Gary D. Bader
A5010789029- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- Biomedical Text Mining and Ontologies
- Gene Regulatory Network Analysis
- Genetics, Bioinformatics, and Biomedical Research
- Cell Image Analysis Techniques
- Cancer-related gene regulation
- Acute Myeloid Leukemia Research
- RNA Research and Splicing
- MicroRNA in disease regulation
- Glioma Diagnosis and Treatment
- Genomics and Rare Diseases
- Ubiquitin and proteasome pathways
- RNA modifications and cancer
- Immune cells in cancer
- Protein Structure and Dynamics
- Cancer Cells and Metastasis
- Histone Deacetylase Inhibitors Research
- Genomics and Chromatin Dynamics
- Scientific Computing and Data Management
University of Toronto
2016-2025
Lunenfeld-Tanenbaum Research Institute
2016-2025
University Health Network
2020-2025
Princess Margaret Cancer Centre
2020-2025
Canadian Institute for Advanced Research
2023-2025
Mount Sinai Hospital
2010-2024
Cellular Research (United States)
2024
University of Waterloo
2024
Sinai Health System
2020-2024
Donnelly College
2012-2023
Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks. Initial mapping efforts already produced wealth data. As the size set increases, databases computational methods will be required store, visualize analyze information order effectively aid knowledge discovery. This paper describes novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that...
GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing lists and prioritizing genes functional assays. Given query list, extends the list with functionally similar that it identifies using available genomics proteomics data. also reports weights indicate predictive value of each selected data set query. Six organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster,...
Abstract Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation this variation at whole-genome scale 1–3 . Here we report integrative analysis 2,658 whole-cancer genomes their matching normal tissues across 38 tumour types from Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium International Genome (ICGC) The Atlas (TCGA). We describe generation PCAWG resource, facilitated international data sharing using compute clouds. On...
A genome-scale genetic interaction map was constructed by examining 5.4 million gene-gene pairs for synthetic interactions, generating quantitative profiles approximately 75% of all genes in the budding yeast, Saccharomyces cerevisiae. network based on reveals a functional cell which similar biological processes cluster together coherent subsets, and highly correlated delineate specific pathways to define gene function. The global identifies cross-connections between bioprocesses, mapping...
In Saccharomyces cerevisiae , more than 80% of the ∼6200 predicted genes are nonessential, implying that genome is buffered from phenotypic consequences genetic perturbation. To evaluate function, we developed a method for systematic construction double mutants, termed synthetic array (SGA) analysis, in which query mutation crossed to an ∼4700 deletion mutants. Inviable double-mutant meiotic progeny identify functional relationships between genes. SGA analysis with roles cytoskeletal...
Background Gene-set enrichment analysis is a useful technique to help functionally characterize large gene lists, such as the results of expression experiments. This finds coherent gene-sets, pathways, that are statistically over-represented in given list. Ideally, number resulting sets smaller than genes list, thus simplifying interpretation. However, increasing and redundancy gene-sets used by many current software works against this ideal. Principal Findings To overcome gene-set...
A genetic interaction network containing approximately 1000 genes and 4000 interactions was mapped by crossing mutations in 132 different query into a set of 4700 viable gene yeast deletion mutants scoring the double mutant progeny for fitness defects. Network connectivity predictive function because often occurred among functionally related genes, similar patterns tended to identify components same pathway. The exhibited dense local neighborhoods; therefore, position on partially is other...
The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary acquired disease processes. are annotated as ordered network transformations single consistent data model. thus functions digital archive human tool for discovering functional relationships such gene expression profiles or somatic mutation catalogs from tumor...
The Biomolecular Interaction Network Database (BIND; http://binddb.org) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development the BIND 2.0 data model has led incorporation virtually all components mechanisms including interactions between any two molecules composed proteins, nucleic acids small molecules. Chemical reactions, photochemical activation conformational changes can also be described. Everything from molecule biochemistry...
The liver is the largest solid organ in body and critical for metabolic immune functions. However, little known about cells that make up human its microenvironment. Here we report a map of cellular landscape using single-cell RNA sequencing. We provide transcriptional profiles 8444 parenchymal non-parenchymal obtained from fractionation fresh hepatic tissue five livers. Using gene expression patterns, flow cytometry, immunohistochemical examinations, identify 20 discrete cell populations...
Pathway Commons ( http://www.pathwaycommons.org ) is a collection of publicly available pathway data from multiple organisms. provides web-based interface that enables biologists to browse and search comprehensive pathways sources represented in common language, download site integrated bulk sets information standard or convenient formats web service software developers can use conveniently query access all data. Database providers share their via repository. Pathways include biochemical...
The Biomolecular Interaction Network Database (BIND: http://bind.ca ) archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view submit records. BIND continues grow with the addition of individual submissions as well interaction data from PDB a number large-scale mapping experiments using yeast two hybrid, mass spectrometry, genetic interactions phage display. We have developed new graphical analysis tool that provides users domain...
GeneMANIA (http://genemania.org) is a flexible user-friendly web site for generating hypotheses about gene function, analyzing lists and prioritizing genes functional assays. Given query list, finds functionally similar using wealth of genomics proteomics data. In this mode, it weights each genomic dataset according to its predictive value the query. Another use function prediction. single gene, likely share with based on their interactions it. Enriched Gene Ontology categories among set can...
Abstract Cytoscape is one of the most popular open‐source software tools for visual exploration biomedical networks composed protein, gene, and other types interactions. It offers researchers a versatile interactive visualization interface exploring complex biological interconnections supported by diverse annotation experimental data, thereby facilitating research tasks such as predicting gene function constructing pathways. provides core functionality to load, visualize, search, filter,...