Explore UCD

UCD Home >


Peer-reviewed Articles and Reviews

(122) Lin J, McCann AP, Sereesongsaeng N, Burden JM, Alsa’d AA, Burden RE, Micu I, Williams R, van Schaeybroeck S, Evergren E, Mullan P, Simpson JC, Scott CJ & Burrows JF (2022). USP17 is required for peripheral trafficking of lysosomes. EMBO Reports, in press.

(121) Melling GE, Conlon R, Pantazi P, Dellar E, Samuel P, Baena Lopez A, Simpson JC & Carter DRF (2022). Confocal microscopy analysis reveals that only a small proportion of extracellular vesicles are successfully labelled with commonly utilised staining methods. Scientific Reports, 12(1):262

(120) Yaothak J, Simpson JC, Heffernan LF, Tsai Y-S & Lin C-C (2022). 2D-GolgiTrack - A Semi-automated Tracking System to Quantify Morphological Changes and Dynamics of the Golgi Apparatus and Golgi-derived Membrane Tubules. Medical & Biological Engineering & Computing, 60(1):151-169.

(119) Chalkley AS, Mysior MM & Simpson JC (2021). A robust method for the large-scale production of spheroids for high-content screening and analysis applications. Journal of Visualized Experiments, 178:e63436.

(118) Mysior MM & Simpson JC (2021). Cell3: A new vision for study of the endomembrane system in mammalian cells. Bioscience Reports, 41(12):BSR20210850C.

(117) Kelly S, Byrne MH, Quinn SJ & Simpson JC (2021). Multiparametric nanoparticle-induced toxicity readouts with single cell resolution in HepG2 multicellular tumour spheroids. Nanoscale, 13(41):17615-17628.

(116) Yaothak J, Simpson JC, Heffernan LF, Tsai Y-S & Lin C-C (2021). Development of a 2D Automated Tracking System to Characterize Golgi-derived Membrane Tubule Fission and Fusion Dynamics. Journal of Medical and Biological Engineering, 41:812-825.

(115) Garcia-Pardo ME, Simpson JC & O’Sullivan NC (2021). A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells. BMC Bioinformatics, 22(1):427.

(114) Patange AD, Simpson JC, Curtin JF, Burgess CM, Cullen PJ & Tiwari BK (2021). Inactivation efficiency of atmospheric air plasma and airborne acoustic ultrasound against bacterial biofilms. Scientific Reports, 11:2346.

(113) Whelan MVX, Simpson JC & O’Croinin T (2021). A novel high-content screening approach for the elucidation of C. jejuni biofilm composition and integrity. BMC Microbiology, 21:2.

(112) Yaothak J, Simpson JC, Heffernan LF, Tsai Y-S & Lin C-C (2020). A Semi-Automated 2D Segmentation and Classification System to Quantify and Characterize Morphological Features of Golg-Derived Membrane Structures. American Journal of Biomedical Engineering, 10(2):29-43.

(111) Charoux C, Patange AD, Hinds L, Simpson JC, O’Donnell C & Tiwari BK (2020). Antimicrobial effects of airborne acoustic ultrasound and plasma activated water from cold and thermal plasma systems on biofilms. Scientific Reports, 10:17297.

(110) Hifni B, Khan M, Devereux SJ, Byrne MH, Quinn SJ & Simpson JC (2020). Investigation of the cellular destination of fluorescently labelled carbon nanohorns in cultured cells. ACS Applied Bio Materials, 3(10):6790–6801.

(109) Mysior MM & Simpson JC (2020). The emerging roles for Rho GTPases at the Golgi complex. Small GTPases, 3:1-12.

(108) Long M, Kranjc T, Mysior MM & Simpson JC (2020). RNA interference screening identifies novel roles for RhoBTB1 and RhoBTB3 in membrane trafficking events in cells. Cells, 9(5), E1089.

(107) Simpson JC (2020). Modification of the Mammalian Endomembrane System in Healthy and Diseased Cells. Int. J. Mol. Sci., 21(6), E2133.

(106) Kaleel M, Yandan Z, Jialiang C, Xuanming F, Simpson JC, Pollastri G & Mooney C (2020). SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks. Bioinformatics, btaa156. doi: 10.1093/bioinformatics/btaa156.

(105) Morris S, Geoghegan ND, Sadler JBA, Koester AM, Black HL, Laub M, Miller L, Heffernan LF, Simpson JC, Mastick CC, Cooper J, Gadegaard N, Bryant NJ & Gould GW (2020). Characterisation of GLUT4 trafficking in HeLa cells: comparable kinetics and orthologous trafficking mechanisms to 3T3-L1 adipocytes. PeerJ, 8, e8751.

