Rothamsted Research

where knowledge grows


Chris Rawlings

+44 (0) 1582 763 133 ext: +44 1582 938871
Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ
Past Projects
Principal Investigator
  • Application of statistical methods to predictive biology
  • Biofortifying Brassica with calcium (Ca) and magnesium (Mg) for human health
  • Statistical genomics
  • FUSE: Floodplain Underground Sensors: A high-density, wireless, underground Sensor Network to quantify floodplain hydro-ecological interactions
  • QTLNetMiner: Mining candidate gene networks from genetic studies of crops and animals
Project Leader
  • From data to knowledge: the ONDEX System for integrating life sciences data resources
  • The BBSRC Sustainable Bioenergy Centre (BSBEC): Perennial Bioenergy Crops Programme: BAB component
  • BBSRC Quota Studentship: A systems biology approach to explore host-pathogen interactions
  • The terrestrial carbon cycle under climate variability and extremes (CARBO-Extreme)
  • Development of appropriate variety testing methodology for assessing nitrogen requirements of new varieties in trials undertaken for national listing
  • Accelerating discovery by mining and visualising integrated chemogenomics data
  • Sustainable farm management aimed at reducing threats to Soils under climate change - SmartSOIL
  • Infrastructure for analysis and experimentation on ecosystems - ANAEE
  • Comparison of climate change mitigation options for cropping systems in the Indo-Gangetic Plains
  • The BBSRC Sustainable Bioenergy Centre (BSBEC): Perennial Bioenergy Crops Programme


Bishop, M., Rawlings, C.J. (editors) (1997) DNA and Protein Sequence Analysis: A Practical Approach Oxford University Press, IRL.

Rawlings, C.J. , Clark, D.A., Altman, R., Hunter, L., Lengauer, T., Wodak, S. (editors) (1995) Proceedings of Third International Conference on Intelligent Systems for Molecular Biology (ISMB-95), Cambridge, England, AAAI/MIT Press.

Solomon, E., Rawlings, C.J. (editors) (1991) Human Gene Mapping 11 : 11th International Workshop on Human Gene Mapping. Cytogenetics and Cell Genetics, 58(1-4), pp 1-2200.

Craig, I. , Rawlings, C.J. (editors) (1990) Human Gene Mapping 10.5: Update to the 10th International Workshop on Human Gene Mapping. Cytogenetics and Cell Genetics, 55, pp 1-785.

Bishop, M., Rawlings, C.J. (editors) (1987) DNA and Protein Sequence Analysis: A Practical Approach, IRL Press, Oxford .

Rawlings, C.J. (1986) Directory of Software for Molecular Biologists, Stockton Press, London .


  Balaur, I; Mazein, A; Saqi, M; Lysenko, A; Rawlings, CJ; Auffray, C. (2016) Recon2Neo4j: Applying graph database technologies for managing comprehensive genome-scale networks  Bioinformatics, doi: 10.1093/bioinformatics/btw731  

  Lysenko, L., Roznovţ, IA., Saqi, M., Mazein, A., Rawlings, CJ., Auffray, C. (2016) Representing and querying disease networks using graph databases, BioData Mining. Vol 9:23 DOI: 10.1186/s13040-016-0102-8

  Orr, R. J., Murray, P. J., Eyles, C. J., Blackwell, M. S. A., Cardenas, L. M., Collins, A. L., Dungait, J. A. J., Goulding, K. W. T., Griffith, B. A., Gurr, S. J., Harris, P., Hawkins, J. M. B., Misselbrook, T. H., Rawlings, C., Shepherd, A., Sint, H., Takahashi, T., Tozer, K. N., Whitmore, A.P., Wu, L. and Lee, M. R. F. (2016), The North Wyke Farm Platform: effect of temperate grassland farming systems on soil moisture contents, runoff and associated water quality dynamics. European Journal of Soil Science. Vol 67, Issue 4, 374-385.  doi: 10.1111/ejss.12350

Habash, D., Baudo, M., Hindle, M., Powers, S., Defoin-Platel, M., Mitchell, R., Saqi, M., Rawlings, CJ., Latiri, K., Araus, J., Abdulkader, A, Tuberosa, R. (2014) Systems responses to progressive water stress in durum wheat, PLoS ONE 9(9): e108431. doi:10.1371/journal.pone.0108431 PMID: 25265161 

