David Gilbert

David R. Gilbert

	2011
76		Qian Gao, Fei Liu, David Gilbert, Monika Heiner, David Tree: A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets. CMSB 2011: 209-218
75		Huma Lodhi, David Gilbert: Bootstrapping Parameter Estimation in Dynamic Systems. Discovery Science 2011: 194-208
74		Monika Heiner, David Gilbert: How Might Petri Nets Enhance Your Systems Biology Toolkit. Petri Nets 2011: 17-37
	2010
73		Corrado Priami, Rainer Breitling, David Gilbert, Monika Heiner, Adelinde M. Uhrmacher: Transactions on Computational Systems Biology XII, Special Issue on Modeling Methodologies Springer 2010
72		Zujian Wu, Qian Gao, David Gilbert: Target driven biochemical network reconstruction based on petri nets and simulated annealing. CMSB 2010: 33-42
71		Amit Goel, Heinz Schmidt, David R. Gilbert: Formal Models of Virtual Enterprise Architecture: Motivations and Approaches. PACIS 2010: 117
70		Mallika Veeramalai, David Gilbert, Gabriel Valiente: An optimized TOPS+ comparison method for enhanced TOPS models. BMC Bioinformatics 11: 138 (2010)
69		Rainer Breitling, Robin Donaldson, David R. Gilbert, Monika Heiner: Biomodel Engineering - From Structure to Behavior. T. Comp. Sys. Biology 12: 1-12 (2010)
	2009
68		Amit Goel, Heinz Schmidt, David Gilbert: Towards formalizing Virtual Enterprise Architecture. EDOCW 2009: 238-242
67		Sung-Hee Park, José A. Reyes, David R. Gilbert, Ji Woong Kim, Sangsoo Kim: Prediction of protein-protein interaction types using association rule based classification. BMC Bioinformatics 10: (2009)
66		Monika Heiner, Sebastian Lehrack, David Gilbert, Wolfgang Marwan: Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments. T. Comp. Sys. Biology 11: 138-163 (2009)
	2008
65		Robin Donaldson, David Gilbert: A Model Checking Approach to the Parameter Estimation of Biochemical Pathways. CMSB 2008: 269-287
64		José A. Reyes, David Gilbert: Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions. DILS 2008: 177-191
63		Monika Heiner, David Gilbert, Robin Donaldson: Petri Nets for Systems and Synthetic Biology. SFM 2008: 215-264
62		David Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson: An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. Workshop on Membrane Computing 2008: 13-28
61		Fabien Jourdan, Rainer Breitling, Michael P. Barrett, David Gilbert: MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinformatics 24(1): 143-145 (2008)
60		Mallika Veeramalai, David Gilbert: A novel method for comparing topological models of protein structures enhanced with ligand information. Bioinformatics 24(23): 2698-2705 (2008)
59		Rainer Breitling, David Gilbert, Monika Heiner, Richard J. Orton: A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings in Bioinformatics 9(5): 404-421 (2008)
58		Sebastian Oehm, David Gilbert, Andreas Tauch, Jens Stoye, Alexander Goesmann: Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Research 36(Web-Server-Issue): 433-437 (2008)
	2007
57		Sung-Hee Park, David Gilbert, Keun Ho Ryu: Fast Structural Similarity Search Based on Topology String Matching. APBC 2007: 341-351
56		David Gilbert, Monika Heiner, Sebastian Lehrack: A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets. CMSB 2007: 200-216
55		Ali Al-Shahib, David Gilbert, Rainer Breitling: Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning. IDEAL 2007: 890-897
54		Jean-Christophe Nebel, Pawel Herzyk, David R. Gilbert: Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinformatics 8: (2007)
53		Juris Viksna, David Gilbert: Assessment of the probabilities for evolutionary structural changes in protein folds. Bioinformatics 23(7): 832-841 (2007)
52		José A. Reyes, David Gilbert: Prediction of protein-protein interactions using one-class classification methods and integrating diverse biological data. J. Integrative Bioinformatics 4(3): (2007)
