Ryan R Brinkman

Ryan R Brinkman

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Ryan R Brinkman

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Data-Driven Flow Cytometry Analysis.

Methods Mol Biol 2019 ;1989:245-265

Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada.

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http://dx.doi.org/10.1007/978-1-4939-9454-0_16DOI Listing
March 2020

Occurrence of T-cell and NK-cell subsets with less well-recognized phenotypes in peripheral blood submitted for routine flow cytometry analysis.

Cytometry B Clin Cytom 2020 Mar 28. Epub 2020 Mar 28.

Department of Pathology and Lab Medicine, University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1002/cyto.b.21876DOI Listing
March 2020

Improving the Rigor and Reproducibility of Flow Cytometry-Based Clinical Research and Trials Through Automated Data Analysis.

Authors:
Ryan R Brinkman

Cytometry A 2020 Feb 13;97(2):107-112. Epub 2019 Sep 13.

Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1002/cyto.a.23883DOI Listing
February 2020

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition).

Authors:
Andrea Cossarizza Hyun-Dong Chang Andreas Radbruch Andreas Acs Dieter Adam Sabine Adam-Klages William W Agace Nima Aghaeepour Mübeccel Akdis Matthieu Allez Larissa Nogueira Almeida Giorgia Alvisi Graham Anderson Immanuel Andrä Francesco Annunziato Achille Anselmo Petra Bacher Cosima T Baldari Sudipto Bari Vincenzo Barnaba Joana Barros-Martins Luca Battistini Wolfgang Bauer Sabine Baumgart Nicole Baumgarth Dirk Baumjohann Bianka Baying Mary Bebawy Burkhard Becher Wolfgang Beisker Vladimir Benes Rudi Beyaert Alfonso Blanco Dominic A Boardman Christian Bogdan Jessica G Borger Giovanna Borsellino Philip E Boulais Jolene A Bradford Dirk Brenner Ryan R Brinkman Anna E S Brooks Dirk H Busch Martin Büscher Timothy P Bushnell Federica Calzetti Garth Cameron Ilenia Cammarata Xuetao Cao Susanna L Cardell Stefano Casola Marco A Cassatella Andrea Cavani Antonio Celada Lucienne Chatenoud Pratip K Chattopadhyay Sue Chow Eleni Christakou Luka Čičin-Šain Mario Clerici Federico S Colombo Laura Cook Anne Cooke Andrea M Cooper Alexandra J Corbett Antonio Cosma Lorenzo Cosmi Pierre G Coulie Ana Cumano Ljiljana Cvetkovic Van Duc Dang Chantip Dang-Heine Martin S Davey Derek Davies Sara De Biasi Genny Del Zotto Gelo Victoriano Dela Cruz Michael Delacher Silvia Della Bella Paolo Dellabona Günnur Deniz Mark Dessing James P Di Santo Andreas Diefenbach Francesco Dieli Andreas Dolf Thomas Dörner Regine J Dress Diana Dudziak Michael Dustin Charles-Antoine Dutertre Friederike Ebner Sidonia B G Eckle Matthias Edinger Pascale Eede Götz R A Ehrhardt Marcus Eich Pablo Engel Britta Engelhardt Anna Erdei Charlotte Esser Bart Everts Maximilien Evrard Christine S Falk Todd A Fehniger Mar Felipo-Benavent Helen Ferry Markus Feuerer Andrew Filby Kata Filkor Simon Fillatreau Marie Follo Irmgard Förster John Foster Gemma A Foulds Britta Frehse Paul S Frenette Stefan Frischbutter Wolfgang Fritzsche David W Galbraith Anastasia Gangaev Natalio Garbi Brice Gaudilliere Ricardo T Gazzinelli Jens Geginat Wilhelm Gerner Nicholas A Gherardin Kamran Ghoreschi Lara Gibellini Florent Ginhoux Keisuke Goda Dale I Godfrey Christoph Goettlinger Jose M González-Navajas Carl S Goodyear Andrea Gori Jane L Grogan Daryl Grummitt Andreas Grützkau Claudia Haftmann Jonas Hahn Hamida Hammad Günter Hämmerling Leo Hansmann Goran Hansson Christopher M Harpur Susanne Hartmann Andrea Hauser Anja E Hauser David L Haviland David Hedley Daniela C Hernández Guadalupe Herrera Martin Herrmann Christoph Hess Thomas Höfer Petra Hoffmann Kristin Hogquist Tristan Holland Thomas Höllt Rikard Holmdahl Pleun Hombrink Jessica P Houston Bimba F Hoyer Bo Huang Fang-Ping Huang Johanna E Huber Jochen Huehn Michael Hundemer Christopher A Hunter William Y K Hwang Anna Iannone Florian Ingelfinger Sabine M Ivison Hans-Martin Jäck Peter K Jani Beatriz Jávega Stipan Jonjic Toralf Kaiser Tomas Kalina Thomas Kamradt Stefan H E Kaufmann Baerbel Keller Steven L