Professor David Gilbert

Contact

Research Interests

University Research Centre Membership

Publications

Journal Papers

(2012) Gao, Q., Gilbert, D., Heiner, M., Liu, F., Maccagnola, D. and Tree, D., Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing., IEEE/ACM Trans Comput Biol Bioinform Download publication

(2012) Heiner, M. and Gilbert, D., BioModel engineering for multiscale Systems Biology, Progress in Biophysics and Molecular Biology

(2012) Soldatova, L., Gao, Q. and Gilbert, D., Towards an ontology of biomodelling, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 7605 LNBI 390- 393

(2011) Vijayakrishnan, S., Callow, P., Nutley, MA., McGow, DP., Gilbert, D., Kropholler, P., Cooper, A., Byron, O. and Lindsay, JG., Variation in the organization and subunit composition of the mammalian pyruvate dehydrogenase complex E2/E3BP core assembly, Biochemical Journal 437 (3) : 565- 574

(2010) Gilbert, D., Jaramillo, A., Krasnogor, N. and de Lorenzo, V., Editorial: Synthetic biology gains momentum in Europe, Systems and Synthetic Biology 4 (3) : 145- 147

(2010) Veeramalai, M., Gilbert, D. and Valiente, G., An optimized TOPS plus comparison method for enhanced TOPS models, BMC Bioinformatics 11138 Download publication

(2010) Gilbert, D., Heiner, M., Breitling, R. and Orton, R., Computational modelling of kinase signalling cascades, Methods in Molecular Biology 661 369- 384

(2010) Gu, X., Trybilo, M., Ramsey, S., Jensen, M., Fulton, R., Rosser, S. and Gilbert, D., Engineering a novel self-powering electrochemical biosensor, Systems and Synthetic Biology 4 (3) : 203- 214 Download publication

(2010) Sturm, OE., Orton, R., Grindlay, J., Birtwistle, M., Vyshemirsky, V., Gilbert, D., Calder, M., Pitt, A., Kholodenko, B. and Kolch, W., The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier., Science Signaling 3 (153) : ra90-

(2009) Orton, RJ., Adriaens, ME., Gormand, A., Sturm, OE., Kolch, W. and Gilbert, DR., Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway, BMC Systems Biology 3 100- Download publication

(2009) Torrance, GM., Leader, DP., Gilbert, DR. and Milner-White, EJ., A novel main chain motif in proteins bridged by cationic groups: the niche, Journal of Molecular Biology 385 (4) : 1076- 1086

(2009) von Kriegsheim, A., Baiocchi, D., Birtwistle, M., Sumpton, D., Bienvenut, W., Morrice, N., Yamada, K., Lamond, A., Kalna, G., Orton, R., Gilbert, D. and Kolch, W., Cell fate decisions are specified by the dynamic ERK interactome, Nature Cell Biology 11 (12) : 1458- 1464

(2009) Park, SH., Reyes, JA., Gilbert, DR., Kim, JW. and Kim, S., Prediction of protein-protein interaction types using association rule based classification, BMC Bioinformatics 1036 Download publication

(2008) Veeramalai, M. and Gilbert, D., A novel method for comparing topological models of protein structures enhanced with ligand information, Bioinformatics 24 (23) : 2698- 2705

(2008) Breitling, R., Gilbert, D., Heiner, M. and Orton, R., A structured approach for the engineering of biochemical network models, illustrated for signalling pathways, Briefings in Bioinformatics 9 (5) : 404- 421 Download publication

(2008) Oehm, S., Gilbert, D., Tauch, A., Stoye, J. and Goesmann, A., Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms, Nucleic Acids Research 36 W433- W437

(2008) Orton, RJ., Sturm, OE., Gormand, A., Kolch, W. and Gilbert, DR., Computational modelling reveals feedback redundancy within the epidermal growth factor receptor/extracellular-signal regulated kinase signalling pathway, IET Systems Biology 2 (4) : 173- 183

(2008) Jourdan, F., Breitling, R., Barrett, MP. and Gilbert, D., MetaNetter: inference and visualization of high-resolution metabolomic networks, Bioinformatics 24 (1) : 143- 145

