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Items: 1 to 50 of 209


Organic phase separation opens up new opportunities to interrogate the RNA-binding proteome.

Smith T, Villanueva E, Queiroz RML, Dawson CS, Elzek M, Urdaneta EC, Willis AE, Beckmann BM, Krijgsveld J, Lilley KS.

Curr Opin Chem Biol. 2020 Mar 1;54:70-75. doi: 10.1016/j.cbpa.2020.01.009. [Epub ahead of print] Review.


Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components.

Marondedze C, Thomas L, Lilley KS, Gehring C.

Front Mol Biosci. 2020 Jan 21;6:163. doi: 10.3389/fmolb.2019.00163. eCollection 2019.


Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions.

Minde DP, Ramakrishna M, Lilley KS.

Commun Biol. 2020 Jan 22;3(1):38. doi: 10.1038/s42003-020-0758-y.


The Arabidopsis thaliana N-recognin E3 ligase PROTEOLYSIS1 influences the immune response.

Till CJ, Vicente J, Zhang H, Oszvald M, Deery MJ, Pastor V, Lilley KS, Ray RV, Theodoulou FL, Holdsworth MJ.

Plant Direct. 2019 Dec 26;3(12):e00194. doi: 10.1002/pld3.194. eCollection 2019 Dec.


DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput.

Demichev V, Messner CB, Vernardis SI, Lilley KS, Ralser M.

Nat Methods. 2020 Jan;17(1):41-44. doi: 10.1038/s41592-019-0638-x. Epub 2019 Nov 25.


Mapping the Saccharomyces cerevisiae Spatial Proteome with High Resolution Using hyperLOPIT.

Nightingale DJH, Oliver SG, Lilley KS.

Methods Mol Biol. 2019;2049:165-190. doi: 10.1007/978-1-4939-9736-7_10.


Proteome Mapping of a Cyanobacterium Reveals Distinct Compartment Organization and Cell-Dispersed Metabolism.

Baers LL, Breckels LM, Mills LA, Gatto L, Deery MJ, Stevens TJ, Howe CJ, Lilley KS, Lea-Smith DJ.

Plant Physiol. 2019 Dec;181(4):1721-1738. doi: 10.1104/pp.19.00897. Epub 2019 Oct 2.


Separating Golgi Proteins from Cis to Trans Reveals Underlying Properties of Cisternal Localization.

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.

Plant Cell. 2019 Sep;31(9):2010-2034. doi: 10.1105/tpc.19.00081. Epub 2019 Jul 2.


Author Correction: Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS).

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.

Nat Biotechnol. 2019 Jun;37(6):692. doi: 10.1038/s41587-019-0161-8.


A Bioconductor workflow for the Bayesian analysis of spatial proteomics.

Crook OM, Breckels LM, Lilley KS, Kirk PDW, Gatto L.

F1000Res. 2019 Apr 11;8:446. doi: 10.12688/f1000research.18636.1. eCollection 2019.


Comparison of Drosophila melanogaster Embryo and Adult Proteome by SWATH-MS Reveals Differential Regulation of Protein Synthesis, Degradation Machinery, and Metabolism Modules.

Fabre B, Korona D, Lees JG, Lazar I, Livneh I, Brunet M, Orengo CA, Russell S, Lilley KS.

J Proteome Res. 2019 Jun 7;18(6):2525-2534. doi: 10.1021/acs.jproteome.9b00076. Epub 2019 May 22.


Ketamine's Effects on the Glutamatergic and GABAergic Systems: A Proteomics and Metabolomics Study in Mice.

Weckmann K, Deery MJ, Howard JA, Feret R, Asara JM, Dethloff F, Filiou MD, Labermaier C, Maccarrone G, Lilley KS, Mueller M, Turck CW.

Mol Neuropsychiatry. 2019 Mar;5(1):42-51. doi: 10.1159/000493425. Epub 2018 Nov 15.


Changes in the Arabidopsis RNA-binding proteome reveal novel stress response mechanisms.

Marondedze C, Thomas L, Gehring C, Lilley KS.

BMC Plant Biol. 2019 Apr 11;19(1):139. doi: 10.1186/s12870-019-1750-x.


A proteomic time course through the differentiation of human induced pluripotent stem cells into hepatocyte-like cells.

Hurrell T, Segeritz CP, Vallier L, Lilley KS, Cromarty AD.

Sci Rep. 2019 Mar 1;9(1):3270. doi: 10.1038/s41598-019-39400-1.


Editorial overview: Untangling proteome organization in space and time.

Cristea IM, Lilley KS.

Curr Opin Chem Biol. 2019 Feb;48:A1-A4. doi: 10.1016/j.cbpa.2019.02.001. No abstract available.


Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae.

Dikicioglu D, Nightingale DJH, Wood V, Lilley KS, Oliver SG.

FEMS Yeast Res. 2019 Mar 1;19(2). pii: foz014. doi: 10.1093/femsyr/foz014.