C Ketelaars Ahad Khalilnezhad Srijit Khan Jan Kisielow Paul Klenerman Jasmin Knopf Hui-Fern Koay Katja Kobow Jay K Kolls Wan Ting Kong Manfred Kopf Thomas Korn Katharina Kriegsmann Hendy Kristyanto Thomas Kroneis Andreas Krueger Jenny Kühne Christian Kukat Désirée Kunkel Heike Kunze-Schumacher Tomohiro Kurosaki Christian Kurts Pia Kvistborg Immanuel Kwok Jonathan Landry Olivier Lantz Paola Lanuti Francesca LaRosa Agnès Lehuen Salomé LeibundGut-Landmann Michael D Leipold Leslie Y T Leung Megan K Levings Andreia C Lino Francesco Liotta Virginia Litwin Yanling Liu Hans-Gustaf Ljunggren Michael Lohoff Giovanna Lombardi Lilly Lopez Miguel López-Botet Amy E Lovett-Racke Erik Lubberts Herve Luche Burkhard Ludewig Enrico Lugli Sebastian Lunemann Holden T Maecker Laura Maggi Orla Maguire Florian Mair Kerstin H Mair Alberto Mantovani Rudolf A Manz Aaron J Marshall Alicia Martínez-Romero Glòria Martrus Ivana Marventano Wlodzimierz Maslinski Giuseppe Matarese Anna Vittoria Mattioli Christian Maueröder Alessio Mazzoni James McCluskey Mairi McGrath Helen M McGuire Iain B McInnes Henrik E Mei Fritz Melchers Susanne Melzer Dirk Mielenz Stephen D Miller Kingston H G Mills Hans Minderman Jenny Mjösberg Jonni Moore Barry Moran Lorenzo Moretta Tim R Mosmann Susann Müller Gabriele Multhoff Luis Enrique Muñoz Christian Münz Toshinori Nakayama Milena Nasi Katrin Neumann Lai Guan Ng Antonia Niedobitek Sussan Nourshargh Gabriel Núñez José-Enrique O'Connor Aaron Ochel Anna Oja Diana Ordonez Alberto Orfao Eva Orlowski-Oliver Wenjun Ouyang Annette Oxenius Raghavendra Palankar Isabel Panse Kovit Pattanapanyasat Malte Paulsen Dinko Pavlinic Livius Penter Pärt Peterson Christian Peth Jordi Petriz Federica Piancone Winfried F Pickl Silvia Piconese Marcello Pinti A Graham Pockley Malgorzata Justyna Podolska Zhiyong Poon Katharina Pracht Immo Prinz Carlo E M Pucillo Sally A Quataert Linda Quatrini Kylie M Quinn Helena Radbruch Tim R D J Radstake Susann Rahmig Hans-Peter Rahn Bartek Rajwa Gevitha Ravichandran Yotam Raz Jonathan A Rebhahn Diether Recktenwald Dorothea Reimer Caetano Reis E Sousa Ester B M Remmerswaal Lisa Richter Laura G Rico Andy Riddell Aja M Rieger J Paul Robinson Chiara Romagnani Anna Rubartelli Jürgen Ruland Armin Saalmüller Yvan Saeys Takashi Saito Shimon Sakaguchi Francisco Sala-de-Oyanguren Yvonne Samstag Sharon Sanderson Inga Sandrock Angela Santoni Ramon Bellmàs Sanz Marina Saresella Catherine Sautes-Fridman Birgit Sawitzki Linda Schadt Alexander Scheffold Hans U Scherer Matthias Schiemann Frank A Schildberg Esther Schimisky Andreas Schlitzer Josephine Schlosser Stephan Schmid Steffen Schmitt Kilian Schober Daniel Schraivogel Wolfgang Schuh Thomas Schüler Reiner Schulte Axel Ronald Schulz Sebastian R Schulz Cristiano Scottá Daniel Scott-Algara David P Sester T Vincent Shankey Bruno Silva-Santos Anna Katharina Simon Katarzyna M Sitnik Silvano Sozzani Daniel E Speiser Josef Spidlen Anders Stahlberg Alan M Stall Natalie Stanley Regina Stark Christina Stehle Tobit Steinmetz Hannes Stockinger Yousuke Takahama Kiyoshi Takeda Leonard Tan Attila Tárnok Gisa Tiegs Gergely Toldi Julia Tornack Elisabetta Traggiai Mohamed Trebak Timothy I M Tree Joe Trotter John Trowsdale Maria Tsoumakidou Henning Ulrich Sophia Urbanczyk Willem van de Veen Maries van den Broek Edwin van der Pol Sofie Van Gassen Gert Van Isterdael René A W van Lier Marc Veldhoen Salvador Vento-Asturias Paulo Vieira David Voehringer Hans-Dieter Volk Anouk von Borstel Konrad von Volkmann Ari Waisman Rachael V Walker Paul K Wallace Sa A Wang Xin M Wang Michael D Ward Kirsten A Ward-Hartstonge Klaus Warnatz Gary Warnes Sarah Warth Claudia Waskow James V Watson Carsten Watzl Leonie Wegener Thomas Weisenburger Annika Wiedemann Jürgen Wienands Anneke Wilharm Robert John Wilkinson Gerald Willimsky James B Wing Rieke Winkelmann Thomas H Winkler Oliver F Wirz Alicia Wong Peter Wurst Jennie H M Yang Juhao Yang Maria Yazdanbakhsh Liping Yu Alice Yue Hanlin Zhang Yi Zhao Susanne Maria Ziegler Christina Zielinski Jakob Zimmermann Arturo Zychlinsky

