Centre for Bacterial Cell Biology

Staff Profile

Professor Andrew Filby

Deputy Dean of the Newcastle University Biosciences Institute (NUBI) and Innovation Methodology and Application (IMA) Theme Lead and FCCF Director

Background

I am currently a Deputy Dean for the Newcastle University Biosciences Institute (NUBI) with specific remit for Engagement and Place and Research Technical Professionals (RTPs).


I am also the "Innovation Methodology and Application" (IMA) research Theme in the Faculty of Medical Sciences (FMS). This is a strategic role that aims to bring together technologists and methodologists from all job families in the faculty toward a true "team science", collaborative attitude to conducting cutting-edge research. The IMA will interface with the other 19 research Themes in the FMS and also be extremely outward focused with other faculties, HEIs and industry. I also serve on the Faculty Research and Innovation Committee (FRIC).


In my tertiary function, I am also director of the Newcastle Flow Cytometry Core Facility (FCCF), part of the Newcastle University Single Cell Unit (NUSCU). This is a world-renowned facility supporting cutting-edge research through the provision of a comprehensive cytomics resource to both internal and external groups, operating at the forefront of cytometric applications and method-focused research. As part of this role, my group have been developing, validating and applying both imaging and non-imaging cytometry-based methods to study several important aspects of cell biology and support various key research themes here at NU. 


Having completed my PhD and subsequent post-doctoral work at the NIMR I have a strong grounding in basic and translational research and consistently contribute to high profile publications. I won the award for best paper in Cytometry part A in 2011 and also made key contributions to work published in Nature (2018 and 2019), Science (2012, 2017, 2018, 2019 and 2020) and Cell (2013). Furthermore, I present my method development work at key conferences both nationally and internationally as well as contributing to the presentations and abstracts of others. 


I am on the editorial board of the Cytometry Part A journal, specialising in imaging cytometry data and recently published some guidelines for data standards in the field. I was selected in 2014 by the International Society for the Advancement of Cytometry (ISAC) as one of only three individuals worldwide to be part of the Shared Resource Laboratory (SRL) emerging leaders’ programme. This is a scholarship that recognises exceptional contribution to the worldwide cytometry community from those working in core facilities. I now serve on the ISAC council as member for technology and methodology. I am also a panel member for the UKRI-MRC Multi-user equipment call and the UKRI-BBSRC Transformative Research Technologies programme


Key points and measures of esteem:


  1. The first Research Technical Professional to be made Professor of Practice in the UK
  2. Recognised at an international level as an expert in the field of Cytometry and Core Facility operations.
  3. Strong publication record in high impact journals such as Science, Cell and Nature.
  4. Invited to speak at several national and international Cytometry meetings.
  5. Member of the Cytometry Part A editorial board..
  6. Lead for the FMS IMA Theme, a first for a non-academic track staff member.
  7. Member of the various key funding agency panels
  8. Awarded the Royal Microscopical Medal (RMS) for Flow Cytometry research in 2019
  9. Co-chair of the UK Institute for Technical Skills and Strategy (UK-ITSS) Technical Council.
  10. Co-founder of the UK-ITSS Technology Specialist Network (TSN)


Conferences (highlights)

 

Guest speak at the launch of the Liverpool University RTP promotion pathway. February 2023


Guest speaker at Cyto 2022 in Philadelphia. Plenary speaker


Australian Cytometry Society, October 2019, Melbourne, Plenary speaker.

 

GLIFCA, September 2019, Tory Michigan, Plenary speaker.

 

Canadian Cytometry and Microscopy Society, June 2019, Edmonton, Plenary speaker.

 

Spatial protein multiplexing in health and disease, May 2019, Basel, Invited speaker.

 

I-biology seminar, February 2019, Heidelberg, Invited speaker/tutor.

https://www.ibiology.org/techniques/imaging-flow-cytometry/

 

QUAD meeting, February 2019, Newcastle, Invited speaker.

 

RACE renewal meeting, January 2019, Glasgow, Invited speaker.

 

ELRIG Pharmaceutical Flow and Imaging meeting, November 2018, Invited speaker/session.

 

Institute Pasteur, Montevideo, Uruguay March 2018, Invited Speaker.

https://www.youtube.com/watch?v=Gjcw2lGAqm4

 


Research

My own current research focuses on “cytomics”, the study of all measurable properties of single cells within complex heterogeneous biological systems, with focus on human health and disease. There are four main areas of research in my group:

  1. The use of “label-free” imaging technologies combined with advanced computer vision (machine/deep learning) as a tool for characterising cellular phenotypes and states toward the development of cost-effective, simple, rapid and accurate “point-of-care” diagnostic solutions. Specifically I have been working with Imaging Flow Cytometry (IFC) to address several key areas of single cell biology. My lab were the first to develop a method for classifying the cell cycle stages of cancer cells using only bright-field imagery using machine (Nature Comms 2016 ) and deep learning neural networks (Nature Comms 2017). We also developed an open source analysis pipeline for the community (Methods 2017). Recently we have been applying similar approaches to phenotype human white blood cells; a Wellcome Trust ISF project called “label-free CDs”. We have already published two papers on the output, with more to follow.
  2. Genomic ENd-point CytOMETRY (Genometry), a fusion between single cell RNA sequencing (scRNAseq) and flow cytometry whereby both protein and mRNA expression can be measured simultaneously on thousands of single cells from a “multi-omics” perspective. We are currently using this to study immune cells in Sepsis.
  3. The use of Imaging Mass Cytometry (IMC) to perform highly multi-plexed phenotyping of single cells in tissue preserving spatial context. Our first output from this methodology was published in Nature and maps key cells in the developing Foetal liver.