(104) De Santi C, Fernandez Fernandez E, Gaul R, Vencken S, Glasgow A, Oglesby IK, Hurley K, Hawkins F, Mitash N, Mu F, Raoof R, Henshall D, Cutrona MB, Simpson JC, Harvey BJ, Linnane B, McNally P, Cryan SA, MacLoughlin R, Swiatecka-Urban A & Greene CM (2020). Precise targeting of miRNA sites restores CFTR activity in CF bronchial epithelial cells. Molecular Therapy, 28(4), 1190-1199.

(103) Whelan MVX, Ardill L, Koida K, Nakajima C, Suzuki Y, Simpson JC & O’Croinin T (2019). Acquisition of fluoroquinolone resistance leads to increased biofilm formation and pathogenicity in Campylobacter jejuni. Scientific Reports, 9, 18216.

(102) Fowler PC, Garcia-Pardo ME, Simpson JC & O’Sullivan NC (2019). NeurodegERation: The central role for ER contacts in neuronal function and axonopathy, lessons from heridatoryspastic paraplegias and related diseases. Frontiers in Neuroscience, 13, 1051.

(101) Melling GE, Carollo E, Conlon R, Simpson JC & Carter DRF (2019). The Challenges and Possibilities of Extracellular Vesicles as Therapeutic Vehicles. European Journal of Pharmaceutics and Biopharmaceutics, 144, 50-56. 

(100) Morgan NE, Cutrona MB & Simpson JC (2019). Multitasking Rab proteins in autophagy and membrane trafficking: a focus on Rab33b. Int. J. Mol. Sci., 20(16), E3916.

(99) Kuhns S, Seixas C, Pestana S, Tavares B, Nogueira R, Jacinto R, Ramalho JS, Simpson JC, Andersen JS, Echard A, Lopes SS, Barral DC & Blacque OE (2019). Rab35 controls cilium length, function and membrane composition. EMBO Rep., 20(10), e47625.

(98) Cutrona MB & Simpson JC (2019). A high-throughput automated confocal microscopy platform for quantitative phenotyping of nanoparticle uptake and transport in spheroids. Small, e1902033.

(97) Devereux SJ, Massaro M, Barker A, Hinds DT, Hifni B, Simpson JC & Quinn SJ (2019). Spectroscopic study of the loading of cationic porphyrins by carbon nanohorns as high capacity carriers of photoactive molecules to cells. Journal of Materials Chemistry B, doi:10.1039/C9TB00217K.

(96) O’Brien KT, Golla K, Kranjc T, O’Donovan D, Allen S, Maguire P, Simpson JC, O’Connell D, Moran N & Shields DC (2019). Computational and Experimental Analysis of Bioactive Peptide Linear Motifs in the Integrin Adhesome. PLoS One, 14(1), e0210337.

(95) Lesniak A, Kilinc D, Blasiak A, Galea G, Simpson JC & Lee GU (2019). Rapid growth cone uptake and dynein-mediated axonal retrograde transport of negatively charged nanoparticles in neurons is dependent on size and cell type. Small, e1803758.

(94) Cheung S, Wu D, Daly HC, Busschaert N, Morgunova M, Simpson JC, Scholz D, Gale PA & O’Shea DF (2018). Real-time recording of the cellular effects of the anion transporter prodigiosin. Chem, 4, 879-895.  

(93) Walsh DP, Murphy RD, Panarella A, Raftery RM, Cavanagh B, Simpson JC, O’Brien FJ, Heise A & Cryan SA (2018). Bioinspired Star-Shaped Poly(L-Lysine) Polypeptides; Efficient Polymeric Nanocarriers for the Delivery of DNA to Mesenchymal Stem Cells. Molecular Pharmaceutics, 15(5), 1878-1891.

(92) Cutrona MB, Morgan NE & Simpson JC (2018). Heritable Skeletal Disorders Arising from Defects in Processing and Transport of Type I Procollagen from the ER: Perspectives on Possible Therapeutic Approaches. Handbook of Experimental Pharmacology, 245, 191-225.

(91) Byrne DJ, Harmon MJ, Simpson JC, Blackstone C & O'Sullivan NC (2017). Roles for the VCP co-factors Npl4 and Ufd1 in neuronal function in Drosophila melanogaster. J. Genet. Genomics, 44, 493-501.