Graham, NS, Hammond, JP, Lysenko, A., Mayes, S.,  Ó Lochlainn,S.,  Blascoa, B., Bowen, HC., Rawlings, CJ., Rios, JJ., Welham, S., Carion, PWC., Dupuy, LX.,  King,GJ,  White, PJ. and Broadley MR. (2014) Genetical and Comparative Genomics of Brassica under Altered Ca Supply Identifies Arabidopsis Ca-Transporter Orthologs, Plant Cell 26(7):2818-30. doi: 10.1105/tpc.114.128603  PMID: 25082855

Lysenko A, Hindle MM, Rawlings CJ, Splendiani A (2014) An interactive graph-based approach for mining omics data on the semantic web. Lecture Notes in Computer Science 8452:225-238.

Taubert J, Hassani-Pak K, Castells-Brooke N, Rawlings CJ. (2014) Ondex Web: web-based visualization and exploration of heterogeneous biological networks. Bioinformatics. 30(7):1034-5. doi: 10.1093/bioinformatics/btt740. PMID: 24363379

Horn F, Rittweger M, Taubert J, Lysenko A, Rawlings C, Guthke R. (2014) “Interactive exploration of integrated biological datasets using context-sensitive workflows” Front Genet. 2014 Feb 20;5:21. doi: 10.3389/fgene.2014.00021 PMID: 24600467

Lysenko, A., Urban, U., Bennett, L., Tsoka, S., Janowska-Sejda, EI., Rawlings, CJ, Hammond-Kosack, KE., Saqi, M. (2013) Network-Based Data Integration for Predicting Virulence Proteins in the Cereal Infecting Fungus Fusarium graminearum, PLOS ONE In Press:

Bennett, L., Lysenko, A., Urban, U., Hammond-Kosack, KE., Rawlings, CJ, Saqi, M., Tsoka, S. (2012) Detection of Multi-clustered Genes and Community Structure for the Plant Pathogenic Fungus Fusarium graminearum In: Computational Methods in Systems Biology, Lecture Notes in Computer Science LNBI 7605, Springer, Eds : Gilbert, D, Heiner, M. pp 69-86

Sternberg MJE,  Tamaddoni-Nezhad, A,, Lesk VI, Kay E, Hitchen PG, Cootes A, van Alphen LB, Lamoureux MP, Jarrell HC, Rawlings CJ, Soo EC, Szymanski CM, Dell A,  Wren BW, Muggleton SH (2012) Gene function hypotheses for the Campylobacter jejuni glycome generated by a logic-based approach. J Mol Biol

Love CG, Andongabo AE, Wang J, Carion PW, Rawlings CJ, King GJ (2012) InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data. J. Integr. Plant Biol. 54(5):345-55.

Splendiani, A. Rawlings, C.J., Kuo, S-C, Stevens, R., Lord, P. (2012) Lost in Translation: Data Integration Tools Meet the Semantic Web (Experiences from the Ondex Project).  In: Lecture Notes in Electrical Engineering, Recent Progress in Data Engineering and Internet Technology, Ed. Ford Lumban Gaol. Vol 157, 87-97 DOI: 10.1007/978-3-642-28798-5_13

Defoin-Platel M, Hassani-Pak K, Rawlings C. (2011) Gaining confidence in cross-species annotation transfer:     from simple molecular function to complex phenotypic traits. Aspects of Applied Biology 107, 790-87

Defoin-Platel, M., Hindle, M.W., Lysenko, A., Powers, S.J., Habash, D.Z., Rawlings, C.J.  and Saqi, M. (2011) AIGO: Towards a unified framework for the Analysis and the Inter-comparison of GO functional annotations. BMC Bioinformatics 12:431.

