Ian Overton

2024

QClique: optimizing performance and accuracy in maximum weighted clique

Abbas, Q., Koohi Esfahani, M., Overton, I. & Vandierendonck, H., 26 Aug 2024, Euro-Par 2024: parallel processing: 30th International European Conference on Parallel and Distributed Computing, proceedings, part III. Carretero, J., Shende, S., Garcia-Blas, J., Brandic, I., Olcoz, K. & Schreiber, M. (eds.). Springer, p. 88-102 15 p. (Lecture Notes in Computer Science; vol. 14803)(European Conference on Parallel Processing).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Open Access

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6 Downloads (Pure)

2023

Investigating the effects of chronic low-dose radiation exposure in the liver of a hypothermic zebrafish model

Cahill, T., da Silveira, W. A., Renaud, L., Wang, H., Williamson, T., Chung, D., Chan, S., Overton, I. & Hardiman, G., 17 Jan 2023, (Early online date) In: Scientific Reports. 13, 1, 918.

Research output: Contribution to journal › Article › peer-review

Open Access

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3 Citations (Scopus)

65 Downloads (Pure)

Strategies and techniques for quality control and semantic enrichment with multimodal data: a case study in colorectal cancer with eHDPrep

Toner, T. M., Pancholi, R., Miller, P., Forster, T., Coleman, H. G. & Overton, I. M., 12 May 2023, (Early online date) In: Gigascience. 12, 14 p., giad030.

Research output: Contribution to journal › Article › peer-review

Open Access

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80 Downloads (Pure)

Transcriptome profiling reveals enhanced mitochondrial activity as a cold adaptive strategy to hypothermia in zebrafish muscle

Cahill, T., Chan, S., Overton, I. M. & Hardiman, G., 11 May 2023, In: Cells. 12, 10, 15 p., 1366.

Research output: Contribution to journal › Article › peer-review

Open Access

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1 Citation (Scopus)

74 Downloads (Pure)

Validation of in vitro trained transcriptomic radiosensitivity signatures in clinical cohorts

O'Connor, J. D., Overton, I. M. & McMahon, S. J., 05 Jul 2023, In: Cancers. 15, 13, 14 p., 3504.

Research output: Contribution to journal › Article › peer-review

Open Access

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1 Citation (Scopus)

97 Downloads (Pure)

2022

Immune cell networks uncover candidate biomarkers of melanoma immunotherapy response

Vo, D. H. T., McGleave, G. & Overton, I. M., Jun 2022, In: Journal of Personalized Medicine. 12, 6, 20 p., 958.

Research output: Contribution to journal › Article › peer-review

Open Access

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1 Citation (Scopus)

99 Downloads (Pure)

PTEN protein phosphatase activity is not required for tumour suppression in the mouse prostate

Wise, H. M., Harris, A., Kriplani, N., Schofield, A., Caldwell, H., Arends, M. J., Overton, I. M. & Leslie, N. R., 19 Oct 2022, In: Biomolecules. 12, 10, 15 p., 1511.

Research output: Contribution to journal › Article › peer-review

Open Access

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1 Citation (Scopus)

51 Downloads (Pure)

RadSigBench: a framework for benchmarking functional genomics signatures of cancer cell radiosensitivity

O'Connor, J. D., Overton, I. M. & McMahon, S. J., 22 Jan 2022, (Early online date) In: Briefings in Bioinformatics.

Research output: Contribution to journal › Article › peer-review

Open Access

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3 Citations (Scopus)

169 Downloads (Pure)

2021

Induced Torpor as a Countermeasure for Low Dose Radiation Exposure in a Zebrafish Model

Cahill, T., da Silveira, W. A., Renaud, L., Williamson, T., Wang, H., Chung, D., Overton, I., Chan, S. S. L. & Hardiman, G., 14 Apr 2021, In: Cells. 10, 4, 26 p., 906.