Eur J Immunol 2019 Oct;49(10):1457-1973

Max Planck Institute for Infection Biology, Berlin, Germany.

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http://dx.doi.org/10.1002/eji.201970107DOI Listing
October 2019

Flow cytometry data analysis: Recent tools and algorithms.

Int J Lab Hematol 2019 May;41 Suppl 1:56-62

Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada.

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https://onlinelibrary.wiley.com/doi/abs/10.1111/ijlh.13016
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http://dx.doi.org/10.1111/ijlh.13016DOI Listing
May 2019

Implementation and Validation of an Automated Flow Cytometry Analysis Pipeline for Human Immune Profiling.

Cytometry A 2019 02 20;95(2):183-191. Epub 2018 Dec 20.

Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, Oregon.

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http://dx.doi.org/10.1002/cyto.a.23664DOI Listing
February 2019

Methodology for evaluating and comparing flow cytometers: A multisite study of 23 instruments.

Cytometry A 2018 11 23;93(11):1087-1091. Epub 2018 Sep 23.

Wake Forest University Baptist Medical Center, Comprehensive Cancer Center and Department of Cancer Biology, Winston-Salem, North Carolina.

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http://dx.doi.org/10.1002/cyto.a.23605DOI Listing
November 2018

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

Bioinformatics 2018 08;34(15):2687-2689

Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada.

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http://dx.doi.org/10.1093/bioinformatics/bty136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061851PMC
August 2018

High throughput automated analysis of big flow cytometry data.

Methods 2018 02 27;134-135:164-176. Epub 2017 Dec 27.

Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2017.12.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5815930PMC
February 2018

Use FlowRepository to share your clinical data upon study publication.

Cytometry B Clin Cytom 2018 01 8;94(1):196-198. Epub 2016 Jul 8.

Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.

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http://doi.wiley.com/10.1002/cyto.b.21393
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http://dx.doi.org/10.1002/cyto.b.21393DOI Listing
January 2018

Guidelines for the use of flow cytometry and cell sorting in immunological studies.

Authors:
Andrea Cossarizza Hyun-Dong Chang Andreas Radbruch Mübeccel Akdis Immanuel Andrä Francesco Annunziato Petra Bacher Vincenzo Barnaba Luca Battistini Wolfgang M Bauer Sabine Baumgart Burkhard Becher Wolfgang Beisker Claudia Berek Alfonso Blanco Giovanna Borsellino Philip E Boulais Ryan R Brinkman Martin Büscher Dirk H Busch Timothy P Bushnell Xuetao Cao Andrea Cavani Pratip K Chattopadhyay Qingyu Cheng Sue Chow Mario Clerici Anne Cooke Antonio Cosma Lorenzo Cosmi Ana Cumano Van Duc Dang Derek Davies Sara De Biasi Genny Del Zotto Silvia Della Bella Paolo Dellabona Günnur Deniz Mark Dessing