(2007) Nebel, J-C., Herzyk, P. and Gilbert, DR., Automatic generation of 3D motifs for classification of protein binding sites, BMC Bioinformatics 8321 Download publication

(2007) Gu, X., Gilbert, D., Higham, D. and Houslay, M., Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs (Poster Presentation), BMC Systems Biology 1 (Supplement 1) : P6 Download publication

(2007) Al-Shahib, A., Breitling, R. and Gilbert, DR., Predicting protein function by machine learning on amino acid sequences – a critical evaluation, BMC Genomics 878 Download publication

(2007) Viksna, J. and Gilbert, D., Assessment of the probabilities for evolutionary structural changes in protein folds, Bioinformatics 23 (7) : 832- 841

(2007) Viksna, J. and Gilbert, D., Assessment of the probabilities for evolutionary structural changes in protein folds., Bioinformatics 23 832- 841

(2007) Reyes, JA. and Gilbert, D., Prediction of protein-protein interactions using one-class classification methods and integrating diverse data, Journal of Integrative Bioinformatics 4 (3) : 77- Download publication

(2006) Morrison, JL., Breitling, R., Higham, DJ. and Gilbert, DR., A lock-and-key model for protein-protein interactions., Bioinformatics 22 2012- 2019

(2006) Gilbert, D., Fuß, H., Gu, X., Orton, R., Robinson, S., Vyshemirsky, V., Kurth, MJ., Downes, CS. and Dubitzky, W., Computational methodologies for modelling, analysis and simulation of signalling networks, Briefings in Bioinformatics 7 (4) : 339- 353

(2005) Morrison, JL., Breitling, R., Higham, DJ. and Gilbert, DR., GeneRank: Using search engine technology for the analysis of microarray experiments, BMC Bioinformatics 6233 Download publication

(2005) Orton, RJ., Sturm, OE., Vyshemirsky, V., Calder, M., Gilbert, DR. and Kolch, W., Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway, Biochemical Journal 392 (2) : 249- 261

(2005) Park, S-H., Ryu, KH. and Gilbert, D., Fast similarity search for protein 3d structures using topological pattern matching based on spatial relations., Int. J. Neural Syst. 15 287- 296

(2005) Al-Shahib, A., Breitling, R. and Gilbert, D., Feature selection and the class imbalance problem in predicting protein function from sequence, Applied Bioinformatics 4 (3) : 195- 203

(2005) Al-Shahib, A., Breitling, R. and Gilbert, D., FrankSum: new feature selection method for protein function prediction, International Journal of Neural Systems 15 (4) : 259- 275

(2005) Torrance, GM., Gilbert, DR., Michalopoulos, I. and Westhead, DR., Protein structure topological comparison, discovery and matching service., Bioinformatics 21 2537- 2538

(2005) Kolch, W., Calder, M. and Gilbert, D., When kinases meet mathematics: the systems biology of MAPK signalling, FEBS Letters 579 (8) : 1891- 1895

(2004) Nasir, L., Gault, E., Campbell, S., Veeramalai, M., Gilbert, D., McFarlane, R., Munro, A. and Argyle, DJ., Isolation and expression of the reverse transcriptase component of the Canis familiaris telomerase ribonucleoprotein (dogTERT), Gene 336 (1) : 105- 113

(2004) Ren, T., Veeramalai, M., Tan, AC. and Gilbert, D., MSAT: a multiple sequence alignment tool based on TOPS, Applied Bioinformatics 3 (2-3) : 149- 158

(2004) Michalopoulos, I., Torrance, GM., Gilbert, DR. and Westhead, DR., TOPS: an enhanced database of protein structural topology., Nucleic Acids Research 32 251- 254

(2003) Deville, Y., Gilbert, D., Helden, JV. and Wodak, SJ., An overview of data models for the analysis of biochemical pathways., Briefings in Bioinformatics 4 246- 259

(2003) Jacquet, J-M., Brim, L., Gilbert, D. and Kretínský, M., Coordination by Means of Synchronous and Asynchronous Communication in Concurrent Constraint Programming., Electr. Notes Theor. Comput. Sci. 68 347- 370

