skip to primary navigationskip to content
 

Publications

2016

Wieczorek S, Combes F, Lazar C, Giai Gianetto Q, Gatto L, Dorffer A, Hesse A, Coute Y, Ferro M, Bruley C, and Burger T. DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics Bioinformatics 2016 doi:10.1093/bioinformatics/btw580.

Perez-Riverol Y, Gatto L, et al. Ten Simple Rules for Taking Advantage of Git and GitHub. PLoS Comput Biol. 2016 Jul 14;12(7):e1004947. doi:10.1371/journal.pcbi.1004947.

Lazar C, Gatto L, Ferro M, Bruley C, Burger T. Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies. J Proteome Res. 2016 Apr 1;15(4):1116-25. doi:10.1021/acs.jproteome.5b00981.

Christoforou A, et al A draft map of the mouse pluripotent stem cell spatial proteome Nature Communications (2016) 12;7:9992. doi: 10.1038/ncomms9992.

Marondedze C, et al ,The RNA-binding protein repertoire of Arabidopsis thaliana  Scientific Reports (2016) 6:29766. doi: 10.1038/srep29766

Breckels et al,  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.

Fabre B, et al 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.

Alam MT et al and Ralser M , The metabolic background is a global player in Saccharomyces gene expression epistasis. Nature Microbiol. (2016) Feb 1;1:15030. doi: 10.1038/nmicrobiol.2015.30.

Marondedze C  et al 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.

2015

Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O and Beyer, A Testing and validation of computational methods for mass spectrometry. J Proteome Res. 2015. doi: 10.1002/stem.2067.

Gatto L, Breckels LM, Naake T and Gibb S Visualisation of proteomics data using R and Bioconductor. Proteomics. 2015 Feb 18. doi:10.1002/pmic.201400392.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015 Jan 29;12(2):115-21 doi:10.1038/nmeth.3252.

Chen C, Buhl, E, Xu, M, Croset, V, Rees, JS, Lilley KS, Benton, R, Hodge JL, Stanewsky, R.Drosophila Ionotropic Receptor 25a mediates circadian clock resetting by temperature Nature 2015, 2015 Nov 18. doi: 10.1038/nature16148

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

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. Review.

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.

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. eCollection 2015 Jun.

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.

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.

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) Transgenic Bread Wheat Infected with Fusarium graminearumJ Agric Food Chem. 2015 Apr 22;63(15):3962-9. doi: 10.1021/jf506003t. Epub 2015 Apr 9.

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.

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.

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.

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

2014

Lowe N, et al 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 141(20):3994-4005. doi: 10.1242/dev.111054. (2014)

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

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.13(8):2147-67. doi: 10.1074/mcp.M114.040923. (2014)

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. 13(7):3360-9. doi: 10.1021/pr500220g. (2014).

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. 13(8):1937-52. doi: 10.1074/mcp.M113.036350.(2014)

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. 1156:157-74. doi: 10.1007/978-1-4939-0685-7_10.(2014)

Walzer M, et al. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics. 13(8):1905-13. doi: 10.1074/mcp.M113.035907. (2014).

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. Nature Biotechnol. 32(5):465-72. doi: 10.1038/nbt.2860. (2014)

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.;289(21):14434-47. doi: 10.1074/jbc.M113.529578. (2014).

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. 25(9):2017-27. doi: 10.1681/ASN.2013101066. (2014).

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

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

Gatto L, Breckels LM, Wieczorek S, Burger T, Lilley KS Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata. Bioinformatics. 30(9):1322-4. doi: 10.1093/bioinformatics/btu013. (2014).

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. 13(2):763-76. doi: 10.1021/pr4008464. (2014)

Gillingham AK, Sinka R, Torres IL, Lilley KS, Munro S.Toward a comprehensive map of the effectors of rab GTPases. Developmental Cell. 2014 Nov 10;31(3):358-73. doi: 10.1016/j.devcel.2014.10.007. Epub 2014 Nov 10.

2013

Gatto L. and Christoforou A. Using R and Bioconductor for proteomics data analysis, Biochim Biophys Acta - Proteins and Proteomics, 2013 http://dx.doi.org/10.1016/j.bbapap.2013.04.032.