Collaborations and Networks (highlights)

 

Internal:

Internally, I work collaboratively across all three of the new FMS institute structures:

“Biosciences”: Human Cell Atlas (HCA) Developmental project (Haniffa lab)

“Clinical and Translational”: Immune-phenotyping of COVID post mortem lung tissues (Fisher)

"Public Health Sciences”: CellProthera “EXCELLENT” trial. (Advanced Therapies Facility)

 

External (academic):

Professor Tom Curtis, SAgE. Looking at the microbial communities in drinking water

Professor Facundo Batista, associate director of the Ragon Institute, USA.

Dr Anne Carpenter, imaging platform lead, Broad Institute, USA.

Professor Yvan Saeys, head of computational analysis, VIB Ghent, Belgium.

Professor Paul Rees, machine/deep learning, Swansea University.

Dr Marcelo Comini, single cell analysis of host-parasite interactions, Pasteur Montevideo, Uruguay.

 

External (industrial/commercial):


Proctor and Gamble (P&G): Developing a flow cytometry assay for antimicrobial testing.

Zomp: Scientific Advisory Board for the company developing a 3D Imaging Flow Cytometer

Genentech: The role of biological therapies in IBD.

Becton Dickinson: A multi-omics approach to immune cell phenotyping in Sepsis.

Northumbria Water: Using Flow Cytometry to assess driking water quality





 

Teaching

I am module co-lead for:


MMB8053: Enabling Technologies and Methodologies for Biomedical Research


I currently teach on the following post-graduate courses:


MMB8022 Stem cells and Regenerative Medicine

MMB8015:Applied Immunobiology of Human Disease


I also teach externally on:

