糖心原创

School of Biosciences
 

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Dov Stekel

Professor of Computational Biology, Faculty of Science

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Biography

I am Professor of computational Biology at the , 糖心原创. I have been working at the 糖心原创 since 2009, when I was appointed as Associate Professor, and have been Professor since 2018. Before working at the 糖心原创, I spent five years at the University of Birmingham as Lecturer in Bioinformatics. I studied mathematics at , and for a D.Phil. at the , , supervised by . My D.Phil. topic was on mathematical modeling of T lymphocyte recirculation and virus dynamics. Following my D.Phil., I worked briefly with at the , before taking a position in the Bioinformatics group at (as it was), and then as Head of Bioinformatics at 's microarray company, . I left OGT after receiving a commission from to write , and worked as a free-lance bioinformatics consultant during that time.

Teaching Summary

I teach on a range of modules associated with mathematical and computer modelling in the biological and environmental sciences. Specifically:

  • Computer Modelling in Science: Introduction (D224E4) - Year 2
  • Computer Modelling in Science: Applications (C135E9) - Year 3
  • Project Management - MSci year

Research Summary

We use mathematical, computing and statistical techniques to build predictive models for biological systems. There are three main areas of activity:

  • Antimicrobial resistance. We use mathematical and computer models at both molecular and population levels to study mechanisms for, and spread of, antimicrobial resistance, under the One Health Paradigm. Current work is focussed on the emergence of antimicrobial resistance in the environment, especially in agriculture and the food chain. Past work has included modelling plasmid regulation, and models for molecular mechanisms for antimicrobial metals, including zinc and mercury. We have also carried out in silico evolution of gene network responses to antimicrobial agents.
  • Resilience. We are also interested in using mathematical and computing techniques to describe and understand resilience, and factors that enable resilience. This is in varied domains, including funded work with Unilever on resilience of the oral microbiome, and Wellcome Trust funded work with the University of Pretoria and others on resilience in young people not in education, employment or training.
  • Quantitative bioinformatics. We retain an interest in using statistical and machine learning techniques as applied to large scale quantitative data sets from Omics technologies, including transcriptomics, proteomics and metabolomics.

We try, where possible, to work on projects with active collaborations with experimental biologists. While our main focus is on microbiology, we are happy to foster collaborations with scientists working in any area of biology, and this range is reflected in our publications.