Wilf NM, et al 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. 14:822. doi: 10.1186/1471-2164-14-822.(2013)

King HA, Cobbold LC, Pichon X, Pöyry T, Wilson LA, Booden H, Jukes-Jones R, Cain K, Lilley KS, Bushell M, Willis AE.Remodelling of a polypyrimidine tract-binding protein complex during apoptosis activates cellular IRESs. Cell Death Differ. 21(1):161-71. doi: 10.1038/cdd.2013.135. (2013)

Hemsley PA, Weimar T, Lilley K, Dupree P, Grierson C. Palmitoylation in plants: new insights through proteomics. Plant Signal Behav. 8(8). pii: e25209. doi: 10.4161/psb.25209. (2013).

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. Nature  Med. 19(6):753-9. doi: 10.1038/nm.3212. (2013).

Breckels LM, Gatto L, Christoforou A, Groen AJ, Lilley KS, Trotter MW. The effect of organelle discovery upon sub-cellular protein localisation. J Proteomics. 88:129-40. doi: 10.1016/j.jprot.2013.02.019. (2013).

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. 12(6):2323-39. doi: 10.1021/pr300775k. (2013).

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

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. 13(6):904-9. doi: 10.1002/pmic.201200532. (2013)

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. 11(1):1. doi: 10.1186/1478-811X-11-1.(2013)

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. 2:272. doi: 10.12688/f1000research.2-272.v2. eCollection (2013).

Hemsley PA, Weimar T, Lilley KS, Dupree P, Grierson C A proteomic approach identifies many novel palmitoylated proteins in Arabidopsis. New Phytol. 197(3):805-14. doi: 10.1111/nph.12077. (2013)

2012

Pipeline to assess the greatest source of technical variance in quantitative proteomics using metabolic labelling. Russell MR, Lilley KS. J Proteomics. 2012 

Popular computational methods to assess multi-protein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Armean IM, Lilley KS, Trotter MW. Mol Cell Proteomics. 2012 

Putative glycosyltransferases and other plant golgi apparatus proteins are revealed by LOPIT proteomics. Nikolovski N, Rubtsov D, Segura MP, Miles GP, Stevens TJ, Dunkley TP, Munro S, Lilley KS, Dupree P. Plant Physiol. 2012 

MRMaid 2.0: mining PRIDE for evidence-based SRM transitions. Fan J, Mohareb F, Bond NJ, Lilley KS, Bessant C. OMICS 2012 

Isobaric tagging approaches in quantitative proteomics: the ups and downs. Christoforou AL, Lilley KS. Anal Bioanal Chem. 2012 

Evaluation and properties of the budding yeast phosphoproteome. Amoutzias GD, He Y, Lilley KS, Van de Peer Y, Oliver SG. Mol Cell Proteomics. 2012 

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

Pre - 2012

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

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

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

In Vivo Analyses of the Roles of Essential Omp85-Related Proteins in the Chloroplast Outer Envelope Membrane. Huang WH, Ling QH, Bedard J, Lilley K, Jarvis P Plant Physiology 2011 Sept Volume: 157 Issue: 1 Pages: 147-159 DOI: 10.1104/pp.111.181891 

Method for suppressing non-specific protein interactions observed with affinity resins. Rees JS, Lilley KS. Methods. 2011 Aug;54(4):407-12. Epub 2011 Jun 22. 

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

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

Proteomics of cryoprotective dehydration in Megaphorura arctica Tullberg 1876 (Onychiuridae: Collembola). Thorne MA, Worland MR, Feret R, Deery MJ, Lilley KS, Clark MS. Insect Mol Biol. 2011 Jun;20(3):303-10. doi: 10.1111/j.1365-2583.2010.01062.x. Epub 2010 Dec 29. 

The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses.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. Proteomics. 2011 Apr;11(8):1371-81. doi: 10.1002/pmic.201000736. Epub 2011 Mar 11. 

