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  2021 (4)
A Bayesian semi-parametric model for thermal proteome profiling. Fang, S.; Kirk, P. D. W.; Bantscheff, M.; Lilley, K. S.; and Crook, O. M. Commun Biol, 4(1): 810. 06 2021.
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Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection. Kamel, W.; Noerenberg, M.; Cerikan, B.; Chen, H.; Järvelin, A. I.; Kammoun, M.; Lee, J. Y.; Shuai, N.; Garcia-Moreno, M.; Andrejeva, A.; Deery, M. J.; Johnson, N.; Neufeldt, C. J.; Cortese, M.; Knight, M. L.; Lilley, K. S.; Martinez, J.; Davis, I.; Bartenschlager, R.; Mohammed, S.; and Castello, A. Mol Cell, 81(13): 2851–2867. 07 2021.
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Ultra-fast proteomics with Scanning SWATH. Messner, C. B.; Demichev, V.; Bloomfield, N.; Yu, J. S. L.; White, M.; Kreidl, M.; Egger, A. S.; Freiwald, A.; Ivosev, G.; Wasim, F.; Zelezniak, A.; Jürgens, L.; Suttorp, N.; Sander, L. E.; Kurth, F.; Lilley, K. S.; Mülleder, M.; Tate, S.; and Ralser, M. Nat Biotechnol, 39(7): 846–854. 07 2021.
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Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions. Erady, C.; Boxall, A.; Puntambekar, S.; Suhas Jagannathan, N.; Chauhan, R.; Chong, D.; Meena, N.; Kulkarni, A.; Kasabe, B.; Prathivadi Bhayankaram, K.; Umrania, Y.; Andreani, A.; Nel, J.; Wayland, M. T.; Pina, C.; Lilley, K. S.; and Prabakaran, S. NPJ Genom Med, 6(1): 4. Jan 2021.
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  2020 (14)
Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers. Shin, J. J. H.; Crook, O. M.; Borgeaud, A. C.; Cattin-Ortolá, J.; Peak-Chew, S. Y.; Breckels, L. M.; Gillingham, A. K.; Chadwick, J.; Lilley, K. S.; and Munro, S. Nat Commun, 11(1): 5987. 11 2020.
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A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection. Crook, O. M.; Geladaki, A.; Nightingale, D. J. H.; Vennard, O. L.; Lilley, K. S.; Gatto, L.; and Kirk, P. D. W. PLoS Comput Biol, 16(11): e1008288. 11 2020.
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A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions. Barylyuk, K.; Koreny, L.; Ke, H.; Butterworth, S.; Crook, O. M.; Lassadi, I.; Gupta, V.; Tromer, E.; Mourier, T.; Stevens, T. J.; Breckels, L. M.; Pain, A.; Lilley, K. S.; and Waller, R. F. Cell Host Microbe, 28(5): 752–766. 11 2020.
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Correction: Proteomics of intracellular freezing survival. Thorne, M. A. S.; Britovšek, N. K.; Hawkins, L.; Lilley, K. S.; and Storey, K. B. PLoS One, 15(9): e0239641. 2020.
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Efficient recovery of the RNA-bound proteome and protein-bound transcriptome using phase separation (OOPS). Villanueva, E.; Smith, T.; Queiroz, R. M. L.; Monti, M.; Pizzinga, M.; Elzek, M.; Dezi, V.; Harvey, R. F.; Ramakrishna, M.; Willis, A. E.; and Lilley, K. S. Nat Protoc, 15(8): 2568–2588. 08 2020.
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Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection. Messner, C. B.; Demichev, V.; Wendisch, D.; Michalick, L.; White, M.; Freiwald, A.; Textoris-Taube, K.; Vernardis, S. I.; Egger, A. S.; Kreidl, M.; Ludwig, D.; Kilian, C.; Agostini, F.; Zelezniak, A.; Thibeault, C.; Pfeiffer, M.; Hippenstiel, S.; Hocke, A.; von Kalle, C.; Campbell, A.; Hayward, C.; Porteous, D. J.; Marioni, R. E.; Langenberg, C.; Lilley, K. S.; Kuebler, W. M.; Mülleder, M.; Drosten, C.; Suttorp, N.; Witzenrath, M.; Kurth, F.; Sander, L. E.; and Ralser, M. Cell Syst, 11(1): 11–24. 07 2020.
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Moving Profiling Spatial Proteomics Beyond Discrete Classification. Crook, O. M.; Smith, T.; Elzek, M.; and Lilley, K. S. Proteomics, 20(23): e1900392. 12 2020.
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Proteomics of intracellular freezing survival. Thorne, M. A. S.; Britovšek, N. K.; Hawkins, L.; Lilley, K. S.; and Storey, K. B. PLoS One, 15(5): e0233048. 2020.
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Changes in the Oligodendrocyte Progenitor Cell Proteome with Ageing. de la Fuente, A. G.; Queiroz, R. M. L.; Ghosh, T.; McMurran, C. E.; Cubillos, J. F.; Bergles, D. E.; Fitzgerald, D. C.; Jones, C. A.; Lilley, K. S.; Glover, C. P.; and Franklin, R. J. M. Mol Cell Proteomics, 19(8): 1281–1302. 08 2020.
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A direct role for SNX9 in the biogenesis of filopodia. Jarsch, I. K.; Gadsby, J. R.; Nuccitelli, A.; Mason, J.; Shimo, H.; Pilloux, L.; Marzook, B.; Mulvey, C. M.; Dobramysl, U.; Bradshaw, C. R.; Lilley, K. S.; Hayward, R. D.; Vaughan, T. J.; Dobson, C. L.; and Gallop, J. L. J Cell Biol, 219(4). 04 2020.
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Identification of the cis‑molecular neighbours of the immune checkpoint protein B7‑H4 in the breast cancer cell‑line SK‑BR‑3 by proteomic proximity labelling. Rees, J. S.; Cheung, L. C. C.; Hamaia, S. W.; Davies, G.; Sandercock, A.; Lilley, K. S.; Tigue, N.; and Jackson, A. P. Int J Oncol, 57(1): 87–99. Jul 2020.
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Organic phase separation opens up new opportunities to interrogate the RNA-binding proteome. Smith, T.; Villanueva, E.; Queiroz, R. M. L.; Dawson, C. S.; Elzek, M.; Urdaneta, E. C.; Willis, A. E.; Beckmann, B. M.; Krijgsveld, J.; and Lilley, K. S. Curr Opin Chem Biol, 54: 70–75. 02 2020.
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Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions. Minde, D. P.; Ramakrishna, M.; and Lilley, K. S. Commun Biol, 3(1): 38. 01 2020.
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DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Demichev, V.; Messner, C. B.; Vernardis, S. I.; Lilley, K. S.; and Ralser, M. Nat Methods, 17(1): 41–44. 01 2020.
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  2019 (20)
Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components. Marondedze, C.; Thomas, L.; Lilley, K. S.; and Gehring, C. Front Mol Biosci, 6: 163. 2019.
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N-recognin E3 ligase PROTEOLYSIS1 influences the immune response. Till, C. J.; Vicente, J.; Zhang, H.; Oszvald, M.; Deery, M. J.; Pastor, V.; Lilley, K. S.; Ray, R. V.; Theodoulou, F. L.; and Holdsworth, M. J. Plant Direct, 3(12): e00194. Dec 2019.
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Mapping the Saccharomyces cerevisiae Spatial Proteome with High Resolution Using hyperLOPIT. Nightingale, D. J. H.; Oliver, S. G.; and Lilley, K. S. Methods Mol Biol, 2049: 165–190. 2019.
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Proteome Mapping of a Cyanobacterium Reveals Distinct Compartment Organization and Cell-Dispersed Metabolism. Baers, L. L.; Breckels, L. M.; Mills, L. A.; Gatto, L.; Deery, M. J.; Stevens, T. J.; Howe, C. J.; Lilley, K. S.; and Lea-Smith, D. J. Plant Physiol, 181(4): 1721–1738. 12 2019.
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. Nightingale, D. J. H.; Lilley, K. S.; and Oliver, S. G. Bio Protoc, 9(14): e3303. Jul 2019.
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Reveals Underlying Properties of Cisternal Localization. Parsons, H. T.; Stevens, T. J.; McFarlane, H. E.; Vidal-Melgosa, S.; Griss, J.; Lawrence, N.; Butler, R.; Sousa, M. M. L.; Salemi, M.; Willats, W. G. T.; Petzold, C. J.; Heazlewood, J. L.; and Lilley, K. S. Plant Cell, 31(9): 2010–2034. 09 2019.
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Author Correction: Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS). Queiroz, R. M. L.; Smith, T.; Villanueva, E.; Marti-Solano, M.; Monti, M.; Pizzinga, M.; Mirea, D. M.; Ramakrishna, M.; Harvey, R. F.; Dezi, V.; Thomas, G. H.; Willis, A. E.; and Lilley, K. S. Nat Biotechnol, 37(6): 692. 06 2019.
