ORCID

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Preprints

J. Stiens, Y.Y. Tan, R. Joyce, K.B. Arnvig, S.L. Kendall, I. Nobeli. Using a whole genome co-expression network to inform the functional characterisation of predicted genomic elements from Mycobacterium tuberculosis transcriptomic data. bioRxiv 2022.06.22.497203. DOI:10.1101/2022.06.22.497203

Publications

Gibson AJ, Stiens J, Passmore IJ, Faulkner V, Miculob J, Willcocks S, Coad M, Berg S, Werling D, Wren BW, Nobeli I, Villarreal-Ramos B, Kendall SL. Defining the Genes Required for Survival of Mycobacterium bovis in the Bovine Host Offers Novel Insights into the Genetic Basis of Survival of Pathogenic Mycobacteria. mBio. 2022 Aug 30;13(4):e0067222. PMID: 35862770; PMCID: PMC9426507. Stiens and Gibson are joint first authors. DOI:10.1128/mbio.00672-22

Gibson, A.J., Passmore,I.J., Faulkner,V., Xia,D., Nobeli,I., Stiens,J., Willcocks,S., Werling,D. Villarreal-Ramos,B., Wren,B.W., Kendall, S.L. Probing differences in gene essentiality between the human and animal adapted lineages of the Mycobacterium tuberculosis complex using TnSeq. Front. Vet. Sci., 24 December 2021. DOI:10.3389/fvets.2021.760717

Stiens, J.; Arnvig, K.B.; Kendall, S.L.; Nobeli, I. Challenges in Defining the Functional, Non-Coding, Expressed Genome of Pathogenic Mycobacteria.Mol Microbiol. 2021 Dec 11. DOI:10.1111/mmi.14862.

Szkop, K.J., Moss, D.S., Nobeli, I. (2020). flexiMAP: A regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data. Bioinformatics Jun 16;37(10):1461-1464. DOI.

Abelak, K.K., Bishop-Bailey, D., Nobeli, I. (2019). Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids. BMC Research Notes 12 (1), 760. DOI.

Ozuna, A., Liberto, D., Joyce, R.M., Arnvig, K.B. and Nobeli, I. (2019). baerhunter: An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data. Bioinformatics, btz643, DOI.

Schwenk, S., Moores, A., Nobeli, I., McHugh, T.D., Arnvig, K.B. (2018) Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis. Nucleic Acids Res. gky226. DOI

Nobeli, I. (2018). In praise of slow. Science 359, 602. DOI

Szkop, K.J. and Nobeli, I. (2017). Untranslated parts of genes interpreted: Making heads or tails of high-throughput transcriptomic data via computational methods. Bioessays 39(12), 1700090. DOI

Szkop, K.J., Cooke, P.I.C., Humphries, J.A., Kalna, V., Moss, D.S., Schuster, E.F., Nobeli, I. (2017) Dysregulation of Alternative Poly-adenylation as a Potential Player in Autism Spectrum Disorder. Frontiers in Molecular Neuroscience 10, 279. DOI.

Smith, L.J., Bochkareva, A., Rolfe, M.D., Hunt, D.M., Kahramanoglou, C., Braun, Y., Rodgers, A., Blockley, A., Coade, S., Lougheed, K.E.A., Hafneh, N.A., Glenn, S.M., Crack, J.C., Le Brun, N.E., Saldanha, J.W., Makarov, V., Nobeli, I., Arnvig, K., Mukamolova G.V., ,R.S., Green, J. (2017) Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence. Nucleic Acids Res. DOI

Lee H., Patschull A.O., Bagnéris ., Ryan H., Sanderson C.M., Ebrahimi B., Nobeli, I., Barrett, T.E. (2017). KSHV SOX mediated host shutoff: the molecular mechanism underlying mRNA transcript processing. Nucleic Acids Res. DOI

Proietti G., Abelak K.K., Bishop-Bailey D., Macchiarulo A., Nobeli I. (2016). Computational modelling of the binding of arachidonic acid to the human monooxygenase CYP2J2. Journal of Molecular Modeling 22(11), 279. DOI

Bagneris, C. DeCaen, P.G., Naylor, C.E., Pryde, D.C., Nobeli, I., Clapham, D.E., and Wallace, B.A. (2014). Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism. PNAS 111: 8428-8433. DOI "

Czarnecki, J., Nobeli, I., Smith, A.M., Shepherd, A.J. (2012). A Text-Mining System for Extracting Metabolic Reactions from Full-Text Articles. BMC Bioinformatics 13: 172. DOI

Patschull, A.O.M., Gooptu, B., Ashford, P., Daviter, T., Nobeli, I. (2012). In Silico Assessment of Potential Druggable Pockets on the Surface of a1-Antitrypsin Conformers. PLoS ONE 7: e36612. DOI

Ashford, P., Moss, D.S., Alex, A., Yeap, S.K., Povia, A., Nobeli, I.$, Williams, M.A.$ (2012). Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets. BMC Bioinformatics 13, 39. DOI
$ Williams and Nobeli are corresponding authors.

Favia, A.D., Bottegoni, G., Nobeli, I., Bisignano, P., Cavalli, A. (2011). SERAPhiC: a Benchmark for in Silico Fragment-Based Drug Design. J. Chem. Inf. Model. 51, 2882-2896. DOI

Patschull, A.O.M., Segu, L., Nyon, M.P., Lomas, D.A., Nobeli, I., Barrett, T.E., Gooptu, B. (2011). 1.8 Ang X-ray crystallographic structure of alpha1-antitrypsin characterizes variable features of an important site for allosteric drug design. Acta Cryst. F67, 1492-1497.

