Biocomputation Research GroupPublications since 2001Journal articles2006Maria J. Schilstra, Lu Li, Joanne Matthews, Andrew Finney, Michael Hucka, and Nicolas Le Novère CellML2SBML: conversion of CellML into SBML Bioinformatics, 2006, Advance publication on line. ISSN: Print: 1367-4803 Electronic: 1460-2059 url: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl047v1
M. J. Schilstra and S. R. Martin An elastically tethered viscous load imposes a regular gait on the motion of myosin-V. Simulation of the effect of transient force relaxation on a stochastic process J. Royal. Soc. Interface, Vol 3, pp 153-165, 2006. ISSN: Print: 1742-5689 Electronic: 1742-5662 doi: 10.1098/rsif.2005.0098 url: http://www.journals.royalsoc.ac.uk/openurl.asp?genre=article&id=doi:10.1098/rsif.2005.0098
Nicolas Le Novère, Benjamin Bornstein, A. Broicher, M. Courtot, Marco Donizelli, H. Dharuri, Lu Li, Herbert M. Sauro, Maria J. Schilstra, Bruce E. Shapiro, Jacky L. Snoep, and Michael Hucka BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucl. Acids Res., Vol 34, pp D689-691, 2006. ISSN: Print: 0305-1048 Electronic: 1362-4962 url: http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D689
2005Arumugam Sujatha, Sreedhar Balaji, Rajan Devi, and Wolfgang Marwan Isolation of Physarum polycephalum plasmodial mutants altered in sporulation by chemical mutagenesis of flagellates European Journal of Protistology, Vol 41, p 19, 2005. ISSN: 0932-4739 doi:10.1016/j.ejop.2004.08.001 url: http://www.sciencedirect.com/science/article/B7GW3-4DTKYT2-1/2/a1446d06cde74a06c60034129bfcad23
Irina Abnizova, René te Boekhorst, Klaudia Walter, and Walter Gilks Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test Bmc Bioinformatics, Vol 6, 2005. ISSN: 1471-2105 doi:10.1186/1471-2105-6-109 url: http://www.biomedcentral.com/1471-2105/6/109
Wolfgang Marwan, Arumugam Sujatha, and Christine Starostzik Reconstructing the regulatory network controlling commitment and sporulation in Physarum polycephalum based on hierarchical Petri Net modelling and simulation J. Theor. Biol., Vol 236, pp 349-365, 2005. ISSN: 0022-5193 doi:10.1016/j.jtbi.2005.03.018 url: http://www.sciencedirect.com/science/article/B6WMD-4G65VM2-1/2/c52421e1183b89a9de89de64f4c078ef
Yi Sun, Mark. Robinson, Rod Adams, Paul Kaye, and Neil Davey Integrating binding site predictions using meta classification methods Lecture Notes in Computer Science, 2005.
Dieter Oesterhelt and Wolfgang Marwan Salz in der Suppe des Lebens Biospektrum, Vol 11, pp 60-62, 2005. ISSN: 0947-0867
T. Nutsch, D. Oesterhelt, E.-D. Gilles, and W. Marwan A Quantitative Model of the Switch Cycle of an Archaeal Flagellar Motor and its Sensory Control Biophys. J., Vol 89, pp 2307-2323, 2005. ISSN: Print: 0006-3495 Electronic: 1542-0086 PMID: 16192281 url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16192281&query_hl=2
S.C. Materna and W. Marwan Estimating the number of plasmids taken up by a eukaryotic cell during transfection and evidence that antisense RNA abolishes gene expression in Physarum polycephalum FEMS Microbiol Lett., Vol 243, pp 29-35, 2005. ISSN: 0378-1097 url: http://www.sciencedirect.com/science/article/B6T2W-4DXJVD1-6/2/ab9208e93ffdab9deeb0678855dc015c
2004Michael Hucka, Andrew Finney, Benjamin Bornstein, Sarah M. Keating, Bruce E. Shapiro, Joanne Matthews, Benjamin Kovitz, Maria J. Schilstra, Akira Funahashi, John C. Doyle, and Hiroaki Kitano Evolving a Lingua Franca and Associated Software Infrastructure for Computational Systems Biology: The Systems Biology Markup Language (SBML) Project Systems Biology, Vol 1, pp 41-53, 2004. ISSN: Print: 1741-2471 Electronic: 1741-248X doi: 10.1049/sb:20045008 url: http://dx.doi.org/10.1049/sb:20045008