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A Bioconductor workflow for the Bayesian analysis of spatial proteomics. Crook, O. M.; Breckels, L. M.; Lilley, K. S.; Kirk, P. D. W.; and Gatto, L. F1000Res, 8: 446. 2019.
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Comparison of Drosophila melanogaster Embryo and Adult Proteome by SWATH-MS Reveals Differential Regulation of Protein Synthesis, Degradation Machinery, and Metabolism Modules. Fabre, B.; Korona, D.; Lees, J. G.; Lazar, I.; Livneh, I.; Brunet, M.; Orengo, C. A.; Russell, S.; and Lilley, K. S. J Proteome Res, 18(6): 2525–2534. 06 2019.
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Ketamine's Effects on the Glutamatergic and GABAergic Systems: A Proteomics and Metabolomics Study in Mice. Weckmann, K.; Deery, M. J.; Howard, J. A.; Feret, R.; Asara, J. M.; Dethloff, F.; Filiou, M. D.; Labermaier, C.; Maccarrone, G.; Lilley, K. S.; Mueller, M.; and Turck, C. W. Mol Neuropsychiatry, 5(1): 42–51. Mar 2019.
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Changes in the Arabidopsis RNA-binding proteome reveal novel stress response mechanisms. Marondedze, C.; Thomas, L.; Gehring, C.; and Lilley, K. S. BMC Plant Biol, 19(1): 139. Apr 2019.
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A proteomic time course through the differentiation of human induced pluripotent stem cells into hepatocyte-like cells. Hurrell, T.; Segeritz, C. P.; Vallier, L.; Lilley, K. S.; and Cromarty, A. D. Sci Rep, 9(1): 3270. 03 2019.
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Editorial overview: Untangling proteome organization in space and time. Cristea, I. M.; and Lilley, K. S. Curr Opin Chem Biol, 48: A1-A4. 02 2019.
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Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae. Dikicioglu, D.; Nightingale, D. J. H.; Wood, V.; Lilley, K. S.; and Oliver, S. G. FEMS Yeast Res, 19(2). 03 2019.
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Assessing sub-cellular resolution in spatial proteomics experiments. Gatto, L.; Breckels, L. M.; and Lilley, K. S. Curr Opin Chem Biol, 48: 123–149. 02 2019.
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Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Geladaki, A.; Kočevar Britovšek, N.; Breckels, L. M.; Smith, T. S.; Vennard, O. L.; Mulvey, C. M.; Crook, O. M.; Gatto, L.; and Lilley, K. S. Nat Commun, 10(1): 331. 01 2019.
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Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS). Queiroz, R. M. L.; Smith, T.; Villanueva, E.; Marti-Solano, M.; Monti, M.; Pizzinga, M.; Mirea, D. M.; Ramakrishna, M.; Harvey, R. F.; Dezi, V.; Thomas, G. H.; Willis, A. E.; and Lilley, K. S. Nat Biotechnol, 37(2): 169–178. 02 2019.
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The subcellular organisation of Saccharomyces cerevisiae. Nightingale, D. J.; Geladaki, A.; Breckels, L. M.; Oliver, S. G.; and Lilley, K. S. Curr Opin Chem Biol, 48: 86–95. 02 2019.
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Proteomic responses of HepG2 cell monolayers and 3D spheroids to selected hepatotoxins. Hurrell, T.; Lilley, K. S.; and Cromarty, A. D. Toxicol Lett, 300: 40–50. Jan 2019.
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The Parkinson's Disease-Linked Protein DJ-1 Associates with Cytoplasmic mRNP Granules During Stress and Neurodegeneration. Repici, M.; Hassanjani, M.; Maddison, D. C.; Garção, P.; Cimini, S.; Patel, B.; Szegö, É. M.; Straatman, K. R.; Lilley, K. S.; Borsello, T.; Outeiro, T. F.; Panman, L.; and Giorgini, F. Mol Neurobiol, 56(1): 61–77. Jan 2019.
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  2018 (12)
A Bayesian mixture modelling approach for spatial proteomics. Crook, O. M.; Mulvey, C. M.; Kirk, P. D. W.; Lilley, K. S.; and Gatto, L. PLoS Comput Biol, 14(11): e1006516. 11 2018.
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Ethylene Receptors, CTRs and EIN2 Target Protein Identification and Quantification Through Parallel Reaction Monitoring During Tomato Fruit Ripening. Mata, C. I.; Fabre, B.; Parsons, H. T.; Hertog, M. L. A. T. M.; Van Raemdonck, G.; Baggerman, G.; Van de Poel, B.; Lilley, K. S.; and Nicolaï, B. M. Front Plant Sci, 9: 1626. 2018.
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Cell Suspension Culture Proteome. Alqurashi, M.; Chiapello, M.; Bianchet, C.; Paolocci, F.; Lilley, K. S.; and Gehring, C. Proteomes, 6(4). Oct 2018.
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Identification of the RNA polymerase I-RNA interactome. Piñeiro, D.; Stoneley, M.; Ramakrishna, M.; Alexandrova, J.; Dezi, V.; Juke-Jones, R.; Lilley, K. S.; Cain, K.; and Willis, A. E. Nucleic Acids Res, 46(20): 11002–11013. 11 2018.
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Negative feedback via RSK modulates Erk-dependent progression from naïve pluripotency. Nett, I. R.; Mulas, C.; Gatto, L.; Lilley, K. S.; and Smith, A. EMBO Rep, 19(8). 08 2018.
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Ciprofloxacin binding to GyrA causes global changes in the proteome of Pseudomonas aeruginosa. Jedrey, H.; Lilley, K. S.; and Welch, M. FEMS Microbiol Lett, 365(13). 07 2018.
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Proteomic Comparison of Various Hepatic Cell Cultures for Preclinical Safety Pharmacology. Hurrell, T.; Segeritz, C. P.; Vallier, L.; Lilley, K. S.; and Cromarty, A. D. Toxicol Sci, 164(1): 229–239. 07 2018.
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Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation. Armean, I. M.; Lilley, K. S.; Trotter, M. W. B.; Pilkington, N. C. V.; and Holden, S. B. Bioinformatics, 34(11): 1884–1892. 06 2018.
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Stat3-mediated alterations in lysosomal membrane protein composition. Lloyd-Lewis, B.; Krueger, C. C.; Sargeant, T. J.; D'Angelo, M. E.; Deery, M. J.; Feret, R.; Howard, J. A.; Lilley, K. S.; and Watson, C. J. J Biol Chem, 293(12): 4244–4261. 03 2018.
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Trans-acting translational regulatory RNA binding proteins. Harvey, R. F.; Smith, T. S.; Mulroney, T.; Queiroz, R. M. L.; Pizzinga, M.; Dezi, V.; Villenueva, E.; Ramakrishna, M.; Lilley, K. S.; and Willis, A. E. Wiley Interdiscip Rev RNA, 9(3): e1465. 05 2018.
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N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. Zhang, H.; Gannon, L.; Hassall, K. L.; Deery, M. J.; Gibbs, D. J.; Holdsworth, M. J.; van der Hoorn, R. A. L.; Lilley, K. S.; and Theodoulou, F. L. New Phytol, 218(3): 1106–1126. 05 2018.
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Mass spectrometry approaches to study plant endomembrane trafficking. Parsons, H. T.; and Lilley, K. S. Semin Cell Dev Biol, 80: 123–132. 08 2018.
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  2017 (9)
Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples. Hooper, C. M.; Stevens, T. J.; Saukkonen, A.; Castleden, I. R.; Singh, P.; Mann, G. W.; Fabre, B.; Ito, J.; Deery, M. J.; Lilley, K. S.; Petzold, C. J.; Millar, A. H.; Heazlewood, J. L.; and Parsons, H. T. Plant J, 92(6): 1202–1217. Dec 2017.
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Spectral Libraries for SWATH-MS Assays for Drosophila melanogaster and Solanum lycopersicum. Fabre, B.; Korona, D.; Mata, C. I.; Parsons, H. T.; Deery, M. J.; Hertog, M. L. A. T. M.; Nicolaï, B. M.; Russell, S.; and Lilley, K. S. Proteomics, 17(21). Nov 2017.
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. Loxley, G. M.; Unsworth, J.; Turton, M. J.; Jebb, A.; Lilley, K. S.; Simpson, D. M.; Rigden, D. J.; Hurst, J. L.; and Beynon, R. J. Open Biol, 7(9). 09 2017.