Lesk VI, Taubert J, Rawlings C, Dunbar S and Muggleton SH (2011) WIBL: Workbench for Integrative Biological Learning. J Integ. Bioinf. 2011; 8(2):156

Lysenko, A., Defoin-Platel, M., Hassani-Pak, K., Taubert, J., Hodgman, C., Rawlings,C., Saqi, M. (2011) Assessing the functional coherence of modules found in multiple evidence networks from Arabidopsis.  BMC Bioinformatics 12:203

Hassani-Pak, K., Legaie, R., Canevet, C., van den Berg, H.A., Moore, J.D. Rawlings, C.J. (2010) Enhancing Data Integration with Text Analysis to Find Proteins Implicated in Plant Stress Response J Integrative Bioinformatics 7(3):121. doi:10.2390/biecoll-jib-2010-121

Splendiani, A., Kuiper, M. & Rawlings, C. J. (2009). Toward a new paradigm for user interaction on the semantic web to support life sciences investigation. In proceedings of the 6th International Workshop on Semantic Web User Interaction (SWUI 2009), CEUR-WS Vol. 544, Washington DC, 25 October 2009

Lysenko, A., Hindle, M.,Taubert, J.Saqi, M.A.S., Rawlings, C. J. (2009) Data Integration for Plant Genomics - Exemplars from the Integration of Arabidopsis thaliana databases, Briefings in Bioinformatics 10: 676-693

Taubert, J., Hindle, M., Lysenko, A., Weile, J., Koehler, J. and Rawlings, C. (2009) Linking Life Sciences Data Using Graph-Based Mapping. In Paton, N., Missier, P. and Hedeler, C. (eds), DILS 2009, LNBI 5647. Springer-Verlag Berlin Heidelberg, 16-30.

Pesch, R., Lysenko, A, Hindle, M., Hassani-Pak, K., Thiele, R., Rawlings,C. , Khler, J., Taubert, J. (2008) Graph-based sequence annotation using a data integration approach, J Integrative Bioinformatics 5(2) doi:10.2390/biecoll-jib-2008-94

Winnenburg, R,. Urban, M., Beacham, A., Baldwin, T. K., Holland, S., Lindeberg, M., Hansen, H., Rawlings, C ., Hammond-Kosack K. E. and Koehler, J. (2007) PHI-base update: additions to the pathogen-host interactions database Nucleic Acids Research 2008 36 :D572-D576 doi:10.1093/nar/gkm858

Mitchell, R.A.C., Castells-Brooke, N., Taubert, T., Verrier, P.J., Leader, D.J., Rawlings, C.J. (2007) Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence Nucleic Acids Research 2007; doi: 10.1093/nar/gkm220

Baldwin, T. K., Winnenburg, R., Urban, M., Rawlings, C ., Khler, J. And Hammond-Kosack, K.E. (2006) The Pathogen Hosts-interaction database (Phi-Base) Provides Insights into Generic and Novel Themes of Pathogenicity. Mol. Plant. Microbe Interact, 19(12):1451-1462

Khler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Rueegg, A., Rawlings, C., Verrier, P. & Philippi, S. (2006). Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics , 22 (11):1383-90

Winnenburg, R,. Baldwin, T. K., Urban, M., Rawlings, C., Khler, J. and Hammond-Kosack K. E. (2006) PHI-base: a new database for pathogen host interactions Nucleic Acids Research, 34, D459-D464

Koehler, J., Rawlings, C., Verrier, C., Mitchell, M., Skusa,, A., Ruegg A., and Philippi, S. (2004) Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures. In Silico Biology 5, 0005.


Harris, M., Martin, J.M.R., Peden, J.F., Rawlings, C.J. (2003) SNP cherry picker: maximizing the chance of finding an association with a disease SNP. Bioinformatics 19: 2141-2143 (applications note).

Martin, J.M.R., Mackay, I.J., Rawlings, C.J. (2003) Pedstrip: extracting a maximal subset of available, unrelated individuals from a pedigree, Bioinformatics 19(2): 291-292 (applications note).

