Dr Christopher Greenman
| Job Title | Contact | Location |
|---|---|---|
| Lecturer |
C dot Greenman at uea dot ac dot uk
Tel: +44 (0)1603 59 3639 |
Biology 2.18 |
Career
Following a mathematics degree at Durham University, Chris completed a mathematics PhD at the University of Edinburgh utilizing number theory to study the spacing distributions of quantized harmonic oscillators. He then spent over five years at Bolton Institute (now University) followed by two years of mathematical consultancy in industry examining problems varying from satellite positioning algorithms to machine learning approaches to drug discovery. He then spent seven years at the Sanger Institute developing statistical and mathematical techniques required to analyse cancer genomic data. He started a synergy position between The Genome Analysis Centre (www.tgac.ac.uk/) in Norwich Research Park and the Computational Biology at the School of Computing Sciences in 2011.
PhD Projects
The following opportunity exists to pursue a PhD with Dr. Greenman on the project:
Mathematical and Statistical Models in Genomics
Key Research Interests
- Graph theoretic techniques to analysing rearrangements
- Markov process techniques to examine copy number variation
- dN/dS techniques of examining selection
- Stochastic methods of modelling clonal growth
- Genomics of plants, microbes animals or cancer
Selected publications
- Greenman C et al. Estimation of Rearrangement Phylogeny in Cancer, Submitted.
- Varela I, et al., Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma, Nature, 2011 Jan 27;469(7331):539-42.
- Stephens PJ, et al, Massive genomic rearrangement acquired in a single catastrophic event during cancer development, Cell. 2011 144(1):27-40
- Santarius T, et al. GLO1-A novel amplified gene in human cancer Genes Chromosomes Cancer. 2010 Aug;49(8):711-25.
- Greenman CD, et al., PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics. 2010 Jan;11(1):164-75.
- Bignell GR*, Greenman CD*, et al. Signatures of mutation and selection in the cancer genome. Nature. 2010 Feb 18;463(7283):893-8.
- Pleasance ED, et al. A small-cell lung cancer genome with complex signatures of tobacco exposure Nature. 2010 Jan 14;463(7278):184-90.
- Pleasance ED, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 2010 Jan 14;463(7278):191-6.
- Stephens PJ, et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature. 2009 Dec 24;462(7276):1005-10.
- Dalgliesh GL et al. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes Nature. 2010 Jan 21;463(7279):360-3
- Mahoney et al., LKB1/KRAS mutant lung cancers constitute a genetic subset of NSCLC with increased sensitivity to MAPK and mTOR signalling inhibition, Br.J.Cancer, 2009, 100, 2, 370-375
- Tarpey, P.S. et al., A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation, Nat.Genet., 2009, 41, 5, 535-543
- Van Haaften, G, et al. Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer, Nat.Genet., 2009, 41, 5,
- Bignell GR, et al. Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res. 2007 Sep;17(9):1296-303.
- Dicks E, et al. AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes. Bioinformatics. 2007 Jul 1;23(13):1689-91.
- Greenman C, et al. Patterns of somatic mutation in human cancer genomes. Nature. 2007 Mar 8;446(7132):153-8.
- Edkins S, et al. Recurrent KRAS codon 146 mutations in human colorectal cancer. Cancer Biol Ther. 2006 Aug;5(8):928-32.
- Greenman C, et al. Statistical analysis of pathogenicity of somatic mutations in cancer. Genetics. 2006 Aug;173(4):2187-98.
- Hunter C, et al. A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy. Cancer Res. 2006 Apr 15;66(8):3987-91.
- Davies H, et al. High throughput DNA sequence variant detection by conformation sensitive capillary electrophoresis and automated peak comparison. Genomics. 2006 Mar;87(3):427-32.
- Bignell G, et al. Sequence analysis of the protein kinase gene family in human testicular germ-cell tumors of adolescents and adults. Genes Chromosomes Cancer. 2006 Jan;45(1):42-46.
- Davies H, et al. Somatic mutations of the protein kinase gene family in human lung cancer. Cancer Res. 2005 Sep 1;65(17):7591-5.
- Stephens P, et al. A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer. Nat Genet. 2005 Jun;37(6):590-2.
- Cox C*, Bignell G*, Greenman C*, et al. A survey of homozygous deletions in human cancer genomes. PNAS 2005 Mar 22;102(12):4542-7.
- Stephens P, et al. Lung cancer: intragenic ERBB2 kinase mutations in tumours. Nature. 2004 Sep 30;431(7008):525-6.
- Greenman C, Is the level spacing distribution of the infinite-dimensional harmonic oscillator that of a Poisson process? 1997 J. Phys. A: Math. Gen. 30 927-936.
- Greenman C, Fractal properties of spacing distributions 1997 J. Phys. A: Math. Gen. 30 915-926.
- Greenman C, The generic spacing distribution of the two-dimensional harmonic oscillator 1996 J. Phys. A: Math. Gen. 29 4065-4081.
Article
Greenman, C (2012) Estimation of Rearrangement Phylogeny in Cancer. Genome Research, 22. pp. 346-361.