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A subcellular map of the human proteome. Thul, P. J.; Åkesson, L.; Wiking, M.; Mahdessian, D.; Geladaki, A.; Ait Blal, H.; Alm, T.; Asplund, A.; Björk, L.; Breckels, L. M.; Bäckström, A.; Danielsson, F.; Fagerberg, L.; Fall, J.; Gatto, L.; Gnann, C.; Hober, S.; Hjelmare, M.; Johansson, F.; Lee, S.; Lindskog, C.; Mulder, J.; Mulvey, C. M.; Nilsson, P.; Oksvold, P.; Rockberg, J.; Schutten, R.; Schwenk, J. M.; Sivertsson, Å.; Sjöstedt, E.; Skogs, M.; Stadler, C.; Sullivan, D. P.; Tegel, H.; Winsnes, C.; Zhang, C.; Zwahlen, M.; Mardinoglu, A.; Pontén, F.; von Feilitzen, K.; Lilley, K. S.; Uhlén, M.; and Lundberg, E. Science, 356(6340). 05 2017.
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Using hyperLOPIT to perform high-resolution mapping of the spatial proteome. Mulvey, C. M.; Breckels, L. M.; Geladaki, A.; Britovšek, N. K.; Nightingale, D. J. H.; Christoforou, A.; Elzek, M.; Deery, M. J.; Gatto, L.; and Lilley, K. S. Nat Protoc, 12(6): 1110–1135. Jun 2017.
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Selective Proteomic Proximity Labeling Assay Using Tyramide (SPPLAT): A Quantitative Method for the Proteomic Analysis of Localized Membrane-Bound Protein Clusters. Rees, J. S.; Li, X. W.; Perrett, S.; Lilley, K. S.; and Jackson, A. P. Curr Protoc Protein Sci, 88: 1–19. 04 2017.
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Tracking the embryonic stem cell transition from ground state pluripotency. Kalkan, T.; Olova, N.; Roode, M.; Mulas, C.; Lee, H. J.; Nett, I.; Marks, H.; Walker, R.; Stunnenberg, H. G.; Lilley, K. S.; Nichols, J.; Reik, W.; Bertone, P.; and Smith, A. Development, 144(7): 1221–1234. 04 2017.
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Time, space, and disorder in the expanding proteome universe. Minde, D. P.; Dunker, A. K.; and Lilley, K. S. Proteomics, 17(7). 04 2017.
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In-depth characterization of the tomato fruit pericarp proteome. Mata, C. I.; Fabre, B.; Hertog, M. L.; Parsons, H. T.; Deery, M. J.; Lilley, K. S.; and Nicolaï, B. M. Proteomics, 17(1-2). 01 2017.
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  2016 (13)
A Bioconductor workflow for processing and analysing spatial proteomics data. Breckels, L. M.; Mulvey, C. M.; Lilley, K. S.; and Gatto, L. F1000Res, 5: 2926. 2016.
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embryos. Fabre, B.; Korona, D.; Nightingale, D. J.; Russell, S.; and Lilley, K. S. Data Brief, 9: 991–995. Dec 2016.
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proteome dynamics during embryogenesis. Fabre, B.; Korona, D.; Nightingale, D. J.; Russell, S.; and Lilley, K. S. Data Brief, 9: 771–775. Dec 2016.
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The metabolic background is a global player in Saccharomyces gene expression epistasis. Alam, M. T.; Zelezniak, A.; Mülleder, M.; Shliaha, P.; Schwarz, R.; Capuano, F.; Vowinckel, J.; Radmanesfahar, E.; Krüger, A.; Calvani, E.; Michel, S.; Börno, S.; Christen, S.; Patil, K. R.; Timmermann, B.; Lilley, K. S.; and Ralser, M. Nat Microbiol, 1: 15030. Feb 2016.
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Phosphorylation of the dimeric cytoplasmic domain of the phytosulfokine receptor, PSKR1. Muleya, V.; Marondedze, C.; Wheeler, J. I.; Thomas, L.; Mok, Y. F.; Griffin, M. D.; Manallack, D. T.; Kwezi, L.; Lilley, K. S.; Gehring, C.; and Irving, H. R. Biochem J, 473(19): 3081–3098. 10 2016.
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The RNA-binding protein repertoire of Arabidopsis thaliana. Marondedze, C.; Thomas, L.; Serrano, N. L.; Lilley, K. S.; and Gehring, C. Sci Rep, 6: 29766. 07 2016.
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Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics. Breckels, L. M.; Holden, S. B.; Wojnar, D.; Mulvey, C. M.; Christoforou, A.; Groen, A.; Trotter, M. W.; Kohlbacher, O.; Lilley, K. S.; and Gatto, L. PLoS Comput Biol, 12(5): e1004920. 05 2016.
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Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches. Fabre, B.; Korona, D.; Groen, A.; Vowinckel, J.; Gatto, L.; Deery, M. J.; Ralser, M.; Russell, S.; and Lilley, K. S. Proteomics, 16(15-16): 2068–2080. 08 2016.
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Impact of Azithromycin on the Quorum Sensing-Controlled Proteome of Pseudomonas aeruginosa. Swatton, J. E.; Davenport, P. W.; Maunders, E. A.; Griffin, J. L.; Lilley, K. S.; and Welch, M. PLoS One, 11(1): e0147698. 2016.
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A draft map of the mouse pluripotent stem cell spatial proteome. Christoforou, A.; Mulvey, C. M.; Breckels, L. M.; Geladaki, A.; Hurrell, T.; Hayward, P. C.; Naake, T.; Gatto, L.; Viner, R.; Martinez Arias, A.; and Lilley, K. S. Nat Commun, 7: 8992. Jan 2016.
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A Quantitative Phosphoproteome Analysis of cGMP-Dependent Cellular Responses in Arabidopsis thaliana. Marondedze, C.; Groen, A. J.; Thomas, L.; Lilley, K. S.; and Gehring, C. Mol Plant, 9(4): 621–623. Apr 2016.
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Analysis of temperature-mediated changes in the wine yeast Saccharomyces bayanus var uvarum. An oenological study of how the protein content influences wine quality. Muñoz-Bernal, E.; Deery, M. J.; Rodríguez, M. E.; Cantoral, J. M.; Howard, J.; Feret, R.; Natera, R.; Lilley, K. S.; and Fernández-Acero, F. J. Proteomics, 16(4): 576–592. Feb 2016.
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Sex-Related Differences in Rat Choroid Plexus and Cerebrospinal Fluid: A cDNA Microarray and Proteomic Analysis. Quintela, T.; Marcelino, H.; Deery, M. J.; Feret, R.; Howard, J.; Lilley, K. S.; Albuquerque, T.; Gonçalves, I.; Duarte, A. C.; and Santos, C. R. J Neuroendocrinol, 28(1). Jan 2016.
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  2015 (11)
Drosophila Ionotropic Receptor 25a mediates circadian clock resetting by temperature. Chen, C.; Buhl, E.; Xu, M.; Croset, V.; Rees, J. S.; Lilley, K. S.; Benton, R.; Hodge, J. J.; and Stanewsky, R. Nature, 527(7579): 516–520. Nov 2015.
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Focus on Quantitative Proteomics. Lilley, K. S.; Beynon, R. J.; Eyers, C. E.; and Hubbard, S. J. Proteomics, 15(18): 3101–3103. Sep 2015.
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Protein Neighbors and Proximity Proteomics. Rees, J. S.; Li, X. W.; Perrett, S.; Lilley, K. S.; and Jackson, A. P. Mol Cell Proteomics, 14(11): 2848–2856. Nov 2015.
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α-Klotho Expression in Human Tissues. Lim, K.; Groen, A.; Molostvov, G.; Lu, T.; Lilley, K. S.; Snead, D.; James, S.; Wilkinson, I. B.; Ting, S.; Hsiao, L. L.; Hiemstra, T. F.; and Zehnder, D. J Clin Endocrinol Metab, 100(10): E1308–1318. Oct 2015.
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The chicken B-cell line DT40 proteome, beadome and interactomes. Rees, J. S.; Lilley, K. S.; and Jackson, A. P. Data Brief, 3: 29–33. Jun 2015.
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Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells. Mulvey, C. M.; Schröter, C.; Gatto, L.; Dikicioglu, D.; Fidaner, I. B.; Christoforou, A.; Deery, M. J.; Cho, L. T.; Niakan, K. K.; Martinez-Arias, A.; and Lilley, K. S. Stem Cells, 33(9): 2712–2725. Sep 2015.
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Selective Proteomic Proximity Labeling Assay Using Tyramide (SPPLAT): A Quantitative Method for the Proteomic Analysis of Localized Membrane-Bound Protein Clusters. Rees, J. S.; Li, X. W.; Perrett, S.; Lilley, K. S.; and Jackson, A. P. Curr Protoc Protein Sci, 80: 1–19. Apr 2015.
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Analysis of Quality-Related Parameters in Mature Kernels of Polygalacturonase Inhibiting Protein (PGIP) Transgenic Bread Wheat Infected with Fusarium graminearum. Masci, S.; Laino, P.; Janni, M.; Botticella, E.; Di Carli, M.; Benvenuto, E.; Danieli, P. P.; Lilley, K. S.; Lafiandra, D.; and D'Ovidio, R. J Agric Food Chem, 63(15): 3962–3969. Apr 2015.