Selected Publications

  • SHAW, LAURENCE M., BLANCHARD, ADAM, CHEN, QINGLIN, AN, XINLI, DAVIES, PEERS, TOTEMEYER, SABINE, ZHU, YONG-GUAN and STEKEL, DOV J., 2019. DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples SCIENTIFIC REPORTS. 9,
  • STEKEL, DOV, 2018. Antibiotic resistance pre-dates penicillin NATURE. 562(7726), 192-192
  • ZHU, YONG-GUAN, GILLINGS, MICHAEL, SIMONET, PASCAL, STEKEL, DOV, BANWART, STEVEN and PENUELAS, JOSEP, 2018. Human dissemination of genes and microorganisms in Earth's Critical Zone GLOBAL CHANGE BIOLOGY. 24(4), 1488-1499
  • ZHU, YONG-GUAN, GILLINGS, MICHAEL, SIMONET, PASCAL, STEKEL, DOV, BANWART, STEVE and PENUELAS, JOSEP, 2017. Microbial mass movements SCIENCE. 357(6356), 1099-1100
  • TODMAN, H., HELLIWELL, R., KING, L., BLANCHARD, A., GRAY-HAMMERTON, C. J., HOOTON, S. P., BAKER, M., MARGERISON, J., WILSON, P., DODD, C. E. R., MORRIS, C., RAMAN, S., HUDSON, C., KREFT, J. U., HOBMAN, J. L., KYPRAIOS, T. and STEKEL, D. J., 2024. NPJ Antimicrob Resist. 2(1), 13
  • FLATGARD, B. M., WILLIAMS, A. D., AMIN, M. B., HOBMAN, J. L., STEKEL, D. J., ROUSHAM, E. K. and ISLAM, M. A., 2024. Microbiol Spectr. 12(6), e0395623
  • COCKX, B. J. R., FOSTER, T., CLEGG, R. J., ALDEN, K., ARYA, S., STEKEL, D. J., SMETS, B. F. and KREFT, J. U., 2024. PLoS Comput Biol. 20(2), e1011303
  • COOK, R., BROWN, N., RIHTMAN, B., MICHNIEWSKI, S., REDGWELL, T., CLOKIE, M., STEKEL, D. J., CHEN, Y., SCANLAN, D. J., HOBMAN, J. L., NELSON, A., JONES, M. A., SMITH, D. and MILLARD, A., 2024. Microb Genom. 10(2),
  • ARNOLD, K. E., LAING, G., MCMAHON, B. J., FANNING, S., STEKEL, D. J., PAHL, O., COYNE, L., LATHAM, S. M. and MCINTYRE, K. M., 2024. Lancet Planet Health. 8(2), e124-e133
  • TODMAN, H., ARYA, S., BAKER, M. and STEKEL, D. J., 2023. PLoS One. 18(8), e0289941
  • WEIDMAN, S., LEVINE, D. T., LOUWAGIE, F., BLACKMORE, K., THERON, L. C. and STEKEL, D. J., 2023. Curr Psychol. 1-15
  • IBRAHIM, D. R., DODD, C. E. R., STEKEL, D. J., MESHIOYE, R. T., DIGGLE, M., LISTER, M. and HOBMAN, J. L., 2023. Antibiotics (Basel). 12(1),
  • COOK, R., BROWN, N., REDGWELL, T., RIHTMAN, B., BARNES, M., CLOKIE, M., STEKEL, D. J., HOBMAN, J., JONES, M. A. and MILLARD, A., 2021. Phage (New Rochelle). 2(4), 214-223
  • HASSOUN-KHEIR, N., STABHOLZ, Y., KREFT, J. U., DE LA CRUZ, R., DECHESNE, A., SMETS, B. F., ROMALDE, J. L., LEMA, A., BALBOA, S., GARCIA-RIESTRA, C., TORRES-SANGIAO, E., NEUBERGER, A., GRAHAM, D., QUINTELA-BALUJA, M., STEKEL, D. J., GRAHAM, J., PRUDEN, A., NESME, J., SORENSEN, S. J., HOUGH, R. and PAUL, M., 2021. One Health. 13, 100339
  • HOOTON, S. P. T., PRITCHARD, A. C. W., ASIANI, K., GRAY-HAMMERTON, C. J., STEKEL, D. J., CROSSMAN, L. C., MILLARD, A. D. and HOBMAN, J. L., 2021. Front Microbiol. 12, 723322