The EMBL practical Flow Cytometry Course

The EMBL Fundamentals of Cell sorting Course

The RMS Flow Cytometry Course




Publications

  • Articles

    • Milross L, Hunter B, McDonald D, Merces G, Thomson A, Hilkens CMU, Wills J, Rees P, Jiwa K, Cooper N, Majo J, Ashwin H, Duncan CJA, Kaye PM, Bayraktar OA, Filby A, Fisher AJ. Distinct lung cell signatures define the temporal evolution of diffuse alveolar damage in fatal COVID-19. eBioMedicine 2024, 99, 104945.
    • Musgrave KM, Scott J, Sendama W, Gardner AI, Dewar F, Lake CJ, Spronk HMH, van Oerle R, Visser M, ten Cate H, Kesteven P, Fuller A, McDonald D, Knill C, Hulme G, Filby A, Wright SE, Roy AI, Ruchaud-Sparagano M, Simpson AJ, Rostron AJ. Tissue factor expression in monocyte subsets during human immunothrombosis, endotoxemia and sepsis. Thrombosis Research 2023, 228, 10-20.
    • Lim JX, Lai CY, Mallett GE, McDonald D, Hulme G, Laba S, Shapanis A, Payne M, Patterson W, Alexander M, Coxhead J, Filby A, Plummer R, Lovat PE, Sciume G, Healy E, Amarnath S. Programmed cell death-1 receptor-mediated regulation of Tbet+NK1.1- innate lymphoid cells within the tumor microenvironment. Proceedings of the National Academy of Sciences of the United States of America 2023, 120(18), e2216587120.
    • Chen C, McDonald D, Blain A, Mossman E, Atkin K, Marusich MF, Capaldi R, Bone L, Smith A, Filby A, Erskine D, Russell O, Hudson G, Vincent AE, Reeve AK. Parkinson’s disease neurons exhibit alterations in mitochondrial quality control proteins. npj Parkinson's Disease 2023, 9, 120.
    • Hunter B, Nicorescu I, Foster E, McDonald D, Hulme G, Fuller A, Thomson A, Goldsborough T, Hilkens CMU, Majo J, Milross L, Fisher A, Bankhead P, Wills J, Rees P, Filby A, Merces G. OPTIMAL: An OPTimized Imaging Mass cytometry AnaLysis framework for benchmarking segmentation and data exploration. Cytometry Part A 2024, 105(1), 36-53.
    • Ashwin H, Milross L, Wilson J, Majo J, Hang Lee JT, Calder G, Hunter B, James S, Lagos D, Signoret N, Filby A, Bayraktar OA, Fisher AJ, Kaye PM. Identification of a protein expression signature distinguishing early from organising diffuse alveolar damage in COVID-19 patients. Journal of Clinical Pathology 2023, 76(8), 561-565.
    • Masic D, Fee K, Bell H, Case M, Witherington G, Lansbury S, Ojeda-Garcia J, McDonald D, Schwab C, Van Delft FW, Filby A, Irving JAE. Hyperactive CREB subpopulations increase during therapy in pediatric B-lineage acute lymphoblastic leukemia. Haematologica 2023, 108(4), 981-992.
    • Ajaib S, Lodha D, Pollock S, Hemmings G, Finetti MA, Gusnanto A, Chakrabarty A, Ismail A, Wilson E, Varn FS, Hunter B, Filby A, Brockman AA, McDonald D, Verhaak RGW, Ihrie RA, Stead LF. GBMdeconvoluteR accurately infers proportions of neoplastic and immune cell populations from bulk glioblastoma transcriptomics data. Neuro-Oncology 2023, 25(7), 1236-1248.
    • Dey S, Ashwin H, Milross L, Hunter B, Majo J, Filby AJ, Fisher AJ, Kaye PM, Lagos D. Downregulation of MALAT1 is a hallmark of tissue and peripheral proliferative T cells in COVID-19. Clinical and Experimental Immunology 2023, 212(3), 262-275.
    • Milross L, Majo J, Pulle J, Hoggard S, Cooper N, Hunter B, Duncan CJA, Filby A, Fisher AJ. The trajectory of COVID-19 cardiopulmonary disease: insights from an autopsy study of community-based, pre-hospital deaths. ERJ Open Research 2022, 8(4), 00303-2022.
    • Hipps D, Dobson PF, Warren C, McDonald D, Fuller A, Filby A, Bulmer D, Laude A, Russell O, Deehan DJ, Turnbull DM, Lawless C. Detecting respiratory chain defects in osteoblasts from osteoarthritic patients using imaging mass cytometry. Bone 2022, 158, 116371.
    • Leslie J, Mackey JBG, Jamieson T, Ramon-Gil E, Drake TM, Fercoq F, Clark W, Gilroy K, Hedley A, Nixon C, Luli S, Laszczewska M, Pinyol R, Esteban-Fabro R, Willoughby CE, Haber PK, Andreu-Oller C, Rahbari M, Fan C, Pfister D, Raman S, Wilson N, Muller M, Collins A, Geh D, Fuller A, Mcdonald D, Hulme G, Filby A, Cortes-Lavaud X, Mohamed N-E, Ford CA, Raffo Iraolagoitia XL, Mcfarlane AJ, Mccain MV, Ridgway RA, Roberts EW, Barry ST, Graham GJ, Heikenwalder M, Reeves HL, Llovet JM, Carlin LM, Bird TG, Sansom OJ, Mann DA. CXCR2 inhibition enables NASH-HCC immunotherapy. Gut 2022, 71(10), 2093-2106.
