List of works - Ryan R Brinkman

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

scientific article published on 08 October 2015

A genome scan for modifiers of age at onset in Huntington disease: The HD MAPS study.

scientific article

A new model for prediction of the age of onset and penetrance for Huntington's disease based on CAG length.

scientific article published in April 2004

A standardized immune phenotyping and automated data analysis platform for multicenter biomarker studies

scientific article published on 06 December 2018

A survey of flow cytometry data analysis methods

scientific article

A worldwide assessment of the frequency of suicide, suicide attempts, or psychiatric hospitalization after predictive testing for Huntington disease. ⬇️

scientific article

Allogeneic SCT for relapsed composite and transformed lymphoma using related and unrelated donors: long-term results.

scientific article

Analysis of High-Throughput Flow Cytometry Data Using plateCore

scientific article

Automated analysis of flow cytometry data comes of age.

scientific article published in January 2016

Automated analysis of multidimensional flow cytometry data improves diagnostic accuracy between mantle cell lymphoma and small lymphocytic lymphoma

scientific article

Automated gating of flow cytometry data via robust model-based clustering

scientific article

B cells with high side scatter parameter by flow cytometry correlate with inferior survival in diffuse large B-cell lymphoma

scientific article

BAIT: Organizing genomes and mapping rearrangements in single cells

scientific article

Bim regulates alloimmune-mediated vascular injury through effects on T-cell activation and death.

scientific article

Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII

scientific article

Computational analysis optimizes the flow cytometric evaluation for lymphoma

scientific article published on 03 September 2013

Correlation analysis of intracellular and secreted cytokines via the generalized integrated mean fluorescence intensity.

scientific article

Critical assessment of automated flow cytometry data analysis techniques.

scientific article

Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops

scientific article published on 01 June 2019

Cytogenetic and molecular responses to standard-dose imatinib in chronic myeloid leukemia are correlated with Sokal risk scores and duration of therapy but not trough imatinib plasma levels.

scientific article published on 31 August 2008

Data File Standard for Flow Cytometry, version FCS 3.1.

scientific article

Data quality assessment of ungated flow cytometry data in high throughput experiments

scientific article

Data reduction for spectral clustering to analyze high throughput flow cytometry data

scientific article

Data standards for flow cytometry

scientific article

Data-Driven Flow Cytometry Analysis

scientific article published on 01 January 2019

Deep profiling of multitube flow cytometry data

scientific article

Development of FuGO: an ontology for functional genomics investigations

scientific article published on January 2006

Diffuse large B-cell lymphoma: reduced CD20 expression is associated with an inferior survival

scientific article

Dynamic molecular changes during the first week of human life follow a robust developmental trajectory

scientific article published on 12 March 2019

Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays.

scientific article

Enhanced flowType/RchyOptimyx: a BioConductor pipeline for discovery in high-dimensional cytometry data

scientific article

Evaluating flow cytometer performance with weighted quadratic least squares analysis of LED and multi-level bead data.

scientific article

Evidence for a modifier of onset age in Huntington disease linked to the HD gene in 4p16.

scientific article

FCS 3.1 Implementation guidance

scientific article published on 25 January 2012

Flow cytometry bioinformatics

scientific article published on 5 December 2013

Flow cytometry data analysis: Recent tools and algorithms

scientific article published on 01 May 2019

Flow cytometry data standards

scientific article

FlowRepository: a resource of annotated flow cytometry datasets associated with peer-reviewed publications.

scientific article

Gating-ML: XML-based gating descriptions in flow cytometry

scientific article

GenePattern flow cytometry suite ⬇️

scientific article published on July 3, 2013

Guidelines for the use of flow cytometry and cell sorting in immunological studies

scientific article published on October 2017

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

scientific article published on 01 October 2019

Hematopoietic stem cell subtypes expand differentially during development and display distinct lymphopoietic programs

scientific article published on 01 March 2012

High Throughput Automated Analysis of Big Flow Cytometry Data.

scientific article published on 26 December 2017

High-content flow cytometry and temporal data analysis for defining a cellular signature of graft-versus-host disease

scientific article

Human monogenic disorders - a source of novel drug targets

scientific article

ISAC's classification results file format

scientific article published on 18 November 2014

Identification of a novel gene (HSN2) causing hereditary sensory and autonomic neuropathy type II through the Study of Canadian Genetic Isolates

scientific article

Immune biomarkers predictive of respiratory viral infection in elderly nursing home residents.

