Kathryn Lilley Publications

Roy D, Mehra P, Clark L, Mukkawar V, Bellande K, Martin-Arevalillo R, Ghosh S, Ingole KD, Bhagat PK, Brown A, Sue-Ob K, Jones A, Vermeer JEM, Vernoux T, Lilley KS, Mullineaux P, Bechtold U, Bennett MJ, Sadanandom Redox-regulated Aux/IAA multimerization modulates auxin responses. Science. 2025 Jul 17;389(6757):eadu1470. doi: 10.1126/science.adu1470. Epub 2025 Jul 17.

 Ingole KD, Alekseeva E, Lilley KS, Sadanandom A. Recent advances in proteomic workflows to interrogate the SUMOylome in plants. New Phytol. 2025 Jul;247(1):90-96. doi: 10.1111/nph.70176. Epub 2025 May 6.

 Zhang F, Tang Y, Zhou H, Li K, West JA, Griffin JL, Lilley KS, Zhang N. The Yeast Gsk-3 Kinase Mck1 Is Necessary for Cell Wall Remodeling in Glucose-Starved and Cell Wall-Stressed Cells. Int J Mol Sci. 2025 Apr 9;26(8):3534. doi: 10.3390/ijms26083534.

Christopher JA, Breckels LM, Crook OM, Vazquez-Chantada M, Barratt D, Lilley KS. Global Proteomics Indicates Subcellular-Specific Anti-Ferroptotic Responses to Ionizing Radiation. Mol Cell Proteomics. 2025 Jan;24(1):100888. doi:10.1016/j.mcpro.2024.100888. Epub 2024 Nov 29. PMID: 39617061; PMCID:PMC11780130.

Breckels LM, Hutchings C, Ingole KD, Kim S, Lilley KS, Makwana MV, McCaskie KJA, Villanueva E. Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations. Cell Chem Biol. 2024 Sep 19;31(9):1665-1687. doi: 10.1016/j.chembiol.2024.08.008. PMID: 39303701.

Monti M, Herman R, Mancini L, Capitanchik C, Davey K, Dawson CS, Ule J, Thomas GH, Willis AE, Lilley KS, Villanueva E. Interrogation of RNA-protein interaction dynamics in bacterial growth. Mol Syst Biol. 2024 May;20(5):573-589. doi: 10.1038/s44320-024-00031-y. Epub 2024 Mar 26. PMID: 38531971; PMCID: PMC11066096.

Mulroney TE, Pöyry T, Yam-Puc JC, Rust M, Harvey RF, Kalmar L, Horner E, Booth L, Ferreira AP, Stoneley M, Sawarkar R, Mentzer AJ, Lilley KS, Smales CM, von der Haar T, Turtle L, Dunachie S, Klenerman P, Thaventhiran JED, Willis AE. N¹-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting. Nature. 2024 Jan;625(7993):189-194. doi: 10.1038/s41586-023-06800-3. Epub 2023 Dec 6. PMID: 38057663; PMCID: PMC10764286.

Villanueva E, Smith T, Pizzinga M, Elzek M, Queiroz RML, Harvey RF, Breckels LM, Crook OM, Monti M, Dezi V, Willis AE, Lilley KS. System-wide analysis of RNA and protein subcellular localization dynamics. Nat Methods. 2024 Jan;21(1):60-71. doi: 10.1038/s41592-023-02101-9. Epub 2023 Nov 30. PMID: 38036857; PMCID: PMC10776395.

Hutchings C, Dawson CS, Krueger T, Lilley KS, Breckels LM. A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data. F1000Res. 2023 Oct 24;12:1402. doi: 10.12688/f1000research.139116.1. PMID: 38021401; PMCID: PMC10683783.

Baldrighi M, Doreth C, Li Y, Zhao X, Warner E, Chenoweth H, Kishore K, Umrania Y, Minde DP, Thome S, Yu X, Lu Y, Knapton A, Harrison J, Clarke M, Latz E, de Cárcer G, Malumbres M, Ryffel B, Bryant C, Liu J, Lilley KS, Mallat Z, Li X. PLK1 inhibition dampens NLRP3 inflammasome-elicited response in inflammatorydisease models. J Clin Invest. 2023 Nov 1;133(21):e162129. doi: 10.1172/JCI162129. PMID: 37698938; PMCID: PMC10617773.

Dirnberger B, Korona D, Popovic R, Deery MJ, Barber H, Russell S, Lilley KS. Enrichment of Membrane Proteins for Downstream Analysis Using Styrene Maleic Acid Lipid Particles (SMALPs) Extraction. Bio Protoc. 2023 Aug 5;13(15):e4728. doi: 10.21769/BioProtoc.4728. PMID: 37575399; PMCID: PMC10415199.

Beale AD, Hayter EA, Crosby P, Valekunja UK, Edgar RS, Chesham JE, Maywood ES, Labeed FH, Reddy AB, Wright KP Jr, Lilley KS, Bechtold DA, Hastings MH, O'Neill JS. Mechanisms and physiological function of daily haemoglobin oxidation rhythms in red blood cells. EMBO J. 2023 Oct 4;42(19):e114164. doi: 10.15252/embj.2023114164. Epub 2023 Aug 9. PMID: 37554073; PMCID: PMC10548169.

Moloney NM, Barylyuk K, Tromer E, Crook OM, Breckels LM, Lilley KS, Waller RF, MacGregor P. Mapping diversity in African trypanosomes using high resolution spatial proteomics. Nat Commun. 2023 Jul 21;14(1):4401. doi: 10.1038/s41467-023-40125-z. PMID: 37479728; PMCID: PMC10361982.

Hines AR, Edgeworth M, Devine PWA, Shepherd S, Chatterton N, Turner C, Lilley KS, Chen X, Bond NJ. Multi-Attribute Monitoring Method for Process Development of Engineered Antibody for Site-Specific Conjugation. J Am Soc Mass Spectrom. 2023 Jul 5;34(7):1330-1341. doi: 10.1021/jasms.3c00037. Epub 2023 Jun 2. PMID: 37265400; PMCID: PMC10326913.

Messner CB, Demichev V, Muenzner J, Aulakh SK, Barthel N, Röhl A, Herrera- Domínguez L, Egger AS, Kamrad S, Hou J, Tan G, Lemke O, Calvani E, Szyrwiel L, Mülleder M, Lilley KS, Boone C, Kustatscher G, Ralser M. The proteomic landscape of genome-wide genetic perturbations. Cell. 2023 Apr 27;186(9):2018-2034.e21. doi: 10.1016/j.cell.2023.03.026. Epub 2023 Apr 19. PMID: 37080200; PMCID: PMC7615649.

Guérin A, Strelau KM, Barylyuk K, Wallbank BA, Berry L, Crook OM, Lilley KS, Waller RF, Striepen B. Cryptosporidium uses multiple distinct secretory organelles to interact with and modify its host cell. Cell Host Microbe. 2023 Apr 12;31(4):650-664.e6. doi: 10.1016/j.chom.2023.03.001. Epub 2023 Mar 22. PMID: 36958336.

von der Haar T, Mulroney TE, Hedayioglu F, Kurusamy S, Rust M, Lilley KS, Thaventhiran JE, Willis AE, Smales CM. Translation of in vitro-transcribed RNA therapeutics. Front Mol Biosci. 2023 Feb 8;10:1128067. doi: 10.3389/fmolb.2023.1128067. PMID: 36845540; PMCID: PMC9943971.

Demichev V, Tober-Lau P, Nazarenko T, Lemke O, Kaur Aulakh S, Whitwell HJ, Röhl A, Freiwald A, Mittermaier M, Szyrwiel L, Ludwig D, Correia-Melo C, Lippert LJ, Helbig ET, Stubbemann P, Olk N, Thibeault C, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, PfeifferM, Jürgens L, Denker S, Zickler D, Spies C, Edel A, Müller NB, Enghard P, Zelezniak A, Bellmann-Weiler R, Weiss G, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Müller-Redetzky H, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE; PA-COVID-19 Study group; Kurth F, Ralser M. A proteomic survival predictor for COVID-19 patients in intensive care. PLOS Digit Health. 2022 Jan 18;1(1):e0000007. doi: 10.1371/journal.pdig.0000007. PMID: 36812516; PMCID: PMC9931303.

Crook OM, Lilley KS, Gatto L, Kirk PDW. Semi-Supervised Non-Parametric Bayesian Modelling of Spatial Proteomics. Ann Appl Stat. 2022 Dec 1;16(4):22-aoas1603. doi: 10.1214/22-AOAS1603. PMID: 36507469; PMCID: PMC7613899.

Crook OM, Davies CTR, Breckels LM, Christopher JA, Gatto L, Kirk PDW, Lilley KS. Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE. Nat Commun. 2022 Oct 10;13(1):5948. doi: 10.1038/s41467-022-33570-9. PMID: 36216816; PMCID: PMC9550814.

Kafkia E, Andres-Pons A, Ganter K, Seiler M, Smith TS, Andrejeva A, Jouhten P, Pereira F, Franco C, Kuroshchenkova A, Leone S, Sawarkar R, Boston R, Thaventhiran J, Zaugg JB, Lilley KS, Lancrin C, Beck M, Patil KR. Operation of a TCA cycle subnetwork in the mammalian nucleus. Sci Adv. 2022 Sep 2;8(35):eabq5206. doi: 10.1126/sciadv.abq5206. Epub 2022 Aug 31. PMID: 36044572; PMCID: PMC9432838.

Demichev V, Szyrwiel L, Yu F, Teo GC, Rosenberger G, Niewienda A, Ludwig D, Decker J, Kaspar-Schoenefeld S, Lilley KS, Mülleder M, Nesvizhskii AI, Ralser M. dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts. Nat Commun. 2022 Jul 8;13(1):3944. doi: 10.1038/s41467-022-31492-0. PMID: 35803928; PMCID: PMC9270362.

Braccia C, Christopher JA, Crook OM, Breckels LM, Queiroz RML, Liessi N, Tomati V, Capurro V, Bandiera T, Baldassari S, Pedemonte N, Lilley KS, ArmirottiA. CFTR Rescue by Lumacaftor (VX-809) Induces an Extensive Reorganization of Mitochondria in the Cystic Fibrosis Bronchial Epithelium. Cells. 2022 Jun 16;11(12):1938. doi: 10.3390/cells11121938. PMID: 35741067; PMCID: PMC9222197.

Smith TS, Andrejeva A, Christopher J, Crook OM, Elzek M, Lilley KS. Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments. ACS Meas Sci Au. 2022 Jun 15;2(3):233-240. doi: 10.1021/acsmeasuresciau.1c00053. Epub 2022 Mar 9. PMID: 35726249; PMCID: PMC9204819.

Fabre B, Choteau SA, Duboé C, Pichereaux C, Montigny A, Korona D, Deery MJ, Camus M, Brun C, Burlet-Schiltz O, Russell S, Combier JP, Lilley KS, Plaza S. In Depth Exploration of the Alternative Proteome of Drosophila melanogaster. Front Cell Dev Biol. 2022 May 26;10:901351. doi: 10.3389/fcell.2022.901351. PMID: 35721519; PMCID: PMC9204603.

Korona D, Dirnberger B, Giachello CNG, Queiroz RML, Popovic R, Müller KH, Minde DP, Deery MJ, Johnson G, Firth LC, Earley FG, Russell S, Lilley KS. Drosophila nicotinic acetylcholine receptor subunits and their native interactions with insecticidal peptide toxins. Elife. 2022 May 16;11:e74322. doi: 10.7554/eLife.74322. PMID: 35575460; PMCID: PMC9110030.

Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J. Understudied proteins: opportunities and challenges for functional proteomics. Nat Methods. 2022 Jul;19(7):774-779. doi: 10.1038/s41592-022-01454-x. PMID: 35534633.

Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J. An open invitation to the Understudied Proteins Initiative. Nat Biotechnol. 2022 Jun;40(6):815-817. doi: 10.1038/s41587-022-01316-z. PMID: 35534555. Webb JP, Paiva AC, Rossoni L, Alstrom-Moore A, Springthorpe V, Vaud S, Yeh V, Minde DP, Langer S, Walker H, Hounslow A, Nielsen DR, Larson T, Lilley K, Stephens G, Thomas GH, Bonev BB, Kelly DJ, Conradie A, Green J. Multi-omic based production strain improvement (MOBpsi) for bio-manufacturing of toxic chemicals. Metab Eng. 2022 Jul;72:133-149. doi: 10.1016/j.ymben.2022.03.004. Epub 2022 Mar 11. PMID: 35289291.

