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  2023 (3)
The proteomic landscape of genome-wide genetic perturbations. Messner, C. B.; Demichev, V.; Muenzner, J.; Aulakh, S. K.; Barthel, N.; hl , A.; nguez , L.; Egger, A. S.; Kamrad, S.; Hou, J.; Tan, G.; Lemke, O.; Calvani, E.; Szyrwiel, L.; lleder , M.; Lilley, K. S.; Boone, C.; Kustatscher, G.; and Ralser, M. Cell. Apr 2023.
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Cryptosporidium uses multiple distinct secretory organelles to interact with and modify its host cell. rin , A.; Strelau, K. M.; Barylyuk, K.; Wallbank, B. A.; Berry, L.; Crook, O. M.; Lilley, K. S.; Waller, R. F.; and Striepen, B. Cell Host Microbe, 31(4): 650–664. Apr 2023.
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-transcribed RNA therapeutics. von der Haar, T.; Mulroney, T. E.; Hedayioglu, F.; Kurusamy, S.; Rust, M.; Lilley, K. S.; Thaventhiran, J. E.; Willis, A. E.; and Smales, C. M. Front Mol Biosci, 10: 1128067. 2023.
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  2022 (13)
Semi-Supervised Non-Parametric Bayesian Modelling of Spatial Proteomics. Crook, O. M.; Lilley, K. S.; Gatto, L.; and Kirk, P. D. W. Ann Appl Stat, 16(4). Dec 2022.
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Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE. Crook, O. M.; Davies, C. T. R.; Breckels, L. M.; Christopher, J. A.; Gatto, L.; Kirk, P. D. W.; and Lilley, K. S. Nat Commun, 13(1): 5948. Oct 2022.
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Operation of a TCA cycle subnetwork in the mammalian nucleus. Kafkia, E.; Andres-Pons, A.; Ganter, K.; Seiler, M.; Smith, T. S.; Andrejeva, A.; Jouhten, P.; Pereira, F.; Franco, C.; Kuroshchenkova, A.; Leone, S.; Sawarkar, R.; Boston, R.; Thaventhiran, J.; Zaugg, J. B.; Lilley, K. S.; Lancrin, C.; Beck, M.; and Patil, K. R. Sci Adv, 8(35): eabq5206. Sep 2022.
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dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts. Demichev, V.; Szyrwiel, L.; Yu, F.; Teo, G. C.; Rosenberger, G.; Niewienda, A.; Ludwig, D.; Decker, J.; Kaspar-Schoenefeld, S.; Lilley, K. S.; lleder , M.; Nesvizhskii, A. I.; and Ralser, M. Nat Commun, 13(1): 3944. Jul 2022.
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CFTR Rescue by Lumacaftor (VX-809) Induces an Extensive Reorganization of Mitochondria in the Cystic Fibrosis Bronchial Epithelium. Braccia, C.; Christopher, J. A.; Crook, O. M.; Breckels, L. M.; Queiroz, R. M. L.; Liessi, N.; Tomati, V.; Capurro, V.; Bandiera, T.; Baldassari, S.; Pedemonte, N.; Lilley, K. S.; and Armirotti, A. Cells, 11(12). Jun 2022.
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Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments. Smith, T. S.; Andrejeva, A.; Christopher, J.; Crook, O. M.; Elzek, M.; and Lilley, K. S. ACS Meas Sci Au, 2(3): 233–240. Jun 2022.
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. Fabre, B.; Choteau, S. A.; é, C.; Pichereaux, C.; Montigny, A.; Korona, D.; Deery, M. J.; Camus, M.; Brun, C.; Burlet-Schiltz, O.; Russell, S.; Combier, J. P.; Lilley, K. S.; and Plaza, S. Front Cell Dev Biol, 10: 901351. 2022.
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nicotinic acetylcholine receptor subunits and their native interactions with insecticidal peptide toxins. Korona, D.; Dirnberger, B.; Giachello, C. N. G.; Queiroz, R. M. L.; Popovic, R.; ller , K. H.; Minde, D. P.; Deery, M. J.; Johnson, G.; Firth, L. C.; Earley, F. G.; Russell, S.; and Lilley, K. S. Elife, 11. May 2022.
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Understudied proteins: opportunities and challenges for functional proteomics. Kustatscher, G.; Collins, T.; Gingras, A. C.; Guo, T.; Hermjakob, H.; Ideker, T.; Lilley, K. S.; Lundberg, E.; Marcotte, E. M.; Ralser, M.; and Rappsilber, J. Nat Methods, 19(7): 774–779. Jul 2022.
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An open invitation to the Understudied Proteins Initiative. Kustatscher, G.; Collins, T.; Gingras, A. C.; Guo, T.; Hermjakob, H.; Ideker, T.; Lilley, K. S.; Lundberg, E.; Marcotte, E. M.; Ralser, M.; and Rappsilber, J. Nat Biotechnol, 40(6): 815–817. Jun 2022.
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Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress. Stoneley, M.; Harvey, R. F.; Mulroney, T. E.; Mordue, R.; Jukes-Jones, R.; Cain, K.; Lilley, K. S.; Sawarkar, R.; and Willis, A. E. Mol Cell, 82(8): 1557–1572. Apr 2022.