    • Chen C, Mossman E, Malko P, McDonald D, Blain AP, Bone L, Erskine D, Filby A, Vincent AE, Hudson G, Reeve AK. Astrocytic Changes in Mitochondrial Oxidative Phosphorylation Protein Levels in Parkinson's Disease. Movement Disorders 2022, 37(2), 302-314.
    • Chen C, McDonald D, Blain A, Sachdeva A, Bone L, Smith ALM, Warren C, Pickett SJ, Hudson G, Filby A, Vincent AE, Turnbull DM, Reeve AK. Imaging mass cytometry reveals generalised deficiency in OXPHOS complexes in Parkinson’s disease. npj Parkinson's Disease 2021, 7(1), 39.
    • Reynolds G, Vegh P, Fletcher J, Poyner EFM, Stephenson E, Goh I, Botting RA, Huang N, Olabi B, Dubois A, Dixon D, Green K, Maunder D, Engelbert J, Efremova M, Polański K, Jardine L, Jones C, Ness T, Horsfall D, McGrath J, Carey C, Popescu D-M, Webb S, Wang X-N, Sayer B, Park J-E, Negri VA, Belokhvostova D, Lynch MD, McDonald D, Filby A, Hagai T, Meyer KB, Husain A, Coxhead J, Vento-Tormo R, Behjati S, Lisgo S, Villani A-C, Bacardit J, Jones PH, O'Toole EA, Ogg GS, Rajan N, Reynolds NJ, Teichmann SA, Watt FM, Haniffa M. Developmental cell programs are co-opted in inflammatory skin disease. Science 2021, 371(6527), eaba6500.
    • James DW, Filby A, Brown MR, Summers HD, Francis LW, Rees P. Data Driven Cell Cycle Model to Quantify the Efficacy of Cancer Therapeutics Targeting Specific Cell-Cycle Phases From Flow Cytometry Results. Frontiers in Bioinformatics 2021, 1, 662210.
    • Jardine L, Webb S, Goh I, Quiroga Londono M, Reynolds G, Mather M, Olabi B, Stephenson E, Botting RA, Horsfall D, Engelbert J, Maunder D, Mende N, Murnane C, Dann E, McGrath J, King H, Kucinski I, Queen R, Carey CD, Shrubsole C, Poyner E, Acres M, Jones C, Ness T, Coulthard R, Elliott N, O'Byrne S, Haltalli MLR, Lawrence JE, Lisgo S, Balogh P, Meyer KB, Prigmore E, Ambridge K, Jain MS, Efremova M, Pickard K, Creasey T, Bacardit J, Henderson D, Coxhead J, Filby A, Hussain R, Dixon D, McDonald D, Popescu D-M, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Regev A, Behjati S, Laurenti E, Wilson NK, Roy A, Gottgens B, Roberts I, Teichmann SA, Haniffa M. Blood and immune development in human fetal bone marrow and Down syndrome. Nature 2021, 598, 327-331.
    • Aspland AM, Douagi I, Filby A, Jellison ER, Martinez L, Shinko D, Smith AL, Tang VA, Thornton S. Biosafety during a pandemic: shared resource laboratories rise to the challenge. Cytometry Part A 2021, 99(1), 68-80.
    • Maier R, Bawamia B, Bennaceur K, Dunn S, Marsay L, Amoah R, Kasim A, Filby A, Austin D, Hancock H, Spyridopoulos I. Telomerase activation to reverse immunosenescence in elderly patients with acute coronary syndrome: Protocol for a randomized pilot trial. JMIR Research Protocols 2020, 9(9), e19456.
    • Doan M, Case M, Masic D, Hennig H, McQuin C, Caicedo J, Singh S, Goodman A, Wolkenhauer O, Summers H, Jamieson D, van Delft FW, Filby A, Carpenter A, Rees P, Irving J. Label-Free Leukemia Monitoring by Computer Vision. Cytometry A 2020, 97(4), 407-414.
    • Cytlak U, Resteu A, Pagan S, Green K, Milne P, Maisuria S, McDonald D, Hulme G, Filby A, Carpenter B, Queen R, Hambleton S, Hague R, Lango Allen H, Thaventhiran JED, Doody G, Collin M, Bigley V. Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans. Immunity 2020, 53(2), 353-370.
    • Warren C, McDonald D, Capaldi R, Deehan D, Taylor RW, Filby A, Turnbull DM, Lawless C, Vincent AE. Decoding mitochondrial heterogeneity in single muscle fibres by imaging mass cytometry. Scientific Reports 2020, 10(1), 15336.
    • Park J-E, Botting RA, Dominguez Conde C, Popescu D-M, Lavaert M, Kunz DJ, Goh I, Stephenson E, Ragazzini R, Tuck E, Wilbrey-Clark A, Roberts K, Kedlian VR, Ferdinand JR, He X, Webb S, Maunder D, Vandamme N, Mahbubani KT, Polanski K, Mamanova L, Bolt L, Crossland D, de Rita F, Fuller A, Filby A, Reynolds G, Dixon D, Saeb-Parsy K, Lisgo S, Henderson D, Vento-Tormo R, Bayraktar OA, Barker RA, Meyer KB, Saeys Y, Bonfanti P, Behjati S, Clatworthy MR, Taghon T, Haniffa M, Teichmann SA. A cell atlas of human thymic development defines T cell repertoire formation. Science 2020, 367(6480), eaay3224.
    • Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL, Staniforth JUL, Braga FAV, Botting RA, Popescu D-M, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Polanski K, Efremova M, Green K, Velasco-Herrera MDC, Guzzo C, Collord G, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Lindsay S, Bajenoff M, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Behjati S, Clatworthy MR. Spatiotemporal immune zonation of the human kidney. Science 2019, 365(6460), 1461-1466.
    • Jardine L, Wiscombe S, Reynolds G, McDonald D, Fuller A, Green K, Filby A, Forrest I, Ruchaud-Sparagano MH, Scott J, Collin M, Haniffa M, Simpson AJ. Lipopolysaccharide inhalation recruits monocytes and dendritic cell subsets to the alveolar airspace. Nature Communications 2019, 10, 1999.
    • Nassar M, Doan M, Filby A, Wolkenhauer O, Fogg DK, Piasecka J, Thornton CA, Carpenter AE, Summers HD, Rees P, Hennig H. Label-Free Identification of White Blood Cells Using Machine Learning. Cytometry Part A 2019, 95(8), 836-842.
    • Cossarizza A, Chang H-D, Radbruch A, Acs A, Adam D, Adam-Klages S, Agace WW, Aghaeepour N, Akdis M, Allez M, Almeida LN, Alvisi G, Anderson G, Andra I, Annunziato F, Anselmo A, Bacher P, Baldari CT, Bari S, Barnaba V, Barros-Martins J, Battistini L, Bauer W, Baumgart S, Baumgarth N, Baumjohann D, Baying B, Bebawy M, Becher B, Beisker W, Benes V, Beyaert R, Blanco A, Boardman DA, Bogdan C, Borger JG, Borsellino G, Boulais PE, Bradford JA, Brenner D, Brinkman RR, Brooks AES, Busch DH, Buscher M, Bushnell TP, Calzetti F, Cameron G, Cammarata I, Cao X, Cardell SL, Casola S, Cassatella MA, Cavani A, Celada A, Chatenoud L, Chattopadhyay PK, Chow S, Christakou E, Cicin-Sain L, Clerici M, Colombo FS, Cook L, Cooke A, Cooper AM, Corbett AJ, Cosma A, Cosmi L, Coulie PG, Cumano A, Cvetkovic L, Dang VD, Dang-Heine C, Davey MS, Davies D, De Biasi S, Del Zotto G, Dela Cruz GV, Delacher M, Della Bella S, Dellabona P, Deniz G, Dessing M, Di Santo JP, Diefenbach A, Dieli F, Dolf A, Dorner T, Dress RJ, Dudziak D, Dustin M, Dutertre C-A, Ebner F, Eckle SBG, Edinger M, Eede P, Ehrhardt GRA, Eich M, Engel P, Engelhardt B, Erdei A, Esser C, Everts B, Evrard M, Falk CS, Fehniger TA, Felipo-Benavent M, Ferry H, Feuerer M, Filby A, Filkor K, Fillatreau S, Follo M, Forster I, Foster J, Foulds GA, Frehse B, Frenette PS, Frischbutter S, Fritzsche W, Galbraith DW, Gangaev A, Garbi N, Gaudilliere B, Gazzinelli RT, Geginat J, Gerner W, Gherardin NA, Ghoreschi K, Gibellini L, Ginhoux F, Goda K, Godfrey DI, Goettlinger C, Gonzalez-Navajas JM, Goodyear CS, Gori A, Grogan JL, Grummitt D, Grutzkau A, Haftmann C, Hahn J, Hammad H, Hammerling G, Hansmann L, Hansson G, Harpur CM, Hartmann S, Hauser A, Hauser AE, Haviland DL, Hedley D, Hernandez DC, Herrera G, Herrmann M, Hess C, Hofer T, Hoffmann P, Hogquist K, Holland T, Hollt T, Holmdahl R, Hombrink P, Houston JP, Hoyer BF, Huang B, Huang F-P, Huber JE, Huehn J, Hundemer M, Hunter CA, Hwang WYK, Iannone A, Ingelfinger F, Ivison SM, Jack H-M, Jani PK, Javega B, Jonjic S, Kaiser T, Kalina T, Kamradt T, Kaufmann SHE, Keller B, Ketelaars SLC, Khalilnezhad A, Khan S, Kisielow J, Klenerman P, Knopf J, Koay H-F, Kobow K, Kolls JK, Kong WT, Kopf M, Korn T, Kriegsmann K, Kristyanto H, Kroneis T, Krueger A, Kuhne J, Kukat C, Kunkel D, Kunze-Schumacher H, Kurosaki T, Kurts C, Kvistborg P, Kwok I, Landry J, Lantz O, Lanuti P, LaRosa F, Lehuen A, LeibundGut-Landmann S, Leipold MD, Leung LYT, Levings MK, Lino AC, Liotta F, Litwin V, Liu Y, Ljunggren H-G, Lohoff M, Lombardi G, Lopez L, Lopez-Botet M, Lovett-Racke AE, Lubberts E, Luche H, Ludewig B, Lugli E, Lunemann S, Maecker HT, Maggi L, Maguire O, Mair F, Mair KH, Mantovani A, Manz RA, Marshall AJ, Martinez-Romero A, Martrus G, Marventano I, Maslinski W, Matarese G, Mattioli AV, Maueroder C, Mazzoni A, McCluskey J, McGrath M, McGuire HM, McInnes IB, Mei HE, Melchers F, Melzer S, Mielenz D, Miller SD, Mills KHG, Minderman H, Mjosberg J, Moore J, Moran B, Moretta L, Mosmann TR, Muller S, Multhoff G, Munoz LE, Munz C, Nakayama T, Nasi M, Neumann K, Ng LG, Niedobitek A, Nourshargh S, Nunez G, O'Connor J-E, Ochel A, Oja A, Ordonez D, Orfao A, Orlowski-Oliver E, Ouyang W, Oxenius A, Palankar R, Panse I, Pattanapanyasat K, Paulsen M, Pavlinic D, Penter L, Peterson P, Peth C, Petriz J, Piancone F, Pickl WF, Piconese