Bruce E. Shapiro, Michael Hucka, Andrew Finney, and John Doyle MathSBML: a package for manipulating SBML-based biological models Bioinformatics, Vol 20, pp 2829-2831, 2004. ISSN: Print: 1367-4803 Electronic: 1460-2059 doi:10.1093/bioinformatics/bth271 url: http://bioinformatics.oupjournals.org/cgi/content/abstract/20/16/2829
2003Maria J. Schilstra, Andrew Finney, Michael Hucka, and Herbert M. Sauro Expressing biochemical network models in SBML Fourth European Biophysics Conference, Vol Eur. Biophys. J. 32, p 209, 2003. ISSN: Print: 0175-7571 Electronic: 1432-1017
Michael Hucka, Andrew Finney, Herbert M. Sauro, Hamid Bolouri, John C. Doyle, Hiroaki Kitano, and the rest of the Sbml Forum, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J. H. Hofmeyr, P. J. Hunter, N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novere, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, and J. Wang The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics, Vol 19, pp 524-531, 2003. ISSN: Print: 1367-4803 Electronic: 1460-2059 PMID: 12611808 url: http://bioinformatics.oupjournals.org/cgi/content/abstract/19/4/524
Andrew Finney and Michael Hucka Systems biology markup language: Level 2 and beyond Biochem. Soc. Trans., Vol 31, p 1472–1473, 2003. ISSN: Print: 0300-5127 Electronic: 1470-8752 PMID: 14641091 url: http://www.biochemsoctrans.org/bst/031/1472/bst0311472.htm
2002C. Titus Brown, Alistair G. Rust, Peter J. C. Clarke, Zhengjun Pan, Maria J. Schilstra, Tristan De Buysscher, Gareth Griffin, Barbara J. Wold, R. Andrew Cameron, Eric H. Davidson, and Hamid Bolouri New Computational Approaches for Analysis of cis-Regulatory Networks Developmental Biology, Vol 246, pp 86-102, 2002. ISSN: 0012-1606 doi:10.1006/dbio.2002.0619 url: http://www.sciencedirect.com/science/article/B6WDG-45WRK44-8/2/def3b58adf50a3ec4b287aa04a85c7bc
Eric H. Davidson, Jonathan P. Rast, Paola Oliveri, Andrew Ransick, Cristina Calestani, Chiou-Hwa Yuh, Takuya Minokawa, Gabriele Amore, Veronica Hinman, Cesar Arenas-Mena, Ochan Otim, C. Titus Brown, Carolina B. Livi, Pei Yun Lee, Roger Revilla, Alistair G. Rust, Zheng jun Pan, Maria J. Schilstra, Peter J. C. Clarke, Maria I. Arnone, Lee Rowen, R. Andrew Cameron, David R. McClay, Leroy Hood, and Hamid Bolouri A Genomic Regulatory Network for Development Science, Vol 295, pp 1669-1678, 2002. ISSN: 0036-8075 doi: 10.1126/science.1069883 url: http://www.sciencemag.org/cgi/content/abstract/295/5560/1669
Eric H. Davidson, Jonathan P. Rast, Paola Oliveri, Andrew Ransick, Cristina Calestani, C.-H. Yuh, Takuya Minokawa, Gabriele Amore, Veronica Hinman, Cesar Arenas-Mena, Ochan Otim, C. Titus Brown, Carolina B. Livi, Pei Yun Lee, Roger Revilla, Maria J. Schilstra, Peter J. C. Clarke, Alistair G. Rust, Zhengjun Pan, Maria I. Arnone, Lee Rowen, R. Andrew Cameron, David R. McClay, Leroy Hood, and Hamid Bolouri A provisonal regulatory gene network for specification of endomesoderm in the sea urchin embryo Developmental Biology, Vol 246, pp 162-190, 2002. ISSN: 0012-1606 doi:10.1006/dbio.2002.0635 url: http://www.sciencedirect.com/science/article/B6WDG-45WRK44-F/2/efb4a250a5717db1111e3da7d8cd50e2
