The OWL of Biomedical Investigations. - Mélanie Courtot; William J. Bug; Frank Gibson; Allyson L. Lister; James Malone; Daniel Schober; Ryan Remy Brinkman; Alan Ruttenberg (OWLED, 2008)

A Survey of Flow Cytometry Data Analysis Methods. - Ali Bashashati; Ryan Remy Brinkman (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)

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)

Analysis of High-Throughput Flow Cytometry Data Using plateCore. - Errol Strain; Florian Hahne; Ryan Remy Brinkman; Perry Haaland (Adv. Bioinformatics, 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)

flowClust: a Bioconductor package for automated gating of flow cytometry data. - Kenneth Lo; Florian Hahne; Ryan Remy Brinkman; Raphael Gottardo (BMC Bioinform., 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)

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; et al. (J. Biomed. Semant., 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)

Towards an Adverse Event Reporting Ontology. - Mélanie Courtot; Ryan Remy Brinkman (ICBO, 2011)

Reporting Adverse Events: Basis for a Common Representation. - Mélanie Courtot; Ryan Remy Brinkman; Alan Ruttenberg (ICBO, 2011)

Building the OBO Foundry - One Policy at a Time. - Mélanie Courtot; Chris Mungall; Ryan Remy Brinkman; Alan Ruttenberg (ICBO, 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)

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)

Adverse events following immunization: reporting standardization, automatic case classification and signal detection. - Mélanie Courtot; Ryan Remy Brinkman; Alan Ruttenberg (ICBO, 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)

Diagnostic criteria and clinical guidelines standardization to automate case classification. - Mélanie Courtot; Jie Zheng 001; Christian J. Stoeckert Jr.; Ryan Remy Brinkman; Alan Ruttenberg (ICBO, 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)

Flow Cytometry Bioinformatics. - Kieran O'Neill; Nima Aghaeepour; Josef Spidlen; Ryan Remy Brinkman (PLoS Comput. Biol., 2013)

GenePattern Flow Cytometry Suite. - Josef Spidlen; Aaron Barsky; Karin Breuer; Peter Carr 004; Marc-Danie Nazaire; Barbara A. Hill; Yu Qian; Ted Liefeld; Michael Reich; Jill P. Mesirov; Peter Wilkinson; Richard H. Scheuermann; et al. (Source Code Biol. Medicine, 2013)

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)

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)

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)

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)

ddPCRclust: an R package and Shiny app for automated analysis of multiplexed ddPCR data. - Benedikt G. Brink; Justin Meskas; Ryan Remy Brinkman (Bioinform., 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)