(90) Lyden A, Lombardi L, Sire W, Li P, Simpson JC, Butler G & Lee GU (2017). Characterization of carboxylate nanoparticle adhesion with the fungal pathogen Candida albicans. Nanoscale, 9, 15911-15922.

(89) Kranjc T, Dempsey E, Cagney G, Nakamura N, Shields DC & Simpson JC (2017). Functional characterisation of the YIPF protein family in mammalian cells. Histochemistry and Cell Biology, 147, 439-451.

(88) Caruso ME, Jenna S, Baillie DL, Bossé R, Simpson JC, Chevet E & Taouji S (2017). Systematic functional analysis of the Ras GTPase family unveils a conserved network required for anterograde protein trafficking. Proteomics, 17, 1-2.

(87) Long M & Simpson JC (2017). Rho GTPases operating at the Golgi complex: Implications for membrane traffic and cancer biology. Tissue Cell, 49, 163-169.

(86) Bexiga MG & Simpson JC (2016). Genome-Wide siRNA Screening Using Forward Transfection: Identification of Modulators of Membrane Trafficking in Mammalian Cells. Methods Mol. Biol., 1470, 39-48.

(85) Panarella A, Bexiga MG, Galea G, O' Neill ED, Salvati A, Dawson KA & Simpson JC (2016). A systematic High-Content Screening microscopy approach reveals key roles for Rab33b, OATL1 and Myo6 in nanoparticle trafficking in HeLa cells. Scientific Reports, 6, 28865.

(84) Grossi M, Morgunova M, Cheung S, Scholz D, Conroy E, Terrile M, Panarella A, Simpson JC, Gallagher W & O'Shea D (2016). Lysosome triggered near-infrared fluorescence imaging of cellular trafficking processes in real time. Nature Communications, 7, 10855.

(83) Singan VR & Simpson JC (2016). Implementation of the Rank-Weighted Co-localization (RWC) algorithm in multiple image analysis platforms for quantitative analysis of microscopy images. Source Code for Biology and Medicine, 11, 2.

(82) Murphy CM, Pare S, Galea G, Simpson JC & Smith SG (2016). Accurate and semi-automated analysis of bacterial association with mammalian cells. J. Microbiol. Methods, 122, 8-12.

(81) Galea G & Simpson JC (2015). High-content analysis of Rab protein function at the ER-Golgi interface. BioArchitecture, 5, 44-53.

(80) Galea G, Bexiga MG, Panarella A, O'Neill ED & Simpson JC (2015). A high-content screening microscopy approach to dissect the role of Rab proteins in Golgi-to-ER retrograde trafficking. J. Cell Sci., 128(13), 2339-2349.

(79) Brayden DJ, Cryan SA, Dawson KA, O'Brien PJ & Simpson JC (2015). High-content analysis for drug delivery and nanoparticle applications. Review Article. Drug Discov. Today, 20(8), 942-957.

(78) Lecat S, Matthes HW, Pepperkok R, Simpson JC & Galzi JL (2015). A Fluorescent Live Imaging Screening Assay Based on Translocation Criteria Identifies Novel Cytoplasmic Proteins Implicated in G Protein-coupled Receptor Signaling Pathways. Mol. Cell. Proteomics 14(5), 1385-1399.

(77) Dunne CF, Twomey B, Kelly C, Simpson JC & Stanton KT (2015). Hydroxyapatite and fluorapatite coatings on dental screws: effects of blast coating process and biological response. J. Mater. Sci. Mater. Med. 26(1), 5347.

(76) Carville NC, Collins L, Manzo M, Gallo K, Lukasz BI, McKayed KK, Simpson JC & Rodriguez BJ (2014). Biocompatibility of ferroelectric lithium niobate and the influence of polarization charge on osteoblast proliferation and function. J. Biomed. Mater. Res. A 103(8), 2540-2548.

(75) Varela JA, Aberg C, Simpson JC & Dawson KA (2014). Trajectory-based co-localization measures for nanoparticle-cell interaction studies. Small 11(17), 2026-2031.

(74) Heffernan LH & Simpson JC (2014). The trials and tubule-ations of Rab6 involvement in Golgi-to-ER retrograde transport. Review Article. Biochem. Soc. Trans. 42(5), 1453-1459.

(73) Farrell J, Kelly C, Rauch J, Kida K, Garcia-Munoz A, Monsefi N, Turriziani B, Doherty C, Mehta JP, Matallanas D, Simpson JC, Kolch W & von Kriegsheim A (2014). HGF induces epithelial-to-mesenchymal transition by modulating the mammalian Hippo/MST2 and ISG15 pathways. J. Proteome Res. 13(6), 2874-2886.

