Literature DB >> 24407226

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

Kieran O'Neill1, Adrin Jalali, Nima Aghaeepour, Holger Hoos, Ryan R Brinkman.   

Abstract

We present a significantly improved version of the flowType and RchyOptimyx BioConductor-based pipeline that is both 14 times faster and can accommodate multiple levels of biomarker expression for up to 96 markers. With these improvements, the pipeline is positioned to be an integral part of data analysis for high-throughput experiments on high-dimensional single-cell assay platforms, including flow cytometry, mass cytometry and single-cell RT-qPCR.

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Year:  2014        PMID： 24407226      PMCID： PMC3998128          DOI： 10.1093/bioinformatics/btt770

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  9 in total

1.  Immunophenotyping of acute leukemia: utility of CD45 for blast cell identification.

Authors:  J P Vial; F Lacombe
Journal:  Methods Cell Biol       Date:  2001       Impact factor: 1.441

Review 2.  A chromatic explosion: the development and future of multiparameter flow cytometry.

Authors:  Pratip K Chattopadhyay; Carl-Magnus Hogerkorp; Mario Roederer
Journal:  Immunology       Date:  2008-12       Impact factor: 7.397

3.  Computational analysis optimizes the flow cytometric evaluation for lymphoma.

Authors:  Fiona E Craig; Ryan R Brinkman; Stephen Ten Eyck; Nima Aghaeepour
Journal:  Cytometry B Clin Cytom       Date:  2013-07-19       Impact factor: 3.058

4.  High-throughput microfluidic single-cell RT-qPCR.

Authors:  Adam K White; Michael VanInsberghe; Oleh I Petriv; Mani Hamidi; Darek Sikorski; Marco A Marra; James Piret; Samuel Aparicio; Carl L Hansen
Journal:  Proc Natl Acad Sci U S A       Date:  2011-08-01       Impact factor: 11.205

5.  Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays.

Authors:  Nima Aghaeepour; Pratip K Chattopadhyay; Anuradha Ganesan; Kieran O'Neill; Habil Zare; Adrin Jalali; Holger H Hoos; Mario Roederer; Ryan R Brinkman
Journal:  Bioinformatics       Date:  2012-02-29       Impact factor: 6.937

Review 6.  A deep profiler's guide to cytometry.

Authors:  Sean C Bendall; Garry P Nolan; Mario Roederer; Pratip K Chattopadhyay
Journal:  Trends Immunol       Date:  2012-04-02       Impact factor: 16.687

7.  RchyOptimyx: cellular hierarchy optimization for flow cytometry.

Authors:  Nima Aghaeepour; Adrin Jalali; Kieran O'Neill; Pratip K Chattopadhyay; Mario Roederer; Holger H Hoos; Ryan R Brinkman
Journal:  Cytometry A       Date:  2012-10-08       Impact factor: 4.355

8.  Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery.

Authors:  Federica Villanova; Paola Di Meglio; Margaret Inokuma; Nima Aghaeepour; Esperanza Perucha; Jennifer Mollon; Laurel Nomura; Maria Hernandez-Fuentes; Andrew Cope; A Toby Prevost; Susanne Heck; Vernon Maino; Graham Lord; Ryan R Brinkman; Frank O Nestle
Journal:  PLoS One       Date:  2013-07-03       Impact factor: 3.240

9.  Critical assessment of automated flow cytometry data analysis techniques.

Authors:  Nima Aghaeepour; Greg Finak; Holger Hoos; Tim R Mosmann; Ryan Brinkman; Raphael Gottardo; Richard H Scheuermann
Journal:  Nat Methods       Date:  2013-02-10       Impact factor: 28.547
  9 in total
  14 in total

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

Authors:  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 R Brinkman
Journal:  Bioinformatics       Date:  2014-12-06       Impact factor: 6.937

2.  Deep profiling of multitube flow cytometry data.

Authors:  Kieran O'Neill; Nima Aghaeepour; Jeremy Parker; Donna Hogge; Aly Karsan; Bakul Dalal; Ryan R Brinkman
Journal:  Bioinformatics       Date:  2015-01-18       Impact factor: 6.937

Review 3.  Computational flow cytometry: helping to make sense of high-dimensional immunology data.

Authors:  Yvan Saeys; Sofie Van Gassen; Bart N Lambrecht
Journal:  Nat Rev Immunol       Date:  2016-06-20       Impact factor: 53.106

4.  High throughput automated analysis of big flow cytometry data.

Authors:  Albina Rahim; Justin Meskas; Sibyl Drissler; Alice Yue; Anna Lorenc; Adam Laing; Namita Saran; Jacqui White; Lucie Abeler-Dörner; Adrian Hayday; Ryan R Brinkman
Journal:  Methods       Date:  2017-12-27       Impact factor: 3.608

5.  Automated identification of maximal differential cell populations in flow cytometry data.

Authors:  Alice Yue; Cedric Chauve; Maxwell W Libbrecht; Ryan R Brinkman
Journal:  Cytometry A       Date:  2021-10-22       Impact factor: 4.714

6.  A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

Authors:  Nima Aghaeepour; Pratip Chattopadhyay; Maria Chikina; Tom Dhaene; Sofie Van Gassen; Miron Kursa; Bart N Lambrecht; Mehrnoush Malek; G J McLachlan; Yu Qian; Peng Qiu; Yvan Saeys; Rick Stanton; Dong Tong; Celine Vens; Sławomir Walkowiak; Kui Wang; Greg Finak; Raphael Gottardo; Tim Mosmann; Garry P Nolan; Richard H Scheuermann; Ryan R Brinkman
Journal:  Cytometry A       Date:  2015-10-08       Impact factor: 4.355

7.  Human microglia regional heterogeneity and phenotypes determined by multiplexed single-cell mass cytometry.

Authors:  Chotima Böttcher; Stephan Schlickeiser; Marjolein A M Sneeboer; Lot D de Witte; Josef Priller; Desiree Kunkel; Anniki Knop; Evdokia Paza; Pawel Fidzinski; Larissa Kraus; Gijsje J L Snijders; René S Kahn; Axel R Schulz; Henrik E Mei; Elly M Hol; Britta Siegmund; Rainer Glauben; Eike J Spruth
Journal:  Nat Neurosci       Date:  2018-12-17       Impact factor: 24.884

Review 8.  Biologically Relevant Heterogeneity: Metrics and Practical Insights.

Authors:  Albert Gough; Andrew M Stern; John Maier; Timothy Lezon; Tong-Ying Shun; Chakra Chennubhotla; Mark E Schurdak; Steven A Haney; D Lansing Taylor
Journal:  SLAS Discov       Date:  2017-01-06       Impact factor: 3.341

9.  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
Journal:  Eur J Immunol       Date:  2017-10       Impact factor: 6.688

10.  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
Journal:  Eur J Immunol       Date:  2019-10       Impact factor: 6.688
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