Flow Cytometry Core Facility

Publications

Publications

Overview

Find a list of our publications, and guidelines for acknowledging FCCF's role in your own research.

We have lists of our publications from 2000 - 2009, and from 2010 - present.

Acknowledging our input 

At current rates, FCCF users pay a fraction of our costs. This is thanks largely to faculty subsidy and more accurate yearly capacity figures.

Even without any specific assistance from our members, the reason the instruments are in good working order is because of their efforts and expertise.

Find out how to acknowledge FCCF's role in your research

2010 - Present

A list of our publications from 2010 - present.

Guidelines for the use of flow cytometry and cell sorting in immunological studies
Cossarizza A, Chang H, Radbruch A, Andrä I, Annunziato F, Bacher P, Barnaba V, Battistini L, Bauer W. M, Baumgart S, Becher B, Beisker W, Berek C, Blanco A, Borsellino G, Boulais P.E., Brinkman R.R, Büscher M, Busch D.H., Bushnell T.P., Cao X, Cavani A, Chattopadhyay P. K., Cheng Q, Chow S, Clerici M, Cooke A, Cosma A, Cosmi L, Cumano A, Dang V. D., Davies D, De Biasi S, Del Zotto G, Della Bella S, Dellabona P, Deniz G, Dessing M, Diefenbach A, Di Santo j, Dieli F, Dolf A, Donnenberg V. S., Dörner T, Ehrhardt G. R. A., Endl E, Engel P, Engelhardt B, Esser C, Everts B, Falk C. S., Fehniger T. A., Filby A, et al
Eur. J. Immunol. 2017 October 11. 47: 1584–1797 DOI: 10.1002/eji.201646632 

A human patient-derived cellular model of Joubert syndrome reveals ciliary defects which can be rescued with targeted therapies
Srivastava S, Ramsbottom S.A., Molinari E, Alkanderi S, Filby A, White K, Henry C, Saunier S, Miles C.G, Sayer J.A
Hum Mol Genet. 2017 Sep 11. doi: 10.1093/hmg/ddx34 PMID 28973549 

Imaging cytometry: Automated morphology and feature extraction
Filby A, Houston J.P.
Cytometry A. 2017 Sep;91(9):851-853. doi: 10.1002/cyto.a.23200 
PMID:28940699

Reconstructing cell cycle and disease progression using deep learning
Eulenberg P, Köhler N, Blasi T, Filby A, Carpenter A.E, Rees P, Theis F.J, Wolf F.A.
Nat Commun. 2017 Sept 6, 8:463 doi:10.1038/s41467-017-00623-3

Cellular senescence drives age-dependent hepatic steatosis.

Ogrodnik M, Miwa S, Tchkonia T, Tiniakos D, Wilson CL, Lahat A, Day CP, Burt A, Palmer A, Anstee QM, Grellscheid SN, Hoeijmakers JHJ, Barnhoorn S, Mann DA, Bird TG, Vermeij WP, Kirkland JL, Passos JF, von Zglinicki T, Jurk D
Nat Commun. 2017 Jun 13;8:15691. doi: 10.1038/ncomms15691. PMID: 28608850

Caveolin-1 Influences LFA-1 Redistribution upon TCR Stimulation in CD8 T Cells

Borger JG, Morrison VL, Filby A, Garcia C, Uotila LM, Simbari F, Fagerholm SC, Zamoyska R.
J Immunol. 2017 Jun 21. pii: ji1700431. doi: 10.4049/jimmunol.1700431 PMID 28637901

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
Villani AC, Satija R, Reynolds G, Sarkizova S, Shekhar K, Fletcher J, Griesbeck M, Butler A, Zheng S, Lazo S, Jardine L, Dixon D, Stephenson E, Nilsson E, Grundberg I, McDonald D, Filby A, Li W, De Jager PL, Rozenblatt-Rosen O, Lane A, Haniffa M, Regev A, Hacohen N
Science. 2017 Apr 21;356(6335) pii: eaah4573. doi: 10.1126/science.aah4573 PMID: 28428369 

