Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets
Belkina, Anna C., Ciccolella, Christopher O., Anno, Rina, Halpert, Richard, Spidlen, Josef, Snyder-Cappione, Jennifer E.
Published in Nature communications (28.11.2019)
Published in Nature communications (28.11.2019)
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Journal Article
Flow cytometry bioinformatics
O'Neill, Kieran, Aghaeepour, Nima, Spidlen, Josef, Brinkman, Ryan
Published in PLoS computational biology (01.12.2013)
Published in PLoS computational biology (01.12.2013)
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Journal Article
flowCore: a Bioconductor package for high throughput flow cytometry
Hahne, Florian, LeMeur, Nolwenn, Brinkman, Ryan R, Ellis, Byron, Haaland, Perry, Sarkar, Deepayan, Spidlen, Josef, Strain, Errol, Gentleman, Robert
Published in BMC bioinformatics (09.04.2009)
Published in BMC bioinformatics (09.04.2009)
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Journal Article
AutoSpill is a principled framework that simplifies the analysis of multichromatic flow cytometry data
Roca, Carlos P., Burton, Oliver T., Gergelits, Václav, Prezzemolo, Teresa, Whyte, Carly E., Halpert, Richard, Kreft, Łukasz, Collier, James, Botzki, Alexander, Spidlen, Josef, Humblet-Baron, Stéphanie, Liston, Adrian
Published in Nature communications (17.05.2021)
Published in Nature communications (17.05.2021)
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Journal Article
MIFlowCyt: The minimum information about a flow cytometry experiment
Lee, Jamie A, Spidlen, Josef, Boyce, Keith, Cai, Jennifer, Crosbie, Nicholas, Dalphin, Mark, Furlong, Jeff, Gasparetto, Maura, Goldberg, Michael, Goralczyk, Elizabeth M, Hyun, Bill, Jansen, Kirstin, Kollmann, Tobias, Kong, Megan, Leif, Robert, McWeeney, Shannon, Moloshok, Thomas D, Moore, Wayne, Nolan, Garry, Nolan, John, Nikolich-Zugich, Janko, Parrish, David, Purcell, Barclay, Qian, Yu, Selvaraj, Biruntha, Smith, Clayton, Tchuvatkina, Olga, Wertheimer, Anne, Wilkinson, Peter, Wilson, Christopher, Wood, James, Zigon, Robert, Scheuermann, Richard H, Brinkman, Ryan R
Published in Cytometry. Part A (01.10.2008)
Published in Cytometry. Part A (01.10.2008)
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Journal Article
Methodology for evaluating and comparing flow cytometers: A multisite study of 23 instruments
Parks, David R., Moore, Wayne A., Brinkman, Ryan R., Chen, Yong, Condello, Danilo, El Khettabi, Faysal, Nolan, John P., Perfetto, Stephen P., Redelman, Doug, Spidlen, Josef, Van Dyke, Jonathan, Wang, Lili, Wood, James C. S.
Published in Cytometry. Part A (01.11.2018)
Published in Cytometry. Part A (01.11.2018)
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Journal Article
Data File Standard for Flow Cytometry, version FCS 3.1
Spidlen, Josef, Moore, Wayne, Parks, David, Goldberg, Michael, Bray, Chris, Bierre, Pierre, Gorombey, Peter, Hyun, Bill, Hubbard, Mark, Lange, Simon, Lefebvre, Ray, Leif, Robert, Novo, David, Ostruszka, Leo, Treister, Adam, Wood, James, Murphy, Robert F, Roederer, Mario, Sudar, Damir, Zigon, Robert, Brinkman, Ryan R
Published in Cytometry. Part A (01.01.2010)
Published in Cytometry. Part A (01.01.2010)
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Journal Article
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)
Spidlen, Josef, Breuer, Karin, Brinkman, Ryan
Published in Current protocols in cytometry (01.07.2012)
Published in Current protocols in cytometry (01.07.2012)
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Journal Article
Flow cytometry data standards
Spidlen, Josef, Shooshtari, Parisa, Kollmann, Tobias R, Brinkman, Ryan R
Published in BMC research notes (07.03.2011)
Published in BMC research notes (07.03.2011)
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Journal Article
GenePattern flow cytometry suite
Spidlen, Josef, Barsky, Aaron, Breuer, Karin, Carr, Peter, Nazaire, Marc-Danie, Hill, Barbara Allen, Qian, Yu, Liefeld, Ted, Reich, Michael, Mesirov, Jill P, Wilkinson, Peter, Scheuermann, Richard H, Sekaly, Rafick-Pierre, Brinkman, Ryan R
Published in Source code for biology and medicine (03.07.2013)
Published in Source code for biology and medicine (03.07.2013)
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Journal Article
FuGEFlow: data model and markup language for flow cytometry
Qian, Yu, Tchuvatkina, Olga, Spidlen, Josef, Wilkinson, Peter, Gasparetto, Maura, Jones, Andrew R, Manion, Frank J, Scheuermann, Richard H, Sekaly, Rafick-Pierre, Brinkman, Ryan R
Published in BMC bioinformatics (16.06.2009)
Published in BMC bioinformatics (16.06.2009)
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Journal Article
20,000 layers under the model: Bayesian neural networks improve the robustness of human PBMC classifications using immunologist encoded bias
Velazquez-palafox, Miguel Angel, Taylor, Ian James, Spidlen, Josef, Lai, Janice, Halpert, Richard, Stadnisky, Michael
Published in The Journal of immunology (1950) (01.05.2019)
Published in The Journal of immunology (1950) (01.05.2019)
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Journal Article
Data File Standard for Flow Cytometry, Version FCS 3.2
Spidlen, Josef, Moore, Wayne, Parks, David, Goldberg, Michael, Blenman, Kim, Cavenaugh, James S., Brinkman, Ryan
Published in Cytometry. Part A (01.01.2021)
Published in Cytometry. Part A (01.01.2021)
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Journal Article
Flexible information storage in MUDRII EHR
Špidlen, Josef, Hanzlíček, Petr, Říha, Antonin, Zvárová, Jana
Published in International journal of medical informatics (Shannon, Ireland) (01.03.2006)
Published in International journal of medical informatics (Shannon, Ireland) (01.03.2006)
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Journal Article
Flexible information storage in MUDR II EHR
Špidlen, Josef, Hanzlíček, Petr, Říha, Antonin, Zvárová, Jana
Published in International journal of medical informatics (Shannon, Ireland) (2006)
Published in International journal of medical informatics (Shannon, Ireland) (2006)
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Journal Article