(2003) Tan, AC. and Gilbert, D., Ensemble machine learning on gene expression data for cancer classification, Applied Bioinformatics 2 (3 Suppl) : S75- S83 Download publication

(2003) Tan, AC., Gilbert, D. and Deville, Y., Multi-class protein fold classification using a new ensemble machine learning approach, Genome Informatics 14 206- 217

(2003) Williams, A., Gilbert, D. and Westhead, DR., Multiple structural alignment for distantly related all b structures using TOPS pattern discovery and simulated annealing, Protein Engineering 16 (12) : 913- 923 Download publication

(2002) Brim, L., Kretinsky, M., Jacquet, JM. and Gilbert, D., Modelling multi-agent systems as synchronous concurrent constraint processes, Computing and Informatics 21 (6) : 565- 590

(2001) Gilbert, D., Westhead, V., Viksna, J. and Thornton, J., A computer system to perform structure comparison using TOPS representations of protein structure, Journal of Computers and Chemistry 26 (1) : 23- 30 Download publication

(2001) Eidhammer, I., Jonassen, J., Grindhaug, SH., Gilbert, D. and Ratnayake, M., A constraint based structure description language for Biosequences, Constraints 6 (2/3) : 173- 200 Download publication

(2001) Backofen, R. and Gilbert, D., Bioinformatics and constraints, Constraints 6 (2/3) : 141- 156 Download publication

(2001) Schroeder, M., Gilbert, D., Helden, JV. and Noy, P., Approaches to visualisation in bioinformatics: from dendrograms to space explorer, Information Sciences 139 (1) : 19- 57 Download publication

(2001) Gilbert, D., Backofen, R. and Yap, RHC., Introduction to the Special Issue on Bioinformatics., Constraints 6 139- 139

(2000) Helden, JV., Naim, A., Mancuso, R., Eldridge, M., Wernisch, L., Gilbert, D. and Wodak, SJ., Representing and analysing molecular and cellular function in the computer, Journal of Biological Chemistry 38 (9-10) : 921- 935 Download publication

(2000) Gilbert, DR., Schroeder, M. and Van Helden, J., Interactive visualization and exploration of relationships between biological objects, Trends in Biotechnology 18 (12) : 487- 494

(1999) Gilbert, D., Westhead, DR., Nagano, N. and Thornton, JM., Motif-based searching in TOPS protein topology databases., Bioinformatics 15 317- 326

(1999) Letichevsky, AA., Kapitonova, JV., Volkov, VA., Chugayenko, A., Khomenko, V. and Gilbert, DR., The development of interactive algorithms for the Mathematical Environment., Electr. Notes Theor. Comput. Sci. 23 352- 369

(1998) Letichevsky, AA. and Gilbert, D., A general theory of action languages, Cybernetics and System Analysis 1 16- 37 Download publication

(1998) Brazma, A., Jonassen, I., Eidhammer, I. and Gilbert, D., Approaches to the automatic discovery of patterns in biosequences, Journal of Computational Biology 5 (2) : 279- 305 Download publication

(1998) Brazma, A., Jonassen, I., Eidhammer, I. and Gilbert, D., Approaches to the Automatic Discovery of Patterns in Biosequences., Journal of Computational Biology 5 279- 305

(1996) Gilbert, D., Can computational logic provide a paradigm for both the specification and implementation of concurrent systems?, ACM Computing Surveys (CSUR) 28 (2) : 303- 305 Download publication

Conference Papers

(2011) Gao, Q., Liu, F., Gilbert, D., Heiner, M. and Tree, D., A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured petri nets, 9th International Conference on Computational Methods in Systems Biology (CMSB 2011), ACM digital library 209- 218

(2011) Gilbert, D. and Heiner, M., How might petri nets enhance your systems biology toolkit, Applications and Theory of Petri Nets 32nd International Conference (PETRI NETS 2011), Lecture Notes in Computer Science (6709) : 17- 37

(2011) Gao, Q., Liu, F., Tree, D. and Gilbert, D., Multi-cell modelling using coloured petri nets applied to planar cell polarity, 2nd International Workshop on Biological Processes & Petri Nets (BioPPN 2011), CEUR Workshop Proceedings (http://ceur-ws.org) 135- 150