Andreas Diefenbach James Di Santo Francesco Dieli Andreas Dolf Vera S Donnenberg Thomas Dörner Götz R A Ehrhardt Elmar Endl Pablo Engel Britta Engelhardt Charlotte Esser Bart Everts Anita Dreher Christine S Falk Todd A Fehniger Andrew Filby Simon Fillatreau Marie Follo Irmgard Förster John Foster Gemma A Foulds Paul S Frenette David Galbraith Natalio Garbi Maria Dolores García-Godoy Jens Geginat Kamran Ghoreschi Lara Gibellini Christoph Goettlinger Carl S Goodyear Andrea Gori Jane Grogan Mor Gross Andreas Grützkau Daryl Grummitt Jonas Hahn Quirin Hammer Anja E Hauser David L Haviland David Hedley Guadalupe Herrera Martin Herrmann Falk Hiepe Tristan Holland Pleun Hombrink Jessica P Houston Bimba F Hoyer Bo Huang Christopher A Hunter Anna Iannone Hans-Martin Jäck Beatriz Jávega Stipan Jonjic Kerstin Juelke Steffen Jung Toralf Kaiser Tomas Kalina Baerbel Keller Srijit Khan Deborah Kienhöfer Thomas Kroneis Désirée Kunkel Christian Kurts Pia Kvistborg Joanne Lannigan Olivier Lantz Anis Larbi Salome LeibundGut-Landmann Michael D Leipold Megan K Levings Virginia Litwin Yanling Liu Michael Lohoff Giovanna Lombardi Lilly Lopez Amy Lovett-Racke Erik Lubberts Burkhard Ludewig Enrico Lugli Holden T Maecker Glòria Martrus Giuseppe Matarese Christian Maueröder Mairi McGrath Iain McInnes Henrik E Mei Fritz Melchers Susanne Melzer Dirk Mielenz Kingston Mills David Mirrer Jenny Mjösberg Jonni Moore Barry Moran Alessandro Moretta Lorenzo Moretta Tim R Mosmann Susann Müller Werner Müller Christian Münz Gabriele Multhoff Luis Enrique Munoz Kenneth M Murphy Toshinori Nakayama Milena Nasi Christine Neudörfl John Nolan Sussan Nourshargh José-Enrique O'Connor Wenjun Ouyang Annette Oxenius Raghav Palankar Isabel Panse Pärt Peterson Christian Peth Jordi Petriz Daisy Philips Winfried Pickl Silvia Piconese Marcello Pinti A Graham Pockley Malgorzata Justyna Podolska Carlo Pucillo Sally A Quataert Timothy R D J Radstake Bartek Rajwa Jonathan A Rebhahn Diether Recktenwald Ester B M Remmerswaal Katy Rezvani Laura G Rico J Paul Robinson Chiara Romagnani Anna Rubartelli Beate Ruckert Jürgen Ruland Shimon Sakaguchi Francisco Sala-de-Oyanguren Yvonne Samstag Sharon Sanderson Birgit Sawitzki Alexander Scheffold Matthias Schiemann Frank Schildberg Esther Schimisky Stephan A Schmid Steffen Schmitt Kilian Schober Thomas Schüler Axel Ronald Schulz Ton Schumacher Cristiano Scotta T Vincent Shankey Anat Shemer Anna-Katharina Simon Josef Spidlen Alan M Stall Regina Stark Christina Stehle Merle Stein Tobit Steinmetz Hannes Stockinger Yousuke Takahama Attila Tarnok ZhiGang Tian Gergely Toldi Julia Tornack Elisabetta Traggiai Joe Trotter Henning Ulrich Marlous van der Braber René A W van Lier Marc Veldhoen Salvador Vento-Asturias Paulo Vieira David Voehringer Hans-Dieter Volk Konrad von Volkmann Ari Waisman Rachael Walker Michael D Ward Klaus Warnatz Sarah Warth James V Watson Carsten Watzl Leonie Wegener Annika Wiedemann Jürgen Wienands Gerald Willimsky James Wing Peter Wurst Liping Yu Alice Yue Qianjun Zhang Yi Zhao Susanne Ziegler Jakob Zimmermann