(72) Higa A, Taouji S, Lhomond S, Jensen D, Fernandez-Zapico ME, Simpson JC, Pasquet JM, Schekman R & Chevet E (2014). Endoplasmic reticulum stress-activated transcription factor ATF6α requires the disulfide isomerase PDIA5 to modulate chemoresistance. Mol. Cell Biol. 34(10), 1839-1849.

(71) Sauvageau E, Rochdi MD, Oueslati M, Hamdan FF, Percherancier Y, Simpson JC, Pepperkok R & Bouvier M (2014). CNIH4 interacts with newly synthesized GPCR and control their export from the endoplasmic reticulum. Traffic 15(4), 383-400.

(70) Bexiga MG, Kelly C, Dawson KA & Simpson JC (2014). RNA interference-mediated inhibition of apoptosis fails to prevent cationic nanoparticle-induced cell death in cultured cells. Nanomedicine 9(11), 1651-1664.

(69) Michel G, Matthes HWD, Hachet-Haas M, El Baghdadi K, de May J, Pepperkok R, Simpson JC, Galzi J-L & Lecat S (2014). Plasma membrane translocation of REDD1 governed by GPCRs contributes to mTORC1 activation. J. Cell Sci. 127, 773-787.

(68) Galea G & Simpson JC (2013). High-content screening and analysis of the Golgi complex. Methods Cell Biol. 118, 281-295.

(67) McKayed KK & Simpson JC (2013). Actin in action: Imaging approaches to study cytoskeleton structure and function. Review article. Cells, 2(4), 715-731.

(66) Wang F, Bexiga MG, Anguissola S, Boya P, Simpson JC, Salvati A & Dawson KA (2013). Time resolved study of cell death mechanisms induced by amine-modified polystyrene nanoparticles. Nanoscale 5(22), 10868-10876.

(65) Bexiga MG & Simpson JC (2013). Human diseases associated with form and function of the Golgi complex. Review article. Int. J. Mol. Sci. 14(9), 18670-18681.

(64) Miranda-Caso Luengo AA, Miranda-Caso Luengo R, Lieggi NT, Luo H, Simpson JC & Meijer WG (2013). A real-time impedance based method to assess Rhodococcus equi virulence. PLoS One 8(3), e60612.

(63) Stadler C, Rexhepaj E, Singan VR, Murphy RF, Pepperkok R, Uhlen M, Simpson JC & Lundberg E (2013). Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells. Nature Methods 10(4), 315-323.

(62) McCarthy JM, Franke M, Resenberger UK, Waldron S, Simpson JC, Tatzelt J, Appelhans D & Rogers M (2013). Anti-prion drug mPPIg5 inhibits PrP(C) conversion to PrP(Sc). PLoS One 8(1), e55282.

(61) Yi P, Higa A, Bexiga M, Marza E, Taouji S, Arma D, Castain C, Le Bail B, Simpson JC, Rosenbaum J, Bioulac-Sage P, Blanc J-F & Chevet E (2012). Sorafenib–mediated targeting of the AAA+ ATPase p97/VCP leads to disruption of the secretory pathway, endoplasmic reticulum stress and hepatocellular cancer cell death. Molecular Cancer Therapeutics 11, 2610-2620.

(60) Singan VR, Handzic K & Simpson JC (2012). Quantitative image analysis approaches for probing Rab GTPase function and localisation in mammalian cells. Review Article. Biochem. Soc. Trans. 40(6), 1389-1393.

(59) Roth SD, Schuttrumpf J, Abriss D, Milanov P, Simpson JC, Pepperkok R, Seifried E & Tonn T (2012). Chemical chaperones improve protein secretion and rescue mutant factor VIII in mice with hemophilia A. PLoS One 7(9), e44505.

(58) Varela JA, Bexiga MG, Aberg C, Simpson JC & Dawson KA (2012). Quantifying size-dependent interactions between fluorescently-labeled polystyrene nanoparticles and mammalian cells. J. Nanobiotechnology 10(1), 39.

(57) Simpson JC, Joggerst B, Laketa V, Verissimo F, Cetin C, Erfle H, Bexiga MG, Singan VR, Heriche J-K, Neumann B, Mateos A, Blake J, Bechtel S, Benes V, Wiemann S, Ellenberg J & Pepperkok R (2012). Genome-wide RNAi screening identifies human proteins with a function in the early secretory pathway. Nature Cell Biol. 14, 764-774.