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

Organelle proteomics experimental designs and analysis. Laurent Gatto, Juan Antonio Vizcaíno, Henning Hermjakob, Wolfgang Huber and Kathryn S. Lilley. Proteomics. 2010 Nov 2 

The Drosophila melanogaster sperm proteome-II (DmSP-II) Wasbrough ER, Dorus S, Hester S, Howard-Murkin J, Lilley K, Wilkin E, Polpitiya A, Petritis K, Karr TL Journal of Proteomics 2010 Oct Volume: 73 Issue: 11 Special Issue: SI Pages: 2171-2185 DOI: 10.1016/j.jprot.2010.09.002 

Genomic tagging reveals a random association of endogenous PtdIns5P 4-kinases IIalpha and IIbeta and a partial nuclear localisation of the IIalpha isoform. Wang M, Bond NJ, Letcher AJ, Richardson JP, Lilley KS, Irvine RF, Clarke JH. Biochem J. 2010 Jun 23. 

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, Hurd T, Nadtochiy SM, Brookes PS, Fearnley IM, Lilley KS, Smith RA, Murphy MP. Biochem J. 2010 Jun 10. 

Nutrient control of eukaryote cell growth: a systems biology study in yeast. Gutteridge A, Pir P, Castrillo JI, Charles PD, Lilley KS, Oliver SG. BMC Biol. 2010 May 24;8:68. 

Addressing accuracy and precision issues in iTRAQ quantitation. Karp NA, Huber W, Sadowski PG, Charles PD, Hester SV, Lilley KS. Mol Cell Proteomics. 2010 Apr 10. 

Mutation of nfxB Causes Global Changes in the Physiology and Metabolism of Pseudomonas aeruginosa. Stickland HG, Davenport PW, Lilley KS, Griffin JL, Welch M. J Proteome Res. 2010 Apr 21. 

Mutations in rpsL that confer streptomycin resistance show pleiotropic effects on virulence and the production of a carbapenem antibiotic in Erwinia carotovora. Barnard AM, Simpson NJ, Lilley KS, Salmond GP. Microbiology. 2010 Apr;156(Pt 4):1030-9. 

Measurement of protein synthesis using heavy water labeling and peptide mass spectrometry: Discrimination between major histocompatibility complex allotypes. De Riva A, Deery MJ, McDonald S, Lund T, Busch R. Anal Biochem. 2010 Aug;403(1-2):1-12. 

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

Proteomic analysis reveals the role of synaptic vesicle cycling in sustaining the suprachiasmatic circadian clock. M. J. Deery, E.S. Maywood, J.C. Chesham, M. Sladek, N.A. Karp, E.W. Green, P.D. Charles, A.B. Reddy, C.P. Kyriacou, K.S. Lilley, M.H. Hastings. Current Biology. 2009 19(23), 2031-2036. 

Mapping organelle proteins and protein complexes in Drosophila melanogasterTan D, Dvinge H, Christoforou A, Bertone P, Martinez Arias A, Lilley KS. J Proteome Res. Jun;8(6):2667-78. 

The organelle proteome of the DT40 Lymphocyte cell line. Hall SL, Hester S, Griffin JL, Lilley KS, Jackson AP. Mol Cell Proteomics. Jun;8(6):1295-305. 

The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Fineran PC, Blower TR, Foulds IJ, Humphreys DP, Lilley KS, Salmond GP. Proc Natl Acad Sci U S A. 2009 20;106(3):894-9. 

MRMaid: the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mead JA, Bianco L, Ottone V, Barton C, Kay RG, Lilley KS, Bond NJ, Bessant C. Mol Cell Proteomics. 2009 8(4):696-705. 

Biofilms and type III secretion are not mutually exclusive in Pseudomonas aeruginosaMikkelsen H, Bond NJ, Skindersoe ME, Givskov M, Lilley KS, Welch M. Microbiology. 2009 155(Pt 3):687-98. 

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

Investigating sample pooling strategies for DIGE experiments to address biological variability. Karp NA and Lilley KS. Proteomics. 2009 Jan;9(2):388-97. 

Drosophila Larp associates with poly(A)-binding protein and is required for male fertility and syncytial embryo development. Blagden SP, Gatt MK, Archambault V, Lada K, Ichihara K, *Lilley KS*, Inoue YH, Glover DM. Dev Biol. 2009 334(1):186-97. 

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

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 PP, Deery MJ, Lilley KS, Glover DM. Genes Dev. 2008 1;22(19):2707-20. 