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Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots. Zhang, H.; Deery, M. J.; Gannon, L.; Powers, S. J.; Lilley, K. S.; and Theodoulou, F. L. Proteomics, 15(14): 2447–2457. Jul 2015.
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SILAC-iPAC: a quantitative method for distinguishing genuine from non-specific components of protein complexes by parallel affinity capture. Rees, J. S.; Lilley, K. S.; and Jackson, A. P. J Proteomics, 115: 143–156. Feb 2015.
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Mep72, a metzincin protease that is preferentially secreted by biofilms of Pseudomonas aeruginosa. Passmore, I. J.; Nishikawa, K.; Lilley, K. S.; Bowden, S. D.; Chung, J. C.; and Welch, M. J Bacteriol, 197(4): 762–773. Feb 2015.
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  2014 (17)
Toward a comprehensive map of the effectors of rab GTPases. Gillingham, A. K.; Sinka, R.; Torres, I. L.; Lilley, K. S.; and Munro, S. Dev Cell, 31(3): 358–373. Nov 2014.
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Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library. Lowe, N.; Rees, J. S.; Roote, J.; Ryder, E.; Armean, I. M.; Johnson, G.; Drummond, E.; Spriggs, H.; Drummond, J.; Magbanua, J. P.; Naylor, H.; Sanson, B.; Bastock, R.; Huelsmann, S.; Trovisco, V.; Landgraf, M.; Knowles-Barley, S.; Armstrong, J. D.; White-Cooper, H.; Hansen, C.; Phillips, R. G.; Lilley, K. S.; Russell, S.; and St Johnston, D. Development, 141(20): 3994–4005. Oct 2014.
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Label-free protein quantification for plant Golgi protein localization and abundance. Nikolovski, N.; Shliaha, P. V.; Gatto, L.; Dupree, P.; and Lilley, K. S. Plant Physiol, 166(2): 1033–1043. Oct 2014.
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Deciphering thylakoid sub-compartments using a mass spectrometry-based approach. Tomizioli, M.; Lazar, C.; Brugière, S.; Burger, T.; Salvi, D.; Gatto, L.; Moyet, L.; Breckels, L. M.; Hesse, A. M.; Lilley, K. S.; Seigneurin-Berny, D.; Finazzi, G.; Rolland, N.; and Ferro, M. Mol Cell Proteomics, 13(8): 2147–2167. Aug 2014.
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Additional precursor purification in isobaric mass tagging experiments by traveling wave ion mobility separation (TWIMS). Shliaha, P. V.; Jukes-Jones, R.; Christoforou, A.; Fox, J.; Hughes, C.; Langridge, J.; Cain, K.; and Lilley, K. S. J Proteome Res, 13(7): 3360–3369. Jul 2014.
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A foundation for reliable spatial proteomics data analysis. Gatto, L.; Breckels, L. M.; Burger, T.; Nightingale, D. J.; Groen, A. J.; Campbell, C.; Nikolovski, N.; Mulvey, C. M.; Christoforou, A.; Ferro, M.; and Lilley, K. S. Mol Cell Proteomics, 13(8): 1937–1952. Aug 2014.
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Determining protein subcellular localization in mammalian cell culture with biochemical fractionation and iTRAQ 8-plex quantification. Christoforou, A.; Arias, A. M.; and Lilley, K. S. Methods Mol Biol, 1156: 157–174. 2014.
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qcML: an exchange format for quality control metrics from mass spectrometry experiments. Walzer, M.; Pernas, L. E.; Nasso, S.; Bittremieux, W.; Nahnsen, S.; Kelchtermans, P.; Pichler, P.; van den Toorn, H. W.; Staes, A.; Vandenbussche, J.; Mazanek, M.; Taus, T.; Scheltema, R. A.; Kelstrup, C. D.; Gatto, L.; van Breukelen, B.; Aiche, S.; Valkenborg, D.; Laukens, K.; Lilley, K. S.; Olsen, J. V.; Heck, A. J.; Mechtler, K.; Aebersold, R.; Gevaert, K.; Vizcaíno, J. A.; Hermjakob, H.; Kohlbacher, O.; and Martens, L. Mol Cell Proteomics, 13(8): 1905–1913. Aug 2014.
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Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal. Elliott, T. S.; Townsley, F. M.; Bianco, A.; Ernst, R. J.; Sachdeva, A.; Elsässer, S. J.; Davis, L.; Lang, K.; Pisa, R.; Greiss, S.; Lilley, K. S.; and Chin, J. W. Nat Biotechnol, 32(5): 465–472. May 2014.
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New insights into the DT40 B cell receptor cluster using a proteomic proximity labeling assay. Li, X. W.; Rees, J. S.; Xue, P.; Zhang, H.; Hamaia, S. W.; Sanderson, B.; Funk, P. E.; Farndale, R. W.; Lilley, K. S.; Perrett, S.; and Jackson, A. P. J Biol Chem, 289(21): 14434–14447. May 2014.
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Human urinary exosomes as innate immune effectors. Hiemstra, T. F.; Charles, P. D.; Gracia, T.; Hester, S. S.; Gatto, L.; Al-Lamki, R.; Floto, R. A.; Su, Y.; Skepper, J. N.; Lilley, K. S.; and Karet Frankl, F. E. J Am Soc Nephrol, 25(9): 2017–2027. Sep 2014.
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Protein profiling using two-dimensional difference gel electrophoresis (2-D DIGE). Feret, R.; and Lilley, K. S. Curr Protoc Protein Sci, 75: 1–22. Feb 2014.
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A protocol for the subcellular fractionation of Saccharomyces cerevisiae using nitrogen cavitation and density gradient centrifugation. Wang, Y.; Lilley, K. S.; and Oliver, S. G. Yeast, 31(4): 127–135. Apr 2014.
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Dynamic regulation of the COP9 signalosome in response to DNA damage. Füzesi-Levi, M. G.; Ben-Nissan, G.; Bianchi, E.; Zhou, H.; Deery, M. J.; Lilley, K. S.; Levin, Y.; and Sharon, M. Mol Cell Biol, 34(6): 1066–1076. Mar 2014.
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Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata. Gatto, L.; Breckels, L. M.; Wieczorek, S.; Burger, T.; and Lilley, K. S. Bioinformatics, 30(9): 1322–1324. May 2014.
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Identification of trans-golgi network proteins in Arabidopsis thaliana root tissue. Groen, A. J.; Sancho-Andrés, G.; Breckels, L. M.; Gatto, L.; Aniento, F.; and Lilley, K. S. J Proteome Res, 13(2): 763–776. Feb 2014.
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Remodelling of a polypyrimidine tract-binding protein complex during apoptosis activates cellular IRESs. King, H. A.; Cobbold, L. C.; Pichon, X.; Pöyry, T.; Wilson, L. A.; Booden, H.; Jukes-Jones, R.; Cain, K.; Lilley, K. S.; Bushell, M.; and Willis, A. E. Cell Death Differ, 21(1): 161–171. Jan 2014.
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  2013 (11)
RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006. Wilf, N. M.; Reid, A. J.; Ramsay, J. P.; Williamson, N. R.; Croucher, N. J.; Gatto, L.; Hester, S. S.; Goulding, D.; Barquist, L.; Lilley, K. S.; Kingsley, R. A.; Dougan, G.; and Salmond, G. P. BMC Genomics, 14: 822. Nov 2013.
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Identification of protein biomarkers in human serum using iTRAQ and shotgun mass spectrometry. Koutroukides, T. A.; Jaros, J. A.; Amess, B.; Martins-de-Souza, D.; Guest, P. C.; Rahmoune, H.; Levin, Y.; Deery, M.; Charles, P. D.; Hester, S.; Groen, A.; Christoforou, A.; Howard, J.; Bond, N.; Bahn, S.; and Lilley, K. S. Methods Mol Biol, 1061: 291–307. 2013.
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Cardioprotection by S-nitrosation of a cysteine switch on mitochondrial complex I. Chouchani, E. T.; Methner, C.; Nadtochiy, S. M.; Logan, A.; Pell, V. R.; Ding, S.; James, A. M.; Cochemé, H. M.; Reinhold, J.; Lilley, K. S.; Partridge, L.; Fearnley, I. M.; Robinson, A. J.; Hartley, R. C.; Smith, R. A.; Krieg, T.; Brookes, P. S.; and Murphy, M. P. Nat Med, 19(6): 753–759. Jun 2013.
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The effect of organelle discovery upon sub-cellular protein localisation. Breckels, L. M.; Gatto, L.; Christoforou, A.; Groen, A. J.; Lilley, K. S.; and Trotter, M. W. J Proteomics, 88: 129–140. Aug 2013.
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Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies. Shliaha, P. V.; Bond, N. J.; Gatto, L.; and Lilley, K. S. J Proteome Res, 12(6): 2323–2339. Jun 2013.