(56) Singan VR, Handzic K, Curran KM & Simpson JC (2012). A method for improved clustering and classification of microscopy images using quantitative co-localization coefficients. BMC Res. Notes, 5(1), 281.

(55) Sandin P, Fitzpatrick LW, Simpson JC & Dawson KA (2012). High-speed imaging of Rab family small GTPases reveals rare events in nanoparticle trafficking in living cells. ACS Nano 6, 1513-1521.

(54) Singan VR, Jones TR, Curran KM & Simpson JC (2011). Dual channel rank-based intensity weighting for quantitative co-localization of microscopy images. BMC Bioinformatics 12, 407.

(53) Moore HM, Bai B, Boisvert FM, Latonen L, Rantanen V, Simpson JC, Pepperkok R, Lamond AI & Laiho M (2011). Quantitative proteomics and dynamic imaging of the nucleolus reveals distinct responses to UV and ionizing radiation. Mol. Cell. Proteomics 10.1074.M111.009241.

(52) Tängemo C, Ronchi P, Colombelli J, Haselmann U, Simpson JC, Antony C, Stelzer EHK, Pepperkok R & Reynaud EG (2011). A novel laser nanosurgery approach supports de novo Golgi biogenesis in mammalian cells. J. Cell Sci. 124, 978-987.

(51) Bexiga MG, Varela JA, Wang F, Fenaroli F, Salvati A, Lynch I, Simpson JC & Dawson KA (2011). Cationic nanoparticles induce caspase 3-, 7- and 9-mediated cytotoxicity in a human astrocytoma cell line. Nanotoxicology, 5:557-567.

(50) Simpson JC (2009). Screening the secretion machinery: high throughput imaging approaches to elucidate the secretory pathway. Review Article. Sem. Cell Dev. Biol. 20, 903-909.

(49) Heinz S, Schuttrumpf J, Simpson JC, Pepperkok R, Nicolaes GA, Abriss D, Milanov P, Roth S, Seifried E & Tonn T (2009). FVIII-eGFP fusion proteins with preserved functional activity for the analysis of the early secretory pathway of FVIII. Thrombosis and Haemostasis 102, 925-935.

(48) Burgo A, Sotirakis E, Simmler M-C, Chamot C, Van der Linden A, Simpson JC, Lanzetti L, Proux-Gillardeaux V & Galli T (2009). Role of Varp, a Rab21 exchange factor and TI-VAMP/VAMP7 partner, in neurite growth. EMBO Rep. 10, 1117-1124.

(47) Martinez-Morales JR, Rembold M, Greger K, Simpson JC, Brown KE, Quiring R, Pepperkok R, Martin-Bermudo MD, Himmelbauer H & Wittbrodt J (2009). Ojoplano-mediated basal constriction is essential for optic cup morphogenesis. Development 136, 2165-2175.

(46) Dejgaard SY, Murshid A, Erman A, Kizilay O, Verbich D, Lodge R, Dejgaard K, Ly-Hartig TB, Pepperkok R, Simpson JC & Presley JF (2008). Rab18 and Rab43 have key roles in ER-Golgi trafficking. J. Cell Sci. 121, 2768-2781.

(45) Schallus T, Jaeck C, Feher K, Palma AS, Liu Y, Simpson JC, Mackeen M, Stier G, Gibson TJ, Feizi T, Pieler T & Muhle-Goll C (2008). Malectin: a novel carbohydrate-binding protein in the endoplasmic reticulum with a potential role in the N-glycosylation pathway. Mol. Biol. Cell 19, 3404-3414.

(44) Fladeby C, Gupta SN, Barois N, Lorenzo PI, Simpson JC, Saatcioglu F & Bakke O (2008). Human PARM-1 is a novel mucin-like, androgen-regulated gene exhibiting proliferative effects in prostate cancer cells. Int. J. of Cancer 122, 1229-1235.

(43) Tsai YS, Chung IF, Simpson JC, Lee MI, Hsiung CC, Chiu TY, Kao LS, Chiu TC, Lin CT, Lin WC, Liang SF & Lin CC (2008). Automated recognition system to classify subcellular protein localizations in images of different cell lines acquired by different imaging systems. Microscopy Research and Technique 71, 305-314.

(42) Wessels E & Simpson JC (2007). Impact of live cell imaging on coated vesicle research. Review Article. Sem. Cell Dev. Biol. 18, 412-423.

(41) Lin CC, Tsai YS, Lin YS, Chiu TY, Hsiung CC, Lee MI, Simpson JC & Hsu CN (2007). Boosting multiclass learning with repeating codes and weak detectors for protein subcellular localization. Bioinformatics 23, 3374-3381.