S, Pinti M, Pockley AG, Podolska MJ, Poon Z, Pracht K, Prinz I, Pucillo CEM, Quataert SA, Quatrini L, Quinn KM, Radbruch H, Radstake TRDJ, Rahmig S, Rahn H-P, Rajwa B, Ravichandran G, Raz Y, Rebhahn JA, Recktenwald D, Reimer D, Reis e Sousa C, Remmerswaal EBM, Richter L, Rico LG, Riddell A, Rieger AM, Robinson JP, Romagnani C, Rubartelli A, Ruland J, Saalmuller A, Saeys Y, Saito T, Sakaguchi S, Sala-de-Oyanguren F, Samstag Y, Sanderson S, Sandrock I, Santoni A, Sanz RB, Saresella M, Sautes-Fridman C, Sawitzki B, Schadt L, Scheffold A, Scherer HU, Schiemann M, Schildberg FA, Schimisky E, Schlitzer A, Schlosser J, Schmid S, Schmitt S, Schober K, Schraivogel D, Schuh W, Schuler T, Schulte R, Schulz AR, Schulz SR, Scotta C, Scott-Algara D, Sester DP, Shankey TV, Silva-Santos B, Simon AK, Sitnik KM, Sozzani S, Speiser DE, Spidlen J, Stahlberg A, Stall AM, Stanley N, Stark R, Stehle C, Steinmetz T, Stockinger H, Takahama Y, Takeda K, Tan L, Tarnok A, Tiegs G, Toldi G, Tornack J, Traggiai E, Trebak M, Tree TIM, Trotter J, Trowsdale J, Tsoumakidou M, Ulrich H, Urbanczyk S, van de Veen W, van den Broek M, van der Pol E, Van Gassen S, Van Isterdael G, van Lier RAW, Veldhoen M, Vento-Asturias S, Vieira P, Voehringer D, Volk H-D, von Borstel A, von Volkmann K, Waisman A, Walker RV, Wallace PK, Wang SA, Wang XM, Ward MD, Ward-Hartstonge KA, Warnatz K, Warnes G, Warth S, Waskow C, Watson JV, Watzl C, Wegener L, Weisenburger T, Wiedemann A, Wienands J, Wilharm A, Wilkinson RJ, Willimsky G, Wing JB, Winkelmann R, Winkler TH, Wirz OF, Wong A, Wurst P, Yang JHM, Yang J, Yazdanbakhsh M, Yu L, Yue A, Zhang H, Zhao Y, Ziegler SM, Zielinski C, Zimmermann J, Zychlinsky A. Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition). European Journal of Immunology 2019, 49(10), 1457-1973.
    • Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park JE, Vento-Tormo R, Miao Z, Dixon D, Rowell R, McDonald D, Fletcher J, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young MD, Meyer KB, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani AC, Roy A, Regev A, Chédotal A, Roberts I, Göttgens B, Behjati S, Laurenti E, Teichmann SA, Haniffa M. Decoding human fetal liver haematopoiesis. Nature 2019, 574, 365–371.
    • Lippeveld M, Knill C, Ladlow E, Fuller A, Michaelis LJ, Saeys Y, Filby A, Peralta D. Classification of Human White Blood Cells Using Machine Learning for Stain-Free Imaging Flow Cytometry. Cytometry Part A 2019, 97(3), 308-319.
    • Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, Collord G, Botting RA, Popescu D-M, Loudon KW, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Velasco-Herrera MDC, Guzzo C, Richoz N, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Maxwell PH, Lindsay S, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Clatworthy M, Behjati S. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science 2018, 361(6402), 594-599.
    • Vento-Tormo R, Efremova M, Botting RA, Turco MY, Vento-Tormo M, Meyer KB, Park JE, Stephenson E, Polański K, Goncalves A, Gardner L, Holmqvist S, Henriksson J, Zou A, Sharkey AM, Millar B, Innes B, Wood L, Wilbrey-Clark A, Payne RP, Ivarsson MA, Lisgo S, Filby A, Rowitch DH, Bulmer JN, Wright GJ, Stubbingon MJT, Haniffa M, Moffett A, Teichmann SA. Single-cell reconstruction of the early maternal–fetal interface in humans. Nature 2018, 563, 347-353.
    • Reis M, McDonald D, Nicholson L, Godthardt K, Knobel S, Dickinson AM, Filby A, Wang X-N. Global phenotypic characterisation of human platelet lysate expanded MSCs by high-throughput flow cytometry. Scientific Reports 2018, 8(1), 3907.
    • Villani A-C, 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 AA, Haniffa M, Regev A, Hacohen N. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 2017, 356(6335), eaah4573.
    • Eulenberg P, Köhler N, Blasi T, Filby A, Carpenter AE, Rees P, Theis FJ, Wolf FA. Reconstructing cell cycle and disease progression using deep learning. Nature Communications 2017, (8), 463.