	2006
51		David Gilbert, Monika Heiner: From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis. ICATPN 2006: 181-200
50		Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert: A lock-and-key model for protein-protein interactions. Bioinformatics 22(16): 2012-2019 (2006)
49		David R. Gilbert, Hendrik Fuß, Xu Gu, Richard J. Orton, Steve Robinson, Vladislav Vyshemirsky, Mary Jo Kurth, C. Stephen Downes, Werner Dubitzky: Computational methodologies for modelling, analysis and simulation of signalling networks. Briefings in Bioinformatics 7(4): 339-353 (2006)
48		Muffy Calder, Vladislav Vyshemirsky, David Gilbert, Richard J. Orton: Analysis of Signalling Pathways Using Continuous Time Markov Chains. T. Comp. Sys. Biology: 44-67 (2006)
	2005
47		Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert: GeneRank: Using search engine technology for the analysis of microarray experiments. BMC Bioinformatics 6: 233 (2005)
46		Gilleain M. Torrance, David R. Gilbert, Ioannis Michalopoulos, David R. Westhead: Protein structure topological comparison, discovery and matching service. Bioinformatics 21(10): 2537-2538 (2005)
45		Ali Al-Shahib, Rainer Breitling, David Gilbert: Franksum: new feature selection method for protein function prediction. Int. J. Neural Syst. 15(4): 259-275 (2005)
44		Sung-Hee Park, Keun Ho Ryu, David Gilbert: Fast similarity search for protein 3d structures using topological pattern matching based on spatial relations. Int. J. Neural Syst. 15(4): 287-296 (2005)
43		Dominique Turnbow, Kris Kasianovitz, Lise Snyder, David Gilbert, David Yamamoto: Usability testing for web redesign: a UCLA case study. OCLC Systems & Services 21(3): 226-234 (2005)
	2004
42		Ali Al-Shahib, Chao He, Aik Choon Tan, Mark Girolami, David Gilbert: An Assessment of Feature Relevance in Predicting Protein Function from Sequence. IDEAL 2004: 52-57
41		Janet M. Thornton, David Gilbert, Catherine Brooksbank: ISMB/ECCB 2004. ISMB/ECCB (Supplement of Bioinformatics) 2004: 1-2
40		Janet M. Thornton, David Gilbert, Catherine Brooksbank: ISMB/ECCB 2004 Organization. ISMB/ECCB (Supplement of Bioinformatics) 2004: 3-5
39		Ioannis Michalopoulos, Gilleain M. Torrance, David R. Gilbert, David R. Westhead: TOPS: an enhanced database of protein structural topology. Nucleic Acids Research 32(Database-Issue): 251-254 (2004)
	2003
38		Aik Choon Tan, David Gilbert: An Empirical Comparison of Supervised Machine Learning Techniques in Bioinformatics. APBC 2003: 219-222
37		Yves Deville, David Gilbert, Jacques van Helden, Shoshana J. Wodak: An Overview of Data Models for the Analysis of Biochemical Pathways. CMSB 2003: 174
36		Aik Choon Tan, David Gilbert, Yves Deville: Integrative machine learning approach for multi-class SCOP protein fold classification. German Conference on Bioinformatics 2003: 153-159
35		Juris Viksna, David Gilbert, Gilleain M. Torrance: Protein structure comparison based o n profiles of topological motifs: a feasible way to deal with information from negative examples. German Conference on Bioinformatics 2003: 159-165
34		Yves Deville, David Gilbert, Jacques van Helden, Shoshana J. Wodak: An overview of data models for the analysis of biochemical pathways. Briefings in Bioinformatics 4(3): 246-259 (2003)
33		Jean-Marie Jacquet, Lubos Brim, David Gilbert, Mojmír Kretínský: Coordination by Means of Synchronous and Asynchronous Communication in Concurrent Constraint Programming. Electr. Notes Theor. Comput. Sci. 68(3): 347-370 (2003)
	2002
32		David Gilbert, David R. Westhead, Juris Viksna, Janet M. Thornton: A Computer System to Perform Structure Comparison using Representations of Protein Structure. Computers & Chemistry 26(1): 23-30 (2002)
31		Lubos Brim, Mojmír Kretínský, Jean-Marie Jacquet, David Gilbert: Modelling Multi-Agent Systems as Synchronous Concurrent Constraint Processes. Computers and Artificial Intelligence 21(6): (2002)
