Motivation: High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging. Results: Here, we present GateFinder, an algorithm that enriches high-dimensional cell types with simple, stepwise polygon gates requiring only two markers at a time. A series of case studies of complex cell types illustrates how simplified enrichment strategies can enable more efficient assays, reveal novel biomarkers and clarify underlying biology. Availability and implementation: The GateFinder algorithm is implemented as a free and open-source package for BioConductor: https://nalab.stanford.edu/gatefinder. Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation: High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging. Results: Here, we present GateFinder, an algorithm that enriches high-dimensional cell types with simple, stepwise polygon gates requiring only two markers at a time. A series of case studies of complex cell types illustrates how simplified enrichment strategies can enable more efficient assays, reveal novel biomarkers and clarify underlying biology. Availability and implementation: The GateFinder algorithm is implemented as a free and open-source package for BioConductor: https://nalab.stanford.edu/gatefinder. Supplementary information: Supplementary data are available at Bioinformatics online.
Authors: Lina Han; Peng Qiu; Zhihong Zeng; Jeffrey L Jorgensen; Duncan H Mak; Jared K Burks; Wendy Schober; Teresa J McQueen; Jorge Cortes; Scott D Tanner; Gail J Roboz; Hagop M Kantarjian; Steven M Kornblau; Monica L Guzman; Michael Andreeff; Marina Konopleva Journal: Cytometry A Date: 2015-01-16 Impact factor: 4.355
Authors: Anuradha Ganesan; Pratip K Chattopadhyay; Tess M Brodie; Jing Qin; Wenjuan Gu; John R Mascola; Nelson L Michael; Dean A Follmann; Mario Roederer Journal: J Infect Dis Date: 2010-01-15 Impact factor: 5.226
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
Authors: Trygve Bakken; Lindsay Cowell; Brian D Aevermann; Mark Novotny; Rebecca Hodge; Jeremy A Miller; Alexandra Lee; Ivan Chang; Jamison McCorrison; Bali Pulendran; Yu Qian; Nicholas J Schork; Roger S Lasken; Ed S Lein; Richard H Scheuermann Journal: BMC Bioinformatics Date: 2017-12-21 Impact factor: 3.307
Authors: Satoshi Inoue; Wanda Y Li; Alan Tseng; Isabel Beerman; Andrew J Elia; Sean C Bendall; François Lemonnier; Ken J Kron; David W Cescon; Zhenyue Hao; Evan F Lind; Naoya Takayama; Aline C Planello; Shu Yi Shen; Alan H Shih; Dana M Larsen; Qinxi Li; Bryan E Snow; Andrew Wakeham; Jillian Haight; Chiara Gorrini; Christian Bassi; Kelsie L Thu; Kiichi Murakami; Alisha R Elford; Takeshi Ueda; Kimberly Straley; Katharine E Yen; Gerry Melino; Luisa Cimmino; Iannis Aifantis; Ross L Levine; Daniel D De Carvalho; Mathieu Lupien; Derrick J Rossi; Garry P Nolan; Rob A Cairns; Tak W Mak Journal: Cancer Cell Date: 2016-07-14 Impact factor: 31.743
Authors: D K Gaudilliere; A Culos; K Djebali; A S Tsai; E A Ganio; W M Choi; X Han; A Maghaireh; B Choisy; Q Baca; J F Einhaus; J J Hedou; B Bertrand; K Ando; R Fallahzadeh; M S Ghaemi; R Okada; N Stanley; A Tanada; M Tingle; T Alpagot; J A Helms; M S Angst; N Aghaeepour; B Gaudilliere Journal: J Dent Res Date: 2019-06-21 Impact factor: 6.116
Authors: Thanaphong Phongpreecha; Chandresh R Gajera; Candace C Liu; Kausalia Vijayaragavan; Alan L Chang; Martin Becker; Ramin Fallahzadeh; Rosemary Fernandez; Nadia Postupna; Emily Sherfield; Dmitry Tebaykin; Caitlin Latimer; Carol A Shively; Thomas C Register; Suzanne Craft; Kathleen S Montine; Edward J Fox; Kathleen L Poston; C Dirk Keene; Michael Angelo; Sean C Bendall; Nima Aghaeepour; Thomas J Montine Journal: Sci Adv Date: 2021-12-15 Impact factor: 14.136
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Authors: Karen D Davis; Nima Aghaeepour; Andrew H Ahn; Martin S Angst; David Borsook; Ashley Brenton; Michael E Burczynski; Christopher Crean; Robert Edwards; Brice Gaudilliere; Georgene W Hergenroeder; Michael J Iadarola; Smriti Iyengar; Yunyun Jiang; Jiang-Ti Kong; Sean Mackey; Carl Y Saab; Christine N Sang; Joachim Scholz; Marta Segerdahl; Irene Tracey; Christin Veasley; Jing Wang; Tor D Wager; Ajay D Wasan; Mary Ann Pelleymounter Journal: Nat Rev Neurol Date: 2020-06-15 Impact factor: 42.937