(2010) Wu, Z., Gao, Q. and Gilbert, D., Target driven biochemical network reconstruction based on petri nets and simulated annealing, 8th Conference on Computational Methods in Systems Biology (CMSB 2010)

(2009) Wang, J., Liu, X., Mustafee, N., Gao, Q., Taylor, SJE. and Gilbert, D., Grid-enabled SIMAP utility: motivation, integration technology and performance results, UK e-Science All Hands Meeting (AHM 2009) Download publication

(2007) Park, SH., Gilbert, D. and Ryu, KH., Fast structural similarity search based on topology string matching, 5th Asia-Pacific Bioinformatics Conference (APBC2007)

(2006) Gilbert, D. and Heiner, M., From Petri Nets to differential equations: An integrative approach for biochemical network analysis, 27th International Conference on Application and Theory of Petri Nets and other models of concurrency (ATPN06) Download publication

(2005) Calder, M., Vyshemirsky, V., Gilbert, D. and Orton, R., Analysis of signalling pathways using the prism model checker, 3rd International Computational Methods in Systems Biology (CMSB 2005) Download publication

(2004) Viksna, J., Gilbert, D. and Torrance, G., Domain discovery method for topological profile searches in protein structures, International Conference on Genome Informatics( GIW 2004) Download publication

(2003) Tan, A., Gilbert, D. and Deville, Y., Multi-class protein fold classification using a new ensemble machine learning approach., 14th International Conference on Genome Informatics (GIW 2003) Download publication

(2003) Tan, AC., Gilbert, D. and Deville, Y., Integrative machine learning approach for multi-class SCOP protein fold classification, German Conference on Bioinformatics (GCB 2003) Download publication

(2003) Tan, AC. and Gilbert, D., An empirical comparison of supervised machine learning techniques in bioinformatics, First Asia Pacific Bioinformatics Conference (APBC 2003) Download publication

(2002) Tan, AC., Gilbert, D. and Tuson, A., Characterisation of FAD-family folds using a machine learning approach, International Conference on Bioinformatics, (INCOB 2002) Download publication

(2001) Brim, L., Gilbert, D., Jacquet, JM. and Kretinsky, M., Multi-agent systems as concurrent constraint processes, 28th Conference on Current Trends in Theory and Practice of Informatics Piestany (SOFSEM 2001), Lecture Notes in Computer Science (2234) : 201- 210 Download publication

(2001) Viksna, J. and Gilbert, D., Pattern matching and pattern discovery algorithms for protein topologies, First International Workshop on Algorithms in BioInformatics BRICS Download publication

(2000) Gilbert, D. and Schroeder, M., FURY: Fuzzy unification and resolution based on edit distance, IEEE International Symposium on Bio-Informatics and Biomedical Engineering Download publication

(2000) Gilbert, D. and Palamidessi, C., Concurrent constraint programming with process mobility, 1st International Conference on Computational Logic (CL2000) Download publication

(2000) Helden, JV., Gilbert, D., Wernisch, L., Schroeder, M. and Wodak, SJ., Application of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data, 1st International Conference on Computational Biology, Biology, Informatics, and Mathematics (JOBIM 2000) Download publication

(2000) Gilbert, D., Westhead, D., Viksna, J. and Thorton, J., Topology-based protein structure comparison using a pattern discovery technique, Symposium on AI in Bioinformatics (AISB-00) Download publication

(2000) Gilbert, D., Schroeder, M. and Helden, JV., Interactive visualisation and exploration of biological data, 2nd International Workshop on Biomolecular Informatics in Conjunction with the 5th Joint Conference on Information Sciences Download publication

(1998) Gilbert, D. and Letichevsky, A., Interaction of agents and environments, International Scientific and Practical Conference on Programming Ukrprog'98' Download publication

(1996) Donovan, N. and Gilbert, D., Economic modelling using constraint logic programming, 9th Symposium and Exhibition on Industrial Applications of Prolog (INAP-96) Download publication

(1996) Kambi, M. and Gilbert, D., Timetabling in constraint logic programming, INAP-96: Symposium and Exhibition on Industrial Applications of Prolog Download publication

