A5066447491- Agricultural risk and resilience
- Insurance and Financial Risk Management
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Disaster Management and Resilience
- Poverty, Education, and Child Welfare
- Scientific Computing and Data Management
- Microfinance and Financial Inclusion
- Biomedical Text Mining and Ontologies
- Single-cell and spatial transcriptomics
- Computational Drug Discovery Methods
- Agricultural Economics and Practices
- Research Data Management Practices
- Income, Poverty, and Inequality
- Healthcare Policy and Management
- RNA Research and Splicing
- Healthcare cost, quality, practices
- SARS-CoV-2 and COVID-19 Research
- Ferroptosis and cancer prognosis
- CRISPR and Genetic Engineering
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Data Quality and Management
- State Capitalism and Financial Governance
- Cell Image Analysis Techniques
Icahn School of Medicine at Mount Sinai
2018-2024
Illumina (United States)
2018-2021
Mount Sinai Medical Center
2019-2021
Mount Sinai Health System
2020
Library Network
2020
The Coordinating Center
2019
Fairleigh Dickinson University
2016-2018
Government of the United Kingdom
2016-2017
University of Oxford
2007-2016
University of Kentucky
2016
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...
Rational demand for index insurance products is shown to be fundamentally different that indemnity due the presence of basis risk. In particular, optimal zero infinitely risk-averse individuals, and nonmonotonic in risk aversion, wealth, price. For a given belief, upper bounds are derived from decreasing absolute decision makers. A simple ratio monitoring presented applied explain low level consumer hedging instruments as rational response deadweight costs (JEL D14, D81, G13, G22, Q14)
While gene expression data at the mRNA level can be globally and accurately measured, profiling activity of cell signaling pathways is currently much more difficult.eXpression2Kinases (X2K) computationally predicts involvement upstream pathways, given a signature differentially expressed genes.X2K first computes enrichment for transcription factors likely to regulate genes.The next step X2K connects these enriched through known protein-protein interactions (PPIs) construct subnetwork.The...
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...
Gene and protein set enrichment analysis is a critical step in the of data collected from omics experiments. Enrichr popular gene web-server search engine that contains hundreds thousands annotated sets. While has been useful providing with many libraries different categories, integrating results across domains knowledge can further hypothesis generation. To this end, Enrichr-KG graph database application combines selected for integrative visualization. The are presented as subgraphs made...
Abstract The notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good stewardship prerequisite reproducibility. Nowadays, guides policy actions professional practices in public private sectors. Despite such endorsements, however, Principles are aspirational, remaining elusive at best, intimidating worst. To address lack of practical guidance, help with capability gaps, we developed Cookbook, an open,...
Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%–20% cases have demonstrated durable responses from immune checkpoint blockade. To enhance efficacy immunotherapies, combination therapies suppressing multiple evasion mechanisms are increasingly contemplated. better understand cell surveillance and diverse tumor tissues, we comprehensively characterized landscape more 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic...
Abstract The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program with the goal generating a large-scale and comprehensive catalogue perturbation-response signatures by utilizing diverse collection perturbations across many model systems assay types. LINCS Data Portal (LDP) has been primary access point for compendium data widely utilized. Here, we report first major update LDP (http://lincsportal.ccs.miami.edu/signatures) substantial changes in...
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....
There are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses visualization do not require programming skills. Here we present iLINCS ( http://ilincs.org ), an web-based platform analysis of signatures cellular perturbations. The facilitates mining re-analysis the large collection datasets (>34,000), pre-computed (>200,000), their connections, as well user-submitted diseases workflows vast resources range analytics...
Millions of transcriptome samples were generated by the Library Integrated Network-based Cellular Signatures (LINCS) program. When these data are processed into searchable signatures along with extracted from Genotype-Tissue Expression (GTEx) and Gene Omnibus (GEO), connections between drugs, genes, pathways diseases can be illuminated. SigCom LINCS is a webserver that serves over million gene expression processed, analyzed, visualized LINCS, GTEx, GEO. built Signature Commons,...
Many biomedical research publications contain gene sets in their supporting tables, and these are currently not available for search reuse. By crawling PubMed Central, the Rummagene server provides access to hundreds of thousands such mammalian sets. So far, we scanned 5,448,589 articles find 121,237 that 642,389 These served enrichment analysis, free text, table title search. Investigating statistical patterns within database, demonstrate can be used transcription factor kinase analyses,...
Abstract By processing and abstracting diverse omics datasets into associations between genes their attributes, the Harmonizome database enables researchers to explore integrate knowledge about human from many central resources. Here, we introduce 3.0, a significant upgrade original database. The adds 26 that contribute nearly 12 million various attribute types such as cells tissues, diseases, pathways. has dataset crossing feature identify gene modules are shared across datasets. To further...
Governments play a key role in supporting populations affected by natural disasters, including rebuilding infrastructure to ensure continued services and scaling-up public safety nets prevent widespread hunger poverty. However, the traditional approach of limiting greater spending aftermath disaster has many drawbacks. External support from bilateral or multilateral donors can be slow unreliable. Private sector reinsurance prohibitively expensive. And reallocating budgets toward recovery...
Abstract There are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses visualization do not require programming skills. Among these, iLINCS is unique in scope versatility of the provided analytics facilitated. ( http://ilincs.org ) an web-based platform analysis signatures cellular perturbations. The facilitates user-submitted diseases perturbations context large compendium pre-computed (>200,000), as well mining...
Abstract The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic states associated with diverse diseases. To develop detailed understanding the linkage between changes, we generated comprehensive dataset that catalogs transcriptional, proteomic, epigenomic responses MCF10A mammary epithelial cells...