Sally Cowley | Head

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I joined the Sir William Dunn School of Pathology as a Wellcome Trust Career Re-Entry Fellow in 2007, engaged in a program of research into the differentiation of human Pluripotent Stem Cell-derived macrophages for disease modelling. Induced Pluripotent Stem cells (iPSC) derived from patients with genetic disease offers a new, hugely exciting opportunity to model human diseases in vitro. iPSC are particularly important for modelling neurological conditions, where patient material is generally unavailable until after death, and for rare genetic disorders, where patient material is severely limiting. To harness this potential, with William James, I set up the James Martin Stem Cell Facility (within the Sir William Dunn School of Pathology, University of Oxford, and affiliated to the Oxford Stem Cell Institute), with particular interests in the use of iPSC for modelling disease, and expertise in human iPSC derivation, genetic modification, and differentiation to myeloid and neuronal lineages. With the mounting evidence for a role of microglia in the progression of neurodegenerative diseases, I have focussed my research on using our iPSC models to better understand microglial physiology and pathophysiology. The success of this programme of research has led to establishment of the James and Lillian Martin Centre for Stem Cell Research, which I Head.

Key projects include: 1) Generation of a world-class panel of over 200 iPS cell lines from Parkinson’s patients, as part of a large-scale study within the Oxford Parkinson’s Disease Centre and the EU IMI consortium StemBANCC, to study the early cellular pathology of PD; 2) Pioneering efficient methodologies for differentiation of macrophages and microglia from human iPS cells; 3) Interrogation of the role of the Parkinson’s-associated genes a-synuclein, LRRK2 and PINK1/Parkin in macrophages and microglia; 4) Investigation of the role of Alzheimer’s-associated genes in iPS-macrophages/microglia, in collaboration with the Alzheimer’s Research UK Oxford Drug Discovery Institute; 5) Collaboration with the Cardiff Dementia Research Institute, to derive iPSC from Alzheimer’s patients with high polygenic risk score to study microglial phenotypes.

After graduating in Natural Sciences from Cambridge, I began my research career working  on host-pathogen interactions in mycobacteria (Ph.D, 1990, Royal College of Surgeons, University of London, and later at AHRI, Ethiopia). My post-doctoral work (New England Deaconess Hospital, Boston, and Institute of Cancer Research, London) centred around signal transduction pathways involved in differentiation: I identified and cloned a novel tyrosine kinase, MATK (expressed predominantly in megakaryocytes and implicated in their differentiation [JBC  1994]); and I was the first to demonstrate that the protein kinase MEK (/MKK) is downstream from the product of the important cancer associated genes Ras and Raf, and is critical for signal transduction pathways leading to differentiation and to tumorigenic transformation [Cell  1994 cited over 1800 times; EMBO J. 1994].

I chose to break from full-time lab-work whilst raising young children, continuing to tutor undergraduates part-time at the University of Oxford and the Open University. I subsequently obtained a Wellcome Trust Career Re-entry fellowship and joined the Sir William Dunn School of Pathology in 2007.

Primary Research Publications in Peer-Reviewed Journals


Integration of 3D-printed cerebral cortical tissue into an ex vivo lesioned brain slice. Jin Y, Mikhailova E, Lei M, Cowley SA, Sun T, Yang X, Zhang Y, Liu K, Catarino da Silva D, Campos Soares L, Bandiera S, Szele FG, Molnár Z, Zhou L, Bayley H. Nat Commun. 2023 Oct 4;14(1):5986.

C9orf72-ALS human iPSC microglia are pro-inflammatory and toxic to co-cultured motor neurons via MMP9. Vahsen BF, Nalluru S, Morgan GR, Farrimond L, Carroll E, Xu Y, Cramb KML, Amein B, Scaber J, Katsikoudi A, Candalija A, Carcolé M, Dafinca R, Isaacs AM, Wade-Martins R, Gray E, Turner MR, Cowley SA, Talbot K. Nat Commun. 2023 Sep 22;14(1):5898.

Calcium dysregulation combined with mitochondrial failure and electrophysiological maturity converge in Parkinson’s iPSC-dopamine neurons. Beccano-Kelly DA, Cherubini M, Mousba Y, Cramb KML, Giussani S, Caiazza MC, Rai P, Vingill S, Bengoa-Vergniory N, Ng B, Corda G, Banerjee A, Vowles J, Cowley S, Wade-Martins R. iScience. 2023 Jun 7;26(7):107044.

Post-translational proteomics platform identifies neurite outgrowth impairments in Parkinson’s disease GBA-N370S dopamine neurons. Bogetofte H, Ryan BJ, Jensen P, Schmidt SI, Vergoossen DLE, Barnkob MB, Kiani LN, Chughtai U, Heon-Roberts R, Caiazza MC, McGuinness W, Márquez-Gómez R, Vowles J, Bunn FS, Brandes J, Kilfeather P, Connor JP, Fernandes HJR, Caffrey TM, Meyer M, Cowley SA, Larsen MR, Wade-Martins R. Cell Rep. 2023 Mar 28;42(3):112180.