  • SHAW, LAURENCE M., BLANCHARD, ADAM, CHEN, QINGLIN, AN, XINLI, DAVIES, PEERS, TOTEMEYER, SABINE, ZHU, YONG-GUAN and STEKEL, DOV J., 2019. DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples SCIENTIFIC REPORTS. 9,
  • WILLIAMS, ORLA, CLARK, IAN, GOMES, RACHEL L., PEREHINEC, TANIA, HOBMAN, JON L., STEKEL, DOV J., HYDE, ROBERT, DODDS, CHRIS and LESTER, EDWARD, 2019. SCIENCE OF THE TOTAL ENVIRONMENT. 655, 1139-1149
  • KNIGHT, G. M., DAVIES, N. G., COLIJN, C., COLL, F., DONKER, T., GIFFORD, D. R., GLOVER, R. E., JIT, M., KLEMM, E., LEHTINEN, S., LINDSAY, J. A., LIPSITCH, M., LLEWELYN, M. J., MATEUS, A. L. P., ROBOTHAM, J. V., SHARLAND, M., STEKEL, D., YAKOB, L. and ATKINS, K. E., 2019. BMC Infect Dis. 19(1), 1011
  • SHAW, L. M., BLANCHARD, A., CHEN, Q., AN, X., DAVIES, P., TOTEMEYER, S., ZHU, Y. G. and STEKEL, D. J., 2019. Sci Rep. 9(1), 2373
  • ISHAN AJMERA, JING SHI, JITENDER GIRI, PING WU, DOV J. STEKEL, CHUNGUI LU and CHARLIE HODGMAN, 2018. npj Systems Biology and Applications. 4(4), 8
  • WILLIAMS O, CLARK I, GOMES RL, PEREHINEC T, HOBMAN JL, STEKEL DJ, HYDE R, DODDS C and LESTER E, 2018. The Science of the total environment. 655, 1139-1149
  • STEKEL, DOV, 2018. Antibiotic resistance pre-dates penicillin NATURE. 562(7726), 192-192
  • SAKARIDIS, IOANNIS, ELLIS, RICHARD J, CAWTHRAW, SHAUN A, VAN VLIET, ARNOUD HM, STEKEL, DOV J, PENELL, JOHANNA, CHAMBERS, MARK, LA RAGIONE, ROBERTO M and COOK, ALASDAIR J, 2018. Table_1_Investigating the Association Between the Caecal Microbiomes of Broilers and Campylobacter Burden.DOCX Figshare.
  • SAKARIDIS, IOANNIS, ELLIS, RICHARD J., CAWTHRAW, SHAUN A., VAN VLIET, ARNOUD H. M., STEKEL, DOV J., PENELL, JOHANNA, CHAMBERS, MARK, LA RAGIONE, ROBERTO M. and COOK, ALASDAIR J., 2018. Investigating the Association Between the Caecal Microbiomes of Broilers and Campylobacter Burden FRONTIERS IN MICROBIOLOGY. 9,
  • ZHU, YONG-GUAN, GILLINGS, MICHAEL, SIMONET, PASCAL, STEKEL, DOV, BANWART, STEVEN and PENUELAS, JOSEP, 2018. Human dissemination of genes and microorganisms in Earth's Critical Zone GLOBAL CHANGE BIOLOGY. 24(4), 1488-1499
  • AJMERA, ISHAN, SHI, JING, GIRI, JITENDER, WU, PING, STEKEL, DOV J., LU, CHUNGUI and HODGMAN, T. CHARLIE, 2018. Regulatory feedback response mechanisms to phosphate starvation in rice NPJ SYSTEMS BIOLOGY AND APPLICATIONS. 4,
  • STEKEL, D., 2018. Nature. 562(7726), 192
  • SAKARIDIS, I., ELLIS, R. J., CAWTHRAW, S. A., VAN VLIET, A. H. M., STEKEL, D. J., PENELL, J., CHAMBERS, M., LA RAGIONE, R. M. and COOK, A. J., 2018. Front Microbiol. 9, 927
  • ZHU, Y. G., GILLINGS, M., SIMONET, P., STEKEL, D., BANWART, S. and PENUELAS, J., 2018. Glob Chang Biol. 24(4), 1488-1499
  • PAL C, ASIANI K, ARYA S, RENSING C, STEKEL DJ, LARSSON DGJ and HOBMAN JL, 2017. Advances in Microbial Physiology. 70, 261-313
