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Abenza JF, Chessel A, Raynaud WG, Carazo-Salas RE (2014) Dynamics of cell shape inheritance in fission yeast. PLoS One. 2014 Sep 11; 9(9):e106959. doi: 10.1371/journal. pone.0106959. PMID: 25210736

Bean DM, Heimbach J, Ficorella L, Micklem G, Oliver SG, Favrin G (2014) esyN: network building, sharing and publishing. PLoS One. Sep 2; 9(9):e106035. PMID: 25181461 

Christoforou A, Arias AM, Lilley KS (2014). 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 [PubMed - in process] 

Daphne Ezer, Nicolae Radu Zabet, Boris Adryan (2014)  Physical constraints determine the logic of bacterial promoter architectures. Nucleic Acids Res. April; 42(7): 4196–4207.

Dikicioglu D, Wood V, Rutherford KM, McDowall MD, Oliver SG. Improving functional annotation for industrial microbes: a case study with Pichi pastoris. Trends Biotechnol. 2014 Aug;32(8):396-9.

Elliott TS, Townsley FM, Bianco A, Ernst RJ, Sachdeva A, Elsässer SJ, Davis L, Lang K, Pisa R, Greiss S, Lilley KS, Chin JW (2014) Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal. Nat Biotechnol. 2014 Apr 13. doi: 10.1038/nbt.2860. [Epub ahead of print] PMID:24727715[PubMed - as supplied by publisher]

Ezer, D., Zabet, N. R., & Adryan, B. (2014). Physical constraints determine the logic of bacterial promoter architectures.. Nucleic Acids Res. doi:10.1093/nar/gku078

Feret, R., & Lilley, K. S. (2014). Protein Profiling Using Two-Dimensional Difference Gel Electrophoresis (2-D DIGE).. Curr Protoc Protein Sci, 75, 22.2.1-22.2.17. doi:10.1002/0471140864.ps2202s75

Ferrero E, Fischer B, Russell S (2014) SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete. Genome Biology 15: R74.

Füzesi-Levi, M. G., Ben-Nissan, G., Bianchi, E., Zhou, H., Deery, M. J., Lilley, K. S., . . . Sharon, M. (2014). Dynamic Regulation of the COP9 Signalosome in Response to DNA Damage.. Mol Cell Biol, 34(6), 1066-1076. doi:10.1128/MCB.01598-13

Gatto L, Breckels LM, Burger T, Nightingale DJ, Groen AJ, Campbell C, Nikolovski N, Mulvey CM, Christoforou A, Ferro M, Lilley KS (2014) A foundation for reliable spatial proteomics data analysis. Mol Cell Proteomics. Aug;13(8):1937-52.

Gatto, L., Breckels, L. M., Wieczorek, S., Burger, T., & Lilley, K. S. (2014). Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata.. Bioinformatics. doi:10.1093/bioinformatics/btu013

Graml V, Studera X, Lawson JL, Chessel A, Geymonat M, Bortfeld-Miller M, Walter T, Wagstaff L, Piddini E, Carazo-Salas RE (2014) A genomic Multiprocess survey of machineries that control and link cell shape, microtubule organization, and cell-cycle progression. Dev Cell. Oct 27;31(2):227-39. doi: 10.1016/j.devcel.2014.09.005. PMID: 25373780 

Groen, A. J., Sancho-Andrés, G., Breckels, L. M., Gatto, L., Aniento, F., & Lilley, K. S. (2014). Identification of Trans-Golgi Network Proteins in Arabidopsis thaliana Root Tissue.. J Proteome Res. doi:10.1021/pr4008464

Grüning, N. M., Du, D., Keller, M. A., Luisi, B. F., & Ralser, M. (2014). Inhibition of triosephosphate isomerase by phosphoenolpyruvate in the feedback-regulation of glycolysis.. Open Biol, 4(3), 130232. doi:10.1098/rsob.130232

Hall B, Jackson E, Hajnal A, Fisher J (2014) Logic Programming to Predict Cell Fate Patterns and Retrodict Genotypes during Organogenesis. Royal Society Interface 11: 0140245, Royal Society Publishing, June.