Type I interferon receptor (IFNAR2) deficiency reveals Zika virus cytopathicity in human macrophages and microglia. Hanrath AT, Hatton CF, Gothe F, Browne C, Vowles J, Leary P, Cockell SJ, Cowley SA, James WS, Hambleton S, Duncan CJA. Front Immunol. 2022 Nov 11;13:1035532.

Single-cell transcriptomics defines an improved, validated monoculture protocol for differentiation of human iPSC to microglia. Washer SJ, Perez-Alcantara M, Chen Y, Steer J, James WS, Trynka G, Bassett AR, Cowley SA. Sci Rep. 2022 Nov 14;12(1):19454.

Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer’s disease mouse models. Monzón-Sandoval J, Burlacu E, Agarwal D, Handel AE, Wei L, Davis J, Cowley SA, Cader MZ, Webber C. Dis Model Mech. 2022 Oct 1;15(10):dmm049349.

Human iPSC co-culture model to investigate the interaction between microglia and motor neurons. Vahsen BF, Gray E, Candalija A, Cramb KML, Scaber J, Dafinca R, Katsikoudi A, Xu Y, Farrimond L, Wade-Martins R, James WS, Turner MR, Cowley SA, Talbot K. Sci Rep. 2022 Jul 23;12(1):12606.

Pathogenic LRRK2 regulates centrosome cohesion via Rab10/RILPL1-mediated CDK5RAP2 displacement. Fdez E, Madero-Pérez J, Lara Ordóñez AJ, Naaldijk Y, Fasiczka R, Aiastui A, Ruiz-Martínez J, López de Munain A, Cowley SA, Wade-Martins R, Hilfiker S. iScience. 2022 May 30;25(6):104476.

Microglia integration into human midbrain organoids leads to increased neuronal maturation and functionality. Sabate-Soler S, Nickels SL, Saraiva C, Berger E, Dubonyte U, Barmpa K, Lan YJ, Kouno T, Jarazo J, Robertson G, Sharif J, Koseki H, Thome C, Shin JW, Cowley SA, Schwamborn JC. Glia. 2022 Jul;70(7):1267-1288.

Aberrant inflammatory responses to type I interferon in STAT2 or IRF9 deficiency. Gothe F, Stremenova Spegarova J, Hatton CF, Griffin H, Sargent T, Cowley SA, James W, Roppelt A, Shcherbina A, Hauck F, Reyburn HT, Duncan CJA, Hambleton S. J Allergy Clin Immunol. 2022 Feb 17:S0091-6749(22)00185-3


iPSC-Derived Microglia as a Model to Study Inflammation in Idiopathic Parkinson’s Disease. Badanjak K, Mulica P, Smajic S, Delcambre S, Tranchevent LC, Diederich N, Rauen T, Schwamborn JC, Glaab E, Cowley SA, Antony PMA, Pereira SL, Venegas C, Grünewald A. Front Cell Dev Biol. 2021 Nov 5;9:740758.

Differentiation of human induced pluripotent stem cells to authentic macrophages using a defined, serum-free, open-source medium. Vaughan-Jackson A, Stodolak S, Ebrahimi KH, Browne C, Reardon PK, Pires E, Gilbert-Jaramillo J, Cowley SA, James WS. Stem Cell Reports. 2021 Jul 13;16(7):1735-1748.

Identification of bioactive metabolites in human iPSC-derived dopaminergic neurons with PARK2 mutation: Altered mitochondrial and energy metabolism. Okarmus J, Havelund JF, Ryding M, Schmidt SI, Bogetofte H, Heon-Roberts R, Wade-Martins R, Cowley SA, Ryan BJ, Færgeman NJ, Hyttel P, Meyer M. Stem Cell Reports. 2021 Jun 8;16(6):1510-1526.

Gene therapy restores dopamine transporter expression and ameliorates pathology in iPSC and mouse models of infantile parkinsonism. Ng J, Barral S, De La Fuente Barrigon C, Lignani G, Erdem FA, Wallings R, Privolizzi R, Rossignoli G, Alrashidi H, Heasman S, Meyer E, Ngoh A, Pope S, Karda R, Perocheau D, Baruteau J, Suff N, Antinao Diaz J, Schorge S, Vowles J, Marshall LR, Cowley SA, Sucic S, Freissmuth M, Counsell JR, Wade-Martins R, Heales SJR, Rahim AA, Bencze M, Waddington SN, Kurian MA. Sci Transl Med. 2021 May 19;13(594):eaaw1564.

