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Items: 1 to 20 of 71

1.

Use FlowRepository to share your clinical data upon study publication.

Spidlen J, Brinkman RR.

Cytometry B Clin Cytom. 2016 Jun 25. doi: 10.1002/cyto.b.21393. [Epub ahead of print]

PMID:
27342384
2.

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

Fletez-Brant K, Špidlen J, Brinkman RR, Roederer M, Chattopadhyay PK.

Cytometry A. 2016 May;89(5):461-71. doi: 10.1002/cyto.a.22837. Epub 2016 Mar 18.

PMID:
26990501
3.

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium.

Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K, Devine L, Obermoser G, Pekalski ML, Pontikos N, Diaz A, Heck S, Villanova F, Terrazzini N, Kern F, Qian Y, Stanton R, Wang K, Brandes A, Ramey J, Aghaeepour N, Mosmann T, Scheuermann RH, Reed E, Palucka K, Pascual V, Blomberg BB, Nestle F, Nussenblatt RB, Brinkman RR, Gottardo R, Maecker H, McCoy JP.

Sci Rep. 2016 Feb 10;6:20686. doi: 10.1038/srep20686.

4.

Automated analysis of flow cytometry data comes of age.

Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH.

Cytometry A. 2016 Jan;89(1):13-5. doi: 10.1002/cyto.a.22810. No abstract available.

PMID:
26812230
5.

Publishing code is essential for reproducible flow cytometry bioinformatics.

O'Neill K, Brinkman RR.

Cytometry A. 2016 Jan;89(1):10-1. doi: 10.1002/cyto.a.22805. No abstract available.

PMID:
26812228
6.

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

Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR.

Cytometry A. 2016 Jan;89(1):16-21. doi: 10.1002/cyto.a.22732. Epub 2015 Oct 8.

PMID:
26447924
7.

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

Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH.

Cytometry A. 2015 Jul;87(7):591-3. doi: 10.1002/cyto.a.22707. No abstract available.

8.

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

Spidlen J, Moore W; ISAC Data Standards Task Force, Brinkman RR.

Cytometry A. 2015 Jul;87(7):683-7. doi: 10.1002/cyto.a.22690. Epub 2015 May 14.

9.

Thinking outside the gate: single-cell assessments in multiple dimensions.

Kvistborg P, Gouttefangeas C, Aghaeepour N, Cazaly A, Chattopadhyay PK, Chan C, Eckl J, Finak G, Hadrup SR, Maecker HT, Maurer D, Mosmann T, Qiu P, Scheuermann RH, Welters MJ, Ferrari G, Brinkman RR, Britten CM.

Immunity. 2015 Apr 21;42(4):591-2. doi: 10.1016/j.immuni.2015.04.006. No abstract available.

10.

Deep profiling of multitube flow cytometry data.

O'Neill K, Aghaeepour N, Parker J, Hogge D, Karsan A, Dalal B, Brinkman RR.

Bioinformatics. 2015 May 15;31(10):1623-31. doi: 10.1093/bioinformatics/btv008. Epub 2015 Jan 18.

11.

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

Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR.

Bioinformatics. 2015 Apr 15;31(8):1337-9. doi: 10.1093/bioinformatics/btu807. Epub 2014 Dec 6.

12.

ISAC's classification results file format.

Spidlen J, Bray C; ISAC Data Standards Task Force, Brinkman RR.

Cytometry A. 2015 Jan;87(1):86-8. doi: 10.1002/cyto.a.22586. Epub 2014 Nov 18.

13.

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

Malek M, Taghiyar MJ, Chong L, Finak G, Gottardo R, Brinkman RR.

Bioinformatics. 2015 Feb 15;31(4):606-7. doi: 10.1093/bioinformatics/btu677. Epub 2014 Oct 16.

14.

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

Johnstone J, Parsons R, Botelho F, Millar J, McNeil S, Fulop T, McElhaney J, Andrew MK, Walter SD, Devereaux PJ, Malekesmaeili M, Brinkman RR, Mahony J, Bramson J, Loeb M.

PLoS One. 2014 Oct 2;9(9):e108481. doi: 10.1371/journal.pone.0108481. eCollection 2014.

15.

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

Rothe K, Lin H, Lin KB, Leung A, Wang HM, Malekesmaeili M, Brinkman RR, Forrest DL, Gorski SM, Jiang X.

Blood. 2014 Jun 5;123(23):3622-34. doi: 10.1182/blood-2013-07-516807. Epub 2014 Apr 22.

16.

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

Courtot M, Brinkman RR, Ruttenberg A.

PLoS One. 2014 Mar 25;9(3):e92632. doi: 10.1371/journal.pone.0092632. eCollection 2014.

17.

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

O'Neill K, Jalali A, Aghaeepour N, Hoos H, Brinkman RR.

Bioinformatics. 2014 May 1;30(9):1329-30. doi: 10.1093/bioinformatics/btt770. Epub 2014 Jan 8.

18.

The luminal progenitor compartment of the normal human mammary gland constitutes a unique site of telomere dysfunction.

Kannan N, Huda N, Tu L, Droumeva R, Aubert G, Chavez E, Brinkman RR, Lansdorp P, Emerman J, Abe S, Eaves C, Gilley D.

Stem Cell Reports. 2013 Jun 4;1(1):28-37. doi: 10.1016/j.stemcr.2013.04.003. eCollection 2013.

19.

Computational analysis optimizes the flow cytometric evaluation for lymphoma.

Craig FE, Brinkman RR, Ten Eyck S, Aghaeepour N.

Cytometry B Clin Cytom. 2014 Jan;86(1):18-24. doi: 10.1002/cyto.b.21115. Epub 2013 Sep 3.

20.

Computational analysis optimizes the flow cytometric evaluation for lymphoma.

Craig FE, Brinkman RR, Eyck ST, Aghaeepour N.

Cytometry B Clin Cytom. 2013 Jul 19. doi: 10.1002/cytob.21115. [Epub ahead of print]

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