Stoneley M, Harvey RF, Mulroney TE, Mordue R, Jukes-Jones R, Cain K, Lilley KS, Sawarkar R, Willis AE. Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress. Mol Cell. 2022 Apr 21;82(8):1557-1572.e7. doi: 10.1016/j.molcel.2022.01.019. Epub 2022 Feb 17. PMID: 35180429; PMCID: PMC9098122.

28: Queiroz RML, Piper SC, Rees JS, Strickson S, Briend E, Low CP, Ferguson GJ, Lilley KS, Jackson AP, Finch DK. Proteomic analysis in primary T cells reveals IL-7 alters T cell receptor thresholding via CYTIP/cytohesin/LFA-1 localisation and activation. Biochem J. 2022 Feb 11;479(3):225-243. doi: 10.1042/BCJ20210313. PMID: 35015072; PMCID: PMC8883493.

Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. Mol Cell Proteomics. 2022 Feb;21(2):100186. doi: 10.1016/j.mcpro.2021.100186. Epub 2021 Dec 16. PMID: 34922010; PMCID: PMC8864473.

Elzek MAW, Christopher JA, Breckels LM, Lilley KS. Localization of Organelle Proteins by Isotope Tagging: Current status and potential applications in drugdiscovery research. Drug Discov Today Technol. 2021 Dec;39:57-67. doi: 10.1016/j.ddtec.2021.06.003. Epub 2021 Jul 10. PMID: 34906326.

Mulvey CM, Breckels LM, Crook OM, Sanders DJ, Ribeiro ALR, Geladaki A, Christoforou A, Britovšek NK, Hurrell T, Deery MJ, Gatto L, Smith AM, Lilley KS. Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line. Nat Commun. 2021 Oct 1;12(1):5773. doi: 10.1038/s41467-021-26000-9. PMID: 34599159; PMCID: PMC8486773.

Christopher JA, Stadler C, Martin CE, Morgenstern M, Pan Y, Betsinger CN, Rattray DG, Mahdessian D, Gingras AC, Warscheid B, Lehtiö J, Cristea IM, Foster LJ, Emili A, Lilley KS. Subcellular proteomics. Nat Rev Methods Primers. 2021;1:32. doi: 10.1038/s43586-021-00029-y. Epub 2021 Apr 29. PMID: 34549195; PMCID: PMC8451152.

Fang S, Kirk PDW, Bantscheff M, Lilley KS, Crook OM. A Bayesian semi-parametric model for thermal proteome profiling. Commun Biol. 2021 Jun 29;4(1):810. doi: 10.1038/s42003-021-02306-8. PMID: 34188175; PMCID: PMC8241860.

Demichev V, Tober-Lau P, Lemke O, Nazarenko T, Thibeault C, Whitwell H, Röhl A, Freiwald A, Szyrwiel L, Ludwig D, Correia-Melo C, Aulakh SK, Helbig ET, Stubbemann P, Lippert LJ, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Mittermaier M, Machleidt F, Garcia C, Ruwwe- Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Enghard P, Zelezniak A, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Müller-Redetzky H, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE; PA-COVID-19 Study group; Ralser M, Kurth F. A time-resolved proteomic and prognostic map of COVID-19. Cell Syst. 2021 Aug 18;12(8):780-794.e7. doi: 10.1016/j.cels.2021.05.005. Epub 2021 Jun 14. PMID: 34139154; PMCID: PMC8201874.

Kamel W, Noerenberg M, Cerikan B, Chen H, Järvelin AI, Kammoun M, Lee JY, Shuai N, Garcia-Moreno M, Andrejeva A, Deery MJ, Johnson N, Neufeldt CJ, Cortese M, Knight ML, Lilley KS, Martinez J, Davis I, Bartenschlager R, Mohammed S, Castello A. Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection. Mol Cell. 2021 Jul 1;81(13):2851-2867.e7. doi: 10.1016/j.molcel.2021.05.023. Epub 2021 May 24. PMID: 34118193; PMCID: PMC8142890.

Messner CB, Demichev V, Bloomfield N, Yu JSL, White M, Kreidl M, Egger AS, Freiwald A, Ivosev G, Wasim F, Zelezniak A, Jürgens L, Suttorp N, Sander LE, Kurth F, Lilley KS, Mülleder M, Tate S, Ralser M. Ultra-fast proteomics with Scanning SWATH. Nat Biotechnol. 2021 Jul;39(7):846-854. doi: 10.1038/s41587-021-00860-4. Epub 2021 Mar 25. PMID: 33767396; PMCID: PMC7611254.

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 MT, Pina C, Lilley KS, Prabakaran S. Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions. NPJ Genom Med. 2021 Jan 25;6(1):4. doi:

10.1038/s41525-020-00167-4. PMID: 33495453; PMCID: PMC7835362.

Shin JJH, Crook OM, Borgeaud AC, Cattin-Ortolá J, Peak-Chew SY, Breckels LM, Gillingham AK, Chadwick J, Lilley KS, Munro S. Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers. Nat Commun. 2020 Nov 25;11(1):5987. doi: 10.1038/s41467-020-19840-4. PMID: 33239640; PMCID: PMC7689464.

Crook OM, Geladaki A, Nightingale DJH, Vennard OL, Lilley KS, Gatto L, Kirk PDW. A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection. PLoS Comput Biol. 2020 Nov 9;16(11):e1008288. doi: 10.1371/journal.pcbi.1008288. PMID: 33166281; PMCID: PMC7707549.

Barylyuk K, Koreny L, Ke H, Butterworth S, Crook OM, Lassadi I, Gupta V, Tromer E, Mourier T, Stevens TJ, Breckels LM, Pain A, Lilley KS, Waller RF. A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions. Cell Host Microbe. 2020 Nov 11;28(5):752-766.e9. doi: 10.1016/j.chom.2020.09.011. Epub 2020 Oct 13. PMID: 33053376; PMCID: PMC7670262.

Korona D, Nightingale D, Fabre B, Nelson M, Fischer B, Johnson G, Lees J, Hubbard S, Lilley K, Russell S. Characterisation of protein isoforms encoded by the Drosophila Glycogen Synthase Kinase 3 gene shaggy. PLoS One. 2020 Aug 6;15(8):e0236679. doi: 10.1371/journal.pone.0236679. PMID: 32760087; PMCID: PMC7410302.

Villanueva E, Smith T, Queiroz RML, Monti M, Pizzinga M, Elzek M, Dezi V, Harvey RF, Ramakrishna M, Willis AE, Lilley KS. Efficient recovery of the RNA- bound proteome and protein-bound transcriptome using phase separation (OOPS). Nat Protoc. 2020 Aug;15(8):2568-2588. doi: 10.1038/s41596-020-0344-2. Epub 2020 Jul 10. PMID: 32651564; PMCID: PMC7613161.

Messner CB, Demichev V, Wendisch D, Michalick L, White M, Freiwald A, Textoris-Taube K, Vernardis SI, Egger AS, 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 DJ, Marioni RE, Langenberg C, Lilley KS, Kuebler WM, Mülleder M, Drosten C, Suttorp N, Witzenrath M, Kurth F, Sander LE, Ralser M. Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection. Cell Syst. 2020 Jul 22;11(1):11-24.e4. doi: 10.1016/j.cels.2020.05.012. Epub 2020 Jun 2. PMID: 32619549; PMCID: PMC7264033.

Crook OM, Smith T, Elzek M, Lilley KS. Moving Profiling Spatial Proteomics Beyond Discrete Classification. Proteomics. 2020 Dec;20(23):e1900392. doi: 10.1002/pmic.201900392. Epub 2020 Jul 12. PMID: 32558233.

Thorne MAS, Britovšek NK, Hawkins L, Lilley KS, Storey KB. Proteomics of intracellular freezing survival. PLoS One. 2020 May 26;15(5):e0233048. doi: 10.1371/journal.pone.0233048. Erratum in: PLoS One. 2020 Sep 17;15(9):e0239641. doi: 10.1371/journal.pone.0239641. PMID: 32453791; PMCID: PMC7250440.

de la Fuente AG, Queiroz RML, Ghosh T, McMurran CE, Cubillos JF, Bergles DE, Fitzgerald DC, Jones CA, Lilley KS, Glover CP, Franklin RJM. Changes in the Oligodendrocyte Progenitor Cell Proteome with Ageing. Mol Cell Proteomics. 2020 Aug;19(8):1281-1302. doi: 10.1074/mcp.RA120.002102. Epub 2020 May 20. PMID: 32434922; PMCID: PMC8015006.

Jarsch IK, Gadsby JR, Nuccitelli A, Mason J, Shimo H, Pilloux L, Marzook B, Mulvey CM, Dobramysl U, Bradshaw CR, Lilley KS, Hayward RD, Vaughan TJ, DobsonCL, Gallop JL. A direct role for SNX9 in the biogenesis of filopodia. J Cell Biol. 2020 Apr 6;219(4):e201909178. doi: 10.1083/jcb.201909178. PMID: 32328641; PMCID: PMC7147113.

Rees JS, Cheung LCC, Hamaia SW, Davies G, Sandercock A, Lilley KS, Tigue N, Jackson AP. 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. Int J Oncol. 2020 Jul;57(1):87-99. doi: 10.3892/ijo.2020.5037. Epub 2020 Apr 3. PMID: 32319587; PMCID: PMC7252456.

Smith T, Villanueva E, Queiroz RML, Dawson CS, Elzek M, Urdaneta EC, Willis AE, Beckmann BM, Krijgsveld J, Lilley KS. Organic phase separation opens up new opportunities to interrogate the RNA-binding proteome. Curr Opin Chem Biol. 2020 Feb;54:70-75. doi: 10.1016/j.cbpa.2020.01.009. Epub 2020 Mar 1. PMID: 32131038.

Marondedze C, Thomas L, Lilley KS, Gehring C. Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components. Front Mol Biosci. 2020 Jan 21;6:163. doi: 10.3389/fmolb.2019.00163. PMID: 32039234; PMCID: PMC6985371.

Minde DP, Ramakrishna M, Lilley KS. Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions. Commun Biol. 2020 Jan 22;3(1):38. doi: 10.1038/s42003-020-0758-y. PMID: 31969649; PMCID: PMC6976632.

Till CJ, Vicente J, Zhang H, Oszvald M, Deery MJ, Pastor V, Lilley KS, Ray RV, Theodoulou FL, Holdsworth MJ. The Arabidopsis thaliana N-recognin E3 ligase PROTEOLYSIS1 influences the immune response. Plant Direct. 2019 Dec 26;3(12):e00194. doi: 10.1002/pld3.194. PMID: 31891113; PMCID: PMC6933115.

Demichev V, Messner CB, Vernardis SI, Lilley KS, Ralser M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat Methods. 2020 Jan;17(1):41-44. doi: 10.1038/s41592-019-0638-x. Epub 2019 Nov 25. PMID: 31768060; PMCID: PMC6949130.

Nightingale DJH, Oliver SG, Lilley KS. Mapping the Saccharomyces cerevisiae Spatial Proteome with High Resolution Using hyperLOPIT. Methods Mol Biol. 2019;2049:165-190. doi: 10.1007/978-1-4939-9736-7_10. PMID: 31602611.

Baers LL, Breckels LM, Mills LA, Gatto L, Deery MJ, Stevens TJ, Howe CJ, Lilley KS, Lea-Smith DJ. Proteome Mapping of a Cyanobacterium Reveals Distinct Compartment Organization and Cell-Dispersed Metabolism. Plant Physiol. 2019 Dec;181(4):1721-1738. doi: 10.1104/pp.19.00897. Epub 2019 Oct 2. PMID: 31578229; PMCID: PMC6878006.

Nightingale DJH, Lilley KS, Oliver SG. A Protocol to Map the Spatial Proteome Using HyperLOPIT in Saccharomyces cerevisiae. Bio Protoc. 2019 Jul 20;9(14):e3303. doi: 10.21769/BioProtoc.3303. PMID: 33654815; PMCID: PMC7854154.