In vitro Quantitative Imaging Assay for Phagocytosis of Dead Neuroblastoma Cells by iPSC-Macrophages. Hall-Roberts H, Di Daniel E, James WS, Davis JB, Cowley SA. J Vis Exp. 2021 Feb 14;(168).

Molecular and electrophysiological features of spinocerebellar ataxia type seven in induced pluripotent stem cells. Burman RJ, Watson LM, Smith DC, Raimondo JV, Ballo R, Scholefield J, Cowley SA, Wood MJA, Kidson SH, Greenberg LJ. PLoS One. 2021 Feb 24;16(2):e0247434.

Alzheimer’s Risk Gene TREM2 Determines Functional Properties of New Type of Human iPSC-Derived Microglia. Reich M, Paris I, Ebeling M, Dahm N, Schweitzer C, Reinhardt D, Schmucki R, Prasad M, Köchl F, Leist M, Cowley SA, Zhang JD, Patsch C, Gutbier S, Britschgi M. Front Immunol. 2021 Feb 3;11:617860.

Genome-wide CRISPR/Cas9-knockout in human induced Pluripotent Stem Cell (iPSC)-derived macrophages. Navarro-Guerrero E, Tay C, Whalley JP, Cowley SA, Davies B, Knight JC, Ebner D. Sci Rep. 2021 Feb 19;11(1):4245.

Tissue-resident macrophages regulate lymphatic vessel growth and patterning in the developing heart. Cahill TJ, Sun X, Ravaud C, Villa Del Campo C, Klaourakis K, Lupu IE, Lord AM, Browne C, Jacobsen SEW, Greaves DR, Jackson DG, Cowley SA, James W, Choudhury RP, Vieira JM, Riley PR. Development. 2021 Feb 3;148(3):dev194563.


TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages. Hall-Roberts H, Agarwal D, Obst J, Smith TB, Monzón-Sandoval J, Di Daniel E, Webber C, James WS, Mead E, Davis JB, Cowley SA. Alzheimers Res Ther. 2020 Nov 16;12(1):151

ADAM17-triggered TNF signalling protects the ageing Drosophila retina from lipid droplet-mediated degeneration. Muliyil S, Levet C, Düsterhöft S, Dulloo I, Cowley SA, Freeman M. EMBO J. 2020 Sep 1;39(17):e104415.

Large-Scale Production of Human iPSC-Derived Macrophages for Drug Screening. Gutbier S, Wanke F, Dahm N, Rümmelin A, Zimmermann S, Christensen K, Köchl F, Rautanen A, Hatje K, Geering B, Zhang JD, Britschgi M, Cowley SA, Patsch C. Int J Mol Sci. 2020 Jul 7;21(13):4808.

Profiling of naïve and primed human pluripotent stem cells reveals state-associated miRNAs. Dodsworth BT, Hatje K, Rostovskaya M, Flynn R, Meyer CA, Cowley SA. Sci Rep. 2020 Jun 29;10(1):10542

Rates of homology directed repair of CRISPR-Cas9 induced double strand breaks are lower in naïve compared to primed human pluripotent stem cells. Dodsworth BT, Hatje K, Meyer CA, Flynn R, Cowley SA. Stem Cell Res. 2020 Jul;46:101852.

Correction of amyotrophic lateral sclerosis related phenotypes in induced pluripotent stem cell-derived motor neurons carrying a hexanucleotide expansion mutation in C9orf72 by CRISPR/Cas9 genome editing using homology-directed repair. Ababneh NA, Scaber J, Flynn R, Douglas A, Barbagallo P, Candalija A, Turner MR, Sims D, Dafinca R, Cowley SA, Talbot K. Hum Mol Genet. 2020 Aug 3;29(13):2200-2217.

Generation of twenty four induced pluripotent stem cell lines from twenty four members of the Lothian Birth Cohort 1936. Toombs J, Panther L, Ornelas L, Liu C, Gomez E, Martín-Ibáñez R, Cox SR, Ritchie SJ, Harris SE, Taylor A, Redmond P, Russ TC, Murphy L, Cooper JD, Burr K, Selvaraj BT, Browne C, Svendsen CN, Cowley SA, Deary IJ, Chandran S, Spires-Jones TL, Sareen D. Stem Cell Res. 2020 Jul;46:101851.

Patient fibroblast circadian rhythms predict lithium sensitivity in bipolar disorder. Sanghani HR, Jagannath A, Humberstone T, Ebrahimjee F, Thomas JM, Churchill GC, Cipriani A, Attenburrow MJ, Perestenko OV, Cowley SA, Cader MZ, Peirson SN, Harrison PJ, Foster RG, Goodwin GM, Vasudevan SR. Mol Psychiatry. 2020 May 13.