scientific article

Implementation and Validation of an Automated Flow Cytometry Analysis Pipeline for Human Immune Profiling

scientific article published on 20 December 2018

Improving the Rigor and Reproducibility of Flow Cytometry-Based Clinical Research and Trials Through Automated Data Analysis

scientific article published on 13 September 2019

Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery.

scientific article

Long-term propagation of distinct hematopoietic differentiation programs in vivo

scientific article

MIFlowCyt: the minimum information about a Flow Cytometry Experiment

scientific article

Merging mixture components for cell population identification in flow cytometry

scientific article

Methodology for evaluating and comparing flow cytometers: A multisite study of 23 instruments

scientific article published on 23 September 2018

Modeling biomedical experimental processes with OBI

scientific article

Occurrence of T-cell and NK-cell subsets with less well-recognized phenotypes in peripheral blood submitted for routine flow cytometry analysis

scientific article published on 28 March 2020

OntoFox: web-based support for ontology reuse

scientific article

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates

Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) compliant manuscript using the International Society for Advancement of Cytometry (ISAC) FCS file repository (FlowRepository.org).

scientific article

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

scientific article (publication date: August 2008)

Properties of CD34+ CML stem/progenitor cells that correlate with different clinical responses to imatinib mesylate

scientific article

Psychological consequences and predictors of adverse events in the first 5 years after predictive testing for Huntington's disease.

scientific article published on October 2003

Publishing code is essential for reproducible flow cytometry bioinformatics

scientific article published on 01 January 2016

Rapid cell population identification in flow cytometry data

scientific article

Recent bioinformatics advances in the analysis of high throughput flow cytometry data.

scientific article

Reduction in multi-lineage and erythroid progenitors distinguishes myelodysplastic syndromes from non-malignant cytopenias

scientific article published on 2 May 2009

Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution ⬇️

scientific article published on August 1, 1997

Scoring relevancy of features based on combinatorial analysis of Lasso with application to lymphoma diagnosis

scientific article

Single Cell Phenotypic Profiling of 27 DLBCL Cases Reveals Marked Intertumoral and Intratumoral Heterogeneity

scientific article published on 22 October 2019

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

scientific article

State-of-the-Art in the Computational Analysis of Cytometry Data.

scientific article published in July 2015

T-Cell Phenotypes Predictive of Frailty and Mortality in Elderly Nursing Home Residents

scientific article published on 24 October 2016

The Ontology for Biomedical Investigations

scientific article

The core autophagy protein ATG4B is a potential biomarker and therapeutic target in CML stem/progenitor cells.

scientific article published on 22 April 2014

The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective

scientific article

The luminal progenitor compartment of the normal human mammary gland constitutes a unique site of telomere dysfunction.

scientific article

The phenotypic distribution and functional profile of tuberculin-specific CD4 T-cells characterizes different stages of TB infection.

scientific article published on 7 September 2012

Thinking outside the gate: single-cell assessments in multiple dimensions

scientific article published on April 2015

Toward understanding the molecular pathology of Huntington's disease.

scientific article published on July 1997

Use FlowRepository to Share Your Clinical Data upon Study Publication.

scientific article

VO: Vaccine Ontology

Wrestling with SUMO and bio-ontologies

scientific article

ddPCRclust: an R package and Shiny app for automated analysis of multiplexed ddPCR data

scientific article published on 01 August 2018

flowClean: Automated identification and removal of fluorescence anomalies in flow cytometry data

scientific article

flowClust: a Bioconductor package for automated gating of flow cytometry data

scientific article

flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.

scientific article

flowLearn: Fast and precise identification and quality checking of cell populations in flow cytometry.

scientific article published on 15 February 2018

List of works by Ryan R Brinkman

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

A genome scan for modifiers of age at onset in Huntington disease: The HD MAPS study.

A new model for prediction of the age of onset and penetrance for Huntington's disease based on CAG length.

A standardized immune phenotyping and automated data analysis platform for multicenter biomarker studies

A survey of flow cytometry data analysis methods

A worldwide assessment of the frequency of suicide, suicide attempts, or psychiatric hospitalization after predictive testing for Huntington disease. ⬇️

Allogeneic SCT for relapsed composite and transformed lymphoma using related and unrelated donors: long-term results.

Analysis of High-Throughput Flow Cytometry Data Using plateCore

Automated analysis of flow cytometry data comes of age.

Automated analysis of multidimensional flow cytometry data improves diagnostic accuracy between mantle cell lymphoma and small lymphocytic lymphoma

Automated gating of flow cytometry data via robust model-based clustering

B cells with high side scatter parameter by flow cytometry correlate with inferior survival in diffuse large B-cell lymphoma

BAIT: Organizing genomes and mapping rearrangements in single cells

Bim regulates alloimmune-mediated vascular injury through effects on T-cell activation and death.

Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII

Computational analysis optimizes the flow cytometric evaluation for lymphoma

Correlation analysis of intracellular and secreted cytokines via the generalized integrated mean fluorescence intensity.

Critical assessment of automated flow cytometry data analysis techniques.

Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops

Cytogenetic and molecular responses to standard-dose imatinib in chronic myeloid leukemia are correlated with Sokal risk scores and duration of therapy but not trough imatinib plasma levels.

Data File Standard for Flow Cytometry, version FCS 3.1.

Data quality assessment of ungated flow cytometry data in high throughput experiments

Data reduction for spectral clustering to analyze high throughput flow cytometry data

Data standards for flow cytometry

Data-Driven Flow Cytometry Analysis

Deep profiling of multitube flow cytometry data

Development of FuGO: an ontology for functional genomics investigations

Diffuse large B-cell lymphoma: reduced CD20 expression is associated with an inferior survival

Dynamic molecular changes during the first week of human life follow a robust developmental trajectory

Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays.

Enhanced flowType/RchyOptimyx: a BioConductor pipeline for discovery in high-dimensional cytometry data

Evaluating flow cytometer performance with weighted quadratic least squares analysis of LED and multi-level bead data.

Evidence for a modifier of onset age in Huntington disease linked to the HD gene in 4p16.

FCS 3.1 Implementation guidance

Flow cytometry bioinformatics

Flow cytometry data analysis: Recent tools and algorithms

Flow cytometry data standards

FlowRepository: a resource of annotated flow cytometry datasets associated with peer-reviewed publications.

Gating-ML: XML-based gating descriptions in flow cytometry

GenePattern flow cytometry suite ⬇️

Guidelines for the use of flow cytometry and cell sorting in immunological studies

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

Hematopoietic stem cell subtypes expand differentially during development and display distinct lymphopoietic programs

High Throughput Automated Analysis of Big Flow Cytometry Data.

High-content flow cytometry and temporal data analysis for defining a cellular signature of graft-versus-host disease

Human monogenic disorders - a source of novel drug targets

ISAC's classification results file format

Identification of a novel gene (HSN2) causing hereditary sensory and autonomic neuropathy type II through the Study of Canadian Genetic Isolates

Immune biomarkers predictive of respiratory viral infection in elderly nursing home residents.

Implementation and Validation of an Automated Flow Cytometry Analysis Pipeline for Human Immune Profiling

Improving the Rigor and Reproducibility of Flow Cytometry-Based Clinical Research and Trials Through Automated Data Analysis

Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery.

Long-term propagation of distinct hematopoietic differentiation programs in vivo

MIFlowCyt: the minimum information about a Flow Cytometry Experiment

Merging mixture components for cell population identification in flow cytometry

Methodology for evaluating and comparing flow cytometers: A multisite study of 23 instruments

Modeling biomedical experimental processes with OBI

Occurrence of T-cell and NK-cell subsets with less well-recognized phenotypes in peripheral blood submitted for routine flow cytometry analysis

OntoFox: web-based support for ontology reuse

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates

Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) compliant manuscript using the International Society for Advancement of Cytometry (ISAC) FCS file repository (FlowRepository.org).

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Properties of CD34+ CML stem/progenitor cells that correlate with different clinical responses to imatinib mesylate

Psychological consequences and predictors of adverse events in the first 5 years after predictive testing for Huntington's disease.

Publishing code is essential for reproducible flow cytometry bioinformatics

Rapid cell population identification in flow cytometry data

Recent bioinformatics advances in the analysis of high throughput flow cytometry data.

Reduction in multi-lineage and erythroid progenitors distinguishes myelodysplastic syndromes from non-malignant cytopenias

Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution ⬇️

Scoring relevancy of features based on combinatorial analysis of Lasso with application to lymphoma diagnosis

Single Cell Phenotypic Profiling of 27 DLBCL Cases Reveals Marked Intertumoral and Intratumoral Heterogeneity

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

State-of-the-Art in the Computational Analysis of Cytometry Data.

T-Cell Phenotypes Predictive of Frailty and Mortality in Elderly Nursing Home Residents

The Ontology for Biomedical Investigations

The core autophagy protein ATG4B is a potential biomarker and therapeutic target in CML stem/progenitor cells.

The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective

The luminal progenitor compartment of the normal human mammary gland constitutes a unique site of telomere dysfunction.