Research output: Contribution to journal › Article › peer-review

Open Access

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7 Citations (Scopus)

174 Downloads (Pure)

Long non-coding RNAs and their potential impact on diagnosis, prognosis, and therapy in prostate cancer: racial, ethnic, and geographical considerations

Morgan, R., da Silveira, W. A., Kelly, R. C., Overton, I., Allott, E. H. & Hardiman, G., 02 Dec 2021, In: Expert Review of Molecular Diagnostics. 21, 12, p. 1257-1271

Research output: Contribution to journal › Article › peer-review

Open Access

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8 Citations (Scopus)

138 Downloads (Pure)

SynLeGG: analysis and visualization of multiomics data for discovery of cancer ‘Achilles Heels’ and gene function relationships

Wappett, M., Harris, A., Lubbock, A. L. R., Lobb, I., McDade, S. & Overton, I., 02 Jul 2021, In: Nucleic Acids Research. 49, W1, p. W613-W618

Research output: Contribution to journal › Article › peer-review

Open Access

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5 Citations (Scopus)

272 Downloads (Pure)

2020

Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling

Overton, I. M., Sims, A. H., Owen, J. A., Heale, B. S. E., Ford, M. J., Lubbock, A. L. R., Pairo-Castineira, E. & Essafi, A., 30 Sept 2020, In: Cancers. 12, 10, 34 p., 2823.

Research output: Contribution to journal › Article › peer-review

Open Access

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4 Citations (Scopus)

158 Downloads (Pure)

2019

Using Simple PID-inspired Controllers for Online Resilient Resource Management of Distributed Scientific Workflows

Ferreira da Silva, R., Filgueira, R., Deelman, E., Pairo-Castineira, E., Overton, I. & Atkinson, M., Jun 2019, In: Future Generation Computing Systems. 95, p. 615-628

Research output: Contribution to journal › Article › peer-review

Open Access

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22 Citations (Scopus)

187 Downloads (Pure)

2017

Overcoming Intratumoural Heterogeneity for Reproducible Molecular Risk Stratification: A Case Study in Advanced Kidney Cancer

Lubbock, A., Stewart, G., O'Mahony, F. C., Laird, A., Mullen, P., O'Donnell, M., Powles, T., Harrison, D. J. & Overton, I., 26 Jun 2017, In: BMC Medicine. 15, 118.

Research output: Contribution to journal › Article › peer-review

Open Access

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6 Citations (Scopus)

254 Downloads (Pure)

Quantitative Shotgun Proteomics Unveils Candidate Novel Esophageal Adenocarcinoma (EAC)-specific Proteins

O'neill, J. R., Pak, H.-S., Pairo-Castineira, E., Save, V., Paterson-Brown, S., Nenutil, R., Vojtěšek, B., Overton, I., Scherl, A. & Hupp, T. R., 01 Mar 2017, In: Molecular and Cellular Proteomics. 16, 6, p. 1138-1150

Research output: Contribution to journal › Article › peer-review

Open Access

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17 Citations (Scopus)

282 Downloads (Pure)

2016

Using Simple PID Controllers to Prevent and Mitigate Faults in Scientific Workflows

Ferreira da Silva, R., Filgueira, R., Deelman, E., Pairo-Castineira, E., Overton, I. & Atkinson, M., 14 Nov 2016, Workflows in Support of Large-Scale Science: Proceedings of the 11th Workshop on Workflows in Support of Large-Scale Science co-located with The International Conference for High Performance Computing, Networking, Storage and Analysis (SC 2016). Vol. 1802. p. 15-24 (CEUR Workshop Proceedings).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Open Access

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8 Citations (Scopus)

253 Downloads (Pure)

2015

Method For Predicting Renal Cell Carcinoma (Patent)

Overton, I., Stewart, G., Lubbock, A., Harrison, D. & Powles, T., 01 Nov 2015

Research output: Other contribution

Sunitinib treatment exacerbates intratumoral heterogeneity in metastatic renal cancer