Assessing sub-cellular resolution in spatial proteomics experiments.

Gatto L, Breckels LM, Lilley KS.

Curr Opin Chem Biol. 2019 Feb;48:123-149. doi: 10.1016/j.cbpa.2018.11.015. Epub 2018 Dec 14. Review.


Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics.

Geladaki A, Kočevar Britovšek N, Breckels LM, Smith TS, Vennard OL, Mulvey CM, Crook OM, Gatto L, Lilley KS.

Nat Commun. 2019 Jan 18;10(1):331. doi: 10.1038/s41467-018-08191-w.


Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS).

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.

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.


The subcellular organisation of Saccharomyces cerevisiae.

Nightingale DJ, Geladaki A, Breckels LM, Oliver SG, Lilley KS.

Curr Opin Chem Biol. 2019 Feb;48:86-95. doi: 10.1016/j.cbpa.2018.10.026. Epub 2018 Nov 29. Review.


A Bayesian mixture modelling approach for spatial proteomics.

Crook OM, Mulvey CM, Kirk PDW, Lilley KS, Gatto L.

PLoS Comput Biol. 2018 Nov 27;14(11):e1006516. doi: 10.1371/journal.pcbi.1006516. eCollection 2018 Nov.


Ethylene Receptors, CTRs and EIN2 Target Protein Identification and Quantification Through Parallel Reaction Monitoring During Tomato Fruit Ripening.

Mata CI, Fabre B, Parsons HT, Hertog MLATM, Van Raemdonck G, Baggerman G, Van de Poel B, Lilley KS, Nicolaï BM.

Front Plant Sci. 2018 Nov 8;9:1626. doi: 10.3389/fpls.2018.01626. eCollection 2018.


Proteomic responses of HepG2 cell monolayers and 3D spheroids to selected hepatotoxins.

Hurrell T, Lilley KS, Cromarty AD.

Toxicol Lett. 2019 Jan;300:40-50. doi: 10.1016/j.toxlet.2018.10.030. Epub 2018 Oct 28.


Early Responses to Severe Drought Stress in the Arabidopsis thaliana Cell Suspension Culture Proteome.

Alqurashi M, Chiapello M, Bianchet C, Paolocci F, Lilley KS, Gehring C.

Proteomes. 2018 Oct 2;6(4). pii: E38. doi: 10.3390/proteomes6040038.


Identification of the RNA polymerase I-RNA interactome.

Piñeiro D, Stoneley M, Ramakrishna M, Alexandrova J, Dezi V, Juke-Jones R, Lilley KS, Cain K, Willis AE.

Nucleic Acids Res. 2018 Nov 16;46(20):11002-11013. doi: 10.1093/nar/gky779.


Negative feedback via RSK modulates Erk-dependent progression from naïve pluripotency.

Nett IR, Mulas C, Gatto L, Lilley KS, Smith A.

EMBO Rep. 2018 Aug;19(8). pii: e45642. doi: 10.15252/embr.201745642. Epub 2018 Jun 12.


Ciprofloxacin binding to GyrA causes global changes in the proteome of Pseudomonas aeruginosa.

Jedrey H, Lilley KS, Welch M.

FEMS Microbiol Lett. 2018 Jul 1;365(13). doi: 10.1093/femsle/fny134.


The Parkinson's Disease-Linked Protein DJ-1 Associates with Cytoplasmic mRNP Granules During Stress and Neurodegeneration.

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.

Mol Neurobiol. 2019 Jan;56(1):61-77. doi: 10.1007/s12035-018-1084-y. Epub 2018 Apr 19.


Proteomic Comparison of Various Hepatic Cell Cultures for Preclinical Safety Pharmacology.

Hurrell T, Segeritz CP, Vallier L, Lilley KS, Cromarty AD.

Toxicol Sci. 2018 Jul 1;164(1):229-239. doi: 10.1093/toxsci/kfy084.


Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation.

Armean IM, Lilley KS, Trotter MWB, Pilkington NCV, Holden SB.

Bioinformatics. 2018 Jun 1;34(11):1884-1892. doi: 10.1093/bioinformatics/btx803.


Stat3-mediated alterations in lysosomal membrane protein composition.

Lloyd-Lewis B, Krueger CC, Sargeant TJ, D'Angelo ME, Deery MJ, Feret R, Howard JA, Lilley KS, Watson CJ.

J Biol Chem. 2018 Mar 23;293(12):4244-4261. doi: 10.1074/jbc.RA118.001777. Epub 2018 Jan 17.


Trans-acting translational regulatory RNA binding proteins.

Harvey RF, Smith TS, Mulroney T, Queiroz RML, Pizzinga M, Dezi V, Villenueva E, Ramakrishna M, Lilley KS, Willis AE.

Wiley Interdiscip Rev RNA. 2018 May;9(3):e1465. doi: 10.1002/wrna.1465. Epub 2018 Jan 17. Review.


N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway.