Fischer, A, Greenman, C and Mustonen, V (2011) Germline Fitness Based Scoring of Cancer Mutations. Genetics, 188 (2). pp. 383-393. ISSN 1943-2631
Varela, I, Tarpey, P, Raine, K, Huang, D, Ong, CK, Stephens, P, Davies, H, Jones, D, Lin, M-L, Teague, J, Bignell, G, Butler, A, Cho, J, Dalgliesh, GL, Galappaththige, D, Greenman, C, Hardy, C, Jia, M, Latimer, C, Lau, KW, Marshall, J, McLaren, S, Menzies, A, Mudie, L, Stebbings, L, Largaespada, DA, Wessels, LFA, Richard, S, Kahnoski, RJ, Anema, J, Tuveson, DA, Perez-Mancera, PA, Mustonen, V, Fischer, A, Adams, DJ, Rust, A, Chan-on, W, Subimerb, C, Dykema, K, Furge, K, Campbell, PJ, Teh, BT, Stratton, MR and Futreal, PA (2011) Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature, 469 (7331). pp. 539-542. ISSN 1476-4687
Stephens, PJ, Greenman, CD, Fu, B, Yang, F, Bignell, GR, Mudie, LJ, Pleasance, ED, Lau, KW, Beare, D, Stebbings, LA, McLaren, S, Lin, M-L, McBride, DJ, Varela, I, Nik-Zainal, S, Leroy, C, Jia, M, Menzies, A, Butler, AP, Teague, JW, Quail, MA, Burton, J, Swerdlow, H, Carter, NP, Morsberger, LA, Iacobuzio-Donahue, C, Follows, GA, Green, AR, Flanagan, AM, Stratton, MR, Futreal, PA and Campbell, PJ (2011) Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell, 144 (1). pp. 27-40. ISSN 1097-4172
Stjernqvist, S, Ryden, T and Greenman, CD (2011) Model-Integrated Estimation of Normal Tissue Contamination for Cancer SNP Allelic Copy Number Data. Cancer Informatics, 10. pp. 159-173. ISSN 1176-9351
Bignell, GR, Greenman, CD, Davies, H, Butler, AP, Edkins, S, Andrews, JM, Buck, G, Chen, L, Beare, D, Latimer, C, Widaa, S, Hinton, J, Fahey, C, Fu, B, Swamy, S, Dalgliesh, GL, Teh, BT, Deloukas, P, Yang, F, Campbell, PJ, Futreal, PA and Stratton, MR (2010) Signatures of mutation and selection in the cancer genome. Nature, 463 (7283). pp. 893-898. ISSN 1476-4687
Dalgliesh, GL, Furge, K, Greenman, C, Chen, L, Bignell, G, Butler, A, Davies, H, Edkins, S, Hardy, C, Latimer, C, Teague, J, Andrews, J, Barthorpe, S, Beare, D, Buck, G, Campbell, PJ, Forbes, S, Jia, M, Jones, D, Knott, H, Kok, CY, Lau, KW, Leroy, C, Lin, M-L, McBride, DJ, Maddison, M, Maguire, S, McLay, K, Menzies, A, Mironenko, T, Mulderrig, L, Mudie, L, O'Meara, S, Pleasance, E, Rajasingham, A, Shepherd, R, Smith, R, Stebbings, L, Stephens, P, Tang, G, Tarpey, PS, Turrell, K, Dykema, KJ, Khoo, SK, Petillo, D, Wondergem, B, Anema, J, Kahnoski, RJ, Teh, BT, Stratton, MR and Futreal, PA (2010) Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature, 463 (7279). pp. 360-363. ISSN 1476-4687
Greenman, CD, Bignell, G, Butler, A, Edkins, S, Hinton, J, Beare, D, Swamy, S, Santarius, T, Chen, L, Widaa, S, Futreal, PA and Stratton, MR (2010) PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics (Oxford, England), 11 (1). pp. 164-75. ISSN 1468-4357
Pleasance, ED, Cheetham, RK, Stephens, PJ, McBride, DJ, Humphray, SJ, Greenman, CD, Varela, I, Lin, ML, Ordóñez, GR, Bignell, GR, Ye, K, Alipaz, J, Bauer, MJ, Beare, D, Butler, A, Carter, RJ, Chen, L, Cox, AJ, Edkins, S, Kokko-Gonzales, PI, Gormley, NA, Grocock, RJ, Haudenschild, CD, Hims, MM, James, T, Jia, M, Kingsbury, Z, Leroy, C, Marshall, J, Menzies, A, Mudie, LJ, Ning, Z, Royce, T, Schulz-Trieglaff, OB, Spiridou, A, Stebbings, LA, Szajkowski, L, Teague, J, Williamson, D, Chin, L, Ross, MT, Campbell, PJ, Bentley, DR, Futreal, PA and Stratton, MR (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, 463 (7278). pp. 191-6. ISSN 1476-4687