Optimizing the difference gel electrophoresis (DIGE) technology. Friedman DB, Lilley KS. Methods Mol Biol. 2008 428:93-124. 

Sub-cellular localization of membrane proteins. Sadowski, PG, Groen AJ, Dupree P and Lilley KS. Proteomics. 2008 8(19):3991-4011. 

A proteomics approach to membrane trafficking. Groen AJ, de Vries SC, Lilley KS. Plant Physiol. 2008 Aug;147(4):1584-9. 

Identification of internal ribosome entry segment (IRES)-trans-acting factors for the Myc family of IRESs. Cobbold LC, Spriggs KA, Haines SJ, Dobbyn HC, Hayes C, de Moor CH, Lilley KS, Bushell M, Willis AE. Mol Cell Biol. 2008 28(1):40-9. 

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

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

Proteomic analysis of the EhV-86 virion Allen MJ, Howard JA, Lilley KS, Wilson WH. Proteome Sci. 2008 Mar 17;6(1):11 

Interaction between Anillin and RacGAP50C connects the actomyosin contractile ring with spindle microtubules at the cell division site. D'Avino PP, Takeda T, Capalbo L, Zhang W, Lilley KS, Laue ED, Glover DM. J Cell Sci. 2008 121(Pt 8):1151-8. 

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

Determination of genuine residents of plant endomembrane organelles using isotope tagging and multivariate statistics. Lilley KS, Dunkley TP. Methods Mol Biol. 2008;432:373-87. 

Isolation and preparation of chloroplasts from Arabidopsis thaliana plants. Kubis SE, Lilley KS, Jarvis P. Methods Mol Biol2008;425:171-86. 

DsbA plays a critical and multi-faceted role in the production of secreted virulence factors by the phytopathogen, Erwinia carotovora subsp. atroseptica Coulthurst SJ, Lilley KS, Hedley PE, Liu H, Toth IK, Salmond GP. J Biol Chem. 2008 Jun 18. 283(35):23739-53 

Independent protein-profiling studies show a decrease in apolipoprotein A1 levels in schizophrenia CSF, brain and peripheral tissues. Huang JT, Wang L, Prabakaran S, Wengenroth M, Lockstone HE, Koethe D, Gerth CW, Gross S, Schreiber D, *Lilley K,* Wayland M, Oxley D, Leweke FM, Bahn S. Mol Psychiatry. 2008 13(12):1118-28. 

Guidelines for reporting the use of gel electrophoresis in proteomics. 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. Nat Biotechnol. 2008 26(8):863-4. 

2-D DIGE Analysis of Liver and Red Blood Cells Provides Further Evidence for Oxidative Stress in Schizophrenia. Prabakaran. S., Wengenroth, M., Lockstone, H.E, Lilley, K, Leweke,F.M. and Bahn S.(2007) J. Prot Res. 6 (1) 141-149 

Inter-relationships between colonies, biofilms, and planktonic cells of Pseudomonas aeruginosa. Mikkelsen H, Duck Z, Lilley KS, Welch M. J Bacteriol. 2007 Mar;189(6):2411-6 

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

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

Identification of clock genes using difference gel electrophoresis. Karp NA, Lilley KS. Methods Mol Biol. 2007;362:265-87. 

Experimental and statistical considerations to avoid false conclusions in proteomic studies using differential in-gel electrophoresis. Karp NA, McCormick PS, Russell MR, Lilley KS. Mol Cell Proteomics 2007 Aug;6(8):1354-64 

Detection of ros-sensitive thiol proteins by redox-difference gel electrophoresis (redox-dige): Implications for mitochondrial redox signalling. Hurd TR, Prime TA, Harbour ME, Lilley KS, Murphy MP. J Biol Chem. 2007 Jul 27;282(30):22040-51 

Recruitment of Polo Kinase to the Spindle Midzone during Cytokinesis Requires the Feo/Klp3A Complex. D'Avino PP, Archambault V, Przewloka MR, Zhang W, Lilley KS, Laue E, Glover DM. PLoS ONE. 2007 