Mannini B, Vecchi G, Labrador-Garrido A, Fabre B, Fani G, Franco JM, Lilley K, Pozo D, Vendruscolo M, Chiti F, Dobson CM, Roodveldt C. Differential Interactome and Innate Immune Response Activation of Two Structurally Distinct Misfolded Protein Oligomers. ACS Chem Neurosci. 2019 Aug 21;10(8):3464-3478. doi: 10.1021/acschemneuro.9b00088. Epub 2019 Aug 2. PMID: 31313906.

Parsons HT, Stevens TJ, McFarlane HE, Vidal-Melgosa S, Griss J, Lawrence N, Butler R, Sousa MML, Salemi M, Willats WGT, Petzold CJ, Heazlewood JL, Lilley KS. Separating Golgi Proteins from Cis to Trans Reveals Underlying Properties of Cisternal Localization. Plant Cell. 2019 Sep;31(9):2010-2034. doi: 10.1105/tpc.19.00081. Epub 2019 Jul 2. PMID: 31266899; PMCID: PMC6751122.

Webb J, Springthorpe V, Rossoni L, Minde DP, Langer S, Walker H, Alstrom-Moore A, Larson T, Lilley K, Eastham G, Stephens G, Thomas GH, Kelly DJ, Green J. Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate. mSystems. 2019 Jun 11;4(4):e00187-19. doi: 10.1128/mSystems.00187-19. PMID: 31186337; PMCID: PMC6561320.

Queiroz RML, Smith T, Villanueva E, Marti-Solano M, Monti M, Pizzinga M, Mirea DM, Ramakrishna M, Harvey RF, Dezi V, Thomas GH, Willis AE, Lilley KS. Author Correction: Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS). Nat Biotechnol. 2019 Jun;37(6):692. doi: 10.1038/s41587-019-0161-8.

Crook OM, Breckels LM, Lilley KS, Kirk PDW, Gatto L. A Bioconductor workflow for the Bayesian analysis of spatial proteomics. F1000Res. 2019 Apr 11;8:446. doi: 10.12688/f1000research.18636.1. PMID: 31119032; PMCID: PMC6509962.

Fabre B, Korona D, Lees JG, Lazar I, Livneh I, Brunet M, Orengo CA, Russell S, Lilley KS. Comparison of Drosophila melanogaster Embryo and Adult Proteome by SWATH-MS Reveals Differential Regulation of Protein Synthesis, Degradation Machinery, and Metabolism Modules. J Proteome Res. 2019 Jun 7;18(6):2525-2534.doi: 10.1021/acs.jproteome.9b00076. Epub 2019 May 22. PMID: 31083952.

Weckmann K, Deery MJ, Howard JA, Feret R, Asara JM, Dethloff F, Filiou MD, Labermaier C, Maccarrone G, Lilley KS, Mueller M, Turck CW. Ketamine's Effects on the Glutamatergic and GABAergic Systems: A Proteomics and Metabolomics Study in Mice. Mol Neuropsychiatry. 2019 Mar;5(1):42-51. doi: 10.1159/000493425. Epub 2018 Nov 15. PMID: 31019917; PMCID: PMC6465744.

Marondedze C, Thomas L, Gehring C, Lilley KS. Changes in the Arabidopsis RNA-binding proteome reveal novel stress response mechanisms. BMC Plant Biol. 2019 Apr 11;19(1):139. doi: 10.1186/s12870-019-1750-x. PMID: 30975080; PMCID: PMC6460520.

Hurrell T, Segeritz CP, Vallier L, Lilley KS, Cromarty AD. A proteomic time course through the differentiation of human induced pluripotent stem cells into hepatocyte-like cells. Sci Rep. 2019 Mar 1;9(1):3270. doi: 10.1038/s41598-019-39400-1. PMID: 30824743; PMCID: PMC6397265.

Cristea IM, Lilley KS. Editorial overview: Untangling proteome organization in space and time. Curr Opin Chem Biol. 2019 Feb;48:A1-A4. doi: 10.1016/j.cbpa.2019.02.001. PMID: 30782346.

Dikicioglu D, Nightingale DJH, Wood V, Lilley KS, Oliver SG. Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae. FEMS Yeast Res. 2019 Mar 1;19(2):foz014. doi: 10.1093/femsyr/foz014. PMID: 30753445.

Gatto L, Breckels LM, Lilley KS. Assessing sub-cellular resolution in spatial proteomics experiments. Curr Opin Chem Biol. 2019 Feb;48:123-149. doi: 10.1016/j.cbpa.2018.11.015. Epub 2018 Dec 14. PMID: 30711721; PMCID: PMC6391913.

Geladaki A, Kočevar Britovšek N, Breckels LM, Smith TS, Vennard OL, Mulvey CM, Crook OM, Gatto L, Lilley KS. Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Nat Commun. 2019 Jan 18;10(1):331. doi: 10.1038/s41467-018-08191-w. PMID: 30659192; PMCID: PMC6338729.

Queiroz RML, Smith T, Villanueva E, Marti-Solano M, Monti M, Pizzinga M, Mirea DM, Ramakrishna M, Harvey RF, Dezi V, Thomas GH, Willis AE, Lilley KS. Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS). Nat Biotechnol. 2019 Feb;37(2):169-178. doi: 10.1038/s41587-018-0001-2. Epub 2019 Jan 3. Erratum in: Nat Biotechnol. 2019 Jun;37(6):692. doi: 10.1038/s41587-019-0161-8. PMID: 30607034; PMCID: PMC6591131.

Nightingale DJ, Geladaki A, Breckels LM, Oliver SG, Lilley KS. The subcellular organisation of Saccharomyces cerevisiae. Curr Opin Chem Biol. 2019 Feb;48:86-95. doi: 10.1016/j.cbpa.2018.10.026. Epub 2018 Nov 29. PMID: 30503867; PMCID: PMC6391909.

Crook OM, Mulvey CM, Kirk PDW, Lilley KS, Gatto L. A Bayesian mixture modelling approach for spatial proteomics. PLoS Comput Biol. 2018 Nov 27;14(11):e1006516. doi: 10.1371/journal.pcbi.1006516. PMID: 30481170; PMCID: PMC6258510.

Mata CI, Fabre B, Parsons HT, Hertog MLATM, Van Raemdonck G, Baggerman G, Van de Poel B, Lilley KS, Nicolaï BM. Ethylene Receptors, CTRs and EIN2 Target Protein Identification and Quantification Through Parallel Reaction Monitoring During Tomato Fruit Ripening. Front Plant Sci. 2018 Nov 8;9:1626. doi: 10.3389/fpls.2018.01626. PMID: 30467512; PMCID: PMC6235968.

Hurrell T, Lilley KS, Cromarty AD. Proteomic responses of HepG2 cell monolayers and 3D spheroids to selected hepatotoxins. Toxicol Lett. 2019 Jan;300:40-50. doi: 10.1016/j.toxlet.2018.10.030. Epub 2018 Oct 28. PMID: 30381255.

Alqurashi M, Chiapello M, Bianchet C, Paolocci F, Lilley KS, Gehring C. Early Responses to Severe Drought Stress in the Arabidopsis thaliana Cell Suspension Culture Proteome. Proteomes. 2018 Oct 2;6(4):38. doi: 10.3390/proteomes6040038. PMID: 30279377; PMCID: PMC6313886.

Piñeiro D, Stoneley M, Ramakrishna M, Alexandrova J, Dezi V, Juke-Jones R, Lilley KS, Cain K, Willis AE. Identification of the RNA polymerase I-RNA interactome. Nucleic Acids Res. 2018 Nov 16;46(20):11002-11013. doi: 10.1093/nar/gky779. PMID: 30169671; PMCID: PMC6237751.

Nett IR, Mulas C, Gatto L, Lilley KS, Smith A. Negative feedback via RSK modulates Erk-dependent progression from naïve pluripotency. EMBO Rep. 2018 Aug;19(8):e45642. doi: 10.15252/embr.201745642. Epub 2018 Jun 12. PMID: 29895711; PMCID: PMC6073214.

Segeritz CP, Rashid ST, de Brito MC, Serra MP, Ordonez A, Morell CM, Kaserman JE, Madrigal P, Hannan NRF, Gatto L, Tan L, Wilson AA, Lilley K, Marciniak SJ, Gooptu B, Lomas DA, Vallier L. hiPSC hepatocyte model demonstrates the role of unfolded protein response and inflammatory networks in α₁-antitrypsin deficiency. J Hepatol. 2018 Oct;69(4):851-860. doi: 10.1016/j.jhep.2018.05.028. Epub 2018 Jun 5. PMID: 29879455; PMCID: PMC6562205.

Jedrey H, Lilley KS, Welch M. Ciprofloxacin binding to GyrA causes global changes in the proteome of Pseudomonas aeruginosa. FEMS Microbiol Lett. 2018 Jul 1;365(13):fny134. doi: 10.1093/femsle/fny134. PMID: 29846552; PMCID: PMC5995189.

Repici M, Hassanjani M, Maddison DC, Garção P, Cimini S, Patel B, Szegö ÉM, Straatman KR, Lilley KS, Borsello T, Outeiro TF, Panman L, Giorgini F. The Parkinson's Disease-Linked Protein DJ-1 Associates with Cytoplasmic mRNP Granules During Stress and Neurodegeneration. Mol Neurobiol. 2019 Jan;56(1):61-77. doi: 10.1007/s12035-018-1084-y. Epub 2018 Apr 19. PMID: 29675578; PMCID: PMC6334738.

Hurrell T, Segeritz CP, Vallier L, Lilley KS, Cromarty AD. Proteomic Comparison of Various Hepatic Cell Cultures for Preclinical Safety Pharmacology. Toxicol Sci. 2018 Jul 1;164(1):229-239. doi: 10.1093/toxsci/kfy084. PMID: 29635369.

Armean IM, Lilley KS, Trotter MWB, Pilkington NCV, Holden SB. Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation. Bioinformatics. 2018 Jun 1;34(11):1884-1892. doi: 10.1093/bioinformatics/btx803. PMID: 29390084; PMCID: PMC5972588.

Lloyd-Lewis B, Krueger CC, Sargeant TJ, D'Angelo ME, Deery MJ, Feret R, Howard JA, Lilley KS, Watson CJ. Stat3-mediated alterations in lysosomal membrane protein composition. J Biol Chem. 2018 Mar 23;293(12):4244-4261. doi: 10.1074/jbc.RA118.001777. Epub 2018 Jan 17. PMID: 29343516; PMCID: PMC5868265.

Harvey RF, Smith TS, Mulroney T, Queiroz RML, Pizzinga M, Dezi V, Villenueva E, Ramakrishna M, Lilley KS, Willis AE. Trans-acting translational regulatory RNA binding proteins. Wiley Interdiscip Rev RNA. 2018 May;9(3):e1465. doi: 10.1002/wrna.1465. Epub 2018 Jan 17. PMID: 29341429; PMCID: PMC5947564.

Zhang H, Gannon L, Hassall KL, Deery MJ, Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL. N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. New Phytol. 2018 May;218(3):1106-1126. doi: 10.1111/nph.14909. Epub 2017 Nov 23. PMID: 29168982; PMCID: PMC5947142.

Weckmann K, Deery MJ, Howard JA, Feret R, Asara JM, Dethloff F, Filiou MD, Iannace J, Labermaier C, Maccarrone G, Webhofer C, Teplytska L, Lilley K, Müller MB, Turck CW. Ketamine's antidepressant effect is mediated by energy metabolism and antioxidant defense system. Sci Rep. 2017 Nov 17;7(1):15788. doi: 10.1038/s41598-017-16183-x. PMID: 29150633; PMCID: PMC5694011.

Parsons HT, Lilley KS. Mass spectrometry approaches to study plant endomembrane trafficking. Semin Cell Dev Biol. 2018 Aug;80:123-132. doi: 10.1016/j.semcdb.2017.10.014. Epub 2017 Nov 13. PMID: 29042236.

Hooper CM, Stevens TJ, Saukkonen A, Castleden IR, Singh P, Mann GW, Fabre B, Ito J, Deery MJ, Lilley KS, Petzold CJ, Millar AH, Heazlewood JL, Parsons HT. Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples. Plant J. 2017 Dec;92(6):1202-1217. doi: 10.1111/tpj.13743. Epub 2017 Nov 20. PMID: 29024340; PMCID: PMC5863471.