(40) von Brunn A, Teepe C, Simpson JC, Pepperkok R, Friedel CC, Zimmer R, Koszinowski U, Roberts R, Baric R & Haas J (2007). Cloning of the SARS coronavirus (SARS-CoV) ORFeome and genome-wide analysis for intraviral protein-protein interactions. PloS ONE 2(5), e459.

(39) Simpson JC, Mateos A & Pepperkok R (2007). Maturation of the mammalian secretome. Review Article, Genome Biology 8, 211.1-211.4.

(38) Simpson JC, Cetin C, Erfle H, Joggerst B, Liebel U, Ellenberg J & Pepperkok R (2007). An RNAi screening platform to identify secretion machinery in mammalian cells. J. Biotechnology 129, 352-365.

(37)Laketa V, Simpson JC, Bechtel S, Wiemann S & Pepperkok R (2007). High-content microscopy identifies new neurite outgrowth regulators. Mol. Biol. Cell 18, 242-252.

(36) Stauber T, Simpson JC, Pepperkok R & Vernos I (2006). A role for Kinesin-2 in COPI-dependent recycling between the ER and Golgi complex. Current Biology 16, 2245-2251.

(35) Stertz S, Reichelt M, Krijnse-Locker J, Mackenzie J, Simpson JC, Haller O, & Kochs G (2006). Interferon-induced, antiviral human MxA protein localizes to a distinct subcompartment of the smooth Endoplasmic Reticulum. J. Interferon Cytokine Res. 26, 650-660.

(34) Simpson JC & Pepperkok R (2006). The subcellular localization of the mammalian proteome comes a fraction closer. Review Article. Genome Biology 7, 213.1-213.3.

(33) Simpson JC, Nilsson T & Pepperkok R (2006). Biogenesis of tubular ER-to-Golgi transport intermediates. Mol. Biol. Cell 17, 723-737.

(32) Kolb-Kokocinski A, Mehrle A, Bechtel S, Simpson JC, Kioschis P, Wiemann S, Wellenreuther R & Poustka A (2006). The systematic functional characterisation of Xq28 genes prioritises candidate disease genes. BMC Genomics 7, 29.

(31) Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, Bechtel S, Simpson J, Hofmann O, Hide W, Glatting KH, Huber W, Pepperkok R, Poustka A & Wiemann S (2006). The LIFEdb database in 2006. Nucleic Acids Res. 34, D415-418.

(30) Al-Taei S, Penning NA, Simpson JC, Futaki S, Takeuchi T, Nakase I & Jones AT (2006). Intracellular Traffic and Fate of Protein Transduction Domains HIV-1 TAT Peptide and Octaarginine. Implications for Their Utilization as Drug Delivery Vectors. Bioconj. Chem. 17, 90-100.

(29) Pepperkok R, Simpson JC, Rietdorf J, Cetin C, Liebel U, Terjung S & Zimmermann (2005). Imaging platforms for measurement of membrane trafficking. Review article. Methods Enzymol. 404, 8-18.

(28) Arlt D, Huber W, Liebel U, Schmidt C, Majety M, Sauermann M, Rosenfelder H, Bechtel S, Mehrle A, Bannasch D, Schupp I, Seiler M, Simpson JC, Hahne F, Moosmayer P, Ruschhaupt M, Guilleaume B, Wellenreuther R, Pepperkok R, Sultmann H, Poustka A & Wiemann S (2005). Functional profiling: From microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle. Cancer Res. 65, 7733-7742.

(27) Welsch T, Endlich N, Goekce G, Doroshenko E, Simpson JC, Kriz W, Shaw AS & Endlich K (2005). Association of CD2AP with dynamic actin on vesicles in podocytes. Am. J. Physiol. Renal Physiol. 289, F1134-1143.

(26) Neubrand VE, Will RD, Mobius W, Poustka A, Wiemann S, Schu P, Dotti CG, Pepperkok R & Simpson JC (2005). γ-BAR, a novel AP-1 interacting protein involved in post-Golgi trafficking. EMBO J. 24, 1122-1133.

(25) Simpson JC & Jones AT (2005). Lipids, Rafts and Traffic - Early endocytic Rabs: functional prediction to functional characterization. Review Article. Biochem. Soc. Symp. 72, 99-108.

(24) Simpson JC, Griffiths G, Wessling-Resnick M, Fransen JAM, Bennett H & Jones AT (2004). A role for the small GTPase Rab21 in the early endocytic pathway. J. Cell Sci. 117, 6297-6311.