  • MUDASSAR IQBAL, NEIL DOHERTY, ANNA PAGE, SAARA QAZI, ISHAN AJMERA, PETER LUND, THEODORE KYPRAIOS, DAVID SCOTT, PHILIP HILL and DOV STEKEL, 2017. Reconstructing promoter activity from Lux bioluminescent reporters PLoS Computational Biology. in press(in press), in press (In Press.)
  • IQBAL, MUDASSAR, DOHERTY, NEIL, PAGE, ANNA M. L., QAZI, SAARA N. A., AJMERA, ISHAN, LUND, PETER A., KYPRAIOS, THEODORE, SCOTT, DAVID J., HILL, PHILIP J. and STEKEL, DOV J., 2017. PLOS COMPUTATIONAL BIOLOGY. 13(9),
  • ZHU, YONG-GUAN, GILLINGS, MICHAEL, SIMONET, PASCAL, STEKEL, DOV, BANWART, STEVE and PENUELAS, JOSEP, 2017. Microbial mass movements SCIENCE. 357(6356), 1099-1100
  • PAL, CHANDAN, ASIANI, KARISHMA, ARYA, SANKALP, RENSING, CHRISTOPHER, STEKEL, DOV J., LARSSON, D. G. JOAKIM and HOBMAN, JON L., 2017. MICROBIOLOGY OF METAL IONS. 70, 261-313
  • ZHU, Y. G., GILLINGS, M., SIMONET, P., STEKEL, D., BANWART, S. and PENUELAS, J., 2017. Science. 357(6356), 1099-1100
  • IBRAHIM, DELVEEN R, DODD, CHRISTINE E R, STEKEL, DOV J, RAMSDEN, STEPHEN J and HOBMAN, JON L, 2016. FEMS microbiology ecology. 92(4),
  • BAKER, MICHELLE, HOBMAN, JON L, DODD, CHRISTINE E R, RAMSDEN, STEPHEN J and STEKEL, DOV J, 2016. FEMS microbiology ecology. 92(4),
  • DIANE LEVINE and DOV STEKEL, 2016. Computers in Human Behaviour. 63, 25鈥�34
  • MATTHIAS GERSTGRASSER, SARAH NICHOLLS, MICHAEL STOUT, KATHERINE SMART, CHRIS POWELL, THEODORE KYPRAIOS and DOV STEKEL, 2016. Journal of Bioinformatics and Computational Biology. 14(3), 1650007
  • IBRAHIM, DELVEEN R., DODD, CHRISTINE E. R., STEKEL, DOV J., RAMSDEN, STEPHEN J. and HOBMAN, JON L., 2016. FEMS MICROBIOLOGY ECOLOGY. 92(4),
  • BAKER, MICHELLE, HOBMAN, JON L., DODD, CHRISTINE E. R., RAMSDEN, STEPHEN J. and STEKEL, DOV J., 2016. FEMS MICROBIOLOGY ECOLOGY. 92(4),
  • GERSTGRASSER, M., NICHOLLS, S., STOUT, M., SMART, K., POWELL, C., KYPRAIOS, T. and STEKEL, D, 2016. Journal of Bioinformatics and Computational Biology. 14, 1-23
  • LEVINE, DIANE T. and STEKEL, DOV J., 2016. So why have you added me? Adolescent girls' technology-mediated attachments and relationships COMPUTERS IN HUMAN BEHAVIOR. 63, 25-34
  • GERSTGRASSER, MATTHIAS, NICHOLLS, SARAH, STOUT, MICHAEL, SMART, KATHERINE, POWELL, CHRIS, KYPRAIOS, THEODORE and STEKEL, DOV, 2016. A Bayesian approach to analyzing phenotype microarray data enables estimation of microbial growth parameters JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY. 14(3),
  • TAKAHASHI H, OSHIMA T, HOBMAN JL, DOHERTY N, CLAYTON SR, IQBAL M, HILL PJ, TOBE T, OGASAWARA N, KANAYA S and STEKEL DJ, 2015. Journal of the Royal Society, Interface / the Royal Society. 12(106),