Fabre B, Korona D, Mata CI, Parsons HT, Deery MJ, Hertog MLATM, Nicolaï BM, Russell S, Lilley KS. Spectral Libraries for SWATH-MS Assays for Drosophila melanogaster and Solanum lycopersicum. Proteomics. 2017 Nov;17(21):10.1002/pmic.201700216. doi: 10.1002/pmic.201700216. PMID: 28922568; PMCID: PMC5821221.

Loxley GM, Unsworth J, Turton MJ, Jebb A, Lilley KS, Simpson DM, Rigden DJ, Hurst JL, Beynon RJ. Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus. Open Biol. 2017 Sep;7(9):170135. doi: 10.1098/rsob.170135. PMID: 28878040; PMCID: PMC5627053.

Thul PJ, Åkesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, Alm T, Asplund A, Björk L, Breckels LM, 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 CM, Nilsson P, Oksvold P, Rockberg J, Schutten R, Schwenk JM, Sivertsson Å, Sjöstedt E, Skogs M, Stadler C, Sullivan DP, Tegel H, Winsnes C, Zhang C, Zwahlen M, Mardinoglu A, Pontén F, von Feilitzen K, Lilley KS, Uhlén M, Lundberg E. A subcellular map of the human proteome. Science. 2017 May 26;356(6340):eaal3321. doi: 10.1126/science.aal3321. Epub 2017 May 11. PMID: 28495876.

Mulvey CM, Breckels LM, Geladaki A, Britovšek NK, Nightingale DJH, Christoforou A, Elzek M, Deery MJ, Gatto L, Lilley KS. Using hyperLOPIT to perform high-resolution mapping of the spatial proteome. Nat Protoc. 2017 Jun;12(6):1110-1135. doi: 10.1038/nprot.2017.026. Epub 2017 May 4. PMID: 28471460.

Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP. Selective Proteomic Proximity Labeling Assay Using Tyramide (SPPLAT): A Quantitative Method for the Proteomic Analysis of Localized Membrane-Bound Protein Clusters. Curr Protoc Protein Sci. 2017 Apr 3;88:19.27.1-19.27.18. doi: 10.1002/cpps.27. PMID: 28369668.

Kalkan T, Olova N, Roode M, Mulas C, Lee HJ, Nett I, Marks H, Walker R, Stunnenberg HG, Lilley KS, Nichols J, Reik W, Bertone P, Smith A. Tracking the embryonic stem cell transition from ground state pluripotency. Development. 2017 Apr 1;144(7):1221-1234. doi: 10.1242/dev.142711. Epub 2017 Feb 7. PMID: 28174249; PMCID: PMC5399622.

Minde DP, Dunker AK, Lilley KS. Time, space, and disorder in the expanding proteome universe. Proteomics. 2017 Apr;17(7):1600399. doi: 10.1002/pmic.201600399. Epub 2017 Mar 20. PMID: 28145059; PMCID: PMC5573936.

Breckels LM, Mulvey CM, Lilley KS, Gatto L. A Bioconductor workflow for processing and analysing spatial proteomics data. F1000Res. 2016 Dec 28;5:2926. doi: 10.12688/f1000research.10411.2. PMID: 30079225; PMCID: PMC6053703.

Mata CI, Fabre B, Hertog ML, Parsons HT, Deery MJ, Lilley KS, Nicolaï BM. In-depth characterization of the tomato fruit pericarp proteome. Proteomics. 2017 Jan;17(1-2). doi: 10.1002/pmic.201600406. PMID: 27957804.

Fabre B, Korona D, Nightingale DJ, Russell S, Lilley KS. SWATH-MS dataset of heat-shock treated Drosophila melanogaster embryos. Data Brief. 2016 Nov 16;9:991-995. doi: 10.1016/j.dib.2016.11.028. PMID: 27900350; PMCID: PMC5123040.

Fabre B, Korona D, Nightingale DJ, Russell S, Lilley KS. SWATH-MS data of Drosophila melanogaster proteome dynamics during embryogenesis. Data Brief. 2016 Oct 24;9:771-775. doi: 10.1016/j.dib.2016.10.009. PMID: 27844044; PMCID: PMC5097952.

Alam MT, 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 KR, Timmermann B, Lilley KS, Ralser M. The metabolic background is a global player in Saccharomyces gene expression epistasis. Nat Microbiol. 2016 Feb 1;1:15030. doi: 10.1038/nmicrobiol.2015.30. PMID: 27572163; PMCID: PMC5131842.

Muleya V, Marondedze C, Wheeler JI, Thomas L, Mok YF, Griffin MD, Manallack DT, Kwezi L, Lilley KS, Gehring C, Irving HR. Phosphorylation of the dimeric cytoplasmic domain of the phytosulfokine receptor, PSKR1. Biochem J. 2016 Oct 1;473(19):3081-98. doi: 10.1042/BCJ20160593. Epub 2016 Aug 3. PMID: 27487840.

Marondedze C, Thomas L, Serrano NL, Lilley KS, Gehring C. The RNA-binding protein repertoire of Arabidopsis thaliana. Sci Rep. 2016 Jul 11;6:29766. doi: 10.1038/srep29766. PMID: 27405932; PMCID: PMC4942612.

Batalha IL, Zhou H, Lilley K, Lowe CR, Roque AC. Mimicking nature: Phosphopeptide enrichment using combinatorial libraries of affinity ligands. J Chromatogr A. 2016 Jul 29;1457:76-87. doi: 10.1016/j.chroma.2016.06.032. Epub 2016 Jun 11. PMID: 27345211.

Breckels LM, Holden SB, Wojnar D, Mulvey CM, Christoforou A, Groen A, Trotter MW, Kohlbacher O, Lilley KS, Gatto L. Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics. PLoS Comput Biol. 2016 May 13;12(5):e1004920. doi: 10.1371/journal.pcbi.1004920. PMID: 27175778; PMCID: PMC4866734.

Fabre B, Korona D, Groen A, Vowinckel J, Gatto L, Deery MJ, Ralser M, Russell S, Lilley KS. Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches. Proteomics. 2016 Aug;16(15-16):2068-80. doi: 10.1002/pmic.201500482. Epub 2016 May 10. PMID: 27029218; PMCID: PMC5737838.

Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Martinez Arias A, Lilley KS. A draft map of the mouse pluripotent stem cell spatial proteome. Nat Commun. 2016 Jan 12;7:8992. doi: 10.1038/ncomms9992. PMID: 26754106; PMCID: PMC4729960.

Syed YA, Zhao C, Mahad D, Möbius W, Altmann F, Foss F, González GA, Sentürk A, Acker-Palmer A, Lubec G, Lilley K, Franklin RJM, Nave KA, Kotter MRN. Antibody-mediated neutralization of myelin-associated EphrinB3 accelerates CNS remyelination. Acta Neuropathol. 2016 Feb;131(2):281-298. doi: 10.1007/s00401-015-1521-1. Epub 2015 Dec 19. PMID: 26687980; PMCID: PMC4713754.

Marondedze C, Groen AJ, Thomas L, Lilley KS, Gehring C. A Quantitative Phosphoproteome Analysis of cGMP-Dependent Cellular Responses in Arabidopsis thaliana. Mol Plant. 2016 Apr 4;9(4):621-3. doi: 10.1016/j.molp.2015.11.007. Epub 2015 Nov 30. PMID: 26658240.

Muñoz-Bernal E, Deery MJ, Rodríguez ME, Cantoral JM, Howard J, Feret R, Natera R, Lilley KS, Fernández-Acero FJ. Analysis of temperature-mediated changes in the wine yeast Saccharomyces bayanus var uvarum. An oenological study of how the protein content influences wine quality. Proteomics. 2016 Feb;16(4):576-92. doi: 10.1002/pmic.201500137. Epub 2016 Jan 25. PMID: 26621492.

Chen C, Buhl E, Xu M, Croset V, Rees JS, Lilley KS, Benton R, Hodge JJ, Stanewsky R. Drosophila Ionotropic Receptor 25a mediates circadian clock resetting by temperature. Nature. 2015 Nov 26;527(7579):516-20. doi: 10.1038/nature16148. Epub 2015 Nov 18. PMID: 26580016.

Lilley KS, Beynon RJ, Eyers CE, Hubbard SJ. Focus on Quantitative Proteomics. Proteomics. 2015 Sep;15(18):3101-3. doi: 10.1002/pmic.201570163. PMID: 26372724.

Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP. Protein Neighbors and Proximity Proteomics. Mol Cell Proteomics. 2015 Nov;14(11):2848-56. doi: 10.1074/mcp.R115.052902. Epub 2015 Sep 8. PMID: 26355100; PMCID: PMC4638030.

Lim K, Groen A, Molostvov G, Lu T, Lilley KS, Snead D, James S, Wilkinson IB, Ting S, Hsiao LL, Hiemstra TF, Zehnder D. α-Klotho Expression in Human Tissues. J Clin Endocrinol Metab. 2015 Oct;100(10):E1308-18. doi: 10.1210/jc.2015-1800. Epub 2015 Aug 17. PMID: 26280509; PMCID: PMC4596032.

Rees JS, Lilley KS, Jackson AP. The chicken B-cell line DT40 proteome, beadome and interactomes. Data Brief. 2015 Jan 13;3:29-33. doi: 10.1016/j.dib.2014.12.006. PMID: 26217713; PMCID: PMC4509924.

Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez-Arias A, Lilley KS. Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells. Stem Cells. 2015 Sep;33(9):2712-25. doi: 10.1002/stem.2067. Epub 2015 Jun 23. PMID: 26059426.

Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP. Selective Proteomic Proximity Labeling Assay Using Tyramide (SPPLAT): A Quantitative Method for the Proteomic Analysis of Localized Membrane-Bound Protein Clusters. Curr Protoc Protein Sci. 2015 Apr 1;80:19.27.1-19.27.18. doi: 10.1002/0471140864.ps1927s80. PMID: 25829300.

Masci S, Laino P, Janni M, Botticella E, Di Carli M, Benvenuto E, Danieli PP, Lilley KS, Lafiandra D, D'Ovidio R. Analysis of Quality-Related Parameters in Mature Kernels of Polygalacturonase Inhibiting Protein (PGIP) TransgenicBread Wheat Infected with Fusarium graminearum. J Agric Food Chem. 2015 Apr 22;63(15):3962-9. doi: 10.1021/jf506003t. Epub 2015 Apr 9. PMID: 25823882.

Zhang H, Deery MJ, Gannon L, Powers SJ, Lilley KS, Theodoulou FL. Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots. Proteomics. 2015 Jul;15(14):2447-57. doi: 10.1002/pmic.201400530. Epub 2015 Apr 17. PMID: 25728785; PMCID: PMC4692092.

Marondedze C, Wong A, Groen A, Serrano N, Jankovic B, Lilley K, Gehring C, Thomas L. Exploring the Arabidopsis proteome: influence of protein solubilization buffers on proteome coverage. Int J Mol Sci. 2014 Dec 31;16(1):857-70. doi: 10.3390/ijms16010857. PMID: 25561235; PMCID: PMC4307279.

Rees JS, Lilley KS, Jackson AP. SILAC-iPAC: a quantitative method for distinguishing genuine from non-specific components of protein complexes by parallel affinity capture. J Proteomics. 2015 Feb 6;115:143-56. doi: 10.1016/j.jprot.2014.12.006. Epub 2014 Dec 20. PMID: 25534881; PMCID: PMC4329988.

Passmore IJ, Nishikawa K, Lilley KS, Bowden SD, Chung JC, Welch M. Mep72, a metzincin protease that is preferentially secreted by biofilms of Pseudomonas aeruginosa. J Bacteriol. 2015 Feb 15;197(4):762-73. doi: 10.1128/JB.02404-14. Epub 2014 Dec 8. PMID: 25488299; PMCID: PMC4334185.

Gillingham AK, Sinka R, Torres IL, Lilley KS, Munro S. Toward a comprehensive map of the effectors of rab GTPases. Dev Cell. 2014 Nov 10;31(3):358-373. doi: 10.1016/j.devcel.2014.10.007. Epub 2014 Nov 10. PMID: 25453831; PMCID: PMC4232348.