Muggleton, S.H. Bryant, C.H., Srinivasan, A., Whittaker A, Topp S., Rawlings C.J. (2001) Are grammatical representations useful for learning from biological sequence data? - a case study, Journal of Computational Biology 8(5): 493-522

Rawlings, C.J. , Searls, D.B. (1997) Computational gene discovery and human disease, Curr. Op. Gen Dev, 7:416-423

Brown, N.P., Whittaker, A.J., Newell, W.R., Rawlings, C.J., Beck, S. (1995) Identification and Analysis of Multigene Families by Comparison of Exon Fingerprints J. Mol. Biol. 249, 342-359

Rawlings, C.J. Fox, J.P. (1994) Artificial intelligence in molecular biology: a review and assessment. Philosophical Transactions of the Royal Society [ London ] , 344 , 353-363

Clark , D. A, Rawlings, C. J, and Doursenot, S. (1994) Genetic Map Construction with Constraints, Proceedings, Second International Conference on Intelligent Systems for Molecular Biology, (eds. R. Altman, D. Brutlag, P. Karp, R. Lathrop, and D. Searls) AAAI/MIT Press, Menlo Park CA, 78-86

Clark, D. A. and Rawlings, C. J. (1994) Intelligent Systems for Molecular Biology: Review of the First International Conference, CABIOS 10(2), 199-206.

Clark , D. A, Rawlings, C. J. and Parson, S. (1993) Current Research in Artificial Intelligence and Molecular Biology, Knowledge Engineering Review, 8(4), 349-357.

Clark , D. A, Rawlings, C. J., Doursenot, S. and Veron, A. (1994) Genetic Mapping with Constraints, Proceedings, The Second International Conference on the Practical Application of Prolog (Ed) Sterling, L, 151-164.

Clark , D. A, Rawlings, C. J., and Shirazi (1994) The Application of Parallel Constraint Logic Programming to Molecular Biology and Genetics, In High Performance Computing and Networking. Eds: W. Gentzsch and U. Harms. Lecture Notes in Computer Science 1994, 236-237, Springer-Verlag.

Clark, D.A., Rawlings, C.J., Shirazi, J.,L i, L-L, Schuerman, K., Reeve, M., Vron, A. (1993) Solving Large Combinatorial Problems in Molecular Biology Using the ElipSys Parallel Constraint Logic Programming System, Computer Journal 36(4) 690-701

Rawlings, C.J. (1993) Introduction to Human Genome Data Resources Part 1: Basic Tools for Internet Users Genome Digest, 1(1) 10-13

Doursenot, S., Clark, D., Rawlings, C.J., Vron, A (1993) Contig Mapping using ElipSys. In Proceedings of Workshop AI and The Genome, IJCAI-93, Chambery , France

Li, L-L., Reeve, M., Schuerman, K., Vron, A., Bellone, J., Pradelles, C., Palaskas, Z., Stamatopoulos, T., Clark , D. A,. Doursenot, S., Rawlings, C.J., Shirazi J., and Sardu, G. (1993) APPLAUSE: Applications Using the ElipSys Parallel CLP System, In Logic Programming" - Proceedings of the 10th International Conference on Logic Programming (Ed) Warren, D. S. MIT Press, pp 847-848.

Clark, D.A., Rawlings, C.J., Shirazi, J., Vron, A, Reeve, M (1993) Protein Topology Prediction through Parallel Constraint Logic Programming. In Hunter, Searls, Shavlik (eds) ISMB-93. Proceedings First International Conference on Intelligent Systems for Molecular Biology. AAAI Press. pp 83-91

Li, L-L, Reeve, M, Schuerman, K., Vron, A., Bellone, J., Pradelle, C., Kolokouris, A., Stamatopolous, T., Clark, D., Rawlings, C.J., Shirazi, J., Sardu, G (1993) APPLAUSE: Application and Assessment of Parallel Programming using Logic. In Bode, Reeve and Wolfe (eds) PARLE 93 Parallel Architechtures in Europe , Springer-Verlag , Berlin . pp 756-759

Barton, G.J. Rawlings, C.J. (1992) A PROLOG Approach to Analysing Protein Structure, Tetrahedron Computer Methodology, 3 739-756

Rawlings, C.J. , Brunn, C., Bryant, S., Robbins, R.J., Lucier, R. (1991) Report of the Informatics Committee. In Human Gene Mapping 11: 11th International Workshop on Human Gene Mapping. Cytogenetics and Cell Genetics, 58(3-4), pp. 1833-1838

Clark, D.A., Shirazi, J., Rawlings, C.J. (1991) Protein topology prediction through constraint-based search and the evaluation of topological folding rules, Protein Engineering 4(7), 751-760