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Improving qualitative and quantitative performance for MS(E)-based label-free proteomics. Bond, N. J.; Shliaha, P. V.; Lilley, K. S.; and Gatto, L. J Proteome Res, 12(6): 2340–2353. Jun 2013.
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Interlaboratory studies and initiatives developing standards for proteomics. Ivanov, A. R.; Colangelo, C. M.; Dufresne, C. P.; Friedman, D. B.; Lilley, K. S.; Mechtler, K.; Phinney, B. S.; Rose, K. L.; Rudnick, P. A.; Searle, B. C.; Shaffer, S. A.; and Weintraub, S. T. Proteomics, 13(6): 904–909. Mar 2013.
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Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins. Marondedze, C.; Turek, I.; Parrott, B.; Thomas, L.; Jankovic, B.; Lilley, K. S.; and Gehring, C. Cell Commun Signal, 11(1): 1. Jan 2013.
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The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics. Vowinckel, J.; Capuano, F.; Campbell, K.; Deery, M. J.; Lilley, K. S.; and Ralser, M. F1000Res, 2: 272. 2013.
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A proteomic approach identifies many novel palmitoylated proteins in Arabidopsis. Hemsley, P. A.; Weimar, T.; Lilley, K. S.; Dupree, P.; and Grierson, C. S. New Phytol, 197(3): 805–814. Feb 2013.
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Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Armean, I. M.; Lilley, K. S.; and Trotter, M. W. Mol Cell Proteomics, 12(1): 1–13. Jan 2013.
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  2012 (6)
Pipeline to assess the greatest source of technical variance in quantitative proteomics using metabolic labelling. Russell, M. R.; and Lilley, K. S. J Proteomics, 77: 441–454. Dec 2012.
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Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. Nikolovski, N.; Rubtsov, D.; Segura, M. P.; Miles, G. P.; Stevens, T. J.; Dunkley, T. P.; Munro, S.; Lilley, K. S.; and Dupree, P. Plant Physiol, 160(2): 1037–1051. Oct 2012.
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MRMaid 2.0: mining PRIDE for evidence-based SRM transitions. Fan, J.; Mohareb, F.; Bond, N. J.; Lilley, K. S.; and Bessant, C. OMICS, 16(9): 483–488. Sep 2012.
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Isobaric tagging approaches in quantitative proteomics: the ups and downs. Christoforou, A. L.; and Lilley, K. S. Anal Bioanal Chem, 404(4): 1029–1037. Sep 2012.
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Evaluation and properties of the budding yeast phosphoproteome. Amoutzias, G. D.; He, Y.; Lilley, K. S.; Van de Peer, Y.; and Oliver, S. G. Mol Cell Proteomics, 11(6): M111.009555. Jun 2012.
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MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Gatto, L.; and Lilley, K. S. Bioinformatics, 28(2): 288–289. Jan 2012.
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  2011 (11)
Uromodulin exclusion list improves urinary exosomal protein identification. Hiemstra, T. F.; Charles, P. D.; Hester, S. S.; Karet, F. E.; and Lilley, K. S. J Biomol Tech, 22(4): 136–145. Dec 2011.
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Taming the isobaric tagging elephant in the room in quantitative proteomics. Christoforou, A.; and Lilley, K. S. Nat Methods, 8(11): 911–913. Oct 2011.
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LC-MS/MS methods for absolute quantification and identification of proteins associated with chimeric plant oil bodies. Capuano, F.; Bond, N. J.; Gatto, L.; Beaudoin, F.; Napier, J. A.; Benvenuto, E.; Lilley, K. S.; and Baschieri, S. Anal Chem, 83(24): 9267–9272. Dec 2011.
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Method for suppressing non-specific protein interactions observed with affinity resins. Rees, J. S.; and Lilley, K. S. Methods, 54(4): 407–412. Aug 2011.
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ABRF-PRG07: advanced quantitative proteomics study. Falick, A. M.; Lane, W. S.; Lilley, K. S.; MacCoss, M. J.; Phinney, B. S.; Sherman, N. E.; Weintraub, S. T.; Witkowska, H. E.; and Yates, N. A. J Biomol Tech, 22(1): 21–26. Apr 2011.
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In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry. Rees, J. S.; Lowe, N.; Armean, I. M.; Roote, J.; Johnson, G.; Drummond, E.; Spriggs, H.; Ryder, E.; Russell, S.; St Johnston, D.; and Lilley, K. S. Mol Cell Proteomics, 10(6): M110.002386. Jun 2011.
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The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses. Friedman, D. B.; Andacht, T. M.; Bunger, M. K.; Chien, A. S.; Hawke, D. H.; Krijgsveld, J.; Lane, W. S.; Lilley, K. S.; MacCoss, M. J.; Moritz, R. L.; Settlage, R. E.; Sherman, N. E.; Weintraub, S. T.; Witkowska, H. E.; Yates, N. A.; and Turck, C. W. Proteomics, 11(8): 1371–1381. Apr 2011.
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Challenges for proteomics core facilities. Lilley, K. S.; Deery, M. J.; and Gatto, L. Proteomics, 11(6): 1017–1025. Mar 2011.
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Proteomics of cryoprotective dehydration in Megaphorura arctica Tullberg 1876 (Onychiuridae: Collembola). Thorne, M. A.; Worland, M. R.; Feret, R.; Deery, M. J.; Lilley, K. S.; and Clark, M. S. Insect Mol Biol, 20(3): 303–310. Jun 2011.
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Proteomic approaches to the characterization of protein thiol modification. Chouchani, E. T.; James, A. M.; Fearnley, I. M.; Lilley, K. S.; and Murphy, M. P. Curr Opin Chem Biol, 15(1): 120–128. Feb 2011.
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Two-dimensional differential in gel electrophoresis (2D-DIGE) analysis of grape berry proteome during postharvest withering. Di Carli, M.; Zamboni, A.; Pè, M. E.; Pezzotti, M.; Lilley, K. S.; Benvenuto, E.; and Desiderio, A. J Proteome Res, 10(2): 429–446. Feb 2011.
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  2010 (15)
Proteomic analysis of the adaptive responses of Pseudomonas aeruginosa to aminoglycoside antibiotics. Mikkelsen, H.; Swatton, J. E.; Lilley, K. S.; and Welch, M. FEMS Microbiol Lett. Aug 2010.
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Proteomics of total membranes and subcellular membranes. Groen, A. J.; and Lilley, K. S. Expert Rev Proteomics, 7(6): 867–878. Dec 2010.
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Organelle proteomics experimental designs and analysis. Gatto, L.; Vizcaíno, J. A.; Hermjakob, H.; Huber, W.; and Lilley, K. S. Proteomics, 10(22): 3957–3969. Nov 2010.
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Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions. Trotter, M. W.; Sadowski, P. G.; Dunkley, T. P.; Groen, A. J.; and Lilley, K. S. Proteomics, 10(23): 4213–4219. Dec 2010.
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Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay. McGlincy, N. J.; Tan, L. Y.; Paul, N.; Zavolan, M.; Lilley, K. S.; and Smith, C. W. BMC Genomics, 11: 565. Oct 2010.
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Quantification and identification of mitochondrial proteins containing vicinal dithiols. Requejo, R.; Chouchani, E. T.; James, A. M.; Prime, T. A.; Lilley, K. S.; Fearnley, I. M.; and Murphy, M. P. Arch Biochem Biophys, 504(2): 228–235. Dec 2010.
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Identification of putative stage-specific grapevine berry biomarkers and omics data integration into networks. Zamboni, A.; Di Carli, M.; Guzzo, F.; Stocchero, M.; Zenoni, S.; Ferrarini, A.; Tononi, P.; Toffali, K.; Desiderio, A.; Lilley, K. S.; Pè, M. E.; Benvenuto, E.; Delledonne, M.; and Pezzotti, M. Plant Physiol, 154(3): 1439–1459. Nov 2010.
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Proteomics for the food industry: opportunities and challenges. Pedreschi, R.; Hertog, M.; Lilley, K. S.; and Nicolaï, B. Crit Rev Food Sci Nutr, 50(7): 680–692. Aug 2010.
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Proteomic complex detection using sedimentation (ProCoDeS): screening for proteins in stable complexes and their candidate interaction partners. Segura, M. P.; Lilley, K. S.; and Dupree, P. Biochem Soc Trans, 38(4): 923–927. Aug 2010.
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Genomic tagging reveals a random association of endogenous PtdIns5P 4-kinases IIalpha and IIbeta and a partial nuclear localization of the IIalpha isoform. Wang, M.; Bond, N. J.; Letcher, A. J.; Richardson, J. P.; Lilley, K. S.; Irvine, R. F.; and Clarke, J. H. Biochem J, 430(2): 215–221. Sep 2010.
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Identification of S-nitrosated mitochondrial proteins by S-nitrosothiol difference in gel electrophoresis (SNO-DIGE): implications for the regulation of mitochondrial function by reversible S-nitrosation. Chouchani, E. T.; Hurd, T. R.; Nadtochiy, S. M.; Brookes, P. S.; Fearnley, I. M.; Lilley, K. S.; Smith, R. A.; and Murphy, M. P. Biochem J, 430(1): 49–59. Aug 2010.