Sample preparation for flow cytometry benefits from some lateral thinking.
Filby A.
Cytometry. 2016 Nov 22. doi:10.1002/cyto.a.23021

An open-source solution for advanced imaging flow cytometry data analysis using machine learning.
Hennig H, Rees P, Blasi T, Kamentsky L, Hung J, Dao D, Carpenter AE, Filby A.
Methods. 2016 Sep 1. pii: S1046-2023(16)30291-2. doi: 10.1016/j.ymeth.2016.08.018. [Epub ahead of print] PMID 27594698

Early PREdiction of Severe Sepsis (ExPRES-Sepsis) study: protocol for an observational derivation study to discover potential leucocyte cell surface biomarkers.
Datta D, Conway Morris A, Antonelli J, Warner N, Brown KA, Wright J, Simpson AJ, Rennie J, Hulme G, Lewis SM, Mare TA, Cookson S, Weir CJ, Dimmick I, Keenan J, Rossi AG, Shankar-Hari M, Walsh TS; ExPRES Sepsis Investigators
BMJ Open. 2016 Aug 1;6(8):e011335. doi: 10.1136/bmjopen-2016-011335.PMID 27481622

Predictive value of cell-surface markers in infections in critically ill patients: protocol for an observational study (ImmuNe FailurE in Critical Therapy (INFECT) Study).
Conway Morris A, Datta D, Shankar-Hari M, Weir CJ, Rennie J, Antonelli J, Rossi AG, Warner N, Keenan J, Wang A, Brown KA, Lewis S, Mare T, Simpson AJ, Hulme G, Dimmick I, Walsh TS.
BMJ Open. 2016 Jul 18;6(7):e011326. doi: 10.1136/bmjopen-2016-011326.

Long-term in vitro maintenance of clonal abundance and leukaemia-initiating potential in acute lymphoblastic leukaemia.
Pal D, Blair HJ, Elder A, Dormon K, Rennie KJ, Coleman DJ, Weiland J, Rankin KS, Filby A, Heidenreich O, Vormoor J 
Leukemia. 2016 Apr 25. doi: 10.1038/leu.2016.79. [Epub ahead of print]
PMID: 27109511

Frequency and dynamics of leukemia-initiating cells during short-term ex vivo culture informs outcomes in acute myeloid leukemia patients.
Griessinger E, Anjos-Afonso F, Vargaftig J, Taussig D, Lassailly F, Prebet T, Imbert V, Nebout M, Vey N,Chabannon C, Filby A, Bollet-Quivogne F, Gribben JG, Peyron J, Bonnet D.
Cancer Res. 2016 Mar 9. pii: canres.2063.2015. [Epub ahead of print]
PubMed PMID: 26960976

Stepwise B-cell-dependent expansion of T helper clonotypes diversifies the T-cell response
Merkenschlager J, Ploquin MJ, Eksmond U, Andargachew R, Thorborn G, Filby A, Pepper M, Evavold B, Kassiotis G
Nat Commun. 2016 Jan 5;7:10281. doi: 
10.1038/ncomms10281. PubMed PMID: 26728651.

Label-free cell cycle analysis for high-throughput imaging flow cytometry
Blasi T, Hennig H, Summers HD, Theis FJ, Cerveira J, Patterson JO, Davies D, Filby A, Carpenter AE, Rees P
Nat Commun. 2016 Jan 7;7:10256. doi: 10.1038/ncomms10256
PubMed PMID: 26739115

The Analysis of Cell Cycle, Proliferation and Asymmetirc Cell Division by Imaging Flow Cytometry
Andrew Filby, William Day, Sukhveer Purewal and Nuria Martinez-Martin
Chapter 5 in Imaging Flow Cytometry: Methods and Protocols. Methods in Molecular Biology, 2016.