Eur J Immunol 2017 10;47(10):1584-1797

Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse, Bern.

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http://doi.wiley.com/10.1002/eji.201646632
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http://dx.doi.org/10.1002/eji.201646632DOI Listing
October 2017

T-Cell Phenotypes Predictive of Frailty and Mortality in Elderly Nursing Home Residents.

J Am Geriatr Soc 2017 01 24;65(1):153-159. Epub 2016 Oct 24.

Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada.

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http://dx.doi.org/10.1111/jgs.14507DOI Listing
January 2017

flowClean: Automated identification and removal of fluorescence anomalies in flow cytometry data.

Cytometry A 2016 05 18;89(5):461-71. Epub 2016 Mar 18.

Vaccine Research Center, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Baltimore, Maryland.

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http://dx.doi.org/10.1002/cyto.a.22837DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522377PMC
May 2016

Publishing code is essential for reproducible flow cytometry bioinformatics.

Cytometry A 2016 Jan;89(1):10-1

Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1002/cyto.a.22805DOI Listing
January 2016

Automated analysis of flow cytometry data comes of age.

Cytometry A 2016 Jan;89(1):13-5

J. Craig Venter Institute, La Jolla, California.

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http://dx.doi.org/10.1002/cyto.a.22810DOI Listing
January 2016

ISAC's Gating-ML 2.0 data exchange standard for gating description.

Cytometry A 2015 Jul 14;87(7):683-7. Epub 2015 May 14.

Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1002/cyto.a.22690DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874733PMC
July 2015

State-of-the-Art in the Computational Analysis of Cytometry Data.

Cytometry A 2015 Jul;87(7):591-3

J. Craig Venter Institute, La Jolla, California.

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http://dx.doi.org/10.1002/cyto.a.22707DOI Listing
July 2015

Immune biomarkers predictive of respiratory viral infection in elderly nursing home residents.

PLoS One 2014 2;9(9):e108481. Epub 2014 Oct 2.

Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada; Department of Medicine, McMaster University, Hamilton, Ontario, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada; Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0108481PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183538PMC
June 2015

Deep profiling of multitube flow cytometry data.

Bioinformatics 2015 May 18;31(10):1623-31. Epub 2015 Jan 18.

Terry Fox Laboratory, BC Cancer Agency, Bioinformatics Graduate Program, University of British Columbia, Department of Hematopathology, Vancouver General Hospital and Faculty of Medical Genetics, University of British Columbia, Vancouver, Canada Terry Fox Laboratory, BC Cancer Agency, Bioinformatics Graduate Program, University of British Columbia, Department of Hematopathology, Vancouver General Hospital and Faculty of Medical Genetics, University of British Columbia, Vancouver, Canada.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/content/early/2015/
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btv008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426837PMC
May 2015

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

Bioinformatics 2015 Apr 6;31(8):1337-9. Epub 2014 Dec 6.

Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
Web Search
http://bioinformatics.oxfordjournals.org/content/early/2014/
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btu807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393520PMC
April 2015

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

Bioinformatics 2015 Feb 16;31(4):606-7. Epub 2014 Oct 16.

Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btu677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325545PMC
February 2015

ISAC's classification results file format.

Cytometry A 2015 Jan 18;87(1):86-8. Epub 2014 Nov 18.

Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1002/cyto.a.22586DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874736PMC
January 2015

The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective.

PLoS One 2014 25;9(3):e92632. Epub 2014 Mar 25.

School of Dental Medicine, University at Buffalo, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092632PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965435PMC
December 2014

The core autophagy protein ATG4B is a potential biomarker and therapeutic target in CML stem/progenitor cells.

Blood 2014 Jun 22;123(23):3622-34. Epub 2014 Apr 22.

Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics and Department of Medicine, University of British Columbia, Vancouver, BC, Canada;

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http://dx.doi.org/10.1182/blood-2013-07-516807DOI Listing
June 2014

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

Bioinformatics 2014 May 8;30(9):1329-30. Epub 2014 Jan 8.

Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada, Max-Planck-Institut fur Informatik, Saarland University, 66123, Saarbrucken, Germany, Departments of Computer Science and Departments of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btt770DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998128PMC
May 2014

Computational analysis optimizes the flow cytometric evaluation for lymphoma.

Cytometry B Clin Cytom 2014 Jan 3;86(1):18-24. Epub 2013 Sep 3.

Division of Hematopathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.

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http://dx.doi.org/10.1002/cyto.b.21115DOI Listing
January 2014

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

BMC Genomics 2013 21;14 Suppl 1:S14. Epub 2013 Jan 21.

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1186/1471-2164-14-S1-S14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549810PMC
August 2013

Computational analysis optimizes the flow cytometric evaluation for lymphoma.

Cytometry B Clin Cytom 2013 Jul 19. Epub 2013 Jul 19.

University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1002/cytob.21115DOI Listing
July 2013

RchyOptimyx: cellular hierarchy optimization for flow cytometry.

Cytometry A 2012 Dec 8;81(12):1022-30. Epub 2012 Oct 8.

Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1002/cyto.a.22209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726344PMC
December 2012

The phenotypic distribution and functional profile of tuberculin-specific CD4 T-cells characterizes different stages of TB infection.

Cytometry B Clin Cytom 2012 Nov 7;82(6):360-8. Epub 2012 Sep 7.

Institut für Medizinische Immunologie der Charité, Campus Mitte, Charité - Universitätsmedizin Berlin, Campus Mitte, Charitéplatz 1, 10117 Berlin, Germany.

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http://dx.doi.org/10.1002/cyto.b.21041DOI Listing
November 2012

FlowRepository: a resource of annotated flow cytometry datasets associated with peer-reviewed publications.

Cytometry A 2012 Sep 6;81(9):727-31. Epub 2012 Aug 6.

Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1002/cyto.a.22106DOI Listing
September 2012

FCS 3.1 Implementation guidance.