LRRK2 Is Recruited to Phagosomes and Co-recruits RAB8 and RAB10 in Human Pluripotent Stem Cell-Derived Macrophages. Lee H, Flynn R, Sharma I, Haberman E, Carling PJ, Nicholls FJ, Stegmann M, Vowles J, Haenseler W, Wade-Martins R, James WS, Cowley SA. Stem Cell Reports. 2020 May 12;14(5):940-955.

Impairment of Mitochondrial Calcium Buffering Links Mutations in C9ORF72 and TARDBP in iPS-Derived Motor Neurons from Patients with ALS/FTD. Dafinca R, Barbagallo P, Farrimond L, Candalija A, Scaber J, Ababneh NA, Sathyaprakash C, Vowles J, Cowley SA, Talbot K. Stem Cell Reports. 2020 May 12;14(5):892-908.


A causal role for TRESK loss of function in migraine mechanisms. Pettingill P, Weir GA, Wei T, Wu Y, Flower G, Lalic T, Handel A, Duggal G, Chintawar S, Cheung J, Arunasalam K, Couper E, Haupt LM, Griffiths LR, Bassett A, Cowley SA, Cader MZ. Brain. 2019 Dec 1;142(12):3852-3867.

Application of CRISPR/Cas9 editing and digital droplet PCR in human iPSCs to generate novel knock-in reporter lines to visualize dopaminergic neurons. Überbacher C, Obergasteiger J, Volta M, Venezia S, Müller S, Pesce I, Pizzi S, Lamonaca G, Picard A, Cattelan G, Malpeli G, Zoli M, Beccano-Kelly D, Flynn R, Wade-Martins R, Pramstaller PP, Hicks AA, Cowley SA, Corti C. Stem Cell Res. 2019 Dec;41:101656

RNA sequencing reveals MMP2 and TGFB1 downregulation in LRRK2 G2019S Parkinson’s iPSC-derived astrocytes. Booth HDE, Wessely F, Connor-Robson N, Rinaldi F, Vowles J, Browne C, Evetts SG, Hu MT, Cowley SA, Webber C, Wade-Martins R. Neurobiol Dis. 2019 Sep;129:56-66.

An integrated transcriptomics and proteomics analysis reveals functional endocytic dysregulation caused by mutations in LRRK2. Connor-Robson N, Booth H, Martin JG, Gao B, Li K, Doig N, Vowles J, Browne C, Klinger L, Juhasz P, Klein C, Cowley SA, Bolam P, Hirst W, Wade-Martins R. Neurobiol Dis. 2019 Jul;127:512-526.

Proteolytic shedding of the prion protein via activation of metallopeptidase ADAM10 reduces cellular binding and toxicity of amyloid-β oligomers. Jarosz-Griffiths HH, Corbett NJ, Rowland HA, Fisher K, Jones AC, Baron J, Howell GJ, Cowley SA, Chintawar S, Cader MZ, Kellett KAB, Hooper NM. J Biol Chem. 2019 Mar 14.

Cellular α-synuclein pathology is associated with bioenergetic dysfunction in Parkinson’s iPSC-derived dopamine neurons. Zambon F, Cherubini M, Fernandes HJR, Lang C, Ryan BJ, Volpato V, Bengoa-Vergniory N, Vingill S, Attar M, Booth HDE, Haenseler W, Vowles J, Bowden R, Webber C, Cowley SA, Wade-Martins R. Hum Mol Genet. 2019 Feb 11.

Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes. Lang C, Campbell KR, Ryan BJ, Carling P, Attar M, Vowles J, Perestenko OV, Bowden R, Baig F, Kasten M, Hu MT, Cowley SA, Webber C, Wade-Martins R. Cell Stem Cell. 2019 Jan 3;24(1):93-106.e6


RIPK1 is a critical modulator of both tonic and TLR-responsive inflammatory and cell death pathways in human macrophage differentiation. Buchrieser J, Oliva-Martin MJ, Moore MD, Long JCD, Cowley SA, Perez-Simón JA, James W, Venero JL. Cell Death Dis. 2018 Sep 24;9(10):973.

Neurodegeneration in SCA14 is associated with increased PKCγ kinase activity, mislocalization and aggregation. Wong MMK, Hoekstra SD, Vowles J, Watson LM, Fuller G, Németh AH, Cowley SA, Ansorge O, Talbot K, Becker EBE. Acta Neuropathol Commun. 2018 Sep 24;6(1):99.

Genome editing in induced pluripotent stem cells rescues TAF1 levels in X-linked dystonia-parkinsonism. Rakovic A, Domingo A, Grütz K, Kulikovskaja L, Capetian P, Cowley SA, Lenz I, Brüggemann N, Rosales R, Jamora D, Rolfs A, Seibler P, Westenberger A, König I, Klein C. Mov Disord. 2018 Jul;33(7):1108-1118.