  • HAOULA Z, RAVIPATI S, STEKEL DJ, ORTORI CA, HODGMAN C, DAYKIN C, RAINE-FENNING N, BARRETT DA and ATIOMO W, 2015. Metabolomics : Official journal of the Metabolomic Society. 11(3), 657-666
  • SWAN AL, STEKEL DJ, HODGMAN C, ALLAWAY D, ALQAHTANI MH, MOBASHERI A and BACARDIT J, 2015. BMC genomics. 16 Suppl 1, S2
  • HAOULA, ZEINA, RAVIPATI, SRINIVASARAO, STEKEL, DOV J., ORTORI, CATHARINE A., HODGMAN, CHARLIE, DAYKIN, CLARE, RAINE-FENNING, NICK, BARRETT, DAVID A. and ATIOMO, WILLIAM, 2015. METABOLOMICS. 11(3), 657-666
  • IQBAL, M., HODGMAN, T.C. and STEKEL, D.J., 2014. Current Chemical Biology. 7, 234-240
  • FLETCHER SJ, IQBAL M, JABBARI S, STEKEL D and RAPPOPORT JZ, 2014. PloS one. 9(11), e111176
  • GIBBS DJ, VO脽 U, HARDING SA, FANNON J, MOODY LA, YAMADA E, SWARUP K, NIBAU C, BASSEL GW, CHOUDHARY A, LAVENUS J, BRADSHAW SJ, STEKEL DJ, BENNETT MJ and COATES JC, 2014. The New phytologist. 203(4), 1194-207
  • YANG, J, OSMAN, K, IQBAL M, STEKEL, DJ, LUO, Z, ARMSTRONG, SJ and FRANKLIN, FCH, 2013. Frontiers in Plant Sciences. 3, 297
  • SALAMA, R.A. and STEKEL, D.J., 2013. Bioinformatics. 29(21), 2699-2704
  • STEKEL DJ and JENKINS DJ, 2012. Advances in experimental medicine and biology. 751, 301-28
  • HERMAN, D., THOMAS, C.M. and STEKEL, D.J., 2012. PLoS ONE. 7(11), e49678
  • HERBERT JMJ, STEKEL DJ, MURA M, SYCHEV M and BICKNELL R, 2011. Methods In Molecular Biology (Clifton, N.J.). 729, 99-119
  • HERMAN D, THOMAS CM and STEKEL DJ, 2011. Bmc Systems Biology. 5, 119
  • JENKINS, DAFYD J and STEKEL, DOV J, 2010. Journal of molecular evolution. 71, 128-140
  • GASSON, P., MILLER, R., STEKEL, D.J, WHINDER, F. and ZIEMINSKA, Z., 2010. Wood identification of Dalbergia nigra (CITES Appendix I) using quantitative wood anatomy, principal components analysis and naive Bayes classification. Annals of botany. 105(1), 45-56
  • SALAMA, RAFIK A and STEKEL, DOV J, 2010. Nucleic acids research. 38(12), e135
  • JENKINS, DAFYD J and STEKEL, DOV J, 2010. Journal of molecular evolution. 70, 215-231
  • FERNANDO, CHRISANTHA T, GOLDSTEIN, RICHARD A, HUSBANDS, PHIL and STEKEL, DOV J, 2010. In silico biology. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 477-80
  • JENKINS, DAFYD J and STEKEL, DOV J, 2009. Artificial Life. 15(3), 259-91
  • LEADBEATER, BARRY S C, YU, QIBIN, KENT, JOYCE and STEKEL, DOV J, 2009. Proceedings of the Royal Society B: Biological Sciences. 276(1654), 3-11
  • WELHAM, P.A. and STEKEL, D.J., 2009. Molecular BioSystems. 5(1), 68-76
  • MA, H., HAGEN, F., STEKEL, D.J., JOHNSTON, S.A., SIONOV, E., FALK, R., POLACHECK, I., BOEKHOUT, T. and MAY, ROBIN C, 2009. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 106(31), 12980-12985
  • CHAUDHURI, ROY R, PETERS, SARAH E, PLEASANCE, STEPHEN J, NORTHEN, HELEN, WILLERS, CHRISSIE, PATERSON, GAVIN K, CONE, DANIELLE B, ALLEN, ANDREW G, OWEN, PAUL J, SHALOM, GIL, STEKEL, DOV J and CHARLES, IAN, 2009. PLoS pathogens. 5(7), e1000529