	2001
30		Lubos Brim, David Gilbert, Jean-Marie Jacquet, Mojmír Kretínský: Multi-agent Systems as Concurrent Constraint Processes. SOFSEM 2001: 201-210
29		Juris Viksna, David Gilbert: Pattern Matching and Pattern Discovery Algorithms for Protein Topologies. WABI 2001: 98-111
28		David Gilbert, Rolf Backofen, Roland H. C. Yap: Introduction to the Special Issue on Bioinformatics. Constraints 6(2/3): 139 (2001)
27		Rolf Backofen, David Gilbert: Bioinformatics and Constraints. Constraints 6(2/3): 141-156 (2001)
26		Ingvar Eidhammer, Inge Jonassen, Svenn Helge Grindhaug, David Gilbert, Madu Ratnayake: A Constraint Based Structure Description Language for Biosequences. Constraints 6(2/3): 173-200 (2001)
25		Michael Schroeder, David Gilbert, Jacques van Helden, Penny Noy: Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. Inf. Sci. 139(1-2): 19-57 (2001)
	2000
24		David Gilbert, Michael Schroeder: FURY: Fuzzy Unification and Resolution Based on Edit Distance. BIBE 2000: 330-336
23		David Gilbert, Catuscia Palamidessi: Concurrent Constraint Programming with Process Mobility. Computational Logic 2000: 463-477
22		David Gilbert: Tutoriel I: Bioinformatique et contraintes. JFPLC 2000: 13-
21		David Gilbert, David R. Westhead, Janet M. Thornton, Karine Yvon: Une technique déclarative pour filtrer des motifs topologiques de protéines. JFPLC 2000: 165-
20		Jacques van Helden, David Gilbert, Lorenz Wernisch, Michael Schroeder, Shoshana J. Wodak: Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data. JOBIM 2000: 147-164
	1999
19		David Gilbert, Juris Viksna: Pattern discovery methods for protein topology diagrams. German Conference on Bioinformatics 1999: 194-196
18		Jacques van Helden, David Gilbert, Lorenz Wernisch, Renato Mancuso, Matthew Eldridge, Kirill Degtyarenko, Shoshana J. Wodak: Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database. German Conference on Bioinformatics 1999: 227-229
17		Alexander A. Letichevsky, David Gilbert: A Model for Interaction of Agents and Environments. WADT 1999: 311-328
16		David Gilbert, David R. Westhead, N. Nagano, Janet M. Thornton: Motif-based searching in TOPS protein topology databases. Bioinformatics 15(4): 317-326 (1999)
15		Alexander A. Letichevsky, Julia V. Kapitonova, Vladislav A. Volkov, A. Chugayenko, Victor Khomenko, David R. Gilbert: The development of interactive algorithms for the Mathematical Environment. Electr. Notes Theor. Comput. Sci. 23(3): 352-369 (1999)
	1998
14		Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, David Gilbert: Approaches to the Automatic Discovery of Patterns in Biosequences. Journal of Computational Biology 5(2): 277-304 (1998)
	1997
13		William M. Gelbart, Madeline A. Crosby, B. Matthews, W. P. Rindone, J. Chillemi, S. Russo Twombly, David Emmert, Michael Ashburner, Rachel A. Drysdale, E. Whitfield, Gillian H. Millburn, A. de Grey, T. Kaufman, K. Matthews, David Gilbert, Victor B. Strelets, C. Tolstoshev: FlyBase: a Drosophila database. The FlyBase consortium. Nucleic Acids Research 25(1): 63-66 (1997)
	1996
12		Lubos Brim, Jean-Marie Jacquet, David Gilbert, Mojmír Kretínský: A Process Algebra for Synchronous Concurrent Constraint Programming. ALP 1996: 165-178
11		Michael Jampel, Jean-Marie Jacquet, David Gilbert, Sebastian Hunt: Transformations Between HCLP and PCSP. CP 1996: 252-266
10		Michael Jampel, Jean-Marie Jacquet, David Gilbert: A General Framework for Integrating HCLP and PCSP (Poster Abstract). JICSLP 1996: 543
9		David Gilbert: Can Computational Logic Provide a Paradigm for Both the Specification and Implementation of Concurrent Systems? ACM Comput. Surv. 28(2): 303-305 (1996)
	1995
8		Lubos Brim, David Gilbert, Jean-Marie Jacquet, Mojmír Kretínský: Synchronisation in Scc. ILPS 1995: 641
	1994
