses chemical, genetic, and microenvironment perturbations. Responses perturbations were measured by transcriptomics, proteomics, imaging, other high content assays. second phase the LINCS program, which lasted 7 years, involved engagement six data signature generation centers (DSGCs) one coordination integration center (DCIC). DSGCs...
Understanding the underlying molecular and structural similarities between seemingly heterogeneous sets of drugs can aid in identifying drug repurposing opportunities assist discovery novel properties preclinical small molecules. A wealth information about molecule structure, targets, indications side effects; induced gene expression signatures; other attributes are publicly available through web-based tools, databases repositories. By processing, abstracting aggregating from these resources...
The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes Health without requiring owners move, reformat, or rehost those data. This is centered on catalog integrates detailed descriptions biomedical individual Programs' Coordination Centers (DCCs) into uniform metadata model can then be indexed and searched centralized portal. Crosscut Metadata Model (C2M2) supports wide variety...
Abstract The coronavirus (CoV) severe acute respiratory syndrome (SARS)-CoV-2 (COVID-19) pandemic has received rapid response by the research community to offer suggestions for repurposing of approved drugs as well improve our understanding COVID-19 viral life cycle molecular mechanisms. In a short period, tens thousands preprints and other publications have emerged including those that report lists experimentally validated compounds potential therapies. addition, gene sets from interacting...
Abstract The Illuminating the Druggable Genome (IDG) consortium is a National Institutes of Health (NIH) Common Fund program designed to enhance our knowledge under‐studied proteins, more specifically, proteins unannotated within three most commonly drug‐targeted protein families: G‐protein coupled receptors, ion channels, and kinases. Since 2014, IDG Knowledge Management Center (IDG‐KMC) has generated several open‐access datasets resources that jointly serve as highly translational...
While hundreds of genes have been associated with pain, much the molecular mechanisms pain remain unknown. As a result, current analgesics are limited to few clinically validated targets. Here, we trained machine learning (ML) ensemble model predict new targets for 17 categories pain. The utilizes features from transcriptomics, proteomics, and gene ontology prioritize modulating We focused on identifying novel G-protein-coupled receptors (GPCRs), ion channels, protein kinases because these...
The coronavirus (CoV) severe acute respiratory syndrome (SARS)-CoV-2 (COVID-19) pandemic has received rapid response by the research community to offer suggestions for repurposing of approved drugs as well improve our understanding COVID-19 viral life cycle molecular mechanisms. In a short period, tens thousands preprints and other publications have emerged including those that report lists experimentally validated compounds potential therapies. addition, gene sets from interacting...
Abstract The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables users to discover datasets from across the U.S. National Institutes Health without requiring owners move, reformat, or rehost those data. CFDE’s is centered on catalog ingests metadata individual Program’s Coordination Centers (DCCs) into uniform model can then be indexed and searched centralized portal. This Crosscut Metadata Model (C2M2) supports wide variety types terms used by...
Abstract Motivation Many biological and biomedical researchers commonly search for information about genes drugs to gather knowledge from these resources. For the most part, such is served as landing pages in disparate data repositories web portals. Results The Gene Drug Landing Page Aggregator (GDLPA) provides users with access 50 gene-centric 19 drug-centric repositories, enabling them retrieve corresponding their gene drug queries. Bringing resources together into one dashboard that...