    • Cossarizza A, Chang H-D, Radbruch A, Andra I, Annunziato F, Bacher P, Barnaba V, Battistini L, Bauer WM, Baumgart S, Becher B, Beisker W, Berek C, Blanco A, Borsellino G, Boulais PE, Brinkman RR, Buscher M, Busch DH, Bushnell TP, Cao X, Cavani A, Chattopadhyay PK, Cheng Q, Chow S, Clerici M, Cooke A, Cosma A, Cosmi L, Cumano A, Dang VD, 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 VS, Dorner T, Ehrhardt GRA, Endl E, Engel P, Engelhardt B, Esser C, Everts B, Falk CS, Fehniger TA, Filby A, Fillatreau S, Follo M, Forster I, Foster J, Foulds GA, Frenette PS, Galbraith D, Garbi N, Garcia-Godoy MD, Ghoreschi K, Gibellini L, Goettlinger C, Goodyear CS, Gori A, Grogan J, Gross M, Grutzkau A, Grummitt D, Hahn J, Hammer Q, Hauser AE, Haviland DL, Hedley D, Herrera G, Herrmann M, Hiepe F, Holland T, Hombrink P, Houston JP, Hoyer BF, Huang B, Hunter CA, Iannone A, Jack H-M, Javega B, Jonjic S, Juelke K, Jung S, Kaiser T, Kalina T, Keller B, Khan S, Kienhofer D, Kroneis T, Kunkel D, Kurts C, Kvistborg P, Lannigan J, Lantz O, Larbi A, LeibundGut-Landmann S, Leipold MD, Levings MK, Litwin V, Liu Y, Lohoff M, Lombardi G, Lopez L, Lovett-Racke A, Lubberts E, Ludewig B, Lugli E, Maecker HT, Martrus G, Matarese G, Maueroder C, McGrath M, McInnes I, Mei HE, Melchers F, Melzer S, Mielenz D, Mills K, Mjosberg J, Moore J, Moran B, Moretta A, Moretta L, Mosmann TR, Muller S, Muller W, Munz C, Multhoff G, Munoz LE, Murphy KM, Nakayama T, Nasi M, Neudorfl C, Nolan J, Nourshargh S, O'Connor J-E, Ouyang W, Oxenius A, Palankar R, Panse I, Peterson P, Peth C, Petriz J, Philips D, Pickl W, Piconese S, Pinti M, Pockley AG, Podolska MJ, Pucillo C, Quataert SA, Radstake TRDJ, Rajwa B, Rebhahn JA, Recktenwald D, Remmerswaal EBM, Rezvani K, Rico LG, Robinson JP, Romagnani C, Rubartelli A, Ruland J, Sakaguchi S, Sala-de-Oyanguren F, Samstag Y, Sanderson S, Sawitzki B, Scheffold A, Schiemann M, Schildberg F, Schimisky E, Schmid SA, Schmitt S, Schober K, Schuler T, Schulz AR, Schumacher T, Scotta C, Shankey TV, Shemer A, Simon A-K, Spidlen J, Stall AM, Stark R, Stehle C, Stein M, Steinmetz T, Stockinger H, Takahama Y, Tarnok A, Tian Z, Toldi G, Tornack J, Traggiai E, Trotter J, Ulrich H, van der Braber M, van Lier RAW, Veldhoen M, Vento-Asturias S, Vieira P, Voehringer D, Volk H-D, von Volkmann K, Waisman A, Walker R, Ward MD, Warnatz K, Warth S, Watson JV, Watzl C, Wegener L, Wiedemann A, Wienands J, Willimsky G, Wing J, Wurst P, Yu L, Yue A, Zhang Q, Zhao Y, Ziegler S, Zimmermann J. Guidelines for the use of flow cytometry and cell sorting in immunological studies. European Journal of Immunology 2017, 47(10), 1584-1797.
    • Borger JG, Morrison VL, Filby A, Garcia C, Uotila LM, Simbari F, Fagerholm SC, Zamoyska R. Caveolin-1 Influences LFA-1 Redistribution upon TCR Stimulation in CD8 T Cells. Journal of Immunology 2017, 199(3), 874-884.
    • Hennig H, Rees P, Blasi T, Kamentsky L, Hung J, Dao D, Carpenter AE, Filby A. An open-source solution for advanced imaging flow cytometry data analysis using machine learning. Methods 2017, 112, 201-210.
    • Srivastava S, Ramsbottom SA, Molinari E, Alkanderi S, Filby A, White K, Henry C, Saunier S, Miles CG, Sayer JA. A human patient-derived cellular model of Joubert syndrome reveals ciliary defects which can be rescued with targeted therapies. Human Molecular Genetics 2017, 26(23), 4657-4667.
    • Merkenschlager J, Ploquin MJ, Eksmond U, Andargachew R, Thorborn G, Filby A, Pepper M, Evavold B, Kassiotis G. Stepwise B-cell-dependent expansion of T helper clonotypes diversifies the T-cell response. Nature Communications 2016, 7, 10281.
    • Filby A. Sample preparation for flow cytometry benefits from some lateral thinking. Cytometry Part A 2016, 89(12), 1054-1056.
    • Pal D, Blair HJ, Elder A, Dormon K, Rennie KJ, Coleman DJL, Weiland J, Rankin KS, Filby A, Heidenreich O, Vormoor J. Long-term in vitro maintenance of clonal abundance and leukaemia-initiating potential in acute lymphoblastic leukaemia. Leukemia 2016, 30, 1691-1700.
    • Blasi T, Hennig H, Summers HD, Theis FJ, Cerveira J, Patterson JO, Davies D, Filby A, Carpenter AE, Rees P. Label-free cell cycle analysis for high-throughput imaging flow cytometry. Nature Communications 2016, 7, 10256.
    • Griessinger E, Anjos-Afonso F, Vargaftig J, Taussig DC, Lassailly F, Prebet T, Imbert V, Nebout M, Vey N, Chabannon C, Filby A, Bollet-Quivogne F, Gribben JG, Peyron JF, Bonnet D. Frequency and Dynamics of Leukemia-Initiating Cells during Short-term Ex Vivo Culture Informs Outcomes in Acute Myeloid Leukemia Patients. Cancer Research 2016, 76(8), 2082-2086.