(23) Nakase I, Niwa M, Takeuchi T, Sonomura K, Kawabata N, Koike Y, Takehashi M, Tanaka S, Ueda K, Simpson JC, Jones AT, Sugiura Y & Futaki S (2004). Cellular uptake of arginine-rich peptides: roles for macropinocytosis and actin rearrangement. Molecular Therapy 10, 1011-1022.

(22) Starkuviene V, Liebel U, Simpson JC, Erfle H, Poustka A, Wiemann S & Pepperkok R (2004). High-content screening microscopy identifies novel proteins with a putative role in secretory membrane traffic. Genome Res. 14, 1948-1956.

(21) Erfle H, Simpson JC, Bastiaens PIH & Pepperkok R (2004). siRNA cell arrays for high content screening microscopy. Biotechniques 37, 454-462.

(20) Becker S, Simpson JC, Pepperkok R, Heinz S, Herder C, Grez M, Seifried E & Tonn T (2004). Confocal microscopy analysis of native, full length and B-domain deleted coagulation factor VIII trafficking in mammalian cells. Thrombosis and Haemostasis 92, 23-35.

(19) Schmidt M, Gerlach F, Avivi A, Laufs T, Wystub S, Simpson JC, Nevo E, Saaler-Reinhardt S, Reuss S, Hankeln T & Burmester T (2004). Cytoglobin is a respiratory protein in connective tissue and neurons that is up-regulated by hypoxia. J. Biol. Chem. 279, 8063-8069.

(18) Schlickum S, Moghekar A, Simpson JC, Steglich C, O`Brien RJ, Winterpacht A & Endele SU (2004). LETM1, a gene deleted in Wolf-Hirschhorn syndrome, encodes an evolutionarily conserved mitochondrial protein. Genomics 83, 254-261.

(17) Simpson JC & Pepperkok R (2003). Localizing the proteome. Review Article. Genome Biology 4 (12), 240.1-240.4.

(16) Liebel U, Starkuviene V, Erfle H, Simpson JC, Poustka A, Wiemann S & Pepperkok R (2003). A microscope-based screening platform for large scale functional analysis in intact cells. FEBS Lett. 554, 394-398.

(15) Elsner S, Hashimoto H, Simpson JC, Cassel D, Nilsson T & Weiss M (2003). Spatio-temporal dynamics of the COPI vesicle machinery. EMBO Rep. 4, 1000-1005.

(14) Reynaud E & Simpson JC (2002). Navigating the secretory pathway: Conference on exocytosis membrane structure and dynamics. EMBO Rep. 3, 828-833.

(13) Brown WL, Mastico RA, Wu M, Heal KG, Adams CJ, Murray JB, Simpson JC, Lord JM, Taylor-Robinson AW, Stockley PG (2002). RNA bacteriophage capsid-mediated drug delivery and epitope presentation. Intervirology 45, 371-80.

(12) Kerkhoff E, Simpson JC, Leberfinger CB, Otto IM, Doerks T, Bork P, Rapp UR, Raabe T & Pepperkok R (2001). The Spir actin organizers are involved in vesicle transport processes. Current Biology 11, 1963-1968.

(11) Pepperkok R, Simpson JC & Wiemann S (2001). Being in the right location at the right time. Review Article. Genome Biology 2 (9), 1024.1-1024.4.

(10) Simpson JC, Neubrand VE, Wiemann S & Pepperkok R (2001). Illuminating the human genome. Review Article. Histochem. Cell Biol. 115, 23-29.

(9) Simpson JC, Wellenreuther R, Poustka A, Pepperkok R & Wiemann S (2000). Systematic subcellular localisation of novel proteins identified by large-scale cDNA sequencing. EMBO Rep. 1, 287-292.

(8) Girod A, Storrie B, Simpson JC, Johannes L, Goud B, Roberts LM, Lord JM, Nilsson T & Pepperkok R (1999). Evidence for a COP-I-independent transport route from the Golgi complex to the endoplasmic reticulum. Nature Cell Biol. 1, 423-430.

(7) Simpson JC, Roberts LM, Romisch K, Davey J, Wolf DH & Lord JM (1999). Ricin A chain utilises the endoplasmic reticulum-associated protein degradation pathway to enter the cytosol of yeast. FEBS Lett. 459, 80-84.

(6) Jackson ME, Simpson JC, Girod A, Pepperkok R, Roberts LM & Lord JM (1999). The KDEL retrieval system is exploited by Pseudomonas exotoxin A, but not by Shiga-like toxin-1, during retrograde transport from the Golgi complex to the endoplasmic reticulum. J. Cell Sci. 112, 467-475.