Hiemstra TF, Charles PD, Gracia T, Hester SS, Gatto L, Al-Lamki R, Floto RA, Su Y, Skepper JN, Lilley KS, Karet Frankl FE (2014) Human Urinary Exosomes as Innate Immune Effectors. J Am Soc Nephrol. 2014 Apr 3. [Epub ahead of print] PMID:24700864 [PubMed - as supplied by publisher]

Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ. A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics. 2014 May 21;15(1):155.

Jones, O. A. H., Sdepanian, S., Lofts, S., Svendsen, C., Spurgeon, D. J., Maguire, M. L., . . . Griffin, J. L. (2014). Metabolomic analysis of soil communities can be used for pollution assessment. Environmental Toxicology and Chemistry, 33(1), 61-64.

Kalderimis, A., Stepan, R., Sullivan, J., Lyne, R., Lyne, M., & Micklem, G. (2014). BioJS DAGViewer: A reusable JavaScript component for displaying directed graphs.. F1000Res, 3, 51. doi:10.12688/f1000research.3-51.v1

Keller MA, Turchyn AV, Ralser M (2014) Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean ocean. Mol Syst Biol. Apr 25;10:725. doi: 10.1002/msb.20145228. PubMed PMID: 24771084; PubMed Central PMCID: PMC4023395

Khabirova E, Moloney A, Marciniak SJ, Williams J, Lomas DA, Oliver SG, Favrin G, Sattelle DB, Crowther DC. (2014). The TRiC/CCT Chaperone Is Implicated in Alzheimer's Disease Based on Patient GWAS and an RNAi Screen in Aβ-Expressing Caenorhabditis elegans. PLoS One. 2014 Jul 31;9(7):e102985. doi: 10.1371/journal.pone.0102985. 

King, H. A., Cobbold, L. C., Pichon, X., Pöyry, T., Wilson, L. A., Booden, H., . . . Willis, A. E. (2014). Remodelling of a polypyrimidine tract-binding protein complex during apoptosis activates cellular IRESs. Cell Death and Differentiation, 21(1), 161-171.

Koulman, A., Prentice, P., Wong, M. C. Y., Matthews, L., Bond, N. J., Eiden, M., . . . Dunger, D. B. (2014). The development and validation of a fast and robust dried blood spot based lipid profiling method to study infant metabolism. Metabolomics, 1-8.

Li XW, Rees JS, Xue P, Zhang H, Hamaia SW, Sanderson B, Funk PE, Farndale RW, Lilley KS, Perrett S, Jackson AP (2014) New Insights into the DT40 B-Cell Receptor Cluster using a Proteomic Proximity Labeling Assay. J Biol Chem. 2014 Apr 4. [Epub ahead of print] PMID:24706754[PubMed - as supplied by publisher] Free Article

Neville, M. C., Nojima, T., Ashley, E., Parker, D. J., Walker, J., Southall, T.,Russell, S. . . . Goodwin, S. F. (2014). Male-specific fruitless isoforms target neurodevelopmental genes to specify a sexually dimorphic nervous system.. Curr Biol, 24(3), 229-241. doi:10.1016/j.cub.2013.11.035

Oliver, S. (2014). The harder we work ….. Yeast, 31(3), 81-82. doi:10.1002/yea.3000

Patel MN, Bernard WG, Milev NB, Cawthorn WP, Figg N, Hart D, Prieur X, Virtue S, Hegyi K, Bonnafous S, Bailly-Maitre B, Chu Y, Griffin JL, Mallat Z, Considine RV, Tran A, Gual P, Takeuchi O, Akira S, Vidal-Puig A, Bennett MR, Sethi JK (2014) Hematopoietic IKBKE limits the chronicity of inflammasome priming and metaflammation. Proc Natl Acad Sci U S A Dec, 24. pii: 201414536.