(1996) Shankar, A., Gilbert, D. and Jampel, M., Transient analysis and synthesis of linear circuits using constraint logic programming, INAP-96: The 9th Symposium and Exhibition on Industrial Applications of Prolog Download publication

(1996) Brim, L., Gilbert, D., Jacquet, JM. and Kretinsky, M., A process algebra for synchronous concurrent constraint programming, 5th International Conference on Algebraic and Logic Programming (ALP96) Download publication

(1996) Jampel, M., Jacquet, JM., Gilbert, D. and Hunt, S., Transformations between HCLP and PCSP, CP96: Second International Conference on Principles and Practice of Constraint Programming Download publication

(1994) Gilbert, D., Hogger, C. and Zlatuska, J., Transforming specifications of observable behaviour into programs, 4th International Workshop on Logic Programming Synthesis and Transformation (LOPSTR '94) Download publication

(2010) Kolch, W., Birtwistle, M., Kholodenko, B., Grindlay, J., Sturm, O., Orton, R., Gilbert, D. and von Kriegsheim, A., From benchside to byteside: what we can learn from computational modelling, 21st Meeting of the European-Association-for-Cancer-Research, EJC SUPPLEMENTS (8) : 3- 3

(2007) Al-Shahib, A., Gilbert, D. and Breitling, R., Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning., , IDEAL (4881) : 890- 897

(2004) Thornton, JM., Gilbert, D. and Brooksbank, C., ISMB/ECCB 2004 Organization., , ISMB/ECCB (Supplement of Bioinformatics) 3- 5

(2003) Viksna, J., Gilbert, D. and Torrance, GM., Protein structure comparison based o n profiles of topological motifs: a feasible way to deal with information from negative examples., , German Conference on Bioinformatics 159- 165

(2000) Gilbert, D., Tutoriel I: Bioinformatique et contraintes., , JFPLC 13- 13

(2000) Gilbert, D., Westhead, DR., Thornton, JM. and Yvon, K., Une technique déclarative pour filtrer des motifs topologiques de protéines., , JFPLC 165- 165

(1999) Letichevsky, AA. and Gilbert, D., A Model for Interaction of Agents and Environments., , WADT (1827) : 311- 328

(1999) Helden, JV., Gilbert, D., Wernisch, L., Mancuso, R., Eldridge, M., Degtyarenko, K. and Wodak, SJ., Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database., , German Conference on Bioinformatics 227- 229

(1999) Gilbert, D. and Viksna, J., Pattern discovery methods for protein topology diagrams., , German Conference on Bioinformatics 194- 196

(1996) Jampel, M., Jacquet, J-M. and Gilbert, D., A General Framework for Integrating HCLP and PCSP (Poster Abstract)., , JICSLP 543- 543

(1995) Brim, L., Gilbert, D., Jacquet, J-M. and Kretínský, M., Synchronisation in Scc., , ILPS 641- 641

(1992) Gilbert, D. and Hogger, CJ., Logic for Representing and Implementing Knwoledge about System Behaviour., , Advanced Topics in Artificial Intelligence (617) : 42- 49

(1991) Gilbert, D. and Hogger, CJ., Deriving Logic Programs from Observations., , ICLP Workshop on Construction of Logic Programs 113- 126

(1989) Gilbert, D., Specifying Concurrent Systems Using Logic., , FORTE 245- 260

(1988) Gilbert, D., A LOTOS to PARLOG Translator., , FORTE 31- 44

(1988) Gilbert, D., Specification and Implementation of Concurrent Systems using PARLOG., , Specification and Verification of Concurrent Systems 455- 473

(1987) Gilbert, D., Executable LOTOS: Using PARLOG to Implement an FDT., , PSTV 281- 294

Book Chapters

(2011) Lodhi, H. and Gilbert, D., Bootstrapping parameter estimation in dynamic systems. In: Elomaa, T., Hollmen, J. and Mannila, H. eds. Discovery Science: Proceedings of the 14th International Conference, DS 2011, Espoo, Finland, October 5-7, 2011. Springer (6926) : 194- 208

(2010) Breitling, R., Donaldson, RA., Gilbert, DR. and Heiner, M., Biomodel engineering – from structure to behavior. In: Priami, C., Donaldson, RA., Gilbert, DR. and Heiner, M. eds. Transactions on Computational Systems Biology XII. Berlin/Heidelberg : Springer (5945/2010) : 1- 12