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Nutrient control of eukaryote cell growth: a systems biology study in yeast. Gutteridge, A.; Pir, P.; Castrillo, J. I.; Charles, P. D.; Lilley, K. S.; and Oliver, S. G. BMC Biol, 8: 68. May 2010.
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Addressing accuracy and precision issues in iTRAQ quantitation. Karp, N. A.; Huber, W.; Sadowski, P. G.; Charles, P. D.; Hester, S. V.; and Lilley, K. S. Mol Cell Proteomics, 9(9): 1885–1897. Sep 2010.
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Mutation of nfxB causes global changes in the physiology and metabolism of Pseudomonas aeruginosa. Stickland, H. G.; Davenport, P. W.; Lilley, K. S.; Griffin, J. L.; and Welch, M. J Proteome Res, 9(6): 2957–2967. Jun 2010.
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Mutations in rpsL that confer streptomycin resistance show pleiotropic effects on virulence and the production of a carbapenem antibiotic in Erwinia carotovora. Barnard, A. M. L.; Simpson, N. J. L.; Lilley, K. S.; and Salmond, G. P. C. Microbiology (Reading), 156(Pt 4): 1030–1039. Apr 2010.
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  2009 (10)
Proteomic analysis reveals the role of synaptic vesicle cycling in sustaining the suprachiasmatic circadian clock. Deery, M. J.; Maywood, E. S.; Chesham, J. E.; Sládek, M.; Karp, N. A.; Green, E. W.; Charles, P. D.; Reddy, A. B.; Kyriacou, C. P.; Lilley, K. S.; and Hastings, M. H. Curr Biol, 19(23): 2031–2036. Dec 2009.
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Gel-based proteomics approach to the study of metabolic changes in pear tissue during storage. Pedreschi, R.; Hertog, M.; Robben, J.; Lilley, K. S.; Karp, N. A.; Baggerman, G.; Vanderleyden, J.; and Nicolaï, B. J Agric Food Chem, 57(15): 6997–7004. Aug 2009.
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Drosophila Larp associates with poly(A)-binding protein and is required for male fertility and syncytial embryo development. Blagden, S. P.; Gatt, M. K.; Archambault, V.; Lada, K.; Ichihara, K.; Lilley, K. S.; Inoue, Y. H.; and Glover, D. M. Dev Biol, 334(1): 186–197. Oct 2009.
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Chapter 19 Measuring redox changes to mitochondrial protein thiols with redox difference gel electrophoresis (redox-DIGE). Hurd, T. R.; James, A. M.; Lilley, K. S.; and Murphy, M. P. Methods Enzymol, 456: 343–361. 2009.
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Mapping organelle proteins and protein complexes in Drosophila melanogaster. Tan, D. J.; Dvinge, H.; Christoforou, A.; Bertone, P.; Martinez Arias, A.; and Lilley, K. S. J Proteome Res, 8(6): 2667–2678. Jun 2009.
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Biofilms and type III secretion are not mutually exclusive in Pseudomonas aeruginosa. Mikkelsen, H.; Bond, N. J.; Skindersoe, M. E.; Givskov, M.; Lilley, K. S.; and Welch, M. Microbiology (Reading), 155(Pt 3): 687–698. Mar 2009.
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The organelle proteome of the DT40 lymphocyte cell line. Hall, S. L.; Hester, S.; Griffin, J. L.; Lilley, K. S.; and Jackson, A. P. Mol Cell Proteomics, 8(6): 1295–1305. Jun 2009.
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The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Fineran, P. C.; Blower, T. R.; Foulds, I. J.; Humphreys, D. P.; Lilley, K. S.; and Salmond, G. P. Proc Natl Acad Sci U S A, 106(3): 894–899. Jan 2009.
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Investigating sample pooling strategies for DIGE experiments to address biological variability. Karp, N. A.; and Lilley, K. S. Proteomics, 9(2): 388–397. Jan 2009.
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MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mead, J. A.; Bianco, L.; Ottone, V.; Barton, C.; Kay, R. G.; Lilley, K. S.; Bond, N. J.; and Bessant, C. Mol Cell Proteomics, 8(4): 696–705. Apr 2009.
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  2008 (14)
Sequestration of Polo kinase to microtubules by phosphopriming-independent binding to Map205 is relieved by phosphorylation at a CDK site in mitosis. Archambault, V.; D'Avino, P. P.; Deery, M. J.; Lilley, K. S.; and Glover, D. M. Genes Dev, 22(19): 2707–2720. Oct 2008.
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Sub-cellular localization of membrane proteins. Sadowski, P. G.; Groen, A. J.; Dupree, P.; and Lilley, K. S. Proteomics, 8(19): 3991–4011. Oct 2008.
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Guidelines for reporting the use of gel electrophoresis in proteomics. Gibson, F.; Anderson, L.; Babnigg, G.; Baker, M.; Berth, M.; Binz, P. A.; Borthwick, A.; Cash, P.; Day, B. W.; Friedman, D. B.; Garland, D.; Gutstein, H. B.; Hoogland, C.; Jones, N. A.; Khan, A.; Klose, J.; Lamond, A. I.; Lemkin, P. F.; Lilley, K. S.; Minden, J.; Morris, N. J.; Paton, N. W.; Pisano, M. R.; Prime, J. E.; Rabilloud, T.; Stead, D. A.; Taylor, C. F.; Voshol, H.; Wipat, A.; and Jones, A. R. Nat Biotechnol, 26(8): 863–864. Aug 2008.
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A proteomics approach to membrane trafficking. Groen, A. J.; de Vries, S. C.; and Lilley, K. S. Plant Physiol, 147(4): 1584–1589. Aug 2008.
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DsbA plays a critical and multifaceted role in the production of secreted virulence factors by the phytopathogen Erwinia carotovora subsp. atroseptica. Coulthurst, S. J.; Lilley, K. S.; Hedley, P. E.; Liu, H.; Toth, I. K.; and Salmond, G. P. J Biol Chem, 283(35): 23739–23753. Aug 2008.
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A combined metabolomic and proteomic investigation of the effects of a failure to express dystrophin in the mouse heart. Gulston, M. K.; Rubtsov, D. V.; Atherton, H. J.; Clarke, K.; Davies, K. E.; Lilley, K. S.; and Griffin, J. L. J Proteome Res, 7(5): 2069–2077. May 2008.
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Determination of genuine residents of plant endomembrane organelles using isotope tagging and multivariate statistics. Lilley, K. S.; and Dunkley, T. P. Methods Mol Biol, 432: 373–387. 2008.
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Isolation and preparation of chloroplasts from Arabidopsis thaliana plants. Kubis, S. E.; Lilley, K. S.; and Jarvis, P. Methods Mol Biol, 425: 171–186. 2008.
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Interaction between Anillin and RacGAP50C connects the actomyosin contractile ring with spindle microtubules at the cell division site. D'Avino, P. P.; Takeda, T.; Capalbo, L.; Zhang, W.; Lilley, K. S.; Laue, E. D.; and Glover, D. M. J Cell Sci, 121(Pt 8): 1151–1158. Apr 2008.
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Proteomic analysis of the EhV-86 virion. Allen, M. J.; Howard, J. A.; Lilley, K. S.; and Wilson, W. H. Proteome Sci, 6: 11. Mar 2008.
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Identification by 2-D DIGE of apoplastic proteins regulated by oligogalacturonides in Arabidopsis thaliana. Casasoli, M.; Spadoni, S.; Lilley, K. S.; Cervone, F.; De Lorenzo, G.; and Mattei, B. Proteomics, 8(5): 1042–1054. Mar 2008.
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Optimizing the difference gel electrophoresis (DIGE) technology. Friedman, D. B.; and Lilley, K. S. Methods Mol Biol, 428: 93–124. 2008.
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Comparison of DIGE and post-stained gel electrophoresis with both traditional and SameSpots analysis for quantitative proteomics. Karp, N. A.; Feret, R.; Rubtsov, D. V.; and Lilley, K. S. Proteomics, 8(5): 948–960. Mar 2008.
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Identification of internal ribosome entry segment (IRES)-trans-acting factors for the Myc family of IRESs. Cobbold, L. C.; Spriggs, K. A.; Haines, S. J.; Dobbyn, H. C.; Hayes, C.; de Moor, C. H.; Lilley, K. S.; Bushell, M.; and Willis, A. E. Mol Cell Biol, 28(1): 40–49. Jan 2008.
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  2007 (15)
Plant organelle proteomics. Lilley, K. S.; and Dupree, P. Curr Opin Plant Biol, 10(6): 594–599. Dec 2007.
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Design and analysis issues in quantitative proteomics studies. Karp, N. A.; and Lilley, K. S. Proteomics, 7 Suppl 1: 42–50. Sep 2007.