FRMD8 promotes inflammatory and growth factor signalling by stabilising the iRhom/ADAM17 sheddase complex. Künzel U, Grieve AG, Meng Y, Sieber B, Cowley SA, Freeman M. Elife. 2018 Jun 13;7.

LRRK2 is a negative regulator of Mycobacterium tuberculosis phagosome maturation in macrophages. Härtlova, A., Herbst, S., Peltier, J., Rodgers, A., Bilkei-Gorzo, O., Fearns, A., Dill, B. D., Lee, H., Flynn, R., Cowley, S. A., Davies, P., Lewis, P. A., Ganley, I. G., Martinez, J., Alessi, D. R., Reith, A. D., Trost, M., and Gutierrez, M. G. EMBO J. 2018 Jun 15;37(12)

Stem cell modeling of mitochondrial parkinsonism reveals key functions of OPA1. Jonikas, M., Madill, M., Mathy, A., Zekoll, T., Zois, C. E., Wigfield, S., Kurzawa-Akanbi, M., Browne, C., Sims, D., Chinnery, P. F., Cowley, S. A., and Tofaris, G. K.  Ann Neurol. 2018 May;83(5):915-925

A simplified method for generating purkinje cells from Human-Induced pluripotent stem cells. Watson, L. M., Wong, M. M. K., Vowles, J., Cowley, S. A., and Becker, E. B. E.  Cerebellum. 2018 Aug;17(4):419-427


Heman-Ackah, S. M., Manzano, R., Hoozemans, J. J. M., Scheper, W., Flynn, R., Haerty, W., Cowley, S. A., Bassett, A. R., and Wood, M. J. A. (2017). Alpha-Synuclein induces the unfolded protein response in parkinson’s disease SNCA triplication iPSC-derived neurons. Human molecular genetics, 15;26(22):4441-4450.

Haenseler, W., Zambon, F., Lee, H., Vowles, J., Rinaldi, F., Duggal, G., Houlden, H., Gwinn, K., Wray, S., Luk, K. C., Wade-Martins, R., James, W. S., and Cowley, S. A. (2017). Excess α-synuclein compromises phagocytosis in iPSC-derived macrophages. Scientific reports, 7(1).

Beevers, J. E., Lai, M. C. C., Collins, E., Booth, H. D. E., Zambon, F., Parkkinen, L., Vowles, J., Cowley, S. A., Wade-Martins, R., and Caffrey, T. M. (2017). MAPT genetic variation and neuronal maturity alter isoform expression affecting axonal transport in iPSC-derived dopamine neurons. Stem cell reports, 9(2):587-599.

Haenseler, W., Sansom, S. N., Buchrieser, J., Newey, S. E., Moore, C. S., Nicholls, F. J., Chintawar, S., Schnell, C., Antel, J. P., Allen, N. D., Cader, M. Z., Wade-Martins, R., James, W. S., and Cowley, S. A. (2017). A highly efficient human pluripotent stem cell microglia model displays a Neuronal-Co-culture-Specific expression profile and inflammatory response. Stem cell reports, 8(6):1727-1742.

Sandor, C., Robertson, P., Lang, C., Heger, A., Booth, H., Vowles, J., Witty, L., Bowden, R., Hu, M., Cowley, S.A., Wade-Martins, R. and Webber, C. (2017). Transcriptomic profiling of purified patient-derived dopamine neurons identifies convergent perturbations and therapeutics for Parkinson’s disease. Human molecular genetics.26(3):552-566.

Baud, A., Wessely, F., Mazzacuva, F., McCormick, J., Camuzeaux, S., Heywood, W., Little, D., Vowles, J., Tuefferd, M., Mosaku,O., Lako, M., Armstrong, L., Webber, C., Cader, M.Z., Peeters, P., Gissen, P., Cowley, S.A., and Mills, K.O. (2017). Multiplex High-Throughput Targeted Proteomic Assay To Identify Induced Pluripotent Stem Cells. Analytical chemistry 89, 2440-2448


Vazquez-Arango, P., Vowles, J., Browne, C., Hartfield, E., Fernandes, H. J., Mandefro, B., Sareen, D., James, W., Wade-Martins, R., Cowley, S. A., Murphy, S., and O’Reilly, D. (2016). Variant u1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease. Nucleic acids research. 44, 10960-10973.

Dafinca, R., Scaber, J., Ababneh, N., Lalic, T., Weir, G., Christian, H., Vowles, J., Douglas, A. G., Fletcher-Jones, A., Browne, C., Nakanishi, M., Turner, M. R., Wade-Martins, R., Cowley, S. A., and Talbot, K. (2016). C9orf72 hexanucleotide expansions are associated with altered endoplasmic reticulum calcium homeostasis and stress granule formation in induced pluripotent stem Cell-Derived neurons from patients with amyotrophic lateral sclerosis and frontotemporal dementia. Stem cells (Dayton, Ohio), 34(8):2063-2078.