New, clear fusion from the cellular perspective: Measuring cellular fusion in Saccharomyces cerevisiae by flow cytometry
Filby A.
Cytometry A. 2015 Jun 26.
doi: 10.1002/cyto.a.22714. [Epub ahead of print] PubMed PMID: 26115228.

An imaging flow cytometry-based approach to measuring the spatiotemporal calcium mobilisation in activated T cells.
Cerveira J, Begum J, Di Marco Barros R, van der Veen AG, Filby A.
J Immunol Methods. 2015 Aug;423:120-130. doi: 
10.1016/j.jim.2015.04.030. Epub 2015 May 9. PubMed PMID: 25967946.

An Imaging Flow Cytometry-based approach to analyse the fission yeast cell cycle in fixed cells
Patterson JO, Swaffer M, Filby A
Methods. 2015 Jul
1;82:74-84. doi: 10.1016/j.ymeth.2015.04.026. Epub 2015 May 4. PubMed PMID: 25952947.

Appraising the suitability of succinimidyl and lipophilic fluorescent dyes to track proliferation in non-quiescent cells by dye dilution
Filby A, Begum J, Jalal M, Day W. 
Methods. 2015 Jul 1;82:29-37. doi: 10.1016/j.ymeth.2015.02.016.
Epub 2015 Mar 20. PubMed PMID: 25802116.

Dual proteolytic pathways govern glycolysis and immune competence.
Lu W, Zhang Y, McDonald DO, Jing H, Carroll B, Robertson N, Zhang Q, Griffin H, Sanderson S, Lakey JH, Morgan NV, Reynard LN, Zheng L, Murdock HM, Turvey SE, Hackett SJ, Prestidge T, Hall JM, Cant AJ, Matthews HF, Koref MF, Simon AK, Korolchuk VI, Lenardo MJ, Hambleton S, Su HC.
Cell. 2014 Dec 18;159(7):1578-90. doi: 10.1016/j.cell.2014.12.001.PMID: 25525876 [PubMed - indexed for MEDLINE]

"Mega" cytometry for a "mega" challenging cell type.
Filby A
Cytometry A. 2014 Apr;85(4):289-91. doi: 10.1002/cyto.a.22435. Epub 2014 Jan 16. PubMed PMID: 24436289.

A method for evaluating the use of fluorescent dyes to track proliferation in cell lines by dye dilution
Begum J, Day W, Henderson C, Purewal S, Cerveira J, Summers H, Rees P, Davies D, Filby A.
Cytometry A. 2013 Dec;83(12):1085-95. doi: 10.1002/cyto.a.22403. Epub 2013 Oct 25. PubMed PMID: 24166880.

Genetic tracing via DNGR-1 expression history defines dendritic cells as a hematopoietic lineage
Schraml BU, van Blijswijk J, Zelenay S, Whitney PG, Filby A, Acton SE, Rogers 
NC, Moncaut N, Carvajal JJ, Reis e Sousa C. 
Cell. 2013 Aug
15;154(4):843-58. doi: 10.1016/j.cell.2013.07.014. PubMed PMID: 23953115.

Regulation of asymmetric cell division and polarity by Scribble is not required for humoral immunity.
Hawkins ED, Oliaro J, Kallies A, Belz GT, Filby A, Hogan T, Haynes N, Ramsbottom KM, Van Ham V, Kinwell T, Seddon B, Davies D, Tarlinton D, Lew AM, Humbert PO, Russell SM. 
Nat Commun. 2013;4:1801. doi:
10.1038/ncomms2796. PubMed PMID: 23653213.

Differential polarization of C-terminal Src kinase between naive and antigen-experienced CD8+ T cells.
Borger JG, Filby A, Zamoyska R. 
J Immunol. 2013 Apr 1;190(7):3089-99. doi: 10.4049/jimmunol.1202408. Epub 2013 Feb 20. PubMed PMID: 23427257.

Reporting imaging flow cytometry data for publication: why mask the detail?
Filby A, Davies D.
Cytometry A. 2012 Aug;81(8):637-42. doi: 10.1002/cyto.a.22091.
Epub 2012 Jul 3. PubMed PMID: 22760920.