7		David Gilbert, Christopher J. Hogger, Jirí Zlatuska: Transforming Specifications of Observable Behaviour into Programs. LOPSTR 1994: 88-103
	1992
6		David Gilbert, Christopher J. Hogger: Logic for Representing and Implementing Knwoledge about System Behaviour. Advanced Topics in Artificial Intelligence 1992: 42-49
	1991
5		David Gilbert, Christopher J. Hogger: Deriving Logic Programs from Observations. ICLP Workshop on Construction of Logic Programs 1991: 113-126
	1989
4		David Gilbert: Specifying Concurrent Systems Using Logic. FORTE 1989: 245-260
	1988
3		David Gilbert: A LOTOS to PARLOG Translator. FORTE 1988: 31-44
2		David Gilbert: Specification and Implementation of Concurrent Systems using PARLOG. Specification and Verification of Concurrent Systems 1988: 455-473
	1987
1		David Gilbert: Executable LOTOS: Using PARLOG to Implement an FDT. PSTV 1987: 281-294

Coauthor Index

1	Ali Al-Shahib	[42] [45] [55]
2	Michael Ashburner	[13]
3	Rolf Backofen	[27] [28]
4	Michael P. Barrett	[61]
5	Alvis Brazma	[14]
6	Rainer Breitling	[45] [47] [50] [55] [59] [61] [62] [69] [73]
7	Lubos Brim	[8] [12] [30] [31] [33]
8	Catherine Brooksbank	[40] [41]
9	Muffy Calder (Muffy Thomas)	[48]
10	J. Chillemi	[13]
11	A. Chugayenko	[15]
12	Madeline A. Crosby	[13]
13	Kirill Degtyarenko	[18]
14	Yves Deville	[34] [36] [37]
15	Robin Donaldson	[62] [63] [65] [69]
16	C. Stephen Downes	[49]
17	Rachel A. Drysdale	[13]
18	Werner Dubitzky	[49]
19	Ingvar Eidhammer	[14] [26]
20	Matthew Eldridge	[18]
21	David Emmert	[13]
22	Hendrik Fuß	[49]
23	Qian Gao	[72] [76]
24	William M. Gelbart	[13]
25	Mark A. Girolami (Mark Girolami)	[42]
26	Amit Goel	[68] [71]
27	Alexander Goesmann	[58]
28	A. de Grey	[13]
29	Svenn Helge Grindhaug	[26]
30	Xu Gu	[49]
31	Chao He	[42]
32	Monika Heiner	[51] [56] [59] [62] [63] [66] [69] [73] [74] [76]
33	Jacques van Helden	[18] [20] [25] [34] [37]
34	Pawel Herzyk	[54]
35	Desmond J. Higham	[47] [50]
36	Christopher J. Hogger	[5] [6] [7]
37	Sebastian Hunt	[11]
38	Jean-Marie Jacquet	[8] [10] [11] [12] [30] [31] [33]
39	Michael Jampel	[10] [11]
40	Inge Jonassen	[14] [26]
41	Fabien Jourdan	[61]
42	Julia V. Kapitonova	[15]
43	Kris Kasianovitz	[43]
44	T. Kaufman	[13]
45	Victor Khomenko	[15]
46	Ji Woong Kim	[67]
47	Sangsoo Kim	[67]
48	Mojmír Kretínský	[8] [12] [30] [31] [33]
49	Mary Jo Kurth	[49]
50	Sebastian Lehrack	[56] [66]
51	Alexander A. Letichevsky	[15] [17]
52	Fei Liu	[76]
53	Huma Lodhi	[75]
54	Renato Mancuso	[18]
55	Wolfgang Marwan	[66]
56	B. Matthews	[13]
57	K. Matthews	[13]
58	Ioannis Michalopoulos	[39] [46]
59	Gillian H. Millburn	[13]
60	Julie L. Morrison	[47] [50]
61	N. Nagano	[16]
62	Jean-Christophe Nebel	[54]
63	Penny Noy	[25]
64	Sebastian Oehm	[58]
65	Richard J. Orton	[48] [49] [59]
66	Catuscia Palamidessi	[23]
67	Sung-Hee Park	[44] [57] [67]
68	Corrado Priami	[73]
69	Madu Ratnayake	[26]
70	José A. Reyes	[52] [64] [67]
71	W. P. Rindone	[13]
72	Steve Robinson	[49]
73	Keun Ho Ryu	[44] [57]
74	Heinz Schmidt	[68] [71]
75	Michael Schroeder	[20] [24] [25]
76	Lise Snyder	[43]
77	Jens Stoye	[58]
78	Victor B. Strelets	[13]
79	Aik Choon Tan	[36] [38] [42]
80	Andreas Tauch	[58]
81	Janet M. Thornton	[16] [21] [32] [40] [41]
82	C. Tolstoshev	[13]
83	Gilleain M. Torrance	[35] [39] [46]
84	David Tree	[76]
85	Dominique Turnbow	[43]
86	S. Russo Twombly	[13]
87	Adelinde M. Uhrmacher (Adelinde Uhrmacher)	[73]
88	Gabriel Valiente	[70]
89	Mallika Veeramalai	[60] [70]
90	Juris Viksna	[19] [29] [32] [35] [53]
91	Vladislav A. Volkov	[15]
92	Vladislav Vyshemirsky	[48] [49]
93	Lorenz Wernisch	[18] [20]
94	David R. Westhead	[16] [21] [32] [39] [46]
95	E. Whitfield	[13]
96	Shoshana J. Wodak	[18] [20] [34] [37]
97	Zujian Wu	[72]
98	David Yamamoto	[43]
99	Roland H. C. Yap	[28]
100	Karine Yvon	[21]
101	Jirí Zlatuska	[7]

Colors in the list of coauthors

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