Knox, R., Lydall, D.A., Friedlos, F., Basham, C., Rawlings, C.J., Roberts, J.J. (1991) The Walker 256 carcinoma: a cell type inherently sensitive only to those difunctional agents that can form DNA interstrand crosslinks , Mutation Research 255, pp 227-240

Bowers, D.S., Rawlings, C.J. (1990) Constraints and Deduction: Convergent Evolution?, In Data and Knowledge Base Integration, Ed. Deen M., Pitman Publishing, London

Clark, D.A., Barton, G., Rawlings, C.J. (1990) A Knowledge-Based Architecture for Protein Sequence Analysis and Structure Prediction, J. Mol. Graphics, 8(2) , 94-107

Clark , D.A., Rawlings, C.J., Barton, G.J., Archer, I. (1990) Knowledge-based orchestration of protein sequence analysis and knowledge aquisition for protein structure prediction, Proceedings: AAAI Spring Symposium 1990, 28-32

Rawlings, C.J. , Lucier, R. (1990) Report of the Informatics Committee. In Human Gene Mapping 10.5: Update to the 10th International Workshop on Human Gene Mapping, Cytogenetics and Cell Genetics, 55, 779-782.

Rawlings, C.J. , Clark, D.A., Barton, G.J., Archer, I., Saldanha, J. (June 1990) Large knowledge based applications on molecular biology and genetics, Proceedings of IEE Colloquium "Very Large Knowledge-Based Systems", Institute of Electrical Engineers, London

Rawlings, C.J. (1989) 1st Interim Report from the Computer Working Group to the MRC/ICRF Joint Advisory Board for the UK Human Genome Mapping Project , G-STRING: The Newsletter of the UK Human Genome Mapping Project, No.2, 12-26.

Rawlings, C.J. (1989) Databases, AI and Knowledge Based Systems for Molecular Biology, Biochemical Society Transactions, 17, 851-855

Rawlings, C.J. (1988) Natural Language Processing by H.R. Noble. Book Review. CABIOS, 4, 515-514.

Rawlings, C.J. (1988) Convergence of AI and Software Engineering. The Knowledge Engineering Review, 3, 159-169.

Rawlings, C.J. (1988) Designing Databases for Molecular Biology, Nature, 334, 477.

Rawlings, C.J. (1988) Expert Systems in Molecular Biology, IUSC Workshop on Molecular Biology Software, Cambridge . Tech. Report. BCU-TR-60.

Seifert, K.L., Rawlings, C.J. (1988) GRIPE: A graphical Interface to a knowledge based system which reasons about protein topology, In People and Computers, ed. D.M Jones and R. Winder, IV, 391-406, Cambridge Press.

Bishop, M.J., Ginsburg, M., Rawlings, C.J., Wakeford, R. (1987) Molecular Sequence Databases, In Nucleic Acid and Protein Sequence Analysis, ed. Bishop, M.J., Rawlings, C.J., Practical Approach Series, IRL Press, Oxford

Rawlings, C.J. (1987) Analysis and Prediction of Protein Structure using Artificial Intelligence, Proceedings: 4th European Seminar in Computer Aided Molecular Design, IBC Press

Rawlings, C.J. (1987) Artificial Intelligence and Protein Structure, Proceedings of Biotechnology Information 86, 59-77, IRL Press,

Rawlings, C.J. , Saldanha, J.W., Seifert, K.L., Addis, T.R., Elleby, P., Nissanke, N., Byrne, C., Foster, A. (1987) The CARDS Project. A Conceptual and Relational Database Server for Large Knowledge Bases, Tech. Report BCU-TR-42, Imperial Cancer Research Fund, Biomedical Computing Unit,

Rawlings, C.J. , Seifert, K., Saldanha, J. (1987) A Large Knowledge Based System for Molecular Biology Proceedings of the first workshop of the special interest group on knowledge manipulation engines, Institute of Electrical Engineers , Reading University

Rawlings, C.J. , Roberts, J.J. (1986) Walker rat carcinoma cells are exceptionally sensitive to cis-diamminedichloroplatinum(II) and other difunctional agents but not defective in the removal of platinum-DNA adducts , Mutation Research, 166, 157-168

Rawlings, C.J. , Taylor, W.R.T., Nyakairu, J., Fox, J., Sternberg, M.J.E. (1986) Using Prolog to Represent and Reason about Protein Structure, Lecture Notes in Computer Science, 225, Springer-Verlag, Berlin.