Prigione, A., Rohwer, N., Hoffmann, S., Mlody, B., Drews, K., Bukowiecki, R.,Ralser M. . . . Adjaye, J. (2014). HIF1α modulates cell fate reprogramming through early glycolytic shift and upregulation of PDK1-3 and PKM2.. Stem Cells, 32(2), 364-376. doi:10.1002/stem.1552

Roberts LD, Ashmore T, Kotwica AO, Murfitt SA, Fernandez BO, Feelisch M, Murray AJ, Griffin JL (2014) Inorganic Nitrate Promotes the Browning of White Adipose Tissue through the Nitrate-Nitrite-Nitric Oxide Pathway. Diabetes Sep 23. pii: DB_140496.

Roberts, L. D., Koulman, A., & Griffin, J. L. (2014). Towards metabolic biomarkers of insulin resistance and type 2 diabetes: Progress from the metabolome. The Lancet Diabetes and Endocrinology, 2(1), 65-75.

Roberts, L. D., West, J. A., Vidal-Puig, A., & Griffin, J. L. (2014). Methods for performing lipidomics in white adipose tissue.. Methods Enzymol, 538, 211-231. doi:10.1016/B978-0-12-800280-3.00012-8

Rutherford, K. M., Harris, M. A., Lock, A., Oliver, S. G., & Wood, V. (2014). Canto: an online tool for community literature curation.. Bioinformatics. doi:10.1093/bioinformatics/btu103

Schmidt HG, Sewitz S, Andrews SS,  Lipkow K (2014) An Integrated Model of Transcription Factor Diffusion Shows the Importance of Intersegmental Transfer and Quaternary Protein Structure for Target Site Finding. PLOS ONE 9(10), e108575.  

Schoech A P,  Zabet NR (2014) Facilitated diffusion buffers noise in gene expression. Phys. Rev. E 90(3): 032701, doi:10.1103/PhysRevE.90.032701.

Torella R, Li J, Kinrade E, Cerda-Moya G, Contreras AN, Foy R, Stojnic R, Glen RC, Kovall RA, Adryan B, Bray SJ (2014) A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL. Nucleic Acids Res.42(16):10550-63. doi: 10.1093/nar/gku730. Epub 2014 Aug 11. PMID:     25114055

Tzanis, A., Dalton, K. A., Hesketh, A., den Hengst, C. D., Buttner, M. J., Thibessard, A., . . . Kelemen, G. H. (2014). A sporulation-specific, sigF-dependent protein, SspA, affects septum positioning in Streptomyces coelicolor.. Mol Microbiol, 91(2), 363-380. doi:10.1111/mmi.12466

Walzer M, Pernas LE, .... Lilley KS, et al. (2014) qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics. 2014 Apr 23. [Epub ahead of print] PMID:24760958[PubMed - as supplied by publisher] Free Article

Vaggi, F., Schiavinotto, T., Lawson, J. L., Chessel, A., Dodgson, J., Geymonat, M., Carazo-Salas, R. E.,. . . Csikász-Nagy, A. (2014). A network approach to mixing delegates at meetings.. Elife, 3, e02273. doi:10.7554/eLife.02273

Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H (2014) ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. Mar;32(3):223-6.

Wang, Y., Lilley, K. S., & Oliver, S. G. (2014). A protocol for the sub-cellular fractionation of Saccharomyces cerevisiae using nitrogen cavitation and density gradient centrifugation.. Yeast. doi:10.1002/yea.3002

Xi, W., Schmidt, C. K., Sanchez, S., Gracias, D. H., Carazo-Salas, R. E., Jackson, S. P., . . . Schmidt, O. G. (2014). Rolled-up Functionalized Nanomembranes as Three-Dimensional Cavities for Single Cell Studies.. Nano Lett. doi:10.1021/nl4042565