Stewart, G. D., O'Mahony, F. C., Laird, A., Eory, L., Lubbock, A., Mackay, A., Nanda, J., O'Donnell, M., Mullen, P., McNeill, A., Riddick, A., Berney, D., Bex, A., Aitchison, M., Overton, I. M., Harrison, D. J. & Powles, T., 01 Sept 2015, In: Clinical Cancer Research. 21, 18

Research output: Contribution to journal › Article › peer-review

30 Citations (Scopus)

2014

Carbonic Anhydrase 9 Expression Increases with Vascular Endothelial Growth Factor-Targeted Therapy and Is Predictive of Outcome in Metastatic Clear Cell Renal Cancer

Stewart, G. D., O'Mahony, F. C., Laird, A., Rashid, S., Martin, S. A., Eory, L., Lubbock, A. L. R., Nanda, J., O'Donnell, M., Mackay, A., Mullen, P., McNeill, S. A., Riddick, A. C. P., Aitchison, M., Berney, D., Bex, A., Overton, I. M., Harrison, D. J. & Powles, T., Nov 2014, In: European Urology. 66, 5, p. 956–963 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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40 Citations (Scopus)

256 Downloads (Pure)

2013

Analyzing Gene Expression Imaging Data in Developmental Biology

Han, L., van Hemert, J., Overton, I., Besana, P. & Baldock, R., 09 Apr 2013, The DATA Bonanza: Improving Knowledge Discovery in Science, Engineering, and Business. John Wiley & Sons Ltd, p. 327-351 25 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

The ADAR RNA editing enzyme controls neuronal excitability in Drosophila melanogaster

Li, X., Overton, I. M., Baines, R. A., Keegan, L. P. & O'Connell, M. A., 01 Oct 2013, In: Nucleic Acids Research.

Research output: Contribution to journal › Article › peer-review

19 Citations (Scopus)

The Use of Reverse Phase Protein Arrays (RPPA) to Explore Protein Expression Variation within Individual Renal Cell Cancers

O'Mahony, F. C., Nanda, J., Laird, A., Mullen, P., Caldwell, H., Overton, I. M., Eory, L., O'Donnell, M., Faratian, D., Powles, T., Harrison, D. J. & Stewart, G. D., 01 Jan 2013, In: Journal of visualized experiments : JoVE. 71

Research output: Contribution to journal › Article › peer-review

9 Citations (Scopus)

TMA Navigator: network inference, patient stratification and survival analysis with tissue microarray data

Lubbock, A. L. R., Katz, E., Harrison, D. J. & Overton, I. M., 01 Jul 2013, In: Nucleic Acids Research. 41, W1, p. W562-W568

Research output: Contribution to journal › Article › peer-review

14 Citations (Scopus)

2012

Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies

Blakeley, P., Overton, I. M. & Hubbard, S. J., 01 Nov 2012, In: Journal of Proteome Research. 11, 11, p. 5221-34

Research output: Contribution to journal › Article › peer-review

70 Citations (Scopus)

2011

Computational approaches to selecting and optimising targets for structural biology

Overton, I. M. & Barton, G. J., 2011, In: Methods. 55, 1, p. 3-11 9 p.

Research output: Contribution to journal › Article › peer-review

8 Citations (Scopus)

Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus

Overton, I. M., Graham, S., Gould, K. A., Hinds, J., Botting, C. H., Shirran, S., Barton, G. J. & Coote, P. J., 2011, In: BMC Systems Biology. 5, p. 68 (online only)

Research output: Contribution to journal › Article › peer-review

33 Citations (Scopus)

XANNpred neural nets that predict the propensity of a protein to yield diffraction-quality crystals

Overton, I. M., Niekerk, C. A. J. & Barton, G. J., 2011, In: Proteins: Structure, Function and Bioinformatics. 79, 4, p. 1027-33