Asymmetric segregation of polarized antigen on B cell division shapes presentation capacity.
Thaunat O, Granja AG, Barral P, Filby A, Montaner B, Collinson L, Martinez-Martin N, Harwood NE, Bruckbauer A, Batista FD.
Science.2012 Jan 27;335(6067):475-9. doi: 10.1126/science.1214100. PubMed PMID: 22282815.

Exome sequencing identifies GATA-2 mutation as the cause of dendritic cell, monocyte, B and NK lymphoid deficiency.
Dickinson RE, Griffin H, Bigley V, Reynard LN, Hussain R, Haniffa M, Lakey JH, Rahman T, Wang XN, McGovern N, Pagan S, Cookson S, McDonald D, Chua I, Wallis J, Cant A, Wright M, Keavney B, Chinnery PF, Loughlin J, Hambleton S, Santibanez-Koref M, Collin M.
Blood. 2011 Sep 8;118(10):2656-8. doi: 10.1182/blood-2011-06-360313. Epub 2011 Jul 15.
PMID: 21765025

An imaging flow cytometric method for measuring cell division history and molecular symmetry during mitosis.
Filby A, Perucha E, Summers H, Rees P, Chana P, Heck S, Lord GM, Davies D. 
Cytometry A. 2011 Jul;79(7):496-506. doi:
10.1002/cyto.a.21091. Epub 2011 Jun 2. PubMed PMID: 21638766.

IRF8 mutations and human dendritic-cell immunodeficiency.
Hambleton S, Salem S, Bustamante J, Bigley V, Boisson-Dupuis S, Azevedo J, Fortin A, Haniffa M, Ceron-Gutierrez L, Bacon CM, Menon G, Trouillet C, McDonald D, Carey P, Ginhoux F, Alsina L, Zumwalt TJ, Kong XF, Kumararatne D, Butler K, Hubeau M, Feinberg J, Al-Muhsen S, Cant A, Abel L, Chaussabel D, Doffinger R, Talesnik E, Grumach A, Duarte A, Abarca K, Moraes-Vasconcelos D, Burk D, Berghuis A, Geissmann F, Collin M, Casanova JL, Gros P.
N Engl J Med. 2011 Jul 14;365(2):127-38. doi: 10.1056/NEJMoa1100066. Epub 2011 Apr 27.
PMID: 21524210

Heterogeneous sensitivity of human acute myeloid leukemia to β-catenin down-modulation
Gandillet A, Park S, Lassailly F, Griessinger E, Vargaftig J, Filby A, Lister TA, Bonnet D.
Leukemia. 2011 May;25(5):770-80. doi:
10.1038/leu.2011.17. Epub 2011 Feb 22. PubMed PMID: 21339756; PubMed Central
PMCID: PMC4289854.

Mutation in the TCRα subunit constant gene (TRAC) leads to a human immunodeficiency disorder characterized by a lack of TCRαβ+ T cells.
Morgan NV, Goddard S, Cardno TS, McDonald D, Rahman F, Barge D, Ciupek A, Straatman-Iwanowska A, Pasha S, Guckian M, Anderson G, Huissoon A, Cant A, Tate WP, Hambleton S, Maher ER.
J Clin Invest. 2011 Feb;121(2):695-702. doi: 10.1172/JCI41931. Epub 2011 Jan 4.
PMID: 21206088

Mislocalization of Lck impairs thymocyte differentiation and can promote development of thymomas
Salmond RJ, Filby A, Pirinen N, Magee AI, Zamoyska R. 
Blood.2011 Jan 6;117(1):108-17. doi: 10.1182/blood-2010-03-277160. Epub 2010 Sep 28.
PubMed PMID: 20876849.