Cytometry A 2012 Jun 25;81(6):523-6. Epub 2012 Jan 25.

Verity Software House, Topsham, Maine, USA.

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http://dx.doi.org/10.1002/cyto.a.22018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676281PMC
June 2012

Analysis of High-Throughput Flow Cytometry Data Using plateCore.

Adv Bioinformatics 2009 11:356141. Epub 2009 Oct 11.

FDA-Center for Food Safety and Nutrition, HFS-013 5100 Paint Branch Parkway, College Park, MD 20740, USA.

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http://dx.doi.org/10.1155/2009/356141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777006PMC
July 2011

A survey of flow cytometry data analysis methods.

Adv Bioinformatics 2009 6:584603. Epub 2009 Dec 6.

Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3.

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http://dx.doi.org/10.1155/2009/584603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798157PMC
July 2011

Recent bioinformatics advances in the analysis of high throughput flow cytometry data.

Adv Bioinformatics 2009 9:461763. Epub 2010 Feb 9.

Computational Biology Unit, Clinical Research Institute Montréal (IRCM), 110 Avenue des Pins Ouest, Montréal, Québec, Canada H2W 1R7.

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http://www.hindawi.com/journals/abi/2009/461763/
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http://dx.doi.org/10.1155/2009/461763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2821639PMC
July 2011

Flow cytometry data standards.

BMC Res Notes 2011 Mar 7;4:50. Epub 2011 Mar 7.

Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/1756-0500-4-50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060130PMC
March 2011

Rapid cell population identification in flow cytometry data.

Cytometry A 2011 Jan;79(1):6-13

Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1002/cyto.a.21007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137288PMC
January 2011

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

BMC Bioinformatics 2010 Jul 28;11:403. Epub 2010 Jul 28.

Terry Fox Laboratory, BC Cancer Agency, 675 W 10th Ave, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/1471-2105-11-403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923634PMC
July 2010

OntoFox: web-based support for ontology reuse.

BMC Res Notes 2010 Jun 22;3:175. Epub 2010 Jun 22.

Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

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http://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0
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http://dx.doi.org/10.1186/1756-0500-3-175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911465PMC
June 2010

Reduction in multi-lineage and erythroid progenitors distinguishes myelodysplastic syndromes from non-malignant cytopenias.

Leuk Res 2009 Dec 2;33(12):1636-42. Epub 2009 May 2.

Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, Canada.

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http://linkinghub.elsevier.com/retrieve/pii/S014521260900142
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http://dx.doi.org/10.1016/j.leukres.2009.03.019DOI Listing
December 2009

FuGEFlow: data model and markup language for flow cytometry.

BMC Bioinformatics 2009 Jun 16;10:184. Epub 2009 Jun 16.

Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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http://dx.doi.org/10.1186/1471-2105-10-184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711079PMC
June 2009

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

BMC Bioinformatics 2009 May 14;10:145. Epub 2009 May 14.

Department of Statistics, University of British Columbia, 333-6356 Agricultural Road, Vancouver, BC, V6T1Z2, Canada.

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http://dx.doi.org/10.1186/1471-2105-10-145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701419PMC
May 2009

flowCore: a Bioconductor package for high throughput flow cytometry.

BMC Bioinformatics 2009 Apr 9;10:106. Epub 2009 Apr 9.

Life Sciences Department, Computational Biology Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA.

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http://dx.doi.org/10.1186/1471-2105-10-106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684747PMC
April 2009

Gating-ML: XML-based gating descriptions in flow cytometry.

Cytometry A 2008 Dec;73A(12):1151-7

Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1002/cyto.a.20637DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2585156PMC
December 2008

Human monogenic disorders - a source of novel drug targets.

Nat Rev Genet 2006 Apr;7(4):249-60

British Columbia Cancer Research Centre, University of British Columbia, Vancouver, British Columbia V5Z 1C3, Canada.

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http://www.nature.com/doifinder/10.1038/nrg1828
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April 2006