Research output: Contribution to journal › Article › peer-review

23 Citations (Scopus)

2010

The Scottish Structural Proteomics Facility: targets, methods and outputs

Oke, M., Carter, L. G., Johnson, K. A., Liu, H., Mcmahon, S. A., Yan, X., Kerou, M., Weikart, N. D., Kadi, N., Sheikh, M. A., Schmelz, S., Dorward, M., Zawadzki, M., Cozens, C., Falconer, H., Powers, H., Overton, I. M., Niekerk, C. A. J., Peng, X. & Patel, P. & 11 others, Garrett, R. A., Prangishvili, D., Botting, C. H., Coote, P. J., Dryden, D. T. F., Barton, G. J., Schwarz-linek, U., Challis, G. L., Taylor, G. L., White, M. F. & Naismith, J. H., 01 Jun 2010, In: Journal of Structural and Functional Genomics. 11, 2, p. 167-180 14 p.

Research output: Contribution to journal › Article › peer-review

101 Citations (Scopus)

2008

ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction

Overton, I. M., Padovani, G., Girolami, M. A. & Barton, G. J., 01 Apr 2008, In: Bioinformatics. 24, 7, p. 901-907 7 p.

Research output: Contribution to journal › Article › peer-review

61 Citations (Scopus)

TarO: a target optimisation system for structural biology

Overton, I., vanNiekerk, C. A. J., Carter, L., Dawson, A., Martin, D., Cameron, S., McMahon, S., White, M. F., Hunter, W., Naismith, J. H. & Barton, G. J., 2008, In: Nucleic Acids Research. 36, suppl. 2, p. W190-W196

Research output: Contribution to journal › Article › peer-review

30 Citations (Scopus)

2007

Expression, purification, crystallization, data collection and preliminary biochemical characterization of methicillin-resistant Staphylococcus aureus Sar2028, an aspartate/tyrosine/phenylalanine pyridoxal-5'-phosphate-dependent aminotransferase

Seetharamappa, J., Oke, M., Liu, H., McMahon, S. A., Johnson, K. A., Carter, L., Dorward, M., Zawadzki, M., Overton, I. M., van Niekirk, C. A. J., Graham, S., Botting, C. H., Taylor, G. L., White, M. F., Barton, G. J., Coote, P. J. & Naismith, J. H., 01 May 2007, In: Acta Crystallographica Section F Structural Biology and Crystallization Communications. 63, Pt 5, p. 452-6

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

Purification, crystallization and data collection of methicillin-resistant Staphylococcus aureus Sar2676, a pantothenate synthetase

Seetharamappa, J., Oke, M., Liu, H., McMahon, S. A., Johnson, K. A., Carter, L., Dorward, M., Zawadzki, M., Overton, I. M., van Niekirk, C. A. J., Graham, S., Botting, C. H., Taylor, G. L., White, M. F., Barton, G. J., Coote, P. J. & Naismith, J. H., 01 Jun 2007, In: Acta Crystallographica Section F Structural Biology and Crystallization Communications. 63, Pt 6, p. 488-91

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis

Yard, B., Carter, L., Johnson, K. A., Overton, I., Dorward, M., Liu, H., McMahon, S., Oke, M., Puech, D., Barton, G. J., Naismith, J. H. & Campopiano, D. J., 2007, In: Journal of Molecular Biology. 370, 5, p. 870-886 17 p.

Research output: Contribution to journal › Article › peer-review

118 Citations (Scopus)

2006

A normalised scale for structural genomics target ranking: the OB-Score

Overton, I. & Barton, G. J., 01 Jul 2006, In: FEBS Letters. 580, 16, p. 4005-4009 5 p.

Research output: Contribution to journal › Article › peer-review

56 Citations (Scopus)

2005

Structures of three HIV-1 HLA-B* 5703-peptide complexes and identification of related HLAs potentially associated with long-term nonprogression

Stewart-Jones, G., Gillespie, G., Overton, I., Kaul, R., Roche, P., McMichael, A. J., Rowland-Jones, S. & Jones, E. Y., 01 Aug 2005, In: Journal of Immunology. 175, 4, p. 2459-2468 10 p.