(2009) Gilbert, D., Breitling, R., Heiner, M. and Donaldson, R., An introduction to BioModel Engineering, illustrated for signal transduction pathways. In: Corne, DW., Frisco, P., Paun, G., Rozenberg, G. and Salomaa, A. eds. Membrane Computing. (5391/2009) : 13- 28 Download publication

(2009) Heiner, M., Lehrack, S., Gilbert, D. and Marwan, W., Extended stochastic petri nets for model-based design of wetlab experiments. In: Transactions on Computational Systems Biology XI. Berlin/Heidelberg : Springer (5750/2009) : 138- 163

(2008) Gilbert, D., Heiner, M., Rosser, S., Fulton, R., Gu, X. and Trybilo, M., A case study in model-driven synthetic biology. In: Hinchey, M., Pagnoni, A., Rammig, FJ. and Schmeck, H. eds. Biologically-Inspired Collaborative Computing. (268/2008) : 163- 175 Download publication

(2008) Donaldson, R. and Gilbert, D., A model checking approach to the parameter estimation of biochemical pathways. In: Heiner, M. and Uhrmacher, AM. eds. Computational Methods in Systems Biology. (5307/2008) : 269- 287 Download publication

(2008) Liu, X., Jiang, J., Ajayi, O., Gu, X., Gilbert, D. and Sinnott, R., BioNessieG - a grid enabled biochemical networks simulation environment. In: Solomonides, T., Silverstein, JC., Saltz, J., Legré, Y., Kratz, M., Foster, I., Breton, V. and Beck, JR. eds. Studies in Health Technology and Informatics. (138) : 147- 157 Download publication

(2008) Reyes, JA. and Gilbert, D., Combining one-class classification models based on diverse biological data for prediction of protein-protein interactions. In: Bairoch, A., Cohen-Boulakia, S. and Froidevaux, C. eds. Data Integration in the Life Sciences. (5109/2008) : 177- 191

(2008) Heiner, M., Gilbert, D. and Donaldson, R., Petri nets for systems and synthetic biology. In: Formal Methods for Computational Systems Biology. Berlin/Heidelberg : Springer (5016/2008) : 215- 264 Download publication

(2007) Gilbert, D., Heiner, M. and Lehrack, S., A unifying framework for modelling and analysing biochemical pathways using Petri nets. In: Calder, M. and Gilmore, S. eds. Computational Methods in Systems Biology. (4695/2007) : 200- 216

(2006) Calder, M., Vyshemirsky, V., Gilbert, D. and Orton, R., Analysis of signalling pathways using continuous time Markov chains. In: Priami, C. and Plotkin, G. eds. Transactions on Computational Systems Biology VI. (4220/2006) : 44- 67

(2006) Gilbert, D. and Heiner, M., From Petri nets to differential equations - An integrative approach for biochemical network analysis. In: Donatelli, S. and Thiagarajan, PS. eds. Petri Nets and Other Models of Concurrency - ICATPN 2006. (4024/2006) : 181- 200 Download publication

(2004) Al-Shahib, A., He, C., Tan, AC., Girolami, M. and Gilbert, D., An assessment of feature relevance in predicting protein function from sequence. In: Yang, ZR., Everson, R. and Yin, H. eds. Intelligent Data Engineering and Automated Learning – IDEAL 2004. (3177/2004) : 52- 57

(2003) Deville, Y., Gilbert, D., van Helden, J. and Wodak, S., An overview of data models for the analysis of biochemical pathways (Abstract only). In: Priami, C. ed. Computational Methods in Systems Biology. (2602/2003) : 174-

(2003) Gilbert, D., Westhead, D. and Viksna, J., Techniques for comparison, pattern matching and pattern discovery: from sequences to protein topology. In: Frasconi, P. and Shamir, S. eds. Artificial intelligence and heuristic methods in bioinformatics. (183) : 128- 147

Books

(2010) Priami, C., Breitling, R., Gilbert, D., Heiner, M. and Uhrmacher, AM., Transactions on computational systems biology XII. Springer