(5) Simpson JC, Smith DC, Roberts LM & Lord JM (1998). Expression of mutant dynamin protects cells against diphtheria toxin but not against ricin. Exp. Cell Res. 239, 293-300.

(4) Simpson JC, Roberts LM & Lord JM (1996). Free ricin A chain reaches an early compartment of the secretory pathway before it enters the cytosol. Exp. Cell Res. 229, 447-451.

(3) Simpson JC, Dascher C, Roberts LM, Lord JM & Balch WE (1995). Ricin cytotoxicity is sensitive to recycling between the endoplasmic reticulum and the Golgi complex. J. Biol. Chem. 270, 20078-20083.

(2) Simpson JC, Lord JM & Roberts LM (1995). Point mutations in the hydrophobic C-terminal region of ricin A chain indicate that Pro250 plays a key role in membrane translocation. Eur. J. Biochem. 232, 458-463.

(1) Simpson JC, Roberts LM & Lord JM (1995). Catalytic and cytotoxic activities of recombinant ricin A chain mutants with charged residues added at the carboxyl terminus. Prot. Expr. Purif. 6, 665-670.

Conference Publications

Ahmad T, Simpson JC & Brayden DJ (2011). Uptake of glucan particles via dectin-1 receptor mediated endocytosis in Peyer’s patches? Transactions of the 38th Int. Soc. Controlled Release Society, Maryland, Abstract 524.

Rietdorf J, Stephens DJ, Squire A, Simpson J, Shima DT, Paccaud J-P, Bastiaens PIH & Pepperkok R (2000). Illuminating cellular structure and function in the early secretory pathway by multispectral 3D imaging in living cells. Proceedings of SPIE - The International Society for Optical Engineering 3921, 232-241.

Book Chapters

Chalkley AS, Kelly S, Mysior MM & Simpson JC (2020). High throughput automated subcellular localisation. eLS, in press.

Simpson JC (2006). Functional assays. In Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine. (Ed. Ganten D & Ruckpaul K) Springer Verlag. Part 6. doi 10.1007/3-540-29623-9_3700.

Simpson JC & Pepperkok R (2006). Systematic sub-cellular localisation of novel proteins. In Cell Biology: A Laboratory Handbook, 3rd Ed. (Ed. Celis CE) Academic Press. Chapter 12, pp121-127.

Lord JM, Day PJ, Jackson ME, Owens SR, Simpson JC, Smith DC & Roberts LM (2002). Pathways of delivering toxins into the cytosol of target cells. In ‘Chimeric Toxins:Mechanisms of action and therapeutic applications’ (Ed. Lazarovici P & Lorberboum-Galski H). Taylor and Francis, London and New York. pp 86-98.

Pepperkok R, Girod A, Simpson JC & Rietdorf J (2000). Immunofluorescence microscopy. In Monoclonal Antibodies. (Ed. Shepherd P & Dean C) Oxford University Press, UK. pp 355-370.

Other Written Contributions

Mysior MM & Simpson JC (2020). Data, data and still more data: the challenges of imaging and analysing 3D cell models. Drug Target Review, Issue 2, Summer 2020, 50-53.

Mysior MM & Simpson JC (2019). High-content imaging: challenges of the 3D world. Drug Target Review, Issue 02, Summer 2019, 40-42.

Simpson JC (2015). It’s the ‘content’ of cells that matters in biomedical research. openAccessGovernment, 2-22452. https://www.openaccessgovernment.org/profile-content-cells-matters-biomedical-research-2/22452/

Scholz D & Simpson JC (2015). Trends in contemporary microscopy. Drug Target Review, Volume 2, Issue 3, 46-49.

Simpson JC (2014). High content screening microscopy: It’s all about numbers. Physiology News, Summer 2014, Issue 95, 28-31.


Simpson JC (2019). Moving from 2D to 3D cell culture: Overcoming challenges to achieving high-quality high-content results. Webcast. https://www.nature.com/webcasts/event/moving-from-2d-to-3d-cell-culture/

Simpson JC (2011). Discovering New Drugs for Disease: Advancing Imaging in the Well. Webcast. https://www.sciencemag.org/custom-publishing/webinars/discovering-new-drugs-disease-advancing-imaging-well

Contact UCD Cell Screening Laboratory

O'Brien Centre for Science, University College Dublin, Belfield, Dublin 4, Ireland.
T: +353 1 716 2345