Ryan R. Brinkman
A5035285628- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- Cell Image Analysis Techniques
- Biomedical Text Mining and Ontologies
- Lymphoma Diagnosis and Treatment
- Immune Cell Function and Interaction
- Genetic Neurodegenerative Diseases
- Semantic Web and Ontologies
- Chronic Myeloid Leukemia Treatments
- Chronic Lymphocytic Leukemia Research
- Gene Regulatory Network Analysis
- Mitochondrial Function and Pathology
- T-cell and B-cell Immunology
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- vaccines and immunoinformatics approaches
- Acute Myeloid Leukemia Research
- Neurological disorders and treatments
- Scientific Computing and Data Management
- Hematopoietic Stem Cell Transplantation
- Neonatal Respiratory Health Research
- Eosinophilic Disorders and Syndromes
- Microfluidic and Bio-sensing Technologies
- Immune responses and vaccinations
- Genomics and Rare Diseases
University of British Columbia
2015-2024
Terry Fox Research Institute
2008-2024
BC Cancer Agency
2014-2024
John Wiley & Sons (United States)
2017-2021
Medical Genetics Center
2020
Université Paris Cité
2017-2018
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2017-2018
New York Medical College
2017-2018
Hudson Institute
2018
Environmental Protection Agency
2017
These guidelines are a consensus work of considerable number members the immunology and flow cytometry community. They provide theory key practical aspects enabling immunologists to avoid common errors that often undermine immunological data. Notably, there comprehensive sections all major immune cell types with helpful Tables detailing phenotypes in murine human cells. The latest techniques applications also described, featuring examples data can be generated and, importantly, how analysed....
Huntington's disease (HD) is a neurodegenerative disorder caused by an unstable CAG repeat. For patients at risk, participating in predictive testing and learning of having expansion, major unanswered question shifts from “Will I get HD?” to “When will it manifest?” Using the largest cohort HD analyzed date (2913 individuals 40 centers worldwide), we developed parametric survival model based on repeat length predict probability neurological onset (based motor symptoms rather than psychiatric...
In this analysis, the authors directly compared performance of flow cytometry data processing algorithms to manual gating approaches. The results offer information practical utility about as applied different sets and challenges. Traditional methods for (FCM) rely on subjective gating. Recently, several groups have developed computational identifying cell populations in multidimensional FCM data. Flow Cytometry: Critical Assessment Population Identification Methods (FlowCAP) challenges were...
Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often clinical trials or drug discovery settings. However, management and analysis methods not advanced sufficiently far from initial small-scale studies to support modeling presence multiple covariates. We developed a set flexible open source computational tools R package flowCore facilitate these data. A key component which is having suitable...
The marriage between immunology and cytometry is one of the most stable productive in recent history science. A rapid search PubMed shows that, as July 2017, using "flow immunology" a term yields more than 68 000 articles, first which, interestingly, not about lymphocytes. It might be stated after short engagement, exchange wedding rings officially occurred when idea to link fluorochromes monoclonal antibodies came about. After this, recognizing different types cells became relatively easy...
Abstract A fundamental tenet of scientific research is that published results are open to independent validation and refutation. Minimum data standards aid providers, users, publishers by providing a specification what required unambiguously interpret experimental findings. Here, we present the Information about Flow Cytometry Experiment (MIFlowCyt) standard, stating minimum information report flow cytometry (FCM) experiments. We brought together cross‐disciplinary international...
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies provide a representation biomedical knowledge from Open Biological Ontologies (OBO) project adds ability this was derived. We here state several applications using it, such as adding semantic expressivity existing databases, building data entry forms,...
Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange information retrieval.
Abstract Standardization of immunophenotyping requires careful attention to reagents, sample handling, instrument setup, and data analysis, is essential for successful cross-study cross-center comparison data. Experts developed five standardized, eight-color panels identification major immune cell subsets in peripheral blood. These were produced as pre-configured, lyophilized, reagents 96-well plates. We present the results a coordinated analysis samples across nine laboratories using these...
Systems biology can unravel complex but has not been extensively applied to human newborns, a group highly vulnerable wide range of diseases. We optimized methods extract transcriptomic, proteomic, metabolomic, cytokine/chemokine, and single cell immune phenotyping data from <1 ml blood, volume readily obtained newborns. Indexing baseline applying innovative integrative computational reveals dramatic changes along remarkably stable developmental trajectory over the first week life. This is...
The complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII reveals that it contains 269 predicted or known genes (300 base pairs larger). Fifty-nine these (22 percent) were previously identified. Of the 210 novel genes, 65 are to encode proteins similar other function. Sixteen appear be relatively recently duplicated. On average, there is one gene approximately every 2 kilobases. Although coding density and composition across not uniform, no regular pattern variation apparent.
Abstract The capability of flow cytometry to offer rapid quantification multidimensional characteristics for millions cells has made this technology indispensable health research, medical diagnosis, and treatment. However, the lack statistical bioinformatics tools parallel recent high‐throughput technological advancements hindered from reaching its full potential. We propose a flexible model‐based clustering approach identifying cell populations in data based on t ‐mixture models with...
Abstract We have developed flowMeans, a time‐efficient and accurate method for automated identification of cell populations in flow cytometry (FCM) data based on K‐means clustering. Unlike traditional K‐means, flowMeans can identify concave by modelling single population with multiple clusters. uses change point detection algorithm to determine the number sub‐populations, enabling be used high throughput FCM analysis pipelines. Our approach compares favorably manual human experts current...
<b><i>Objective:</i></b> There is increasing evidence that neuron loss precedes the phenotypic expression of Huntington’s disease (HD). As genes for late-onset neurodegenerative diseases are identified, need accurate assessment phenoconversion (i.e., transition from health to phenotype) will be important. <b><i>Methods:</i></b> Prospective longitudinal evaluation using Unified Disease Rating Scale (UHDRS) was conducted by Huntington Study Group members 36 sites. were 260 persons considered...
Ontology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, OBO Foundry principles require that these ontologies be open non-redundant, avoiding duplication terms through re-use existing resources. As current options to do so present various difficulties, new approach, MIREOT, allows specifying import single terms. Initial implementations allow for controlled selected annotations...
As a high-throughput technology that offers rapid quantification of multidimensional characteristics for millions cells, flow cytometry (FCM) is widely used in health research, medical diagnosis and treatment, vaccine development. Nevertheless, there an increasing concern about the lack appropriate software tools to provide automated analysis platform parallelize data-generation platform. Currently, large extent, FCM data relies on manual selection sequential regions 2-D graphical...
Abstract Background Recent biological discoveries have shown that clustering large datasets is essential for better understanding biology in many areas. Spectral particular has proven to be a powerful tool amenable applications. However, it cannot directly applied due time and memory limitations. To address this issue, we modified spectral by adding an information preserving sampling procedure applying post-processing stage. We call entire algorithm SamSPECTRAL. Results tested our on flow...