Search Results - "Spidlen, Josef"

Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets by Belkina, Anna C., Ciccolella, Christopher O., Anno, Rina, Halpert, Richard, Spidlen, Josef, Snyder-Cappione, Jennifer E.

“…Accurate and comprehensive extraction of information from high-dimensional single cell datasets necessitates faithful visualizations to assess biological…”
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Flow cytometry bioinformatics by O'Neill, Kieran, Aghaeepour, Nima, Spidlen, Josef, Brinkman, Ryan

“…Flow cytometry bioinformatics is the application of bioinformatics to flow cytometry data, which involves storing, retrieving, organizing, and analyzing flow…”
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flowCore: a Bioconductor package for high throughput flow cytometry by Hahne, Florian, LeMeur, Nolwenn, Brinkman, Ryan R, Ellis, Byron, Haaland, Perry, Sarkar, Deepayan, Spidlen, Josef, Strain, Errol, Gentleman, Robert

“…Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in…”
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AutoSpill is a principled framework that simplifies the analysis of multichromatic flow cytometry data by 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

“…Compensating in flow cytometry is an unavoidable challenge in the data analysis of fluorescence-based flow cytometry. Even the advent of spectral cytometry…”
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flowClean: Automated identification and removal of fluorescence anomalies in flow cytometry data by Fletez‐Brant, Kipper, Špidlen, Josef, Brinkman, Ryan R., Roederer, Mario, Chattopadhyay, Pratip K.

“…Modern flow cytometry systems can be coupled to plate readers for high‐throughput acquisition. These systems allow hundreds of samples to be analyzed in a…”
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MIFlowCyt: The minimum information about a flow cytometry experiment by 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

“…A fundamental tenet of scientific research is that published results are open to independent validation and refutation. Minimum data standards aid data…”
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Methodology for evaluating and comparing flow cytometers: A multisite study of 23 instruments by 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.

“…We demonstrate improved methods for making valid and accurate comparisons of fluorescence measurement capabilities among instruments tested at different sites…”
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Data File Standard for Flow Cytometry, version FCS 3.1 by 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

“…The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file…”
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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) by Spidlen, Josef, Breuer, Karin, Brinkman, Ryan

“…FlowRepository.org is a Web-based flow cytometry data repository provided by the International Society for Advancement of Cytometry (ISAC). It supports…”
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Flow cytometry data standards by Spidlen, Josef, Shooshtari, Parisa, Kollmann, Tobias R, Brinkman, Ryan R

“…Flow cytometry is a widely used analytical technique for examining microscopic particles, such as cells. The Flow Cytometry Standard (FCS) was developed in…”
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GenePattern flow cytometry suite by 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

“…Traditional flow cytometry data analysis is largely based on interactive and time consuming analysis of series two dimensional representations of up to 20…”
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FuGEFlow: data model and markup language for flow cytometry by 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

“…Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of…”
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Obstacles to Implementing an Execution Engine for Clinical Guidelines Formalized in GLIF by Kolesa, Petr, Spidlen, Josef, Zvárová, Jana

“…This article is on obstacles we faced when developing an executable representation of guidelines formalized the Guideline Interchange Format (GLIF). The GLIF…”
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FlowRepository: A resource of annotated flow cytometry datasets associated with peer‐reviewed publications by Spidlen, Josef, Breuer, Karin, Rosenberg, Chad, Kotecha, Nikesh, Brinkman, Ryan R.

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ICEFormat—the image cytometry experiment format by Spidlen, Josef, Novo, David

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20,000 layers under the model: Bayesian neural networks improve the robustness of human PBMC classifications using immunologist encoded bias by Velazquez-palafox, Miguel Angel, Taylor, Ian James, Spidlen, Josef, Lai, Janice, Halpert, Richard, Stadnisky, Michael

“…Abstract Accurate classification of immunological subsets is a cornerstone of routine assays in basic research and the clinic. This process generates terabytes…”
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Data File Standard for Flow Cytometry, Version FCS 3.2 by Spidlen, Josef, Moore, Wayne, Parks, David, Goldberg, Michael, Blenman, Kim, Cavenaugh, James S., Brinkman, Ryan

“…FCS 3.2 is a revision of the flow cytometry data standard based on a decade of suggested improvements from the community as well as industry needs to capture…”
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Use FlowRepository to share your clinical data upon study publication by Spidlen, Josef, Brinkman, Ryan R.

“…A fundamental tenet of scientific research is that published results including underlying data should be open to independent validation and refutation. Data…”
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ISAC 's G ating‐ ML 2.0 data exchange standard for gating description by Spidlen, Josef, Moore, Wayne, Brinkman, Ryan R.

“…Abstract The lack of software interoperability with respect to gating has traditionally been a bottleneck preventing the use of multiple analytical tools and…”
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Flow Cytometry Bioinformatics: e1003365 by Aghaeepour, Nima, Spidlen, Josef, Brinkman, Ryan

“…Flow cytometry bioinformatics is the application of bioinformatics to flow cytometry data, which involves storing, retrieving, organizing, and analyzing flow…”
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