January 2008

Favia, A.D. and Nobeli, Irene and Glaser, F. and Thornton, Janet M. (2008) Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. Journal of Molecular Biology 375 (3), pp. 855-874. ISSN 0022-2836.

Bashton, M. and Nobeli, Irene and Thornton, Janet M. (2008) Procognate: a cognate ligand domain mapping for enzymes. Nucleic Acids Research 36 , D618-D622. ISSN 0305-1048.

June 2008

Thornton, Janet M. and Favia, A.D. and Nobeli, Irene and Furnham, N. (2008) The evolution of specificity in large protein families. In: 33rd FEBS Congress & 11th IUBMB Conference: Biochemistry of Cell Regulation, June 28-July 3 2008, Athens, Greece.

9 February 2009

Nobeli, Irene and Favia, A.D. and Thornton, Janet M. (2009) Protein promiscuity and its implications for biotechnology. Nature Biotechnology 27 , pp. 157-167. ISSN 1087-0156.

April 2009

Gooptu, Bibek and Miranda, E. and Nobeli, Irene and Mallya, M. and Purkiss, Andrew G. and Leigh Brown, S.C. and Summers, C. and Phillips, R.L. and Lomas, D.A. and Barrett, Tracey E. (2009) Crystallographic and cellular characterisation of two mechanisms stabilising the native fold of α1-Antitrypsin: implications for disease and drug design. Journal of Molecular Biology 387 (4), pp. 857-868. ISSN 0022-2836.

October 2009

Macchiarulo, A. and Thornton, Janet M. and Nobeli, Irene (2009) Mapping human metabolic pathways in the small molecule chemical space. Journal of Chemical Information and Modelling 49 (10), pp. 2272-2289. ISSN 1549-9596.

2011

Patschull, Anathe O.M. and Segu, Lakshmi and Nyon, Mun Peak and Lomas, D.A. and Nobeli, Irene and Barrett, Tracey E. and Gooptu, Bibek (2011) Therapeutic target-site variability in α1-antitrypsin characterized at high resolution. Acta Crystallographica Section F Structural Biology and Crystallization Communications 67 (12), pp. 1492-1497. ISSN 1744-3091.

August 2011

Guzman, Juan D. and Wube, A. and Evangelopoulos, Dimitrios and Gupta, Antima and Hufner, A. and Basavannacharya, Chandrakala and Rahman, M.M. and Thomaschitz, C. and Bauer, R. and McHugh, T.D. and Nobeli, Irene and Prieto, J.M. and Gibbons, S. and Bucar, F. and Bhakta, Sanjib (2011) Interaction of N-methyl-2-alkenyl-4-quinolones with ATP-dependent MurE ligase of Mycobacterium tuberculosis: antibacterial activity, molecular docking and inhibition kinetics. Journal of Antimicrobial Chemotherapy 66 (8), pp. 1766-1772. ISSN 0305-7453.

November 2011

Favia, A.D. and Nobeli, Irene (2011) Using chemical structure to infer biological function. In: Guha, R. and Bender, A. (eds.) Computational Approaches in Cheminformatics and Bioinformatics. Hoboken, U.S.: Wiley, pp. 211-238. ISBN 9780470384411.

5 December 2011

Chang, Y.-P. and Mahadeva, R. and Patschull, A.O.M. and Nobeli, Irene and Ekeowa, U.I. and McKay, A.R. and Thalassinos, Konstantinos and Irving, J.A. and Haq, I. and Nyon, Mun Peak and Christodoulou, John and Ordóñez, A. and Miranda, E. and Gooptu, Bibek (2011) Targeting serpins in high-throughput and structure-based drug design. In: Whisstock, J.C. and Bird, P.I. (eds.) Serpin Structure and Evolution. Methods In Enzymology 501. New York, U.S.: Elsevier, pp. 139-175. ISBN 9780123859501.

14 March 2012

Ashford, Paul and Moss, David S. and Alex, A. and Yeap, S.K. and Povia, Alice and Nobeli, Irene and Williams, Mark A. (2012) Visualization of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets. BMC Bioinformatics 13 , p. 39. ISSN 1471-2105.

May 2012

Patschull, Anathe O.M. and Gooptu, Bibek and Ashford, Paul and Daviter, Tina and Nobeli, Irene (2012) In silico assessment of potential druggable pockets on the surface of α1-Antitrypsin conformers. PLoS One 7 (5), ISSN 1932-6203.

23 July 2012

Czarnecki, Jan M. and Nobeli, Irene and Smith, Adrian M.L. and Shepherd, Adrian J. (2012) A text-mining system for extracting metabolic reactions from full-text articles. BMC Bioinformatics 13 (172), ISSN 1471-2105.

10 June 2014

Bagneris, Claire and DeCaen, P.G. and Naylor, Claire E. and Pryde, D.C. and Nobeli, Irene and Clapham, D.E. and Wallace, Bonnie A. (2014) Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism. Proceedings of the National Academy of Sciences of the United States of America 111 (23), pp. 8428-8433. ISSN 0027-8424.