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

Molecular Analysis of Core Kinetochore Composition and Assembly in Drosophila melanogaster. Przewloka MR, Zhang W, Costa P, Archambault V, D'Avino PP, Lilley KS, Laue ED, McAinsh AD, Glover DM. PLoS ONE. 2007 

Nuclear Phospholipase C Gamma: Punctate Distribution and Association with the Promyelocytic Leukemia Protein. Ferguson BJ, Dovey CL, Lilley K, Wyllie AH, Rich T Journal of Proteome Research 2007 6(1):141-9 

Comparative proteomic analysis reveals differential expression of Hsp25 following the directed differentiation of mouse embryonic stem cells. Battersby A, Jones RD, Lilley KS, McFarlane RJ, Braig HR, Allen ND, Wakeman JA. Biochim Biophys Acta. 2007 1773(2):147-56. 

A comprehensive Growth control of the eukaryotic cell: a systems biology study in yeast. Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DCJ, Cornell MJ, Petty J, Hakes L, Wardleworth L, Rash B, Brown M, Dunn WB, Broadhurst D, Hart SR, Jackson CS, O'Donoghue K, Hester S, Dunkley T, Swainston N. Li P, Gaskell SJ, Paton NW, Lilley KS, Kell DB, Oliver SG. Journal of Biology. 2007 6: 4 

The minimum information about a proteomics experiment (MIAPE). 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. Nat Biotechnol. 2007 25(8):887-93 

FlyMine: an integrated database for Drosophila and Anopheles genomics. 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. Genome Biol. 2007 8(7):R129 

The association of biomolecular resource facilities proteomics research group 2006 study: relative protein quantitation. Turck CW, Falick AM, Kowalak JA, Lane WS, Lilley KS, Phinney BS, Weintraub ST, Witkowska HE, Yates NA. Mol Cell. Proteomics. 2007 6(8):1291-8 

Virulence and prodigiosin antibiotic biosynthesis in Serratia are regulated pleiotropically by the GGDEF/EAL domain protein, PigX. Fineran PC, Williamson NR, Lilley KS, Salmond GP. J Bacteriol. 2007 189 (21) 7653-62 

Design and analysis issues in quantitative proteomics studies Proteomics. Karp, NA, Lilley KS. Proteomics. 2007 7(S1):42-50 

Plant organelle proteomics. Lilley KS, Dupree, P Curr. Opin. Plant Biol. 2007 10 (6) 594-9

Genetic and proteomic analysis of the role of luxS in the enteric phytopathogen, Erwinia carotovora. Coulthurst SJ, Lilley,KS and Salmond GPC. Mol. Plant Path. 2006 7 (1) :31-45. 

Methods of Quantitative Proteomics and their application to plant organelle characterization. Lilley KS and Dupree P. Journal of Experimental Botany. 2006 57(7):1493-9. 

TNP-8N3-ADP Photoaffinity Labeling of Two Na,K-ATPase Sequences under Separate Na + plus K + Control. Ward DG, Taylor, M, Lilley KS, Cavieres JD. J. Biol. Chem. 2006 45(10):3460-71 

Mapping the Arabidopsis Organelle Proteome. Dunkley, TPJ., Hester S., Shadforth, IP, Runions, J, Weimar, T, Hanton, SL, Griffin, JL, Bessant C, Brandizzi ,F, Hawes, C, Watson, RB, Dupree P and Lilley KS. Prot. Natl. Acad. Sci. 2006 25;103(17):6518-23 

Differential gel electrophoresis and transgenic mitochondrial calcium reporters demonstrate spatiotemporal filtering in calcium control of mitochondria. (2006) Terhzaz S, Southall TD, Lilley KS, Kean L, Allan AK, Davies SA, Dow JA. J Biol Chem. 2006 281(27):18849-58

Circadian orchestration of the hepatic proteome. 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. Curr Biol. 2006 16(11):1107-15. 

The tip-link antigen, a protein associated with the transduction complex of sensory hair cells, is protocadherin-15. 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. J Neurosci. 2006 26(26):7022-34 

Plant endoplasmin supports the protein secretory pathway and has a role in proliferating tissues. Klein EM, Mascheroni L, Pompa A, Ragni L, Weimar T, Lilley KS, Dupree P, Vitale A. Plant J. 2006 48(5):657-73. 