Kapellos, T. S., Taylor, L., Lee, H., Cowley, S. A., James, W. S., Iqbal, A. J., and Greaves, D. R. (2016). A novel real time imaging platform to quantify macrophage phagocytosis. Biochemical pharmacology. 116, 107-119.

Fernandes, H. J., Hartfield, E. M., Christian, H. C., Emmanoulidou, E., Zheng, Y., Booth, H., Bogetofte, H., Lang, C., Ryan, B. J., Sardi, S. P., Badger, J., Vowles, J., Evetts, S., Tofaris, G. K., Vekrellis, K., Talbot, K., Hu, M. T., James, W., Cowley, S. A., and Wade-Martins, R. (2016). ER stress and autophagic perturbations lead to elevated extracellular α-Synuclein in GBA-N370S parkinson’s iPSC-derived dopamine neurons. Stem cell reports, 6(3):342-356.

Handel, A. E., Chintawar, S., Lalic, T., Whiteley, E., Vowles, J., Giustacchini, A., Argoud, K., Sopp, P., Nakanishi, M., Bowden, R., Cowley, S., Newey, S., Akerman, C., Ponting, C. P., and Cader, M. Z. (2016). Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics. Human molecular genetics, 25(5):989-1000.


Flynn, R., Grundmann, A., Renz, P., Hänseler, W., James, W. S., Cowley, S. A., and Moore, M. D. (2015). CRISPR-mediated genotypic and phenotypic correction of a chronic granulomatous disease mutation in human iPS cells. Experimental hematology, 43(10).


van Wilgenburg B, Moore MD, James WS and Cowley SA (2014) The productive entry pathway of HIV-1 in macrophages is dependent on endocytosis through lipid rafts containing CD4. PLoS ONE  DOI: 10.1371/journal.pone.0086071 

 Hartfield EM, Yamasaki-Mann M, Ribeiro Fernandes HJ, Vowles J, James WS, Cowley SA and Wade-Martins R. (2014). Physiological characterisation of human iPS-derived dopaminergic neurons. PloS one, 9(2):e87388+.


Wilgenburg Bv, Browne C, Vowles J, Cowley SA (2013) Efficient, Long Term Production of Monocyte-Derived Macrophages from Human Pluripotent Stem Cells under Partly-Defined and Fully-Defined Conditions. PLoS ONE 8(8): e71098. doi:10.1371/journal.pone.0071098

O’Reilly D, Dienstbier M, Cowley SA, Vazquez P, Drozdz M, Taylor S, James WS, and Murphy S. Differentially expressed, variant u1 snRNAs regulate gene expression in human cells. Genome research 2013, 23(2):281-291.


Jiang Y*, Cowley SA*, Siler U* , Melguzo D, Tilgner K, Browne C, deWilton A, Pryzborski S, Saretzki G,James WS, Reichenbach J, Seger RA, Lako M and Armstrong L. *joint first authors. Derivation and functional analysis of patient specific induced pluripotent stem cells as an in vitro model of Chronic Granulomatous Disease. Stem Cells 2012 30(4):599-611.


Raposo RASA, Trudgian DC, Thomas B, van Wilgenburg B, Cowley SA and James W. Protein Kinase C and NF-κB-dependent CD4 downregulation in macrophages induced by t cell-derived soluble factors: consequences for HIV-1 infection. Journal of immunology 2011 187(2):748-759.

Zhou L, Sokolskaja E, Jolly C, James W, Cowley SA and Fassati A. Transportin 3 Promotes a Nuclear Maturation Step Required for Efficient HIV-1 Integration. PLoS Pathogens 2011 7(8):e1002194+.

Mandegar MA, MoralliD, KhojaS, Cowley S,  ChanDY, YusufM, MukherjeeS, Blundell MP, VolpiEV, ThrasherAJ, JamesW and Monaco ZL. Functional human artificial chromosomes are generated and stably maintained in human embryonic stem cells. Human Molecular Genetics 2011 20(15):2905-2913


Xu X, Cowley S, Flaim CJ, James W, Seymour LW and Cui Z. The role of apoptotic pathways in the low recovery rate after cryopreservation of dissociated human embryonic stem cells. Biotechnology progress 2010 26(3):827-837

Xu X, Cowley S, Flaim CJ, James W, Seymour LW and Cui Z. Enhancement of cell recovery for dissociated human embryonic stem cells after cryopreservation. Biotechnology progress 2010 26(3):781-788

Brook FA, Cowley SA, Evans EP, Turner K, James WS and Mardon HJ. Derivation and characterization of the human embryonic stem cell line, OxF1. In Vitro Cellular and Developmental Biology – Animal  2010 46(3-4):173-177


Karlsson KR, Cowley S, Martinez FO, Shaw M, Minger SL, and James W. Homogeneous monocytes and macrophages from human embryonic stem cells following coculture-free differentiation in M-CSF and IL-3. Experimental Hematology 2008 36 1167–1175



Mache A, Mengistu Y and Cowley S. Shigella serogroups identified from adult diarrhoeal out-patients in Addis Ababa, Ethiopia: antibiotic resistance and plasmid profile analysis. East African Medical Journal 1997 74 179-182.

