Ryan Remy Brinkman

27 papers Journal 21Unranked 6
YearRankTypeTitle / Venue / Authors
2018 J jnl
ddPCRclust: an R package and Shiny app for automated analysis of multiplexed ddPCR data.
Bioinform.
Benedikt G. Brink, Justin Meskas, Ryan Remy Brinkman
2018 J jnl
flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry.
Bioinform.
Markus Lux, Ryan Remy Brinkman, Cédric Chauve, Adam Laing, Anna Lorenc, Lucie Abeler-Dörner, Barbara Hammer
2015 J jnl
Deep profiling of multitube flow cytometry data.
Bioinform.
Kieran O'Neill, Nima Aghaeepour, Jeremy Parker, Donna Hogge, Aly Karsan, Bakul Dalal, Ryan Remy Brinkman
2015 J jnl
flowCL: ontology-based cell population labelling in flow cytometry.
Bioinform.
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
2015 J jnl
flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.
Bioinform.
Mehrnoush Malek, Mohammad Jafar Taghiyar, Lauren Chong, Greg Finak, Raphael Gottardo, Ryan Remy Brinkman
2014 J jnl
Enhanced flowType/RchyOptimyx: a Bioconductor pipeline for discovery in high-dimensional cytometry data.
Bioinform.
Kieran O'Neill, Adrin Jalali, Nima Aghaeepour, Holger H. Hoos, Ryan Remy Brinkman
2013 — conf
Diagnostic criteria and clinical guidelines standardization to automate case classification.
ICBO
Mélanie Courtot, Jie Zheng, Christian J. Stoeckert Jr., Ryan Remy Brinkman, Alan Ruttenberg
2013 J jnl
Flow Cytometry Bioinformatics.
PLoS Comput. Biol.
Kieran O'Neill, Nima Aghaeepour, Josef Spidlen, Ryan Remy Brinkman
2013 J jnl
GenePattern Flow Cytometry Suite.
Source Code Biol. Medicine
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
2013 J jnl
Scoring relevancy of features based on combinatorial analysis of Lasso with application to lymphoma diagnosis.
BMC Genom.
Habil Zare, Gholamreza Haffari, Arvind Gupta, Ryan Remy Brinkman
2012 — conf
Adverse events following immunization: reporting standardization, automatic case classification and signal detection.
ICBO
Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg
2012 J jnl
Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays.
Bioinform.
Nima Aghaeepour, Pratip K. Chattopadhyay, Anuradha Ganesan, Kieran O'Neill, Habil Zare, Adrin Jalali, Holger H. Hoos, Mario Roederer, Ryan Remy Brinkman
2011 — conf
Building the OBO Foundry - One Policy at a Time.
ICBO
Mélanie Courtot, Chris Mungall, Ryan Remy Brinkman, Alan Ruttenberg
2011 J jnl
MIREOT: The minimum information to reference an external ontology term.
Appl. Ontology
Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Remy Brinkman, Alan Ruttenberg
2011 J jnl
Overcoming the ontology enrichment bottleneck with Quick Term Templates.
Appl. Ontology
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
2011 — conf
Reporting Adverse Events: Basis for a Common Representation.
ICBO
Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg
2011 — conf
Towards an Adverse Event Reporting Ontology.
ICBO
Mélanie Courtot, Ryan Remy Brinkman
2010 J jnl
Data reduction for spectral clustering to analyze high throughput flow cytometry data.
BMC Bioinform.
Habil Zare, Parisa Shooshtari, Arvind Gupta, Ryan Remy Brinkman
2010 J jnl
Modeling biomedical experimental processes with OBI.
J. Biomed. Semant.
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.
2009 J jnl
A Survey of Flow Cytometry Data Analysis Methods.
Adv. Bioinformatics
Ali Bashashati, Ryan Remy Brinkman
2009 J jnl
Analysis of High-Throughput Flow Cytometry Data Using plateCore.
Adv. Bioinformatics
Errol Strain, Florian Hahne, Ryan Remy Brinkman, Perry Haaland
2009 J jnl
FuGEFlow: data model and markup language for flow cytometry.
BMC Bioinform.
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
2009 J jnl
Merging Mixture Components for Cell Population Identification in Flow Cytometry.
Adv. Bioinformatics
Greg Finak, Ali Bashashati, Ryan Remy Brinkman, Raphael Gottardo
2009 J jnl
Recent Bioinformatics Advances in the Analysis of High Throughput Flow Cytometry Data.
Adv. Bioinformatics
Raphael Gottardo, Ryan Remy Brinkman, George Luta, Matthew P. Wand
2009 J jnl
flowClust: a Bioconductor package for automated gating of flow cytometry data.
BMC Bioinform.
Kenneth Lo, Florian Hahne, Ryan Remy Brinkman, Raphael Gottardo
2009 J jnl
flowCore: a Bioconductor package for high throughput flow cytometry.
BMC Bioinform.
Florian Hahne, Nolwenn LeMeur, Ryan Remy Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain, Robert Gentleman
2008 — conf
The OWL of Biomedical Investigations.
OWLED
Mélanie Courtot, William J. Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Remy Brinkman, Alan Ruttenberg