Lowe N, Rees JS, Roote J, Ryder E, Armean IM, Johnson G, Drummond E, Spriggs H, Drummond J, Magbanua JP, Naylor H, Sanson B, Bastock R, Huelsmann S, Trovisco V, Landgraf M, Knowles-Barley S, Armstrong JD, White-Cooper H, Hansen C, Phillips RG; UK Drosophila Protein Trap Screening Consortium; Lilley KS, Russell S, St Johnston D. Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library. Development. 2014 Oct;141(20):3994-4005. doi: 10.1242/dev.111054. PMID: 25294943; PMCID: PMC4197710.

Nikolovski N, Shliaha PV, Gatto L, Dupree P, Lilley KS. Label-free protein quantification for plant Golgi protein localization and abundance. Plant Physiol. 2014 Oct;166(2):1033-43. doi: 10.1104/pp.114.245589. Epub 2014 Aug 13. PMID: 25122472; PMCID: PMC4213074.

Tomizioli M, Lazar C, Brugière S, Burger T, Salvi D, Gatto L, Moyet L, Breckels LM, Hesse AM, Lilley KS, Seigneurin-Berny D, Finazzi G, Rolland N, Ferro M. Deciphering thylakoid sub-compartments using a mass spectrometry-based approach. Mol Cell Proteomics. 2014 Aug;13(8):2147-67. doi: 10.1074/mcp.M114.040923. Epub 2014 May 28. PMID: 24872594; PMCID: PMC4125743.

Shliaha PV, Jukes-Jones R, Christoforou A, Fox J, Hughes C, Langridge J, Cain K, Lilley KS. Additional precursor purification in isobaric mass tagging experiments by traveling wave ion mobility separation (TWIMS). J Proteome Res. 2014 Jul 3;13(7):3360-9. doi: 10.1021/pr500220g. Epub 2014 Jun 16. PMID: 24854137.

Gatto L, Breckels LM, Burger T, Nightingale DJ, Groen AJ, Campbell C, Nikolovski N, Mulvey CM, Christoforou A, Ferro M, Lilley KS. A foundation for reliable spatial proteomics data analysis. Mol Cell Proteomics. 2014 Aug;13(8):1937-52. doi: 10.1074/mcp.M113.036350. Epub 2014 May 20. PMID: 24846987; PMCID: PMC4125728.

Christoforou A, Arias AM, Lilley KS. Determining protein subcellular localization in mammalian cell culture with biochemical fractionation and iTRAQ 8-plex quantification. Methods Mol Biol. 2014;1156:157-74. doi: 10.1007/978-1-4939-0685-7_10. PMID: 24791987.

Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics. 2014 Aug;13(8):1905-13. doi: 10.1074/mcp.M113.035907. Epub 2014 Apr 23. PMID: 24760958; PMCID: PMC4125725.

Elliott TS, Townsley FM, Bianco A, Ernst RJ, Sachdeva A, Elsässer SJ, Davis L, Lang K, Pisa R, Greiss S, Lilley KS, Chin JW. Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal. Nat Biotechnol. 2014 May;32(5):465-72. doi: 10.1038/nbt.2860. Epub 2014 Apr 13. PMID: 24727715; PMCID: PMC4107302.

Li XW, Rees JS, Xue P, Zhang H, Hamaia SW, Sanderson B, Funk PE, Farndale RW, Lilley KS, Perrett S, Jackson AP. New insights into the DT40 B cell receptor cluster using a proteomic proximity labeling assay. J Biol Chem. 2014 May 23;289(21):14434-47. doi: 10.1074/jbc.M113.529578. Epub 2014 Apr 4. PMID: 24706754; PMCID: PMC4031500.

Hiemstra TF, Charles PD, Gracia T, Hester SS, Gatto L, Al-Lamki R, Floto RA, Su Y, Skepper JN, Lilley KS, Karet Frankl FE. Human urinary exosomes as innate immune effectors. J Am Soc Nephrol. 2014 Sep;25(9):2017-27. doi: 10.1681/ASN.2013101066. Epub 2014 Apr 3. PMID: 24700864; PMCID: PMC4147985.

Feret R, Lilley KS. Protein profiling using two-dimensional difference gel electrophoresis (2-D DIGE). Curr Protoc Protein Sci. 2014 Feb 3;75:22.2.1-22.2.17. doi: 10.1002/0471140864.ps2202s75. PMID: 24510675.

Wang Y, Lilley KS, Oliver SG. A protocol for the subcellular fractionation of Saccharomyces cerevisiae using nitrogen cavitation and density gradient centrifugation. Yeast. 2014 Apr;31(4):127-35. doi: 10.1002/yea.3002. Epub 2014 Feb 20. PMID: 24510422; PMCID: PMC4282465.

Füzesi-Levi MG, Ben-Nissan G, Bianchi E, Zhou H, Deery MJ, Lilley KS, Levin Y, Sharon M. Dynamic regulation of the COP9 signalosome in response to DNA damage. Mol Cell Biol. 2014 Mar;34(6):1066-76. doi: 10.1128/MCB.01598-13. Epub 2014 Jan 13. PMID: 24421388; PMCID: PMC3958043.

136: Gatto L, Breckels LM, Wieczorek S, Burger T, Lilley KS. Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata. Bioinformatics. 2014 May 1;30(9):1322-4. doi: 10.1093/bioinformatics/btu013. Epub 2014 Jan 11. PMID: 24413670; PMCID: PMC3998135.

Groen AJ, Sancho-Andrés G, Breckels LM, Gatto L, Aniento F, Lilley KS. Identification of trans-golgi network proteins in Arabidopsis thaliana root tissue. J Proteome Res. 2014 Feb 7;13(2):763-76. doi: 10.1021/pr4008464. Epub 2014 Jan 17. PMID: 24344820; PMCID: PMC3929368.

Wilf NM, Reid AJ, Ramsay JP, Williamson NR, Croucher NJ, Gatto L, Hester SS, Goulding D, Barquist L, Lilley KS, Kingsley RA, Dougan G, Salmond GP. 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. BMC Genomics. 2013 Nov 22;14(1):822. doi: 10.1186/1471-2164-14-822. PMID: 24267595; PMCID: PMC4046660.

Koutroukides TA, Jaros JA, Amess B, Martins-de-Souza D, Guest PC, Rahmoune H, Levin Y, Deery M, Charles PD, Hester S, Groen A, Christoforou A, Howard J, Bond N, Bahn S, Lilley KS. Identification of protein biomarkers in human serum using iTRAQ and shotgun mass spectrometry. Methods Mol Biol. 2013;1061:291-307. doi: 10.1007/978-1-62703-589-7_18. PMID: 23963945.

Hemsley PA, Weimar T, Lilley K, Dupree P, Grierson C. Palmitoylation in plants: new insights through proteomics. Plant Signal Behav. 2013 Aug;8(8):e25209. doi: 10.4161/psb.25209. Epub 2013 Jun 5. PMID: 23759553; PMCID: PMC3999067.

Chouchani ET, Methner C, Nadtochiy SM, Logan A, Pell VR, Ding S, James AM, Cochemé HM, Reinhold J, Lilley KS, Partridge L, Fearnley IM, Robinson AJ, Hartley RC, Smith RA, Krieg T, Brookes PS, Murphy MP. Cardioprotection by S-nitrosation of a cysteine switch on mitochondrial complex I. Nat Med. 2013 Jun;19(6):753-9. doi: 10.1038/nm.3212. Epub 2013 May 26. PMID: 23708290; PMCID: PMC4019998.

Marondedze C, Lilley K, Thomas L. Comparative gel-based phosphoproteomics in response to signaling molecules. Methods Mol Biol. 2013;1016:139-54. doi: 10.1007/978-1-62703-441-8_10. PMID: 23681577.

Groen A, Thomas L, Lilley K, Marondedze C. Identification and quantitation of signal molecule-dependent protein phosphorylation. Methods Mol Biol. 2013;1016:121-37. doi: 10.1007/978-1-62703-441-8_9. PMID: 23681576.

Shliaha PV, Bond NJ, Gatto L, Lilley KS. Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies. J Proteome Res. 2013 Jun 7;12(6):2323-39. doi: 10.1021/pr300775k. Epub 2013 May 2. PMID: 23514362.

Bond NJ, Shliaha PV, Lilley KS, Gatto L. Improving qualitative and quantitative performance for MS(E)-based label-free proteomics. J Proteome Res. 2013 Jun 7;12(6):2340-53. doi: 10.1021/pr300776t. Epub 2013 Apr 17. PMID: 23510225.

Ivanov AR, Colangelo CM, Dufresne CP, Friedman DB, Lilley KS, Mechtler K, Phinney BS, Rose KL, Rudnick PA, Searle BC, Shaffer SA, Weintraub ST. Interlaboratory studies and initiatives developing standards for proteomics. Proteomics. 2013 Mar;13(6):904-9. doi: 10.1002/pmic.201200532. Epub 2013 Feb 19. PMID: 23319436; PMCID: PMC3863631.

Marondedze C, Turek I, Parrott B, Thomas L, Jankovic B, Lilley KS, Gehring C. Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins. Cell Commun Signal. 2013 Jan 5;11(1):1. doi: 10.1186/1478-811X-11-1. PMID: 23289948; PMCID: PMC3544604.

Vowinckel J, Capuano F, Campbell K, Deery MJ, Lilley KS, Ralser M. The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics. F1000Res. 2013 Dec 13;2:272. doi: 10.12688/f1000research.2-272.v2. PMID: 24741437; PMCID: PMC3983906.

Hemsley PA, Weimar T, Lilley KS, Dupree P, Grierson CS. A proteomic approach identifies many novel palmitoylated proteins in Arabidopsis. New Phytol. 2013 Feb;197(3):805-814. doi: 10.1111/nph.12077. Epub 2012 Dec 17. PMID: 23252521.

Russell MR, Lilley KS. Pipeline to assess the greatest source of technical variance in quantitative proteomics using metabolic labelling. J Proteomics. 2012 Dec 21;77:441-54. doi: 10.1016/j.jprot.2012.09.020. Epub 2012 Oct 16. PMID: 23079070.

Armean IM, Lilley KS, Trotter MW. Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Mol Cell Proteomics. 2013 Jan;12(1):1-13. doi: 10.1074/mcp.R112.019554. Epub 2012 Oct 15. PMID: 23071097; PMCID: PMC3536891.

Nikolovski N, Rubtsov D, Segura MP, Miles GP, Stevens TJ, Dunkley TP, Munro S, Lilley KS, Dupree P. Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. Plant Physiol. 2012 Oct;160(2):1037-51. doi: 10.1104/pp.112.204263. Epub 2012 Aug 24. PMID: 22923678; PMCID: PMC3461528.

Fan J, Mohareb F, Bond NJ, Lilley KS, Bessant C. MRMaid 2.0: mining PRIDE for evidence-based SRM transitions. OMICS. 2012 Sep;16(9):483-8. doi: 10.1089/omi.2011.0143. Epub 2012 Jul 17. PMID: 22804252; PMCID: PMC3437039.

Christoforou AL, Lilley KS. Isobaric tagging approaches in quantitative proteomics: the ups and downs. Anal Bioanal Chem. 2012 Sep;404(4):1029-37. doi: 10.1007/s00216-012-6012-9. Epub 2012 May 12. PMID: 22580419.

Amoutzias GD, He Y, Lilley KS, Van de Peer Y, Oliver SG. Evaluation and properties of the budding yeast phosphoproteome. Mol Cell Proteomics. 2012 Jun;11(6):M111.009555. doi: 10.1074/mcp.M111.009555. Epub 2012 Jan 27. PMID: 22286756; PMCID: PMC3433898.

Hiemstra TF, Charles PD, Hester SS, Karet FE, Lilley KS. Uromodulin exclusion list improves urinary exosomal protein identification. J Biomol Tech. 2011 Dec;22(4):136-45. PMID: 22131889; PMCID: PMC3221452.

Gatto L, Lilley KS. MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Bioinformatics. 2012 Jan 15;28(2):288-9. doi: 10.1093/bioinformatics/btr645. Epub 2011 Nov 22. PMID: 22113085.

158: Christoforou A, Lilley KS. Taming the isobaric tagging elephant in the room in quantitative proteomics. Nat Methods. 2011 Oct 28;8(11):911-3. doi: 10.1038/nmeth.1736. PMID: 22036744.

Capuano F, Bond NJ, Gatto L, Beaudoin F, Napier JA, Benvenuto E, Lilley KS, Baschieri S. LC-MS/MS methods for absolute quantification and identification of proteins associated with chimeric plant oil bodies. Anal Chem. 2011 Dec 15;83(24):9267-72. doi: 10.1021/ac201733m. Epub 2011 Nov 16. PMID: 22017570.