Mache A, Mengistu Y and Cowley S. Salmonella serogroups identified from adult diarrhoeal out-patients in Addis Ababa, Ethiopia: antibiotic resistance and plasmid profile analysis. East African Medical Journal 1997 74 183-186.


Alessi DR, Cohen P, Ashworth A, Cowley S, Leevers SJ, Marshall CJ. Assay and expression of mitogen-activated protein kinase, MAP kinase kinase, and Raf. Methods in Enzymology 1995 255 279-90.

Towatari M, May GE, Marais R, Perkins G, Marshall CJ, Cowley S and Enver T.   Regulation of GATA-2 phosphorylation by mitogen-activated protein kinase and interleukin- 3.  Journal of Biological Chemistry 1995 270 4101-4107.

Gillespie-Brown J, Fuller SJ, Bogoyevitch MA, Cowley S, Sugden PH. The mitogen-activated protein kinase kinase MEK1 stimulates a pattern of gene expression typical of the hypertrophic phenotype in rat ventricular cardiomyocytes. Journal of  Biological Chemistry 1995 270 28092-6.


Freshney NW, Rawlinson L, Guesdon F, Jones E, Cowley S, Hsuan J and Saklatvala J.  Interleukin-1 activates a novel protein kinase cascade that results in the phosphorylation of hsp27.  Cell 1994 78 1039-1049.

Cowley S, Paterson H, Kemp P and Marshall CJ.  Activation of MAP kinase kinase is necessary and sufficient for PC12 differentiation and for transformation of NIH 3T3 cells.   Cell 1994 77 841-852.

Alessi DR, Saito Y, Campbell DG, Cohen P, Sithanandam G, Rapp U, Ashworth A, Marshall CJ and Cowley S.   Identification of the sites in MAP kinase kinase-1 phosphorylated by p74raf-1.  EMBO J. 1994 13 1610-1619.

Bennett BD*, Cowley S*, Jiang S, London R, Deng B, Grabarek J, Groopman JE, Goeddel DV, Avraham H.  *joint first authors. Identification and characterization of a novel tyrosine kinase from megakaryocytes. Journal of Biological Chemistry 1994 269 1068-1074.


Avraham H, Cowley S, Chi SY, Jiang S, Groopman JE. Characterization of adhesive interactions between human endothelial cells and megakaryocytes. Journal of Clinical Investigation 1993 93 2378-84.


Cowley SA, Groopman JE, Avraham H.  Effects of transforming growth factor beta on megakaryocytic cell fusion and endomitosis.  International Journal of Cell Cloning 1992 10 223-231.

Avraham H, Vannier E, Cowley SA, Jiang S, Chi S, Dinarello CA, Zsebo KM, Groopman JE. Effects of stem cell factor, c-kit ligand, on human megakaryocytic cells. Blood 1992 79365-71.


Gschmeissner SE, Pereira JH, Cowley SA. Rapid assessment of nerve stumps.  Journal of Bone and Joint Surgery 1991 73 688-89.


Pereira JH, Cowley SA, Gschmeissner SE, Bowden REM, Turk JL.  Denatured muscle grafts for nerve repair: an experimental model of nerve damage in leprosy.  Journal of Bone and Joint Surgery 1990 72 874-80.

Cowley SA, Gschmeissner SE, Negesse Y, Curtis J, Turk JL. Major Histocompatibility Complex Class II antigen expression in nerves in leprosy. An immuno-electron microscopical study.  International Journal of Leprosy and other Mycobacterial diseases 1990 58 560-565.


Cowley SA, Butter C, Gschmeissner SE, Curtis J, Turk JL. An immuno-electron microscopical study of the expression of MHC Class II antigens in guinea pig sciatic nerves following induction of intraneural granulomas. Journal of Neuroimmunology 1989 33 223-231.


Cowley SA, Butter C, Verghese S, Curtis J, Turk JL. Nerve damage induced by mycobacterial granulomas in guinea pig sciatic nerves. International Journal of Leprosy and other Mycobacterial diseases 1988 56 283-290.

Review Articles and Book Chapters

Radical-SAM dependent nucleotide dehydratase (SAND), rectification of the names of an ancient iron-sulfur enzyme using NC-IUBMB recommendations. Ji Y, Wei L, Da A, Stark H, Hagedoorn PL, Ciofi-Baffoni S, Cowley SA, Louro RO, Todorovic S, Mroginski MA, Nicolet Y, Roessler MM, Le Brun NE, Piccioli M, James WS, Hagen WR, Ebrahimi KH. Front Mol Biosci. 2022 Oct 21;9:1032220.