Chang, Y-P. et al. (2011). Targeting serpins in high-throughput and structure-based drug design. Methods in Enzymology, 501, 139-175.

Guzman, J.D. et al. (2011). Interaction of N-methyl-2-alkenyl-4-quinolones with ATP-dependent MurE ligase of Mycobacterium tuberculosis: antibacterial activity, molecular docking and inhibition kinetics. J. Antimicrob. Chemother., 66(8), 1766-1772.

Macchiarulo, A., Thornton, J.M., Nobeli, I. (2009). Mapping human metabolic pathways in the small molecule chemical space. J. Chem. Inf. Model., 49, 2272-2289.

Gooptu, B., Miranda, E., Nobeli, I., Mallya, M., Purkiss, A., Brown, S.C., Summers, C., Phillips, R.L., Lomas, D.A., Barrett, T.E. (2009). Crystallographic and cellular characterisation of two mechanisms stabilising the native fold of alpha1-antitrypsin: implications for disease and drug design. J. Mol. Biol., 387, 857-868.

Nobeli, I., Favia, A., and Thornton, J.M. (2009). Protein promiscuity and its implications for biotechnology. Nat. Biotechnol., 27, 157-167.

Favia, A.$, Nobeli, I.$, Glaser, F., and Thornton, J.M. (2008). Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. J. Mol. Biol., 375, 855-874. $ Favia and Nobeli are joint first authors.

Bashton, M., Nobeli, I., and Thornton, J.M. (2008). PROCOGNATE: A cognate ligand domain mapping for enzymes. Nucleic Acids Res., 36, D618-D622.

Bashton, M., Nobeli, I., and Thornton, J.M. (2006). Cognate ligand domain mapping for enzymes. J. Mol. Biol., 364, 836-852.

Nobeli, I. and Thornton, J.M. (2006). A bioinformatician's view of the metabolome. Bioessays, 28, 534-545.

Nobeli, I., Spriggs, R.V., George, R., and Thornton, J.M. (2005). A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E. coli. J. Mol. Biol., 347, 415-436.

Macchiarulo, A., Nobeli, I., and Thornton, J.M. (2004). Ligand selectivity and competition between enzymes in silico. Nat. Biotechnol., 22, 1039-45.

Nobeli, I., Ponstingl, H., Krissinel, E.B., and Thornton, J.M. (2003). A structure-based anatomy of the E. coli metabolome. J. Mol. Biol., 334, 697-71.

Jones, S., Barker, J.A., Nobeli, I., and Thornton, J.M. (2003). Using structural motif templates to identify proteins with DNA binding function. Nucleic Acids Res. 31, 2811-23.

Nobeli, I., Laskowski, R.A., Valdar, W.S.J, and Thornton, J.M. (2001). On the molecular discrimination between adenine and guanine by proteins. Nucleic Acids Res. 29, 4294-309.

Nobeli, I., Mitchell, J.B.O., Alex, A., and Thornton, J.M. (2001). Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes. J. Comput. Chem. 22, 673-88.

Novoa, J.J., Nobeli, I., Grepioni, F., and Braga, D. (2000). Are all short O--H...O contacts hydrogen bonds? A quantitative look at the nature of the O--H...O intermolecular hydrogen bonds. New J. Chem., 24, 5-8.

Nobeli, I. and Price, S.L. (1999). A non-empirical intermolecular potential for oxalic acid crystal structures. J. Phys. Chem. A, 103, 6448-57.

Nobeli, I., Price, S.L., and Wheatley, R.J. (1998). Use of molecular overlap to predict intermolecular repulsion in N--H...O hydrogen bonds. Molec. Phys., 95, 525-37.

Nobeli, I., Price, S.L., Yeoh, S.L., and Taylor, R. (1997). On the hydrogen bonding abilities of phenols and anisoles. Chem. Phys. Letts, 280, 196-202.

Nobeli, I., Price, S.L., Lommerse, J.P.M., and Taylor, R. (1997). Hydrogen bonding properties of oxygen and nitrogen acceptors in aromatic heterocycles. J. Comput. Chem., 18, 2060-74.

Invited contributions

Favia, A.D. and Nobeli, I. (2011). Using chemical structure to infer biological function. In :Computational Approaches in Cheminformatics and Bioinformatics. Guha, R. and Bender, A. (eds). Wiley, ISBN: 978-0-470-38441-1.

Thornton, J.M., Favia, A.D., Nobeli, I., and Furnham, N. The evolution of specificity in large protein families. FEBS J., 275, 23, Suppl. 1, 2008.

Nobeli, I. and Thornton, J.M. The proteome and the metabolome - a structural perspective.Peptide Revolution: Genomics, Proteomics and Therapeutics, Michael Chorev and Tomi K. Sawyer (Editors), American Peptide Society, 2003.

Nobeli, I. and Thornton, J.M. Proteins, small molecules and networks. Proceedings of EuroQSAR 2002, 14th European Symposium on Quantitative Structure Activity Relationships, Bournemouth, UK, 8-13 Sep. 2002.

Theses

Characterising organic hydrogen bonds. PhD thesis (UCL, Chemistry, 1999).

IR-relevant: An information retrieval toolkit. MSc thesis (Birkbeck, Computer Science, 2003).