Whole-exome-sequencing-based discovery of human FADD deficiency.
Bolze A, Byun M, McDonald D, Morgan NV, Abhyankar A, Premkumar L, Puel A, Bacon CM, Rieux-Laucat F, Pang K, Britland A, Abel L, Cant A, Maher ER, Riedl SJ, Hambleton S, Casanova JL.
Am J Hum Genet. 2010 Dec 10;87(6):873-81. doi: 10.1016/j.ajhg.2010.10.028. Epub 2010 Nov 25.
PMID: 21109225

2000-2009

A list of our publications from 2000-2009.

Race between retroviral spread and CD4+ T-cell response determines the outcome of acute Friend virus infection.
Pike R, Filby A, Ploquin MJ, Eksmond U, Marques R, Antunes I, Hasenkrug K, Kassiotis G. 
J Virol. 2009 Nov;83(21):11211-22.doi: 10.1128/JVI.01225-09. Epub 2009 Aug 19. PubMed PMID: 19692462; PubMed
Central PMCID: PMC2772778.

Thyroid peroxidase forms thionamide-sensitive homodimers: relevance for immunomodulation of thyroid autoimmunity.
McDonald DO, Pearce SH.
J Mol Med (Berl). 2009 Oct;87(10):971-80. doi: 10.1007/s00109-009-0511-y. Epub 2009 Aug 8.
PMID: 19669106

T-cell receptor proximal signaling via the Src-family kinases, Lck and Fyn, influences T-cell activation, differentiation, and tolerance.
Salmond RJ, Filby A, Qureshi I, Caserta S, Zamoyska R. 
Immunol Rev. 2009 Mar;228(1):9-22.doi: 10.1111/j.1600-065X.2008.00745.x. Review. PubMed PMID: 19290918.

The tryptophan 620 allele of the lymphoid tyrosine phosphatase (PTPN22) gene predisposes to autoimmune Addison's disease.
Roycroft M, Fichna M, McDonald D, Owen K, Zurawek M, Gryczyńska M, Januszkiewicz-Lewandowska D, Fichna P, Cordell H, Donaldson P, Nowak J, Pearce S.
Clin Endocrinol (Oxf). 2009 Mar;70(3):358-62. doi: 10.1111/j.1365-2265.2008.03380.x. Epub 2008 Aug 15.
PMID: 18710467

Polymorphisms in CLEC16A and CIITA at 16p13 are associated with primary adrenal insufficiency.
Skinningsrud B, Husebye ES, Pearce SH, McDonald DO, Brandal K, Wolff AB, Løvås K, Egeland T, Undlien DE.
J Clin Endocrinol Metab. 2008 Sep;93(9):3310-7. doi: 10.1210/jc.2008-0821. Epub 2008 Jul 1.
PMID: 18593762

Fyn regulates the duration of TCR engagement needed for commitment to effector function.
Filby A, Seddon B, Kleczkowska J, Salmond R, Tomlinson P, Smida M, Lindquist JA, Schraven B, Zamoyska R. 
J Immunol. 2007 Oct 1;179(7):4635-44. PubMed PMID: 17878361.

Lck regulates the threshold of activation in primary T cells, while both Lck and Fyn contribute to the magnitude of the extracellular signal-related kinase response.
Lovatt M, Filby A, Parravicini V, Werlen G, Palmer E, Zamoyska R. 
Mol Cell Biol. 2006 Nov;26(22):8655-65. Epub 2006 Sep 11. PubMed PMID: 16966372; 
PubMed Central PMCID: PMC1636771.

The influence of the src-family kinases, Lck and Fyn, on T cell differentiation, survival and activation.
Zamoyska R, Basson A, Filby A, Legname G, Lovatt M, Seddon B.
Immunol Rev. 2003 Feb;191:107-18. Review. PubMed PMID: 12614355.

Interleukins 5 and 13 characterize immune responses to respiratory sensitizing acid anhydrides
Dearman RJ, Filby A, Humphreys IR, Kimber I.
J Appl Toxicol. 2002 Sep-Oct;22(5):317-25. PubMed PMID: 12355561.