    • Filby A. New, clear fusion from the cellular perspective: Measuring cellular fusion in Saccharomyces cerevisiae by flow cytometry. Cytometry Part A 2015, 87(9), 797-799.
    • Filby A, Begum J, Jalal M, Day W. Appraising the suitability of succinimidyl and lipophilic fluorescent dyes to track proliferation in non-quiescent cells by dye dilution. Methods 2015, 82, 29-37.
    • Cerveira J, Begum J, Barros RD, van der Veen AG, Filby A. An imaging flow cytometry-based approach to measuring the spatiotemporal calcium mobilisation in activated T cells. Journal of Immunological Methods 2015, 423, 120-130.
    • Patterson JO, Swaffer M, Filby A. An Imaging Flow Cytometry-based approach to analyse the fission yeast cell cycle in fixed cells. Methods 2015, 82, 74-84.
    • Filby A. "Mega" cytometry for a "mega" challenging cell type. Cytometry Part A 2014, 85(4), 289-291.
    • Hawkins ED, Oliaro J, Kallies A, Belz GT, Filby A, Hogan T, Haynes N, Ramsbottom KM, VanHam V, Kinwell T, Seddon B, Davies D, Tarlinton D, Lew AM, Humbert PO, Russell SM. Regulation of asymmetric cell division and polarity by Scribble is not required for humoral immunity. Nature Communications 2013.
    • Schraml BU, vanBlijswijk J, Zelenay S, Whitney PG, Filby A, Acton SE, Rogers NC, Moncaut N, Carvaja JJ, ReiseSousa C. Genetic tracing via DNGR-1 expression history defines dendritic cells as a hematopoietic lineage. Cell 2013.
    • Borger JG, Filby A, Zamoyska R. Differential polarization of C-terminal Src kinase between naive and antigen-experienced CD8+ T cells. Journal of Immunology 2013.
    • Begum J, Day W, Henderson C, Purewal S, Cerveira J, Summers H, Rees P, Davies D, Filby A. A method for evaluating the use of fluorescent dyes to track proliferation in cell lines by dye dilution. Cytometry Part A 2013, 83(12), 1085-1095.
    • Filby A, Davies D. Reporting imaging flow cytometry data for publication: why mask the detail?. Cytometry Part A 2012.
    • Thaunat O, Granja AG, Barral P, Filby A, Montaner B, Collinson L, Martinez-Martin N, Harwoo NE, Bruckbauer A, Batista FD. Asymmetric segregation of polarized antigen on B cell division shapes presentation capacity. Science 2012.
    • Gandillet A, Park S, Lassailly F, Griessinger E, Vargaftig J, Filby A, Lister TA, Bonnet D. Heterogeneous sensitivity of human acute myeloid leukemia to β-catenin down-modulation. Leukemia 2011.
    • Filby A, Perucha E, Summers H, Rees P, Chana P, Heck S, Lord GM, Davies D. An imaging flow cytometric method for measuring cell division history and molecular symmetry during mitosis. Cytometry Part A 2011.
    • Salmond RJ, Filby A, Pirinen N, Magee AI, Zamoyska R. Mislocalization of Lck impairs thymocyte differentiation and can promote development of thymomas. Blood 2010.
    • Salmon RJ, Filby A, Qureshi I, Caserta S, Zamoyska R. T-cell receptor proximal signaling via the Src-family kinases, Lck and Fyn, influences T-cell activation, differentiation, and tolerance. Immunological Reviews 2009.
    • Pike R, Filby A, Ploquin MJ, Eksmond U, Marques R, Antunes I, Hasenkrug K, Kassiotis G. Race between retroviral spread and CD4+ T-cell response determines the outcome of acute Friend virus infection. Journal of Virology 2009.
    • Filby A, Seddon B, Kleczkowska J, Salmond R, Tomlinson P, Smida M, Lindquist JA, Schraven B, Zamoyska R. Filby A, Seddon B, Kleczkowska J, Salmond R, Tomlinson P, Smida M, Lindquist JA, Schraven B, Zamoyska R. Journal of Immunology 2007.
    • Lovatt M, Filby A, Parravicini V, Werlen G, Palmer E, Zamoyska R. 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. Molecular and Cellular Biology 2006.
    • Zamoysk R, Basson A, Filby A, Legname G, Lovatt M, Seddon B. The influence of the src-family kinases, Lck and Fyn, on T cell differentiation, survival and activation. Immunological Reviews 2003.
    • Dearman RJ, Filby A, Humphreys IR, Kimber I. Interleukins 5 and 13 characterize immune responses to respiratory sensitizing acid anhydrides. Journal of Applied Toxicology 2002, 22(5), 317-325.

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