Research output: Contribution to journal › Article › peer-review

63 Citations (Scopus)

Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags

Hubbard, S. J., Grafham, D. V., Beattie, K. J., Overton, I. M., McLaren, S. R., Croning, M. D. R., Boardman, P. E., Bonfield, J. K., Burnside, J., Davies, R. M., Farrell, E. R., Francis, M. D., Griffiths-Jones, S., Humphray, S. J., Hyland, C., Scott, C. E., Tang, H., Taylor, R. G., Tickle, C. & Brown, W. R. A. & 3 others, Birney, E., Rogers, J. & Wilson, S. A., 01 Jan 2005, In: Genome Research. 15, 1, p. 174-183 10 p.

Research output: Contribution to journal › Article › peer-review

77 Citations (Scopus)

2004

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

Wong, G.K.-S., Liu, B., Wang, J., Zhang, Z.-Y., Yang, X., Zhang, Z., Meng, Q., Zhou, J., Li, D., Zhang, J., Ni, P., Li, S., Ran, L., Li, H., Zhang, J., Li, R., Li, S., Zheng, H., Lin, W. & Li, G. & 95 others, Wang, X., Zhao, W., Li, J., Ye, C., Dai, M., Ruan, J., Zhou, Y., Li, Y., He, X., Zhang, Y., Wang, J., Huang, X., Tong, W., Chen, J., Ye, J., Chen, C., Wei, N., Li, G., Dong, L., Lan, F., Sun, Y., Zhang, Z., Yang, Z., Yu, Y., Huang, Y., He, D., Xi, Y., Wei, D. Q., Qi, Q., Li, W., Shi, J., Wang, M., Xie, F., Wang, J., Zhang, X., Wang, P., Zhao, Y., Li, N., Yang, N., Dong, W., Hu, S., Zeng, C., Zheng, W., Hao, B., Hillier, L. W., Yang, S.-P., Warren, W. C., Wilson, R. K., Brandström, M., Ellegren, H., Crooijmans, R. P. M. A., van der Poel, J. J., Bovenhuis, H., Groenen, M. A. M., Ovcharenko, I., Gordon, L., Stubbs, L., Lucas, S., Glavina, T., Aerts, A., Kaiser, P., Rothwell, L., Young, J. R., Rogers, S., Walker, B. A., van Hateren, A., Kaufman, J., Bumstead, N., Lamont, S. J., Zhou, H., Hocking, P. M., Morrice, D., de Koning, D.-J., Law, A., Bartley, N., Burt, D. W., Hunt, H., Cheng, H. H., Gunnarsson, U., Wahlberg, P., Andersson, L., Kindlund, E., Tammi, M. T., Andersson, B., Webber, C., Ponting, C., Overton, I. M., Boardman, P. E., Tang, H., Hubbard, S. J., Wilson, S. A., Yu, J., Wang, J., Yang, H. & Consortium, I. C. P. M., 2004, In: Nature. 432, 7018, p. 717-22 694 p.