Rees J, Lilley K. Enabling technologies for yeast proteome analysis. Methods Mol Biol. 2011;759:149-78. doi: 10.1007/978-1-61779-173-4_10. PMID: 21863487.

Huang W, Ling Q, Bédard J, Lilley K, Jarvis P. In vivo analyses of the roles of essential Omp85-related proteins in the chloroplast outer envelope membrane. Plant Physiol. 2011 Sep;157(1):147-59. doi: 10.1104/pp.111.181891. Epub 2011 Jul 14. PMID: 21757633; PMCID: PMC3165866.

Falick AM, Lane WS, Lilley KS, MacCoss MJ, Phinney BS, Sherman NE, Weintraub ST, Witkowska HE, Yates NA. ABRF-PRG07: advanced quantitative proteomics study. J Biomol Tech. 2011 Apr;22(1):21-6. PMID: 21455478; PMCID PMC3059538.

Rees JS, Lowe N, Armean IM, Roote J, Johnson G, Drummond E, Spriggs H, Ryder E, Russell S, St Johnston D, Lilley KS. In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry. Mol Cell Proteomics. 2011 Jun;10(6):M110.002386. doi: 10.1074/mcp.M110.002386. Epub 2011 Mar 29. PMID: 21447707; PMCID: PMC3108830.

Friedman DB, Andacht TM, Bunger MK, Chien AS, Hawke DH, Krijgsveld J, Lane WS, Lilley KS, MacCoss MJ, Moritz RL, Settlage RE, Sherman NE, Weintraub ST, Witkowska HE, Yates NA, Turck CW. The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses. Proteomics. 2011 Apr;11(8):1371-81. doi: 10.1002/pmic.201000736. Epub 2011 Mar 11. PMID: 21394914.

Lilley KS, Deery MJ, Gatto L. Challenges for proteomics core facilities. Proteomics. 2011 Mar;11(6):1017-25. doi: 10.1002/pmic.201000693. Epub 2011 Feb 16. PMID: 21360676.

Mikkelsen H, Swatton JE, Lilley KS, Welch M. Proteomic analysis of the adaptive responses of Pseudomonas aeruginosa to aminoglycoside antibiotics. FEMS Microbiol Lett. 2010 Aug 19. doi: 10.1111/j.1574-6968.2009.01729.x. Epub ahead of print. PMID: 21204916.

Groen AJ, Lilley KS. Proteomics of total membranes and subcellular membranes. Expert Rev Proteomics. 2010 Dec;7(6):867-78. doi: 10.1586/epr.10.85. PMID: 21142888.

Chouchani ET, James AM, Fearnley IM, Lilley KS, Murphy MP. Proteomic approaches to the characterization of protein thiol modification. Curr Opin Chem Biol. 2011 Feb;15(1):120-8. doi: 10.1016/j.cbpa.2010.11.003. Epub 2010 Dec 2. PMID: 21130020; PMCID: PMC3087609. Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS. Organelle proteomics experimental designs and analysis. Proteomics. 2010 Nov;10(22):3957-69. doi: 10.1002/pmic.201000244. Epub 2010 Nov 2. PMID: 21080489.

Trotter MW, Sadowski PG, Dunkley TP, Groen AJ, Lilley KS. Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions. Proteomics. 2010 Dec;10(23):4213-9. doi: 10.1002/pmic.201000359. PMID: 21058340.

McGlincy NJ, Tan LY, Paul N, Zavolan M, Lilley KS, Smith CW. Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay. BMC Genomics. 2010 Oct 14;11:565. doi: 10.1186/1471-2164-11-565. PMID: 20946641; PMCID: PMC3091714.

Di Carli M, Zamboni A, Pè ME, Pezzotti M, Lilley KS, Benvenuto E, Desiderio A. Two-dimensional differential in gel electrophoresis (2D-DIGE) analysis of grape berry proteome during postharvest withering. J Proteome Res. 2011 Feb 4;10(2):429-46. doi: 10.1021/pr1005313. Epub 2010 Dec 1. PMID: 20945943.

Requejo R, Chouchani ET, James AM, Prime TA, Lilley KS, Fearnley IM, Murphy MP. Quantification and identification of mitochondrial proteins containing vicinal dithiols. Arch Biochem Biophys. 2010 Dec 15;504(2):228-35. doi: 10.1016/j.abb.2010.09.003. Epub 2010 Sep 15. PMID: 20836988.

Wasbrough ER, Dorus S, Hester S, Howard-Murkin J, Lilley K, Wilkin E, Polpitiya A, Petritis K, Karr TL. The Drosophila melanogaster sperm proteome-II (DmSP-II). J Proteomics. 2010 Oct 10;73(11):2171-85. doi: 10.1016/j.jprot.2010.09.002. Epub 2010 Sep 15. PMID: 20833280.

Zamboni A, Di Carli M, Guzzo F, Stocchero M, Zenoni S, Ferrarini A, Tononi P, Toffali K, Desiderio A, Lilley KS, Pè ME, Benvenuto E, Delledonne M, Pezzotti M. Identification of putative stage-specific grapevine berry biomarkers and omics data integration into networks. Plant Physiol. 2010 Nov;154(3):1439-59. doi: 10.1104/pp.110.160275. Epub 2010 Sep 8. PMID: 20826702; PMCID: PMC2971619.

Pedreschi R, Hertog M, Lilley KS, Nicolaï B. Proteomics for the food industry: opportunities and challenges. Crit Rev Food Sci Nutr. 2010 Aug;50(7):680-92. doi: 10.1080/10408390903044214. PMID: 20694929.

Segura MP, Lilley KS, Dupree P. Proteomic complex detection using sedimentation (ProCoDeS): screening for proteins in stable complexes and their candidate interaction partners. Biochem Soc Trans. 2010 Aug;38(4):923-7. doi:10.1042/BST0380923. PMID: 20658978.

Wang M, Bond NJ, Letcher AJ, Richardson JP, Lilley KS, Irvine RF, Clarke JH. Genomic tagging reveals a random association of endogenous PtdIns5P 4-kinases IIalpha and IIbeta and a partial nuclear localization of the IIalpha isoform. Biochem J. 2010 Sep 1;430(2):215-21. doi: 10.1042/BJ20100340. PMID: 20569199; PMCID: PMC2943749.

Chouchani ET, Hurd TR, Nadtochiy SM, Brookes PS, Fearnley IM, Lilley KS, Smith RA, Murphy MP. 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. Biochem J. 2010 Aug 15;430(1):49-59. doi: 10.1042/BJ20100633. PMID: 20533907; PMCID: PMC2911678.

Gutteridge A, Pir P, Castrillo JI, Charles PD, Lilley KS, Oliver SG. Nutrient control of eukaryote cell growth: a systems biology study in yeast. BMC Biol. 2010 May 24;8:68. doi: 10.1186/1741-7007-8-68. PMID: 20497545; PMCID: PMC2895586.

Karp NA, Huber W, Sadowski PG, Charles PD, Hester SV, Lilley KS. Addressing accuracy and precision issues in iTRAQ quantitation. Mol Cell Proteomics. 2010 Sep;9(9):1885-97. doi: 10.1074/mcp.M900628-MCP200. Epub 2010 Apr 10. PMID: 20382981; PMCID: PMC2938101.

Stickland HG, Davenport PW, Lilley KS, Griffin JL, Welch M. Mutation of nfxB causes global changes in the physiology and metabolism of Pseudomonas aeruginosa. J Proteome Res. 2010 Jun 4;9(6):2957-67. doi: 10.1021/pr9011415. PMID: 20373734.

Nilo R, Saffie C, Lilley K, Baeza-Yates R, Cambiazo V, Campos-Vargas R, González M, Meisel LA, Retamales J, Silva H, Orellana A. Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE). BMC Genomics. 2010 Jan 18;11:43. doi: 10.1186/1471-2164-11-43. PMID: 20082721; PMCID: PMC2822761.

184: Barnard AML, Simpson NJL, Lilley KS, Salmond GPC. Mutations in rpsL that confer streptomycin resistance show pleiotropic effects on virulence and the production of a carbapenem antibiotic in Erwinia carotovora. Microbiology (Reading). 2010 Apr;156(Pt 4):1030-1039. doi: 10.1099/mic.0.034595-0. Epub 2010 Jan 7. PMID: 20056700.

Deery MJ, Maywood ES, Chesham JE, Sládek M, Karp NA, Green EW, Charles PD, Reddy AB, Kyriacou CP, Lilley KS, Hastings MH. Proteomic analysis reveals the role of synaptic vesicle cycling in sustaining the suprachiasmatic circadian clock. Curr Biol. 2009 Dec 15;19(23):2031-6. doi: 10.1016/j.cub.2009.10.024. Epub 2009 Nov 12. PMID: 19913422.

Pedreschi R, Hertog M, Robben J, Lilley KS, Karp NA, Baggerman G, Vanderleyden J, Nicolaï B. Gel-based proteomics approach to the study of metabolic changes in pear tissue during storage. J Agric Food Chem. 2009 Aug 12;57(15):6997-7004. doi: 10.1021/jf901432h. PMID: 19722581.

Blagden SP, Gatt MK, Archambault V, Lada K, Ichihara K, Lilley KS, Inoue YH, Glover DM. Drosophila Larp associates with poly(A)-binding protein and is required for male fertility and syncytial embryo development. Dev Biol. 2009 Oct 1;334(1):186-97. doi: 10.1016/j.ydbio.2009.07.016. Epub 2009 Jul 22. PMID: 19631203.

Hurd TR, James AM, Lilley KS, Murphy MP. Chapter 19 Measuring redox changes to mitochondrial protein thiols with redox difference gel electrophoresis (redox-DIGE). Methods Enzymol. 2009;456:343-61. doi:

10.1016/S0076-6879(08)04419-4. PMID: 19348898.

Tan DJ, Dvinge H, Christoforou A, Bertone P, Martinez Arias A, Lilley KS. Mapping organelle proteins and protein complexes in Drosophila melanogaster. J Proteome Res. 2009 Jun;8(6):2667-78. doi: 10.1021/pr800866n. PMID: 19317464.

Hall SL, Hester S, Griffin JL, Lilley KS, Jackson AP. The organelle proteome of the DT40 lymphocyte cell line. Mol Cell Proteomics. 2009 Jun;8(6):1295-305. doi: 10.1074/mcp.M800394-MCP200. Epub 2009 Jan 30. PMID: 19181659; PMCID: PMC2690488.

Fineran PC, Blower TR, Foulds IJ, Humphreys DP, Lilley KS, Salmond GP. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin- antitoxin pair. Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):894-9. doi: 10.1073/pnas.0808832106. Epub 2009 Jan 5. PMID: 19124776; PMCID: PMC2630095.

Karp NA, Lilley KS. Investigating sample pooling strategies for DIGE experiments to address biological variability. Proteomics. 2009 Jan;9(2):388-97. doi: 10.1002/pmic.200800485. PMID: 19105178.

Mead JA, Bianco L, Ottone V, Barton C, Kay RG, Lilley KS, Bond NJ, Bessant C. MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mol Cell Proteomics. 2009 Apr;8(4):696-705. doi: 10.1074/mcp.M800192-MCP200. Epub 2008 Nov 15. PMID: 19011259; PMCID: PMC2667351.

Archambault V, D'Avino PP, Deery MJ, Lilley KS, Glover DM. Sequestration of Polo kinase to microtubules by phosphopriming-independent binding to Map205 is relieved by phosphorylation at a CDK site in mitosis. Genes Dev. 2008 Oct 1;22(19):2707-20. doi: 10.1101/gad.486808. PMID: 18832073; PMCID: PMC2559908.

Sadowski PG, Groen AJ, Dupree P, Lilley KS. Sub-cellular localization of membrane proteins. Proteomics. 2008 Oct;8(19):3991-4011. doi: 10.1002/pmic.200800217. PMID: 18780351.

Lindsay HA, Baines R, ffrench-Constant R, Lilley K, Jacobs HT, O'Dell KM. The dominant cold-sensitive Out-cold mutants of Drosophila melanogaster have novel missense mutations in the voltage-gated sodium channel gene paralytic. Genetics. 2008 Oct;180(2):873-84. doi: 10.1534/genetics.108.090951. Epub 2008 Aug 24. PMID: 18723887; PMCID: PMC2567387.