Comparative proteomics of clathrin-coated vesicles. Borner GH, Harbour M, Hester S, Lilley KS and Robinson MS. J Cell Biol. 2006 175(4):571-8. 

Quantitative proteomic approach to study subcellular localization of membrane proteins. Sadowski, PG Dunkley, TPJ, Shadforth, IP,Griffin, JL, Dupree, P, Bessant, C, and Lilley, KS. Nature Protocols. 2006 1 1778 - 1789 

Differentiation of Isomeric N-Glycan Structures by Normal-Phase Liquid Chromatography-MALDI-TOF/TOF Tandem Mass Spectrometry. Maslen, S.; Sadowski, P.; Adam, A.; Lilley, K.; Stephens, E. Anal Chem. 2006 15;78(24):8491-8.

Application of Partial Least Squares Discriminant Analysis to Two Dimensional difference gel studies in expression proteomics. Natasha A. Karp, Julian L. Griffin, and Kathryn S. Lilley. Proteomics. 2005 5 (1): 81-90 

Identification of a New Quorum-Sensing-Controlled Virulence Factor in Erwinia carotovora subsp. atroseptica Secreted via the Type II Targeting Pathway. M. Corbett, S. Virtue, K. Bell, P. Birch, T. Burr, L. Hyman, K. Lilley, S. Poock, I. Toth, and G. Salmond. MPMI. 2005 18 (4): 334-342 

Analysis of detergent-resistant membranes in Arabidopsis. Evidence for plasma membrane lipid rafts Borner GHH. Sherrier DJ, Weimar T, Michaelson LV, Hawkins ND, MacAskill A, Napier JA, Beale MH, Lilley KS, Dupree P. Plant Physiology. 2005 137 (1): 104-116 

Maximising sensitivity for detecting changes in protein expression: experimental design using Minimal CyDyes. Karp, N.A. , and Lilley, K.S. Proteomics. 2005 5 (12):3105 

Impact of replicate types on proteomic expression analysis. Karp, N.A., Spencer, M., Lindsay, H, O´Dell, K. and Lilley, K.S. J. Prot. Res. 2005 4: 1867 

Confident Protein Identification Using the Average Peptide Score Method Coupled with Search-specific, Ab-initio Thresholds. Shadforth, I., Dunkley, T.P.J., Lilley, K.S., Crowther, D. and Bessant, C. Rapid Communications in Mass Spectrometry. 2005 19 : 3363-3368 

i-Tracker: For quantitative proteomics using iTRAQTMShadforth, I., Dunkley, T.P.J., Lilley, K.S. and Bessant, C. BMC Genomics. 2006 6: 145 -150

SETH1 and SETH2, two components of the glycosylphospatidylinositol anchor biosynthetic pathway, are required for pollen germination and tube growth in Arabidopsis. Lalanne, E., Honys, D., Johnson, A., Borner, G.H.H., Lilley, K.S., Dupree, P., Grossniklaus, U., and Twell, D. The Plant Cell. (2004) 16: 229-240 

Detecting a significant change in protein expression by Differential In-gel Analysis of 2-D Difference Gel Electrophoresis. Natasha A Karp, David P Kreil, and Kathryn S Lilley. Proteomics. (2004) 4 (5) 1421-1432 

Protein profiling of human post-mortem brain using 2-dimensional fluorescence difference gel electrophoresis (2-D DIGE). Jane E. Swatton, Sudhakaran Prabakaran, Natasha A. Karp, Kathryn S. Lilley and Sabine Bahn. Molecular Psychiatry. (2004) 9 (2): 128-143 

DNA microarray normalization methods can remove bias from differential protein expression analysis of 2-D difference gel electrophoresis results. Kreil, D.P.,Karp, N.A., and Lilley, K.S. Bioinformatics. (2004) 20(13) 2026-2034 

An integrative functional genomics approach reveals impaired brain energy metabolism in Schizophrenia. Prabakaran,. S., Swatton, J., Ryan, M., Huffaker, S., Griffin, J., Wayland, M., Freeman,, T., Dudridge, F., Lilley, K.S., Karp,,N.A., Hester, S., Tkachev, D., Mimmack, M.L., Huang J. T.-J., Yolken, R. H.,.Webster, M. J, Torrey, F. and Bahn, S. Molecular Psychiatry. (2004) 9 (7): 684-697 