Rawlings, C.J. (1986) Representing protein structures in Prolog: the Prolog representation, Tech. Report BCU-TR-TOPOL-b, Imperial Cancer Research Fund, Biomedical Computing Unit.

Roberts, J.J., Friedlos, F., Scott, D., Ormerod, M.G., Rawlings, C.J. (1986) The unique sensitivity of Walker rat tumour cells to difunctional agents is associated with a failure to recover from inhibition of DNA synthesis and increased chromosome damage, Mutation Research, 166, 169-181

Rawlings, C.J. , Taylor, W.R., Nyakairu, J., Fox, J., Sternberg, M.J.E. (1985) Reasoning about protein topology using the logic programming language PROLOG, Journal of Molecular Graphics, 3, 151-157

Rawlings, C.J. (1984) Large Knowledge Bases... Some Practical Issues, In Proceedings of 1st Workshop on Architectures for Large Knowledge Bases. ed. S. Lavington (ed), The Alvey Directorate.

Rawlings, C.J. (1984) Managing Large Collections of Biological Knowledge in a Frame Based System - Present Methods and Future Requirements, , In Proceedings of 2nd Workshop on Architectures for Large Knowledge Bases. ed. S. Lavington, Alvey Directorate,

Roberts, J.J., Rawlings, C.J., Friedlos, F. (1984) DNA Repair Characteristics of Walker Rat Carcinoma Cells Sensitive and Resistant to cis-diamminedichloroplatinum (II) (Cisplatin) and Difunctional Alkylating Agents, ed. Hacker, M.P., Douple, E.B., Krakoff, I.H., Developments in Oncology, Martinus Nijhoff Publishing.

Rawlings, C.J. , Fox,J. (1983) The UNIT Package...A Critical Appraisal of a Frame-Based Knowledge Representation System, In Expert Systems 83, British Computer Society.

Roberts, J.J., Pera, M.F.P., Rawlings, C.J. (1982) The Role of DNA Repair in the Recovery of Mammalian Cells from cis-diamminedichloroplatinum (II) Induced Damage, Progress in Mutation Research, 4, 223-246

Pera,M.F., Rawlings, C.J., Roberts,J.J (1981) The Role of DNA Repair in the Recovery of Human Cells from Cisplatin Toxicit y , Chem. Biol Interactions, 37, 245-261

Pera,M.F., Rawlings, C.J., Shackleton,J., Roberts,J.J (1981) Quantitative Aspects of the Formation and Loss of DNA Interstrand Crosslinks in Chinese Hamster Cells Following Treatment with cis-diamminedichloroplatinum (II) II. Comparison of Results from Alkaline Elution, DNA renaturation and DNA Sedimentatiion Studie s , Biochim. Biophys. Acta, 655, 152-166

Fraval, H.N.A., Rawlings, C.J., Roberts,J.J. (1978) Increased Sensitivity of UV-repair Deficient Human Cells to DNA bound Platinum Products Which Unlike Thymine Dimers are not Recognisedby an Endonuclease Extracted from Micrococcus luteus, Mutation Research, 51, 121-132



PhD in The Role of DNA Repair in Determining Mammalian Cell Sensitivity to Cytotoxic Agents ()


BSc in Biophysics ()

Measures of esteem


  • Board Member for UK Research Councils - ELIXIR


  • Chairman - EBI Ensembl Genomes Scientific Advisory Board


  • Member - International Wheat Initiative Wheat Information System Expert Working Group


  • International Science Advisory Board - Ensembl Genomes Project - EBI
  • Chair of BBSRC Exploiting New Ways of Working Strategy Advisory Panel
  • European Bioinformatics Institute - International Review of Bioinformatics Services


  • BBSRC Appointments Committee


  • External Examiner - MRes in Comput. Biology, York


  • International Science Advisory Board - Nottingham Centre for Plant Integrative Biology


  • Visiting Professor of Bioinformatics: Imperial College Department of Computer Science