Gibson F, Anderson L, Babnigg G, Baker M, Berth M, Binz PA, Borthwick A, Cash P, Day BW, Friedman DB, Garland D, Gutstein HB, Hoogland C, Jones NA, Khan A, Klose J, Lamond AI, Lemkin PF, Lilley KS, Minden J, Morris NJ, Paton NW, Pisano MR, Prime JE, Rabilloud T, Stead DA, Taylor CF, Voshol H, Wipat A, Jones AR. Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol. 2008 Aug;26(8):863-4. doi: 10.1038/nbt0808-863. PMID: 18688234.

Taylor CF, Binz PA, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn DM, Hühmer A, Kussmann M, Lilley K, Macht M, Mann M, Müller D, Neubert TA, Nickson J, Patterson SD, Raso R, Resing K, Seymour SL, Tsugita A, Xenarios I, Zeng R, Julian RK Jr. Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol. 2008 Aug;26(8):860-1. doi: 10.1038/nbt0808-860. PMID: 18688232.

Groen AJ, de Vries SC, Lilley KS. A proteomics approach to membrane trafficking. Plant Physiol. 2008 Aug;147(4):1584-9. doi: 10.1104/pp.108.123448. PMID: 18678750; PMCID: PMC2492629.

Coulthurst SJ, Lilley KS, Hedley PE, Liu H, Toth IK, Salmond GP. DsbA plays a critical and multifaceted role in the production of secreted virulence factorsby the phytopathogen Erwinia carotovora subsp. atroseptica. J Biol Chem. 2008 Aug 29;283(35):23739-53. doi: 10.1074/jbc.M801829200. Epub 2008 Jun 18. PMID: 18562317; PMCID: PMC3259793.

Lilley KS. Protein profiling using two-dimensional difference gel electrophoresis (2-D DIGE). Curr Protoc Protein Sci. 2003 Feb;Chapter 22:22.2.1-22.2.14. doi: 10.1002/0471140864.ps2202s30. PMID: 18429243.

Gulston MK, Rubtsov DV, Atherton HJ, Clarke K, Davies KE, Lilley KS, Griffin JL. A combined metabolomic and proteomic investigation of the effects of a failure to express dystrophin in the mouse heart. J Proteome Res. 2008 May;7(5):2069-77. doi: 10.1021/pr800070p. Epub 2008 Apr 3. PMID: 18386883.

Lilley KS, Dunkley TP. Determination of genuine residents of plant endomembrane organelles using isotope tagging and multivariate statistics. Methods Mol Biol. 2008;432:373-87. doi: 10.1007/978-1-59745-028-7_25. PMID: 18370031.

Kubis SE, Lilley KS, Jarvis P. Isolation and preparation of chloroplasts from Arabidopsis thaliana plants. Methods Mol Biol. 2008;425:171-86. doi: 10.1007/978-1-60327-210-0_16. PMID: 18369897.

D'Avino PP, Takeda T, Capalbo L, Zhang W, Lilley KS, Laue ED, Glover DM. Interaction between Anillin and RacGAP50C connects the actomyosin contractile ring with spindle microtubules at the cell division site. J Cell Sci. 2008 Apr 15;121(Pt 8):1151-8. doi: 10.1242/jcs.026716. Epub 2008 Mar 18. PMID: 18349071.

Allen MJ, Howard JA, Lilley KS, Wilson WH. Proteomic analysis of the EhV-86 virion. Proteome Sci. 2008 Mar 17;6:11. doi: 10.1186/1477-5956-6-11. PMID: 18346272; PMCID: PMC2322966.

Casasoli M, Spadoni S, Lilley KS, Cervone F, De Lorenzo G, Mattei B. Identification by 2-D DIGE of apoplastic proteins regulated by oligogalacturonides in Arabidopsis thaliana. Proteomics. 2008 Mar;8(5):1042-54. doi: 10.1002/pmic.200700523. PMID: 18324730.

Friedman DB, Lilley KS. Optimizing the difference gel electrophoresis (DIGE) technology. Methods Mol Biol. 2008;428:93-124. doi: 10.1007/978-1-59745-117-8_6. PMID: 18287770.

Karp NA, Feret R, Rubtsov DV, Lilley KS. Comparison of DIGE and post-stained gel electrophoresis with both traditional and SameSpots analysis for quantitative proteomics. Proteomics. 2008 Mar;8(5):948-60. doi: 10.1002/pmic.200700812. PMID: 18246571.

Cobbold LC, Spriggs KA, Haines SJ, Dobbyn HC, Hayes C, de Moor CH, Lilley KS, Bushell M, Willis AE. Identification of internal ribosome entry segment(IRES)-trans-acting factors for the Myc family of IRESs. Mol Cell Biol. 2008 Jan;28(1):40-9. doi: 10.1128/MCB.01298-07. Epub 2007 Oct 29. PMID: 17967896; PMCID: PMC2223313.

Lilley KS, Dupree P. Plant organelle proteomics. Curr Opin Plant Biol. 2007 Dec;10(6):594-9. doi: 10.1016/j.pbi.2007.08.006. Epub 2007 Oct 2. PMID: 17913569.

Karp NA, Lilley KS. Design and analysis issues in quantitative proteomics studies. Proteomics. 2007 Sep;7 Suppl 1:42-50. doi: 10.1002/pmic.200700683. PMID: 17893850.

Fineran PC, Williamson NR, Lilley KS, Salmond GP. Virulence and prodigiosin antibiotic biosynthesis in Serratia are regulated pleiotropically by the GGDEF/EAL domain protein, PigX. J Bacteriol. 2007 Nov;189(21):7653-62. doi: 10.1128/JB.00671-07. Epub 2007 Aug 31. PMID: 17766413; PMCID: PMC2168757.

Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H. The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 2007 Aug;25(8):887-93. doi: 10.1038/nbt1329. PMID: 17687369.

Lyne R, Smith R, Rutherford K, Wakeling M, Varley A, Guillier F, Janssens H, Ji W, Mclaren P, North P, Rana D, Riley T, Sullivan J, Watkins X, Woodbridge M, Lilley K, Russell S, Ashburner M, Mizuguchi K, Micklem G. FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol. 2007;8(7):R129. doi: 10.1186/gb-2007-8-7-r129. PMID: 17615057; PMCID: PMC2323218.

Viale A, Li J, Tiesman J, Hester S, Massimi A, Griffin C, Grills G, Khitrov G, Lilley K, Knudtson K, Ward B, Kornacker K, Chu CY, Auer H, Brooks AI. Big results from small samples: evaluation of amplification protocols for gene expression profiling. J Biomol Tech. 2007 Jul;18(3):150-61. PMID: 17595311; PMCID: PMC2062549.

D'Avino PP, Archambault V, Przewloka MR, Zhang W, Lilley KS, Laue E, Glover DM. Recruitment of Polo kinase to the spindle midzone during cytokinesis requires the Feo/Klp3A complex. PLoS One. 2007 Jun 27;2(6):e572. doi: 10.1371/journal.pone.0000572. PMID: 17593971; PMCID: PMC1894651.

Reddy AB, Maywood ES, Karp NA, King VM, Inoue Y, Gonzalez FJ, Lilley KS, Kyriacou CP, Hastings MH. Glucocorticoid signaling synchronizes the liver circadian transcriptome. Hepatology. 2007 Jun;45(6):1478-88. doi: 10.1002/hep.21571. PMID: 17538967.

Przewloka MR, Zhang W, Costa P, Archambault V, D'Avino PP, Lilley KS, Laue ED, McAinsh AD, Glover DM. Molecular analysis of core kinetochore composition and assembly in Drosophila melanogaster. PLoS One. 2007 May 30;2(5):e478. doi: 10.1371/journal.pone.0000478. PMID: 17534428; PMCID: PMC1868777.

Hurd TR, Prime TA, Harbour ME, Lilley KS, Murphy MP. Detection of reactive oxygen species-sensitive thiol proteins by redox difference gel electrophoresis: implications for mitochondrial redox signaling. J Biol Chem. 2007 Jul 27;282(30):22040-51. doi: 10.1074/jbc.M703591200. Epub 2007 May 24. PMID: 17525152.

Turck CW, Falick AM, Kowalak JA, Lane WS, Lilley KS, Phinney BS, Weintraub ST, Witkowska HE, Yates NA; Association of Biomolecula Resource Facilities Proteomics Research Group. The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 study: relative protein quantitation. Mol Cell Proteomics. 2007 Aug;6(8):1291-8. doi: 10.1074/mcp.M700165-MCP200. Epub 2007 May18. PMID: 17513294.

Karp NA, McCormick PS, Russell MR, Lilley KS. Experimental and statistical considerations to avoid false conclusions in proteomics studies using differential in-gel electrophoresis. Mol Cell Proteomics. 2007 Aug;6(8):1354-64. doi: 10.1074/mcp.M600274-MCP200. Epub 2007 May 17. PMID: 17513293.

Sadowski PG, Dunkley TP, Shadforth IP, Dupree P, Bessant C, Griffin JL, Lilley KS. Quantitative proteomic approach to study subcellular localization of membrane proteins. Nat Protoc. 2006;1(4):1778-89. doi: 10.1038/nprot.2006.254. PMID: 17487160.

Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DC, Cornell MJ, Petty J, Hakes L, Wardleworth L, Rash B, Brown M, Dunn WB, Broadhurst D, O'Donoghue K, Hester SS, Dunkley TP, Hart SR, Swainston N, Li P, Gaskell SJ, Paton NW, Lilley KS, Kell DB, Oliver SG. Growth control of the eukaryote cell: a systems biology study in yeast. J Biol. 2007;6(2):4. doi: 10.1186/jbiol54. PMID: 17439666; PMCID: PMC2373899.

Ferguson BJ, Dovey CL, Lilley K, Wyllie AH, Rich T. Nuclear phospholipase C gamma: punctate distribution and association with the promyelocytic leukemia protein. J Proteome Res. 2007 May;6(5):2027-32. doi: 10.1021/pr060684v. Epub 2007 Apr 10. PMID: 17419608.

Karp NA, Lilley KS. Identification of clock genes using difference gel electrophoresis. Methods Mol Biol. 2007;362:265-87. doi: 10.1007/978-1-59745-257-1_18. PMID: 17417015.

Hartman NT, Sicilia F, Lilley KS, Dupree P. Proteomic complex detection using sedimentation. Anal Chem. 2007 Mar 1;79(5):2078-83. doi: 10.1021/ac061959t. PMID: 17326601.

Chen F, Archambault V, Kar A, Lio' P, D'Avino PP, Sinka R, Lilley K, Laue ED, Deak P, Capalbo L, Glover DM. Multiple protein phosphatases are required for mitosis in Drosophila. Curr Biol. 2007 Feb 20;17(4):293-303. doi: 10.1016/j.cub.2007.01.068. PMID: 17306545.

Prabakaran S, Wengenroth M, Lockstone HE, Lilley K, Leweke FM, Bahn S. 2-D DIGE analysis of liver and red blood cells provides further evidence for oxidative stress in schizophrenia. J Proteome Res. 2007 Jan;6(1):141-9. doi: 10.1021/pr060308a. PMID: 17203958.

Maslen S, Sadowski P, Adam A, Lilley K, Stephens E. Differentiation of isomeric N-glycan structures by normal-phase liquid chromatography-MALDI-TOF/TOF tandem mass spectrometry. Anal Chem. 2006 Dec 15;78(24):8491-8. doi: 10.1021/ac0614137. PMID: 17165844.

Borner GH, Harbour M, Hester S, Lilley KS, Robinson MS. Comparative proteomics of clathrin-coated vesicles. J Cell Biol. 2006 Nov 20;175(4):571-8. doi: 10.1083/jcb.200607164. PMID: 17116749; PMCID: PMC2064594.

Klein EM, Mascheroni L, Pompa A, Ragni L, Weimar T, Lilley KS, Dupree P, Vitale A. Plant endoplasmin supports the protein secretory pathway and has a role in proliferating tissues. Plant J. 2006 Dec;48(5):657-73. doi: 10.1111/j.1365-313X.2006.02904.x. Epub 2006 Oct 19. PMID: 17059403.