Zhang H, Gannon L, Hassall KL, Deery MJ, Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL.

New Phytol. 2018 May;218(3):1106-1126. doi: 10.1111/nph.14909. Epub 2017 Nov 23.


Mass spectrometry approaches to study plant endomembrane trafficking.

Parsons HT, Lilley KS.

Semin Cell Dev Biol. 2018 Aug;80:123-132. doi: 10.1016/j.semcdb.2017.10.014. Epub 2017 Nov 13. Review.


Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples.

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.

Plant J. 2017 Dec;92(6):1202-1217. doi: 10.1111/tpj.13743. Epub 2017 Nov 20.


Spectral Libraries for SWATH-MS Assays for Drosophila melanogaster and Solanum lycopersicum.

Fabre B, Korona D, Mata CI, Parsons HT, Deery MJ, Hertog MLATM, Nicolaï BM, Russell S, Lilley KS.

Proteomics. 2017 Nov;17(21). doi: 10.1002/pmic.201700216.


Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus.

Loxley GM, Unsworth J, Turton MJ, Jebb A, Lilley KS, Simpson DM, Rigden DJ, Hurst JL, Beynon RJ.

Open Biol. 2017 Sep;7(9). pii: 170135. doi: 10.1098/rsob.170135.


A subcellular map of the human proteome.

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.

Science. 2017 May 26;356(6340). pii: eaal3321. doi: 10.1126/science.aal3321. Epub 2017 May 11.


Using hyperLOPIT to perform high-resolution mapping of the spatial proteome.

Mulvey CM, Breckels LM, Geladaki A, Britovšek NK, Nightingale DJH, Christoforou A, Elzek M, Deery MJ, Gatto L, Lilley KS.

Nat Protoc. 2017 Jun;12(6):1110-1135. doi: 10.1038/nprot.2017.026. Epub 2017 May 4.


Selective Proteomic Proximity Labeling Assay Using Tyramide (SPPLAT): A Quantitative Method for the Proteomic Analysis of Localized Membrane-Bound Protein Clusters.

Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP.

Curr Protoc Protein Sci. 2017 Apr 3;88:19.27.1-19.27.18. doi: 10.1002/cpps.27.


Tracking the embryonic stem cell transition from ground state pluripotency.

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.

Development. 2017 Apr 1;144(7):1221-1234. doi: 10.1242/dev.142711. Epub 2017 Feb 7.


Time, space, and disorder in the expanding proteome universe.

Minde DP, Dunker AK, Lilley KS.

Proteomics. 2017 Apr;17(7). doi: 10.1002/pmic.201600399. Epub 2017 Mar 20.


A Bioconductor workflow for processing and analysing spatial proteomics data.

Breckels LM, Mulvey CM, Lilley KS, Gatto L.

Version 2. F1000Res. 2016 Dec 28 [revised 2018 Jan 1];5:2926. doi: 10.12688/f1000research.10411.2. eCollection 2016.


In-depth characterization of the tomato fruit pericarp proteome.

Mata CI, Fabre B, Hertog ML, Parsons HT, Deery MJ, Lilley KS, Nicolaï BM.

Proteomics. 2017 Jan;17(1-2). doi: 10.1002/pmic.201600406.


SWATH-MS dataset of heat-shock treated Drosophila melanogaster embryos.

Fabre B, Korona D, Nightingale DJ, Russell S, Lilley KS.

Data Brief. 2016 Nov 16;9:991-995. eCollection 2016 Dec.


SWATH-MS data of Drosophila melanogaster proteome dynamics during embryogenesis.

Fabre B, Korona D, Nightingale DJ, Russell S, Lilley KS.

Data Brief. 2016 Oct 24;9:771-775. eCollection 2016 Dec.


The metabolic background is a global player in Saccharomyces gene expression epistasis.

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.

Nat Microbiol. 2016 Feb 1;1:15030. doi: 10.1038/nmicrobiol.2015.30.


Phosphorylation of the dimeric cytoplasmic domain of the phytosulfokine receptor, PSKR1.

Muleya V, Marondedze C, Wheeler JI, Thomas L, Mok YF, Griffin MD, Manallack DT, Kwezi L, Lilley KS, Gehring C, Irving HR.

Biochem J. 2016 Oct 1;473(19):3081-98. doi: 10.1042/BCJ20160593. Epub 2016 Aug 3.


The RNA-binding protein repertoire of Arabidopsis thaliana.

Marondedze C, Thomas L, Serrano NL, Lilley KS, Gehring C.

Sci Rep. 2016 Jul 11;6:29766. doi: 10.1038/srep29766.


Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.

Breckels LM, Holden SB, Wojnar D, Mulvey CM, Christoforou A, Groen A, Trotter MW, Kohlbacher O, Lilley KS, Gatto L.

PLoS Comput Biol. 2016 May 13;12(5):e1004920. doi: 10.1371/journal.pcbi.1004920. eCollection 2016 May.

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