Pleasance, ED, Stephens, PJ, O'Meara, S, McBride, DJ, Meynert, A, Jones, D, Lin, ML, Beare, D, Lau, KW, Greenman, C, Varela, I, Nik-Zainal, S, Davies, HR, Ordoñez, GR, Mudie, LJ, Latimer, C, Edkins, S, Stebbings, L, Chen, L, Jia, M, Leroy, C, Marshall, J, Menzies, A, Butler, A, Teague, JW, Mangion, J, Sun, YA, McLaughlin, SF, Peckham, HE, Tsung, EF, Costa, GL, Lee, CC, Minna, JD, Gazdar, A, Birney, E, Rhodes, MD, McKernan, KJ, Stratton, MR, Futreal, PA and Campbell, PJ (2010) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature, 463 (7278). pp. 184-90. ISSN 1476-4687
Santarius, T, Bignell, GR, Greenman, CD, Widaa, S, Chen, L, Mahoney, CL, Butler, A, Edkins, S, Waris, S, Thornalley, PJ, Futreal, PA and Stratton, MR (2010) GLO1-A novel amplified gene in human cancer. Genes, chromosomes & cancer, 49 (8). pp. 711-25. ISSN 1098-2264
Ashwin, Clive, Choudhury, B, Davies, H, Edkins, S, Greenman, C, Haaften, Gvan, Mironenko, T, Santarius, T, Stevens, C, Stratton, MR and Futreal, PA (2009) LKB1/KRAS mutant lung cancers constitute a genetic subset of NSCLC with increased sensitivity to MAPK and mTOR signalling inhibition. British journal of cancer, 100 (2). pp. 370-5. ISSN 1532-1827
Stephens, PJ, McBride, DJ, Lin, ML, Varela, I, Pleasance, ED, Simpson, JT, Stebbings, LA, Leroy, C, Edkins, S, Mudie, LJ, Greenman, CD, Jia, M, Latimer, C, Teague, JW, Lau, KW, Burton, J, Quail, MA, Swerdlow, H, Churcher, C, Natrajan, R, Sieuwerts, AM, Martens, JWM, Silver, DP, Langerød, A, Russnes, HEG, Foekens, JA, Reis-Filho, JS, van 't Veer, L, Richardson, AL, Børresen-Dale, AL, Campbell, PJ, Futreal, PA and Stratton, MR (2009) Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature, 462 (7276). pp. 1005-10. ISSN 1476-4687
Tarpey, PS, Smith, R, Pleasance, E, Whibley, A, Edkins, S, Hardy, C, O'Meara, S, Latimer, C, Dicks, E, Menzies, A, Stephens, P, Blow, M, Greenman, C, Xue, Y, Tyler-Smith, C, Thompson, D, Gray, K, Andrews, J, Barthorpe, S, Buck, G, Cole, J, Dunmore, R, Jones, D, Maddison, M, Mironenko, T, Turner, R, Turrell, K, Varian, J, West, S, Widaa, S, Wray, P, Teague, J, Butler, A, Jenkinson, A, Jia, M, Richardson, D, Shepherd, R, Wooster, R, Tejada, MI, Martinez, F, Carvill, G, Goliath, R, de Brouwer, APM, van Bokhoven, H, Van Esch, H, Chelly, J, Raynaud, M, Ropers, HG, Abidi, FE, Srivastava, AK, Cox, J, Luo, Y, Mallya, U, Moon, J, Parnau, J, Mohammed, S, Tolmie, JL, Shoubridge, C, Corbett, M, Gardner, A, Haan, E, Rujirabanjerd, S, Shaw, M, Vandeleur, L, Fullston, T, Easton, DF, Boyle, J, Partington, M, Hackett, A, Field, M, Skinner, C, Stevenson, RE, Bobrow, M, Turner, G, Schwartz, CE, Gecz, J, Raymond, FL, Futreal, PA and Stratton, MR (2009) A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Nature genetics, 41 (5). pp. 535-43. ISSN 1546-1718
van Haaften, G, Dalgliesh, GL, Davies, H, Chen, L, Bignell, G, Greenman, C, Edkins, S, Hardy, C, O'Meara, S, Teague, J, Butler, A, Hinton, J, Latimer, C, Andrews, J, Barthorpe, S, Beare, D, Buck, G, Campbell, PJ, Cole, J, Forbes, S, Jia, M, Jones, D, Kok, CY, Leroy, C, Lin, ML, McBride, DJ, Maddison, M, Maquire, S, McLay, K, Menzies, A, Mironenko, T, Mulderrig, L, Mudie, L, Pleasance, E, Shepherd, R, Smith, R, Stebbings, L, Stephens, P, Tang, G, Tarpey, PS, Turner, R, Turrell, K, Varian, J, West, S, Widaa, S, Wray, P, Collins, VP, Ichimura, K, Law, S, Wong, J, Yuen, ST, Leung, SY, Tonon, G, DePinho, RA, Tai, YT, Anderson, KC, Kahnoski, RJ, Massie, A, Khoo, SK, Teh, BT, Stratton, MR and Futreal, PA (2009) Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. Nature genetics, 41 (5). pp. 521-3. ISSN 1546-1718