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Virulence and prodigiosin antibiotic biosynthesis in Serratia are regulated pleiotropically by the GGDEF/EAL domain protein, PigX. Fineran, P. C.; Williamson, N. R.; Lilley, K. S.; and Salmond, G. P. J Bacteriol, 189(21): 7653–7662. Nov 2007.
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The minimum information about a proteomics experiment (MIAPE). Taylor, C. F.; Paton, N. W.; Lilley, K. S.; Binz, P. A.; Julian, R. K.; Jones, A. R.; Zhu, W.; Apweiler, R.; Aebersold, R.; Deutsch, E. W.; Dunn, M. J.; Heck, A. J.; Leitner, A.; Macht, M.; Mann, M.; Martens, L.; Neubert, T. A.; Patterson, S. D.; Ping, P.; Seymour, S. L.; Souda, P.; Tsugita, A.; Vandekerckhove, J.; Vondriska, T. M.; Whitelegge, J. P.; Wilkins, M. R.; Xenarios, I.; Yates, J. R.; and Hermjakob, H. Nat Biotechnol, 25(8): 887–893. Aug 2007.
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Recruitment of Polo kinase to the spindle midzone during cytokinesis requires the Feo/Klp3A complex. D'Avino, P. P.; Archambault, V.; Przewloka, M. R.; Zhang, W.; Lilley, K. S.; Laue, E.; and Glover, D. M. PLoS One, 2(6): e572. Jun 2007.
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Glucocorticoid signaling synchronizes the liver circadian transcriptome. Reddy, A. B.; Maywood, E. S.; Karp, N. A.; King, V. M.; Inoue, Y.; Gonzalez, F. J.; Lilley, K. S.; Kyriacou, C. P.; and Hastings, M. H. Hepatology, 45(6): 1478–1488. Jun 2007.
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Molecular analysis of core kinetochore composition and assembly in Drosophila melanogaster. Przewloka, M. R.; Zhang, W.; Costa, P.; Archambault, V.; D'Avino, P. P.; Lilley, K. S.; Laue, E. D.; McAinsh, A. D.; and Glover, D. M. PLoS One, 2(5): e478. May 2007.
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Detection of reactive oxygen species-sensitive thiol proteins by redox difference gel electrophoresis: implications for mitochondrial redox signaling. Hurd, T. R.; Prime, T. A.; Harbour, M. E.; Lilley, K. S.; and Murphy, M. P. J Biol Chem, 282(30): 22040–22051. Jul 2007.
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The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 study: relative protein quantitation. Turck, C. W.; Falick, A. M.; Kowalak, J. A.; Lane, W. S.; Lilley, K. S.; Phinney, B. S.; Weintraub, S. T.; Witkowska, H. E.; and Yates, N. A. Mol Cell Proteomics, 6(8): 1291–1298. Aug 2007.
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Experimental and statistical considerations to avoid false conclusions in proteomics studies using differential in-gel electrophoresis. Karp, N. A.; McCormick, P. S.; Russell, M. R.; and Lilley, K. S. Mol Cell Proteomics, 6(8): 1354–1364. Aug 2007.
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Growth control of the eukaryote cell: a systems biology study in yeast. Castrillo, J. I.; Zeef, L. A.; Hoyle, D. C.; Zhang, N.; Hayes, A.; Gardner, D. C.; Cornell, M. J.; Petty, J.; Hakes, L.; Wardleworth, L.; Rash, B.; Brown, M.; Dunn, W. B.; Broadhurst, D.; O'Donoghue, K.; Hester, S. S.; Dunkley, T. P.; Hart, S. R.; Swainston, N.; Li, P.; Gaskell, S. J.; Paton, N. W.; Lilley, K. S.; Kell, D. B.; and Oliver, S. G. J Biol, 6(2): 4. 2007.
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Identification of clock genes using difference gel electrophoresis. Karp, N. A.; and Lilley, K. S. Methods Mol Biol, 362: 265–287. 2007.
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Proteomic complex detection using sedimentation. Hartman, N. T.; Sicilia, F.; Lilley, K. S.; and Dupree, P. Anal Chem, 79(5): 2078–2083. Mar 2007.
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Interrelationships between colonies, biofilms, and planktonic cells of Pseudomonas aeruginosa. Mikkelsen, H.; Duck, Z.; Lilley, K. S.; and Welch, M. J Bacteriol, 189(6): 2411–2416. Mar 2007.
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Comparative proteomic analysis reveals differential expression of Hsp25 following the directed differentiation of mouse embryonic stem cells. Battersby, A.; Jones, R. D.; Lilley, K. S.; McFarlane, R. J.; Braig, H. R.; Allen, N. D.; and Wakeman, J. A. Biochim Biophys Acta, 1773(2): 147–156. Feb 2007.
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  2006 (12)
Quantitative proteomic approach to study subcellular localization of membrane proteins. Sadowski, P. G.; Dunkley, T. P.; Shadforth, I. P.; Dupree, P.; Bessant, C.; Griffin, J. L.; and Lilley, K. S. Nat Protoc, 1(4): 1778–1789. 2006.
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Comparative proteomics of clathrin-coated vesicles. Borner, G. H.; Harbour, M.; Hester, S.; Lilley, K. S.; and Robinson, M. S. J Cell Biol, 175(4): 571–578. Nov 2006.
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Plant endoplasmin supports the protein secretory pathway and has a role in proliferating tissues. Klein, E. M.; Mascheroni, L.; Pompa, A.; Ragni, L.; Weimar, T.; Lilley, K. S.; Dupree, P.; and Vitale, A. Plant J, 48(5): 657–673. Dec 2006.
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Difference gel electrophoresis DIGE. Lilley, K. S.; and Friedman, D. B. Drug Discov Today Technol, 3(3): 347–353. 2006.
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The tip-link antigen, a protein associated with the transduction complex of sensory hair cells, is protocadherin-15. Ahmed, Z. M.; Goodyear, R.; Riazuddin, S.; Lagziel, A.; Legan, P. K.; Behra, M.; Burgess, S. M.; Lilley, K. S.; Wilcox, E. R.; Riazuddin, S.; Griffith, A. J.; Frolenkov, G. I.; Belyantseva, I. A.; Richardson, G. P.; and Friedman, T. B. J Neurosci, 26(26): 7022–7034. Jun 2006.
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Circadian orchestration of the hepatic proteome. Reddy, A. B.; Karp, N. A.; Maywood, E. S.; Sage, E. A.; Deery, M.; O'Neill, J. S.; Wong, G. K.; Chesham, J.; Odell, M.; Lilley, K. S.; Kyriacou, C. P.; and Hastings, M. H. Curr Biol, 16(11): 1107–1115. Jun 2006.
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The ABRF MARG microarray survey 2005: taking the pulse of the microarray field. Knudtson, K. L.; Auer, H.; Brooks, A. I.; Griffin, C.; Grills, G.; Hester, S.; Khitrov, G.; Lilley, K. S.; Massimi, A.; Tiesman, J. P.; and Viale, A. J Biomol Tech, 17(2): 176–186. Apr 2006.
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Differential gel electrophoresis and transgenic mitochondrial calcium reporters demonstrate spatiotemporal filtering in calcium control of mitochondria. Terhzaz, S.; Southall, T. D.; Lilley, K. S.; Kean, L.; Allan, A. K.; Davies, S. A.; and Dow, J. A. J Biol Chem, 281(27): 18849–18858. Jul 2006.
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Mapping the Arabidopsis organelle proteome. Dunkley, T. P.; Hester, S.; Shadforth, I. P.; Runions, J.; Weimar, T.; Hanton, S. L.; Griffin, J. L.; Bessant, C.; Brandizzi, F.; Hawes, C.; Watson, R. B.; Dupree, P.; and Lilley, K. S. Proc Natl Acad Sci U S A, 103(17): 6518–6523. Apr 2006.
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Methods of quantitative proteomics and their application to plant organelle characterization. Lilley, K. S.; and Dupree, P. J Exp Bot, 57(7): 1493–1499. 2006.
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TNP-8N3-ADP photoaffinity labeling of two Na,K-ATPase sequences under separate Na+ plus K+ control. Ward, D. G.; Taylor, M.; Lilley, K. S.; and Cavieres, J. D. Biochemistry, 45(10): 3460–3471. Mar 2006.
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Genetic and proteomic analysis of the role of luxS in the enteric phytopathogen, Erwinia carotovora. Coulthurst, S. J.; Lilley, K. S.; and Salmond, G. P. Mol Plant Pathol, 7(1): 31–45. Jan 2006.
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  2005 (5)
i-Tracker: for quantitative proteomics using iTRAQ. Shadforth, I. P.; Dunkley, T. P.; Lilley, K. S.; and Bessant, C. BMC Genomics, 6: 145. Oct 2005.
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Impact of replicate types on proteomic expression analysis. Karp, N. A.; Spencer, M.; Lindsay, H.; O'Dell, K.; and Lilley, K. S. J Proteome Res, 4(5): 1867–1871. 2005.
