Ryan Remy Brinkman

According to our database, Ryan Remy Brinkman authored at least 27 papers between 2008 and 2018.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2018

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

Markus Lux, Ryan Remy Brinkman, Cédric Chauve, Adam Laing, Anna Lorenc, Lucie Abeler-Dörner, Barbara Hammer

Bioinform., 2018

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

Benedikt G. Brink, Justin Meskas, Ryan Remy Brinkman

Bioinform., 2018

2015

Deep profiling of multitube flow cytometry data.

Kieran O'Neill, Nima Aghaeepour, Jeremy Parker, Donna Hogge, Aly Karsan, Bakul Dalal, Ryan Remy Brinkman

Bioinform., 2015

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

Mehrnoush Malek, Mohammad Jafar Taghiyar, Lauren Chong, Greg Finak, Raphael Gottardo, Ryan Remy Brinkman

Bioinform., 2015

flowCL: ontology-based cell population labelling in flow cytometry.

Mélanie Courtot, Justin Meskas, Alexander D. Diehl, Radina Droumeva, Raphael Gottardo, Adrin Jalali, Mohammad Jafar Taghiyar, Holden T. Maecker, J. Philip McCoy, Alan Ruttenberg, Richard H. Scheuermann, Ryan Remy Brinkman

Bioinform., 2015

2014

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

Kieran O'Neill, Adrin Jalali, Nima Aghaeepour, Holger H. Hoos, Ryan Remy Brinkman

Bioinform., 2014

2013

GenePattern Flow Cytometry Suite.

Josef Spidlen, Aaron Barsky, Karin Breuer, Peter Carr, Marc-Danie Nazaire, Barbara A. Hill, Yu Qian, Ted Liefeld, Michael Reich, Jill P. Mesirov, Peter Wilkinson, Richard H. Scheuermann, Rafick-Pierre Sekaly, Ryan Remy Brinkman

Source Code Biol. Medicine, 2013

Flow Cytometry Bioinformatics.

Kieran O'Neill, Nima Aghaeepour, Josef Spidlen, Ryan Remy Brinkman

PLoS Comput. Biol., 2013

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

Habil Zare, Gholamreza Haffari, Arvind Gupta, Ryan Remy Brinkman

BMC Genom., 2013

Diagnostic criteria and clinical guidelines standardization to automate case classification.

Mélanie Courtot, Jie Zheng, Christian J. Stoeckert Jr., Ryan Remy Brinkman, Alan Ruttenberg

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

2012

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

Nima Aghaeepour, Pratip K. Chattopadhyay, Anuradha Ganesan, Kieran O'Neill, Habil Zare, Adrin Jalali, Holger H. Hoos, Mario Roederer, Ryan Remy Brinkman

Bioinform., 2012

Adverse events following immunization: reporting standardization, automatic case classification and signal detection.

Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg

Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

2011

Overcoming the ontology enrichment bottleneck with Quick Term Templates.

Philippe Rocca-Serra, Alan Ruttenberg, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober, Jay Greenbaum, Mélanie Courtot, Ryan Remy Brinkman, Susanna-Assunta Sansone, Richard H. Scheuermann, Bjoern Peters

Appl. Ontology, 2011

MIREOT: The minimum information to reference an external ontology term.

Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Remy Brinkman, Alan Ruttenberg

Appl. Ontology, 2011

Building the OBO Foundry - One Policy at a Time.

Mélanie Courtot, Chris Mungall, Ryan Remy Brinkman, Alan Ruttenberg

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Reporting Adverse Events: Basis for a Common Representation.

Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Towards an Adverse Event Reporting Ontology.

Mélanie Courtot, Ryan Remy Brinkman

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2010

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

Habil Zare, Parisa Shooshtari, Arvind Gupta, Ryan Remy Brinkman

BMC Bioinform., 2010

Modeling biomedical experimental processes with OBI.

Ryan Remy Brinkman, Mélanie Courtot, Dirk Derom, Jennifer Fostel, Yongqun He, Phillip W. Lord, James Malone, Helen E. Parkinson, Björn Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Larisa N. Soldatova, Christian J. Stoeckert Jr., Jessica A. Turner, Jie Zheng, et al.

J. Biomed. Semant., 2010

2009

FuGEFlow: data model and markup language for flow cytometry.

Yu Qian, Olga Tchuvatkina, Josef Spidlen, Peter Wilkinson, Maura Gasparetto, Andrew R. Jones, Frank J. Manion, Richard H. Scheuermann, Rafick-Pierre Sekaly, Ryan Remy Brinkman

BMC Bioinform., 2009

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

Kenneth Lo, Florian Hahne, Ryan Remy Brinkman, Raphael Gottardo

BMC Bioinform., 2009

flowCore: a Bioconductor package for high throughput flow cytometry.

Florian Hahne, Nolwenn LeMeur, Ryan Remy Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain, Robert Gentleman

BMC Bioinform., 2009

Analysis of High-Throughput Flow Cytometry Data Using plateCore.

Errol Strain, Florian Hahne, Ryan Remy Brinkman, Perry Haaland

Adv. Bioinformatics, 2009

Recent Bioinformatics Advances in the Analysis of High Throughput Flow Cytometry Data.

Raphael Gottardo, Ryan Remy Brinkman, George Luta, Matthew P. Wand

Adv. Bioinformatics, 2009

Merging Mixture Components for Cell Population Identification in Flow Cytometry.

Greg Finak, Ali Bashashati, Ryan Remy Brinkman, Raphael Gottardo

Adv. Bioinformatics, 2009

A Survey of Flow Cytometry Data Analysis Methods.

Ali Bashashati, Ryan Remy Brinkman

Adv. Bioinformatics, 2009

2008

The OWL of Biomedical Investigations.

Mélanie Courtot, William J. Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Remy Brinkman, Alan Ruttenberg

Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions, 2008