  • FERNANDO, CHRISANTHA T, LIEKENS, ANTHONY M L, BINGLE, LEWIS E H, BECK, CHRISTIAN, LENSER, THORSTEN, STEKEL, DOV J and ROWE, JONATHAN E, 2009. Journal Of The Royal Society Interface. 6(34), 463-9
  • CHAUDHURI, R. R., LOMAN, N. J., SNYDER, L. A., BAILEY, C. M., STEKEL, D. J. and PALLEN, M. J., 2008. xBASE2: a comprehensive resource for comparative bacterial genomics. VOL 36(SUPP/1), D543-D546
  • STEKEL, D.J. and JENKINS, D.J., 2008. BMC Systems Biology. 2, 6
  • HERBERT, JOHN M J, STEKEL, DOV, SANDERSON, SHARON, HEATH, VICTORIA L and BICKNELL, ROY, 2008. BMC Genomics. 9, 153
  • JENKINS, D.J. AND STEKEL. D.J., 2008. Effects of signalling on the evolution of gene regulatory networks In: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems. 289-296
  • BOWLES, EMMA J, LEE, JOON-HEE, ALBERIO, RAMIRO, LLOYD, RHIANNON E I, STEKEL, DOV, CAMPBELL, KEITH H S and ST JOHN, JUSTIN C, 2007. Genetics. 176(3), 1511-26
  • JONES, B, STEKEL, D.J, ROWE, J and FERNANDO, C.T., 2007. Is there a Liquid State Machine in the Bacterium Escherichia Coli? In: Proceedings of IEEE Symposium on Artificial Life. 187-191
  • STEKEL, DOV J, SARTI, DONATELLA, TREVINO, VICTOR, ZHANG, LIHONG, SALMON, MIKE, BUCKLEY, CHRIS D, STEVENS, MARK, PALLEN, MARK J, PENN, CHARLES and FALCIANI, FRANCESCO, 2005. Analysis of host response to bacterial infection using error model based gene expression microarray experiments. Nucleic Acids Research. 33(6), e53
  • STEKEL, D.J., 2003. Microarray Bioinformatics Cambridge University Press.
  • STEKEL, D J, GIT, Y and FALCIANI, F, 2000. Genome Research. 10(12), 2055-61
  • SCHETTINO, G, FOLKARD, M, VOJNOVIC, B, MICHETTE, A.G, STEKEL, D.J, PFAUNTCSH, S.K and PRISE, K.M. AND MICHAEL, B.D., 2000. The ultrasoft X-ray microbeam: a sub-cellular probe of radiation response Radiation Research. 153, 222-225
  • STEKEL, D J, 1998. The simulation of density-dependent effects in the recirculation of T lymphocytes. Scandinavian journal of immunology. 47(5), 426-30
  • STEKEL, D J, PARKER, C E and NOWAK, M A, 1997. A model of lymphocyte recirculation. Immunology Today. 18(5), 216-21
  • MAY, R M, STEKEL, D J and NOWAK, M A, 1997. Mathematical Biosciences. 139(1), 59-68
  • STEKEL, D J, 1997. Journal of Theoretical Biology. 186(4), 491-501
  • RASHBASS, J, STEKEL, D and WILLIAMS, E D, 1996. Journal of Pathology. 179(3), 333-9
  • STEKEL, D J, NOWAK, M A and SOUTHWOOD, T R, 1996. Nature. 381(6578), 119
  • STEKEL, D, RASHBASS, J and WILLIAMS, E D, 1995. Journal of Theoretical Biology. 175(3), 283-93

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糖心原创
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