Battersby A, Jones RD, Lilley KS, McFarlane RJ, Braig HR, Allen ND, Wakeman JA. Comparative proteomic analysis reveals differential expression of Hsp25 following the directed differentiation of mouse embryonic stem cells. Biochim Biophys Acta. 2007 Feb;1773(2):147-56. doi: 10.1016/j.bbamcr.2006.08.030. Epub 2006 Aug 26. PMID: 17030443.

Lilley KS, Friedman DB. Difference gel electrophoresis DIGE. Drug Discov Today Technol. 2006 Autumn;3(3):347-53. doi: 10.1016/j.ddtec.2006.09.013. PMID: 24980539.

Ahmed ZM, Goodyear R, Riazuddin S, Lagziel A, Legan PK, Behra M, Burgess SM, Lilley KS, Wilcox ER, Riazuddin S, Griffith AJ, Frolenkov GI, Belyantseva IA, Richardson GP, Friedman TB. The tip-link antigen, a protein associated with the transduction complex of sensory hair cells, is protocadherin-15. J Neurosci. 2006 Jun 28;26(26):7022-34. doi: 10.1523/JNEUROSCI.1163-06.2006. PMID: 16807332; PMCID: PMC6673907.

Reddy AB, Karp NA, Maywood ES, Sage EA, Deery M, O'Neill JS, Wong GK, Chesham J, Odell M, Lilley KS, Kyriacou CP, Hastings MH. Circadian orchestration of the hepatic proteome. Curr Biol. 2006 Jun 6;16(11):1107-15. doi: 10.1016/j.cub.2006.04.026. PMID: 16753565.

Knudtson KL, Auer H, Brooks AI, Griffin C, Grills G, Hester S, Khitrov G, Lilley KS, Massimi A, Tiesman JP, Viale A. The ABRF MARG microarray survey 2005: taking the pulse of the microarray field. J Biomol Tech. 2006 Apr;17(2):176-86. PMID: 16741246; PMCID: PMC2291780.

Terhzaz S, Southall TD, Lilley KS, Kean L, Allan AK, Davies SA, Dow JA. Differential gel electrophoresis and transgenic mitochondrial calcium reporters demonstrate spatiotemporal filtering in calcium control of mitochondria. J Biol Chem. 2006 Jul 7;281(27):18849-58. doi: 10.1074/jbc.M603002200. Epub 2006 May 2. PMID: 16670086.

Dunkley TP, Hester S, Shadforth IP, Runions J, Weimar T, Hanton SL, Griffin JL, Bessant C, Brandizzi F, Hawes C, Watson RB, Dupree P, Lilley KS. Mapping the Arabidopsis organelle proteome. Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6518-23. doi: 10.1073/pnas.0506958103. Epub 2006 Apr 17. PMID: 16618929; PMCID: PMC1458916.

Lilley KS, Dupree P. Methods of quantitative proteomics and their application to plant organelle characterization. J Exp Bot. 2006;57(7):1493-9. doi: 10.1093/jxb/erj141. PMID: 16617121.

Ward DG, Taylor M, Lilley KS, Cavieres JD. TNP-8N3-ADP photoaffinity labeling of two Na,K-ATPase sequences under separate Na+ plus K+ control. Biochemistry. 2006 Mar 14;45(10):3460-71. doi: 10.1021/bi051927k. PMID: 16519541.

Coulthurst SJ, Lilley KS, Salmond GP. Genetic and proteomic analysis of the role of luxS in the enteric phytopathogen, Erwinia carotovora. Mol Plant Pathol. 2006 Jan 1;7(1):31-45. doi: 10.1111/j.1364-3703.2005.00314.x. PMID: 20507426.

Shadforth IP, Dunkley TP, Lilley KS, Bessant C. i-Tracker: for quantitative proteomics using iTRAQ. BMC Genomics. 2005 Oct 20;6:145. doi: 10.1186/1471-2164-6-145. PMID: 16242023; PMCID: PMC1276793.

Shadforth I, Dunkley T, Lilley K, Crowther D, Bessant C. Confident protein identification using the average peptide score method coupled with search-specific, ab initio thresholds. Rapid Commun Mass Spectrom. 2005;19(22):3363-8. doi: 10.1002/rcm.2203. PMID: 16235224.

Karp NA, Spencer M, Lindsay H, O'Dell K, Lilley KS. Impact of replicate types on proteomic expression analysis. J Proteome Res. 2005 Sep- Oct;4(5):1867-71. doi: 10.1021/pr050084g. PMID: 16212444.

Karp NA, Lilley KS. Maximising sensitivity for detecting changes in protein expression: experimental design using minimal CyDyes. Proteomics. 2005 Aug;5(12):3105-15. doi: 10.1002/pmic.200500083. PMID: 16035117.

Lilley KS, Friedman DB. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics. 2004 Dec;1(4):401-9. doi: 10.1586/14789450.1.4.401. PMID: 15966837.

Corbett M, Virtue S, Bell K, Birch P, Burr T, Hyman L, Lilley K, Poock S, Toth I, Salmond G. Identification of a new quorum-sensing-controlled virulence factor in Erwinia carotovora subsp. atroseptica secreted via the type II targeting pathway. Mol Plant Microbe Interact. 2005 Apr;18(4):334-42. doi: 10.1094/MPMI-18-0334. PMID: 15828685.

Karp NA, Griffin JL, Lilley KS. Application of partial least squares discriminant analysis to two-dimensional difference gel studies in expression proteomics. Proteomics. 2005 Jan;5(1):81-90. doi: 10.1002/pmic.200400881. PMID: 15744836.

Borner GH, Sherrier DJ, Weimar T, Michaelson LV, Hawkins ND, Macaskill A, Napier JA, Beale MH, Lilley KS, Dupree P. Analysis of detergent-resistant membranes in Arabidopsis. Evidence for plasma membrane lipid rafts. Plant Physiol. 2005 Jan;137(1):104-16. doi: 10.1104/pp.104.053041. Epub 2004 Dec 23. PMID: 15618420; PMCID: PMC548842.

Garwood K, McLaughlin T, Garwood C, Joens S, Morrison N, Taylor CF, Carroll K, Evans C, Whetton AD, Hart S, Stead D, Yin Z, Brown AJ, Hesketh A, Chater K, Hansson L, Mewissen M, Ghazal P, Howard J, Lilley KS, Gaskell SJ, Brass A, Hubbard SJ, Oliver SG, Paton NW. PEDRo: a database for storing, searching and disseminating experimental proteomics data. BMC Genomics. 2004 Sep 17;5:68. doi: 10.1186/1471-2164-5-68. PMID: 15377392; PMCID: PMC521486.

Jones AM, Thomas V, Truman B, Lilley K, Mansfield J, Grant M. Specific changes in the Arabidopsis proteome in response to bacterial challenge: differentiating basal and R-gene mediated resistance. Phytochemistry. 2004 Jun;65(12):1805-16. doi: 10.1016/j.phytochem.2004.04.005. PMID: 15276439.

Kubis S, Patel R, Combe J, Bédard J, Kovacheva S, Lilley K, Biehl A, Leister D, Ríos G, Koncz C, Jarvis P. Functional specialization amongst the Arabidopsis Toc159 family of chloroplast protein import receptors. Plant Cell. 2004 Aug;16(8):2059-77. doi: 10.1105/tpc.104.023309. Epub 2004 Jul 23. PMID: 15273297; PMCID: PMC519198.

Lilley KS, Griffiths DR. Proteomics in Drosophila melanogaster. Brief Funct Genomic Proteomic. 2003 Jul;2(2):106-13. doi: 10.1093/bfgp/2.2.106. PMID: 15239931.

Karp NA, Kreil DP, Lilley KS. Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis. Proteomics. 2004 May;4(5):1421-32. doi: 10.1002/pmic.200300681. PMID: 15188411.

Kreil DP, Karp NA, Lilley KS. DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results. Bioinformatics. 2004 Sep 1;20(13):2026-34. doi: 10.1093/bioinformatics/bth193. Epub 2004 Mar 25. PMID: 15044229.

Lalanne E, Honys D, Johnson A, Borner GH, Lilley KS, Dupree P, Grossniklaus U, Twell D. SETH1 and SETH2, two components of the glycosylphosphatidylinositol anchor biosynthetic pathway, are required for pollen germination and tube growth in Arabidopsis. Plant Cell. 2004 Jan;16(1):229-40. doi: 10.1105/tpc.014407. Epub 2003 Dec 11. PMID: 14671020; PMCID: PMC301407.

Tofaris GK, Razzaq A, Ghetti B, Lilley KS, Spillantini MG. Ubiquitination of alpha-synuclein in Lewy bodies is a pathological event not associated with impairment of proteasome function. J Biol Chem. 2003 Nov 7;278(45):44405-11. doi: 10.1074/jbc.M308041200. Epub 2003 Aug 15. PMID: 12923179.

Kubis S, Baldwin A, Patel R, Razzaq A, Dupree P, Lilley K, Kurth J, Leister D, Jarvis P. The Arabidopsis ppi1 mutant is specifically defective in the expression, chloroplast import, and accumulation of photosynthetic proteins. Plant Cell. 2003 Aug;15(8):1859-71. doi: 10.1105/tpc.012955. PMID: 12897258; PMCID: PMC167175.

Borner GH, Lilley KS, Stevens TJ, Dupree P. Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis. Plant Physiol. 2003 Jun;132(2):568-77. doi: 10.1104/pp.103.021170. Epub 2003 May 1. PMID: 12805588; PMCID: PMC166998.

Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, Kell DB, Lilley KS, Roepstorff P, Yates JR 3rd, Brass A, Brown AJ, Cash P, Gaskell SJ, Hubbard SJ, Oliver SG. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol. 2003 Mar;21(3):247-54. doi: 10.1038/nbt0303-247. PMID: 12610571.

Robertson AS, Belorgey D, Lilley KS, Lomas DA, Gubb D, Dafforn TR. Characterization of the necrotic protein that regulates the Toll-mediated immune response in Drosophila. J Biol Chem. 2003 Feb 21;278(8):6175-80. doi: 10.1074/jbc.M209277200. Epub 2002 Oct 31. PMID: 12414799.

Ritchie MA, Gill AC, Deery MJ, Lilley K. Precursor ion scanning fordetection and structural characterization of heterogeneous glycopeptide mixtures. J Am Soc Mass Spectrom. 2002 Sep;13(9):1065-77. doi: 10.1016/S1044-0305(02)00421-X. PMID: 12322954.

Beale M, Dupree P, Lilley K, Beynon J, Trick M, Clarke J, Bevan M, Bancroft I, Jones J, May S, van de Sande K, Leyser O. GARNet, the Genomic Arabidopsis Resource Network. Trends Plant Sci. 2002 Apr;7(4):145-7. doi: 10.1016/s1360-1385(01)02224-5. PMID: 11950604.

Lilley KS, Razzaq A, Dupree P. Two-dimensional gel electrophoresis: recent advances in sample preparation, detection and quantitation. Curr Opin Chem Biol. 2002 Feb;6(1):46-50. doi: 10.1016/s1367-5931(01)00275-7. PMID: 11827822.

Diggle TA, Subkhankulova T, Lilley KS, Shikotra, N, Willis AE, Redpath NT,; Phosphorylation of elongation factor-2 kinase on serine 499 by cAMP-dependent protein kinase induces Ca2+/calmodulin-independent activity. Biochem J 1 February 2001; 353 (3): 621–626. doi: https://doi.org/10.1042/bj3530621

Lilley, KS and Engel, PC (1992), The essentail active-site lysines of clostridial glutamate dehydrogenase. European Journal of Biochemistry, 207: 533-540. https://doi.org/10.1111/j.1432-1033.1992.tb17079.x

Lilley KS, Baker PJ, K. Britton L, Stillman TJ, Brown PE, Moir AJG, Engel PC, Rice DW, Bell JE, Bell E, The partial amino acid sequence of the NAD -dependent glutamate dehydrogenase of Clostridium symbiosum: implications for the evolution and structural basis of coenzyme specificity, Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Volume 1080, Issue 3,1991,Pages 191-197, https://doi.org/10.1016/0167-4838(91)90001-G

Lilley KS., Davison MD. and Rivett AJ (1990), N-Terminal sequence similarities between components of the multicatalytic proteinase complex, FEBS Letters, 262, doi: 10.1016/0014-5793(90)80220-D