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Proteomic analysis in primary T cells reveals IL-7 alters T cell receptor thresholding via CYTIP/cytohesin/LFA-1 localisation and activation. Queiroz, R. M. L.; Piper, S. C.; Rees, J. S.; Strickson, S.; Briend, E.; Low, C. P.; Ferguson, G. J.; Lilley, K. S.; Jackson, A. P.; and Finch, D. K. Biochem J, 479(3): 225–243. Feb 2022.
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Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. Christopher, J. A.; Geladaki, A.; Dawson, C. S.; Vennard, O. L.; and Lilley, K. S. Mol Cell Proteomics, 21(2): 100186. Feb 2022.
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  2021 (7)
Localization of Organelle Proteins by Isotope Tagging: Current status and potential applications in drug discovery research. Elzek, M. A. W.; Christopher, J. A.; Breckels, L. M.; and Lilley, K. S. Drug Discov Today Technol, 39: 57–67. Dec 2021.
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Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line. Mulvey, C. M.; Breckels, L. M.; Crook, O. M.; Sanders, D. J.; Ribeiro, A. L. R.; Geladaki, A.; Christoforou, A.; ek , N. K.; Hurrell, T.; Deery, M. J.; Gatto, L.; Smith, A. M.; and Lilley, K. S. Nat Commun, 12(1): 5773. Oct 2021.
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Subcellular proteomics. Christopher, J. A.; Stadler, C.; Martin, C. E.; Morgenstern, M.; Pan, Y.; Betsinger, C. N.; Rattray, D. G.; Mahdessian, D.; Gingras, A. C.; Warscheid, B.; ö, J.; Cristea, I. M.; Foster, L. J.; Emili, A.; and Lilley, K. S. Nat Rev Methods Primers, 1. 2021.
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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. Jun 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.; rvelin , 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. Jul 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.; rgens , L.; Suttorp, N.; Sander, L. E.; Kurth, F.; Lilley, K. S.; lleder , M.; Tate, S.; and Ralser, M. Nat Biotechnol, 39(7): 846–854. Jul 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.; á, J.; Peak-Chew, S. Y.; Breckels, L. M.; Gillingham, A. K.; Chadwick, J.; Lilley, K. S.; and Munro, S. Nat Commun, 11(1): 5987. Nov 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. Nov 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. Nov 2020.
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Correction: Proteomics of intracellular freezing survival. Thorne, M. A. S.; ek , 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. Aug 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.; lleder , M.; Drosten, C.; Suttorp, N.; Witzenrath, M.; Kurth, F.; Sander, L. E.; and Ralser, M. Cell Syst, 11(1): 11–24. Jul 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. Dec 2020.
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Proteomics of intracellular freezing survival. Thorne, M. A. S.; ek , 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. Aug 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). Apr 2020.
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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. Feb 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. Jan 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. Jan 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. Dec 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. Sep 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. Jun 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. Jun 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. Mar 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. Feb 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). Mar 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. Feb 2019.
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Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Geladaki, A.; ek , 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. Jan 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. Feb 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. Feb 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.; o , P.; Cimini, S.; Patel, B.; ö, 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. Nov 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 ï, 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. eiro , 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. Nov 2018.
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ve pluripotency. Nett, I. R.; Mulas, C.; Gatto, L.; Lilley, K. S.; and Smith, A. EMBO Rep, 19(8). Aug 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). Jul 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. Jul 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. Jun 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. Mar 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. May 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. May 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. Aug 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.; ï, 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). Sep 2017.
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A subcellular map of the human proteome. Thul, P. J.; kesson , L.; Wiking, M.; Mahdessian, D.; Geladaki, A.; Ait Blal, H.; Alm, T.; Asplund, A.; rk , L.; Breckels, L. M.; m , 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.; stedt , E.; Skogs, M.; Stadler, C.; Sullivan, D. P.; Tegel, H.; Winsnes, C.; Zhang, C.; Zwahlen, M.; Mardinoglu, A.; n , F.; von Feilitzen, K.; Lilley, K. S.; n , M.; and Lundberg, E. Science, 356(6340). May 2017.
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Using hyperLOPIT to perform high-resolution mapping of the spatial proteome. Mulvey, C. M.; Breckels, L. M.; Geladaki, A.; ek , 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. Apr 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. Apr 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). Apr 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 ï, B. M. Proteomics, 17(1-2). Jan 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.; lleder , M.; Shliaha, P.; Schwarz, R.; Capuano, F.; Vowinckel, J.; Radmanesfahar, E.; ger , A.; Calvani, E.; Michel, S.; rno , 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. Oct 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. Jul 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. May 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. Aug 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. oz-Bernal , E.; Deery, M. J.; guez , M. E.; Cantoral, J. M.; Howard, J.; Feret, R.; Natera, R.; Lilley, K. S.; and ndez-Acero , F. J. Proteomics, 16(4): 576–592. Feb 2016.
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cDNA Microarray and Proteomic Analysis. Quintela, T.; Marcelino, H.; Deery, M. J.; Feret, R.; Howard, J.; Lilley, K. S.; Albuquerque, T.; alves , 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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-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.; ter , 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.; re , 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.; no , 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.; sser , 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. zesi-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.; s , 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.; yry , 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(1): 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.; é, 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.; è, 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.; no , 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.; è, 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 ï, 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.; dek , 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 ï, 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.