Research output: Contribution to journal › Article › peer-review

379 Citations (Scopus)

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Hillier, L. W., Miller, J. W., Birney, E., Warren, W. C., Hardison, R., Ponting, C., Bork, P., Burt, D. W., Groenen, M. A. M., Delany, M., Dodgson, J., Chinwalla, A., Cliften, P., Clifton, S., Delehaunty, K., Fronick, C., Fulton, R., Graves, T., Kremitzki, C. & Layman, D. & 156 others, Magrini, V., McPherson, J., Miner, T., Minx, P., Nash, W., Nhan, M., Nelson, J., Oddy, L., Pohl, C., Randall-Maher, J., Smith, S., Wallis, J., Yang, S., Romanov, M., Rondelli, C., Paton, B., Smith, J., Morrice, D., Daniels, L., Tempest, H., Robertson, L., Masabanda, J., Griffin, D., Vignal, A., Fillon, V., Jacobbson, L., Kerje, S., Andersson, L. S., Crooijmans, R., Aerts, J., van der Poel, J., Ellegren, H., Caldwell, R., Hubbard, S. J., Grafham, D., Kierzek, A., McLaren, W. M., Overton, I., Arakawa, H., Beattie, K., Bezzubov, Y., Boardman, P. E., Bonfield, J., Croning, M., Davies, R., Francis, M., Humphray, S., Scott, C., Taylor, R., Tickle, C., Brown, W., Rogers, J., Buerstedde, J., Wilson, S., Stubbs, L., Ovcharenko, I., Gordon, L., Lucas, G. S., Miller, M., Inoko, H., Shiina, T., Kaufman, J., Salomonsen, J., Skjoedt, K., Wong, G.K.-S., Wang, J., Liu, B., Wang, J., Yu, J., Yang, H., Nefedov, M., Koriabine, M., deJong, P., Goodstadt, L., Webber, C., Dickens, N. J., Letunic, I., Suyama, M., Torrents, D., von Mering, C., Zdobnov, E., Makova, K., Nekrutenko, A., Elnitski, L., Eswara, P., King, D., Yang, S., Tyekucheva, S., Radakrishnan, A., Harris, R., Chiaromonte, F., Taylor, J., He, J., Rijnkels, M., Griffiths-Jones, S., Ureta-Vidal, A., Hoffman, M., Severin, J., Searle, S., Law, A. S., Speed, J. D., Waddington, D., Cheng, Z., Tuzun, E., Eichler, E. E., Bao, Z., Flicek, P., Shteynberg, D., Brent, M., Bye, J., Huckle, E., Chatterji, S., Dewey, C., Pachter, L., Kouranov, A., Mourelatos, Z., Hatzigeorgiou, A., Paterson, A., Ivarie, R., Brandstrom, M., Axelsson, E., Backstrom, N., Berlin, S., Webster, M., Pourquie, O., Reymond, A., Ucla, C., Antonarakis, S. E., Long, M., Emerson, J., Betran, E., Dupanloup, [. V., Kaessmann, H., Hinrichs, A., Bejerano, G., Furey, T., Harte, R., Raney, B., Siepel, A., Kent, W., Haussler, D., Eyras, E., Castelo, R., Abril, J., Castellano, S., Camara, F., Nates-Parra, G., Guigo, R., Bourque, G., Tesler, G., Pevzner, P., Smit, H. A., Fulton, L., Mardis, E. R., Wilson, R. & Consortium, I. C. G. S., 01 Dec 2004, In: Nature. 432, 7018, p. 695-716 22 p.

Research output: Contribution to journal › Article › peer-review

2259 Citations (Scopus)

2002

A comprehensive collection of chicken cDNAs

Boardman, P. E., Sanz-Ezquerro, J., Overton, I. M., Burt, D. W., Bosch, E., Fong, W. T., Tickle, C., Brown, W. R. A., Wilson, S. A. & Hubbard, S. J., 2002, In: Current Biology. 12, 22, p. 1965-9 1955 p.

Research output: Contribution to journal › Article › peer-review

279 Citations (Scopus)

2001

Translocation portals for the substrates and products of a viral transcription complex: the bluetongue virus core

Diprose, J., Burroughs, J., Sutton, G., Goldsmith, A., Gouet, P., Malby, R., Overton, I., Zientara, S., Mertens, P., Stuart, D. & Grimes, J., 01 Dec 2001, In: The EMBO Journal. 20, 24, p. 7229-7239 11 p.

Research output: Contribution to journal › Article › peer-review

71 Citations (Scopus)

Ian Overton

Research output

Search results