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Maximising sensitivity for detecting changes in protein expression: experimental design using minimal CyDyes. Karp, N. A.; and Lilley, K. S. Proteomics, 5(12): 3105–3115. Aug 2005.
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Application of partial least squares discriminant analysis to two-dimensional difference gel studies in expression proteomics. Karp, N. A.; Griffin, J. L.; and Lilley, K. S. Proteomics, 5(1): 81–90. Jan 2005.
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Analysis of detergent-resistant membranes in Arabidopsis. Evidence for plasma membrane lipid rafts. Borner, G. H.; Sherrier, D. J.; Weimar, T.; Michaelson, L. V.; Hawkins, N. D.; Macaskill, A.; Napier, J. A.; Beale, M. H.; Lilley, K. S.; and Dupree, P. Plant Physiol, 137(1): 104–116. Jan 2005.
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  2004 (9)
All about DIGE: quantification technology for differential-display 2D-gel proteomics. Lilley, K. S.; and Friedman, D. B. Expert Rev Proteomics, 1(4): 401–409. Dec 2004.
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PEDRo: a database for storing, searching and disseminating experimental proteomics data. Garwood, K.; McLaughlin, T.; Garwood, C.; Joens, S.; Morrison, N.; Taylor, C. F.; Carroll, K.; Evans, C.; Whetton, A. D.; Hart, S.; Stead, D.; Yin, Z.; Brown, A. J.; Hesketh, A.; Chater, K.; Hansson, L.; Mewissen, M.; Ghazal, P.; Howard, J.; Lilley, K. S.; Gaskell, S. J.; Brass, A.; Hubbard, S. J.; Oliver, S. G.; and Paton, N. W. BMC Genomics, 5: 68. Sep 2004.
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Localization of organelle proteins by isotope tagging (LOPIT). Dunkley, T. P.; Watson, R.; Griffin, J. L.; Dupree, P.; and Lilley, K. S. Mol Cell Proteomics, 3(11): 1128–1134. Nov 2004.
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Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis. Karp, N. A.; Kreil, D. P.; and Lilley, K. S. Proteomics, 4(5): 1421–1432. May 2004.
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The use of isotope-coded affinity tags (ICAT) to study organelle proteomes in Arabidopsis thaliana. Dunkley, T. P.; Dupree, P.; Watson, R. B.; and Lilley, K. S. Biochem Soc Trans, 32(Pt3): 520–523. Jun 2004.
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Mitochondrial dysfunction in schizophrenia: evidence for compromised brain metabolism and oxidative stress. Prabakaran, S.; Swatton, J. E.; Ryan, M. M.; Huffaker, S. J.; Huang, J. T.; Griffin, J. L.; Wayland, M.; Freeman, T.; Dudbridge, F.; Lilley, K. S.; Karp, N. A.; Hester, S.; Tkachev, D.; Mimmack, M. L.; Yolken, R. H.; Webster, M. J.; Torrey, E. F.; and Bahn, S. Mol Psychiatry, 9(7): 684–697. Jul 2004.
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DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results. Kreil, D. P.; Karp, N. A.; and Lilley, K. S. Bioinformatics, 20(13): 2026–2034. Sep 2004.
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Protein profiling of human postmortem brain using 2-dimensional fluorescence difference gel electrophoresis (2-D DIGE). Swatton, J. E.; Prabakaran, S.; Karp, N. A.; Lilley, K. S.; and Bahn, S. Mol Psychiatry, 9(2): 128–143. Feb 2004.
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SETH1 and SETH2, two components of the glycosylphosphatidylinositol anchor biosynthetic pathway, are required for pollen germination and tube growth in Arabidopsis. Lalanne, E.; Honys, D.; Johnson, A.; Borner, G. H.; Lilley, K. S.; Dupree, P.; Grossniklaus, U.; and Twell, D. Plant Cell, 16(1): 229–240. Jan 2004.
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  2003 (6)
Protein profiling using two-dimensional difference gel electrophoresis (2-D DIGE). Lilley, K. S. Curr Protoc Protein Sci, Chapter 22: Unit 22.2. Feb 2003.
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Proteomics in Drosophila melanogaster. Lilley, K. S.; and Griffiths, D. R. Brief Funct Genomic Proteomic, 2(2): 106–113. Jul 2003.
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Ubiquitination of alpha-synuclein in Lewy bodies is a pathological event not associated with impairment of proteasome function. Tofaris, G. K.; Razzaq, A.; Ghetti, B.; Lilley, K. S.; and Spillantini, M. G. J Biol Chem, 278(45): 44405–44411. Nov 2003.
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Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis. Borner, G. H.; Lilley, K. S.; Stevens, T. J.; and Dupree, P. Plant Physiol, 132(2): 568–577. Jun 2003.
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A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Taylor, C. F.; Paton, N. W.; Garwood, K. L.; Kirby, P. D.; Stead, D. A.; Yin, Z.; Deutsch, E. W.; Selway, L.; Walker, J.; Riba-Garcia, I.; Mohammed, S.; Deery, M. J.; Howard, J. A.; Dunkley, T.; Aebersold, R.; Kell, D. B.; Lilley, K. S.; Roepstorff, P.; Yates, J. R.; Brass, A.; Brown, A. J.; Cash, P.; Gaskell, S. J.; Hubbard, S. J.; and Oliver, S. G. Nat Biotechnol, 21(3): 247–254. Mar 2003.
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Characterization of the necrotic protein that regulates the Toll-mediated immune response in Drosophila. Robertson, A. S.; Belorgey, D.; Lilley, K. S.; Lomas, D. A.; Gubb, D.; and Dafforn, T. R. J Biol Chem, 278(8): 6175–6180. Feb 2003.
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  2002 (1)
Two-dimensional gel electrophoresis: recent advances in sample preparation, detection and quantitation. Lilley, K. S.; Razzaq, A.; and Dupree, P. Curr Opin Chem Biol, 6(1): 46–50. Feb 2002.
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  2001 (1)
Phosphorylation of elongation factor-2 kinase on serine 499 by cAMP-dependent protein kinase induces Ca2+/calmodulin-independent activity. Diggle, T. A.; Subkhankulova, T.; Lilley, K. S.; Shikotra, N.; Willis, A. E.; and Redpath, N. T. Biochem J, 353(Pt 3): 621–626. Feb 2001.
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  1999 (1)
Survey of current trends in DNA synthesis core facilities. Hager, K. M.; Fox, J. W.; Gunthorpe, M.; Lilley, K. S.; and Yeung, A. J Biomol Tech, 10(4): 187–193. Dec 1999.
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  1996 (1)
Mutational spectra of tamoxifen-induced mutations in the livers of lacI transgenic rats. Davies, R.; Oreffo, V. I.; Bayliss, S.; Dinh, P. A.; Lilley, K. S.; White, I. N.; Smith, L. L.; and Styles, J. A. Environ Mol Mutagen, 28(4): 430–433. 1996.
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  1992 (4)
The essential active-site lysines of clostridial glutamate dehydrogenase. A study with pyridoxal-5'-phosphate. Lilley, K. S.; and Engel, P. C. Eur J Biochem, 207(2): 533–540. Jul 1992.
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GroEL proteins from three Pseudomonas species. Fowell, S. L.; Lilley, K. S.; Jones, D.; and Maxwell, A. Mol Microbiol, 6(11): 1575–1576. Jun 1992.
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Subunit assembly and active site location in the structure of glutamate dehydrogenase. Baker, P. J.; Britton, K. L.; Engel, P. C.; Farrants, G. W.; Lilley, K. S.; Rice, D. W.; and Stillman, T. J. Proteins, 12(1): 75–86. Jan 1992.
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Characterization of a kallidin receptor in the eel intestine. Cougnon, N.; Deacon, C. F.; Lilley, K. S.; and Henderson, I. W. Agents Actions Suppl, 38 ( Pt 2): 382–389. 1992.
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  1991 (1)
The partial amino acid sequence of the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum: implications for the evolution and structural basis of coenzyme specificity. Lilley, K. S.; Baker, P. J.; Britton, K. L.; Stillman, T. J.; Brown, P. E.; Moir, A. J.; Engel, P. C.; Rice, D. W.; Bell, J. E.; and Bell, E. Biochim Biophys Acta, 1080(3): 191–197. Nov 1991.
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  1990 (1)
N-terminal sequence similarities between components of the multicatalytic proteinase complex. Lilley, K. S.; Davison, M. D.; and Rivett, A. J. FEBS Lett, 262(2): 327–329. Mar 1990.
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  1989 (1)
Release of iron from ferritin molecules and their iron-cores by 3-hydroxypyridinone chelators in vitro. Brady, M. C.; Lilley, K. S.; Treffry, A.; Harrison, P. M.; Hider, R. C.; and Taylor, P. D. J Inorg Biochem, 35(1): 9–22. Jan 1989.
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