Microglia states and nomenclature: A field at its crossroads. Paolicelli RC, Sierra A, Stevens B, Tremblay ME, Aguzzi A, Ajami B, Amit I, Audinat E, Bechmann I, Bennett M, Bennett F, Bessis A, Biber K, Bilbo S, Blurton-Jones M, Boddeke E, Brites D, Brône B, Brown GC, Butovsky O, Carson MJ, Castellano B, Colonna M, Cowley SA, Cunningham C, Davalos D, De Jager PL, de Strooper B, Denes A, Eggen BJL, Eyo U, Galea E, Garel S, Ginhoux F, Glass CK, Gokce O, Gomez-Nicola D, González B, Gordon S, Graeber MB, Greenhalgh AD, Gressens P, Greter M, Gutmann DH, Haass C, Heneka MT, Heppner FL, Hong S, Hume DA, Jung S, Kettenmann H, Kipnis J, Koyama R, Lemke G, Lynch M, Majewska A, Malcangio M, Malm T, Mancuso R, Masuda T, Matteoli M, McColl BW, Miron VE, Molofsky AV, Monje M, Mracsko E, Nadjar A, Neher JJ, Neniskyte U, Neumann H, Noda M, Peng B, Peri F, Perry VH, Popovich PG, Pridans C, Priller J, Prinz M, Ragozzino D, Ransohoff RM, Salter MW, Schaefer A, Schafer DP, Schwartz M, Simons M, Smith CJ, Streit WJ, Tay TL, Tsai LH, Verkhratsky A, von Bernhardi R, Wake H, Wittamer V, Wolf SA, Wu LJ, Wyss-Coray T. Neuron. 2022 Nov 2;110(21):3458-3483.

Variation on a theme: mapping microglial heterogeneity. Washer SJ, Bassett AR, Cowley SA. Trends Genet. 2021 Dec;37(12):1050-1052.

Non-neuronal cells in amyotrophic lateral sclerosis – from pathogenesis to biomarkers. Vahsen BF, Gray E, Thompson AG, Ansorge O, Anthony DC, Cowley SA, Talbot K, Turner MR. Nat Rev Neurol. 2021 Jun;17(6):333-348.

Honing the Double-Edged Sword: Improving Human iPSC-Microglia Models. Hedegaard A, Stodolak S, James WS, Cowley SA. Front Immunol. 2020 Dec 8;11:614972.

Microglial inflammation and phagocytosis in Alzheimer’s disease: potential therapeutic targets. Nizami S, Hall-Roberts H, Warrier S, Cowley SA, Di Daniel E. Br J Pharmacol. 2019 Feb 10.

Lee, H., James, W. S., and Cowley, S.A. (2017). LRRK2 in peripheral and central nervous system innate immunity: its link to Parkinson’s disease. Biochemical Society transactions 45, 131-139.

Dodsworth, B. T., Flynn, R., and Cowley, S. A. (2015). The current state of naïve human pluripotency. Stem cells (Dayton, Ohio), 33(11):3181-3186.

Hartfield, E. M., Fernandes, H. J., Vowles, J., Cowley, S. A., and Wade-Martins, R. (2012). Cellular reprogramming: a new approach to modelling parkinson’s disease. Biochemical Society transactions, 40(5):1152-1157.

Cowley, S. A., Karlsson, K. R., van Wilgenburg, B., Carter, G., Browne, C., Vowles, J., Martinez Estrada, F., Pelchen-Matthews, A., Miller, J., Moore, M. D., and James, W. (2012). Macrophages from human Pluripotent Stem Cells. Chapter 3 in Handbook of Macrophages: Life Cycle, Functions and Diseases, pages 83-120. Nova Science Publishers, NY.  ISBN: 978-1-62081-162-7

Cowley S Induced pluripotent stem cells and their application into personalised therapy. Chapter in: Comprehensive Biotechnology 2nd Edition. Elsevier. 2011  ISBN 13: 978-0-444-53352-4

Lufino M M P, Popplestone, AR, Cowley SA, Edser PAH, James WS and Wade-Martins R. Episomal transgene expression in pluripotent stem cells. Methods in Molecular Biology 2011 767(27): 369-387. Humana Press, Totowa, NJ.

Cowley S and Romero I. Signal Transduction. Chapter in Molecular and Cell Biology 2004 Open University Press, Milton Keynes.

Cowley S and Romero I. Tumorigenesis. Chapter in Molecular and Cell Biology 2004 Open University Press, Milton Keynes.

Cowley S. The biology of HIV. Leprosy Review 2001 72 212-220.

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