A proteomics method for determining the sub-cellular location of membrane proteins in Arabidopsis thaliana. Dunkley T.P.J., Dupree P., Watson R.B., Lilley K.S. Biochem Soc Trans.(2004) 32 :520-523 

Functional Specialization amongst the Arabidopsis Toc159 Family of Chloroplast Protein Import Receptor. Kubis, S., Patel., R., Combe, J., Bedard, J., Kovacheva, S. , Lilley, K., Biehl, A., Leister, D., Rios, G., Koncz, C., and Jarvis P., Plant Cell. (2004) 16 (8): 2059-2077. 

Specific changes in the Arabidopsis proteome in response to bacterial challenge: differentiating basal and R-gene mediated resistanceJones. AME, Thomas V, Truman B, Lilley K, Mansfield J, Grant M. Phytochemistry. 2004 65 (12): 1805-1816 

Localization of Organelle Proteins by Isotope Tagging (LOPIT). Dunkley T.P.J., Watson R., Griffin J.L., Dupree P. and Lilley K.S. Mol. Cell. Proteomics. (2004) 4 (11) 1128-1134 

PEDRo: A database for storing, searching and disseminating experimental proteomics data. 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 AJP, Hesketh A, Chater K, Hansson L, Mewissen M, Ghazal P, Howard J, Lilley KS, Gaskell SJ, Brass A, Hubbard SJ, Oliver SG, Paton NW. BMC Genomics. (2004) 5: art. no. 68 SEP 17 2004

Characterisation of the Necrotic protein that regulates Toll mediated immune response in Drosophila. Robertson, A.S., Belgorey, D., Lilley, K.S., Lomas, D.A., Gubb, D., and Dafforn, T.R. J. Biol. Chem. (2003) 278 (8 ) 6175-6180 

A Systematic Approach to Modelling, Capturing and Disseminating Proteomics Experimental Data. Taylor CF , Paton NW, Garwood KL , Kirby PL , Stead DA ,Yin Z , Deutsch E , Selway L, Walker J , Riba–Garcia I , Mohammed S , Deery MJ , Howard JA , Dunkley T, Shaw A, Aebersold R , Lilley KS , Roepstorff P , Yates JR III , Kell D, Brass A, Brown A , Cash P , Gaskell S , Hubbard S and, Oliver SG. Nat. Biotech. (2003) 21 (3) 247-254 

Protein Profiling using 2D DIGE. Lilley K.S. Current Protocols in Protein Science. (J. Wiley and Sons, Inc.) Editors Coligan JE,Dunn, BM, Speicher, DW and Wingfield PT. (2003) 

GPI-Anchored proteins in Arabidopsis. Borner, G.H.H., Stevens, T., Lilley, K.S. and Dupree. P Plant Physiol. (2003) 132 568-577 

The Arabidopsis ppi mutant is specifically defective in the expression, chloroplast import, and accumulation of photosynthetic proteins. Kubis, S., Baldwin, A., Patel, R., Razzaq, A., Dupree, P., Lilley, K., Kurth, J., Leister, D and Jarvis, P. The Plant Cell. (2003) 15 1-14 

Proteomics in Drosophila melanogaster. Lilley, K.S. and Griffiths, D.R. Briefings in Functional Genomics and Proteomics. (2003) 2 106-113 

Ubiquitination of a -synuclein in Lewy bodies is a pathological event not associated with impairment of proteasome function. George K.Tofaris, Azam Razzaq, Bernardino Ghetti, Kathryn Lilley and Maria Grazia Spillantini. J. Biol. Chem. (2003) 278 (45): 44405-44411

Two-dimensional gel electrophoresis: recent advances in sample preparation, detection and quantitation. Lilley, K.S., Razzaq, A. and Dupree, P. Current Opinion in Chemical Biology. (2002) 6, 46-50 . 

Precuon scanning for detection and structural characterisation of heterogeneous glycopeptide mixture. Ritchie, M.A., Deery, M.J., Lilley, K.S and Gill, A.C. JASMS. (2002) 13 (9)1065-1077