1 November 2016

Proietti, G and Abelak, K.K. and Bishop-Bailey, D. and Macchiarulo, A. and Nobeli, Irene (2016) Computational modelling of the binding of arachidonic acid to the human monooxygenase CYP2J2. Journal of Molecular Modeling 22 (11), p. 279. ISSN 1610-2940.

5 May 2017

Lee, Hyunah and Patschull, Anathe and Bagneris, Claire and Ryan, H. and Sanderson, C.M. and Ebrahimi, B. and Nobeli, Irene and Barrett, Tracey E. (2017) KSHV SOX mediated host shutoff: the molecular mechanism underlying mRNA transcript processing. Nucleic Acids Research 45 (8), pp. 4756-4767. ISSN 0305-1048.

20 June 2017

Smith, L.J. and Bochkareva, A. and Rolfe, M.D. and Hunt, D.M. and Kahramanoglou, C. and Braun, Y. and Rodgers, A. and Blockley, A. and Coade, S. and Lougheed, K.E.A. and Hafneh, N.A. and Glenn, S.M. and Crack, J.C. and Le Brun, N.E. and Saldanha, J.W. and Makarov, V. and Nobeli, Irene and Arnvig, K. and Mukamolova, G.V. and Buxton, R.S. and Green, J. (2017) Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence. Nucleic Acids Research 45 (11), pp. 6600-6612. ISSN 0305-1048.

13 September 2017

Szkop, Krzysztof J. and Cooke, Peter I.C. and Humphries, Joanne A. and Kalna, Viktoria and Moss, David S. and Schuster, E.F. and Nobeli, Irene (2017) Dysregulation of alternative poly-adenylation as a potential player in Autism Spectrum Disorder. Frontiers in Molecular Neuroscience 10 , ISSN 1662-5099.

December 2017

Szkop, Krzysztof and Nobeli, Irene (2017) Untranslated parts of genes interpreted: making heads or tails of high-throughput transcriptomic data via computational methods. BioEssays 39 (12), ISSN 0265-9247.

29 March 2018

Schwenk, S. and Moores, A. and Nobeli, Irene and McHugh, T.D. and Arnvig, K.B. (2018) Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis. Nucleic Acids Research , ISSN 0305-1048.

21 November 2019

Abelak, K. and Bishop-Bailey, D. and Nobeli, Irene (2019) Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids. BMC Research Notes 12 , p. 760. ISSN 1756-0500.

1 February 2020

Ozuna, A. and Liberto, D. and Joyce, R.M. and Arnvig, K.B. and Nobeli, Irene (2020) baerhunter: an R package for the discovery and anal-ysis of expressed non-coding regions in bacterial RNA-seq data. Bioinformatics 36 (3), pp. 966-969. ISSN 1460-2059.

15 May 2021

Szkop, Krzysztof J. and Moss, David S. and Nobeli, Irene (2021) flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data. Bioinformatics 37 (10), pp. 1461-1464. ISSN 1367-4803.

24 December 2021

Gibson, A.J. and Passmore, I.J. and Faulkner, V. and Xia, D. and Nobeli, Irene and Stiens, J. and Willcocks, S. and Clark, T.G. and Sobkowiak, B. and Werling, D. and Villarreal-Ramos, B. and Wren, B.W. and Kendall, S.L. (2021) Probing differences in gene essentiality between the human and animal adapted lineages of the Mycobacterium tuberculosis complex using TnSeq. Frontiers in Veterinary Science 8 , p. 760717. ISSN 2297-1769.

January 2022

Stiens, Jennifer and Arnvig, Kristine B. and Kendall, S.L. and Nobeli, Irene (2022) Challenges in defining the functional, non-coding, expressed genome of members of the Mycobacterium tuberculosis complex. Molecular Microbiology 117 (1), pp. 20-31. ISSN 0950-382X.

30 August 2022

Gibson, A.J. and Stiens, Jennifer and Passmore, I.J. and Faulkner, V. and Miculob, J. and Willcocks, S. and Coad, M. and Berg, S. and Werling, D. and Wren, B.W. and Nobeli, Irene and Villarreal-Ramos, B. and Kendall, S.L. (2022) 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 13 (4), ISSN 2150-7511.

16 March 2023

Stiens, Jennifer and Tan, Y.Y. and Joyce, R. and Arnvig, K.B. and Kendall, S.L. and Nobeli, Irene (2023) Using a whole genome co-expression network to inform the functional characterisation of predicted genomic elements from Mycobacterium tuberculosis transcriptomic data. Molecular Microbiology , ISSN 0950-382X.

25 October 2023

Aksoylu, I.S. and Martin, P. and Robert, F. and Szkop, K.J. and Redmond, N.E. and Bhattacharyya, S. and Wang, J. and Chen, S. and Beauchamp, R.L. and Nobeli, Irene and Pelletier, J. and Larsson, O. and Ramesh, V. (2023) Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations. Molecular Autism 14 , p. 39. ISSN 2040-2392.

4 April 2024

Curel, Claire J.M. and Nobeli, Irene and Thornton, C. (2024) Leflunomide treatment does not protect neural cells following Oxygen-Glucose Deprivation (OGD) in vitro. Cells 13 (7), p. 631. ISSN 2073-4409.