Maria J. Schilstra, Alistair G. Rust, Rod Adams, and Hamid Bolouri A finite state automaton model for multi-neuron simulations Neurocomputing, Vol 44 - 46C, pp 1141-1148, 2002. ISSN: 0925-2312 doi:10.1016/S0925-2312(02)00438-1 url: http://www.sciencedirect.com/science/article/B6V10-45F90MH-T/2/b9aa84a205464363836a89dd184bdc53
Submitted manuscripts
John F. Eccleston, Stephen R. Martin, and Maria J. Schilstra Rapid Kinetic Techniques Accepted for: Biophysical tools for the biologist, Vol. 1, eds. JJ Correia and WH Dietrich Methods in Molecular Biology, eds L Wilson and PT Matsudaira Elsevier Inc., San Diego (26 June 2006)
Maria J. Schilstra, Stephen R. Martin, and Sarah M. Keating Methods for simulating the dynamics of complex biological processes Accepted for: Biophysical tools for the biologist, Vol. 1, eds. JJ Correia and WH Dietrich Methods in Molecular Biology, eds L Wilson and PT Matsudaira Elsevier Inc., San Diego (9 June 2006)
Stephen R. Martin and Maria J. Schilstra Circular dichroism and its application to the study of biomolecules Accepted for: Biophysical tools for the biologist, Vol. 1, eds. JJ Correia and WH Dietrich Methods in Molecular Biology, eds L Wilson and PT Matsudaira Elsevier Inc., San Diego (30 May 2006)
Maria J. Schilstra and Chrystopher L. Nehaniv Bio-logic: gene expression and the laws of combinatorial logic Accepted by Artificial Life (3 May 2006)
Johannes F. Knabe, Chrystopher L. Nehaniv, and M. J. Schilstra Genetic regulatory network models of biological clocks: evolutionary history matters Accepted by Artificial Life (3 May 2006)
Yi Sun, Mark Robinson, Rod Adams, Paul Kaye, René Te Boekhorst, Alistair G. Rust, and Neil Davey Integrating genomic binding site predictions using real-valued meta classifiers Submitted to Pattern Recognition
Conference proceedingsJohannes F. Knabe, Chrystopher L. Nehaniv, and M. J. Schilstra Evolvability of differentiation in genetic regulatory networks Proceedings of GWAL-7, 2006 Submitted 26 April 2006
Johannes F. Knabe, Chrystopher L. Nehaniv, Maria J. Schilstra, and Tom Quick Evolving Biological Clocks using Genetic Regulatory Networks Proceedings of ALife X, 2006 Submitted 13 January 2006 Available as University of Hertfordshire Technical Report nr 438
Mark Robinson, Yi Sun, René te Boekhorst, Paul Kaye, Rod Adams, Neil Davey, and Alistair G. Rust Improving computational predictions of cis-regulatory binding sites In Proceedings of Pacific Symposium on Biocomputing, Wailea, Maui, Hawaii, 2006
N. Le Novere, B. Bornstein, A. Broicher, M. Courtot, M. Donizelli, H. Dharuri, L. Li, H. Sauro, M. J. Schilstra, J. L. Snoep, and M. Hucka BioModels Database, storage and exchange of curated quantiative models in Systems Biology In Proceedings of International Conference on Systems Biology (ICSB 2005), Harvard University, Boston, MA, USA, 2005
Michael Hucka, Andrew Finney, Benjamin Bornstein, Bruce E. Shapiro, Sarah M. Keating, Maria J. Schilstra, Akira Funahashi, A. Jouraku, Joanne Matthews, and Benjamin Kovitz Software from the SBML Team: LibSBML, MathSBML, SBMLToolbox, CellML2SBML, KEGG2SBML, SBML Test Suite, and the Online Tools In Proceedings of International Conference on Systems Biology (ICSB), Harvard University, Boston, MA, USA, 2005
M. J. Schilstra and S. R. Martin Nano-escapement: the motion of a molecular motor dragging a large viscous load is predicted to be regular and uniform In Proceedings of 6th International Conference on Systems Biology (ICSB 2005), Harvard University, Boston, MA, USA, 2005
Yi Sun, Rod. Adams, Paul Kaye, Alistair G. Rust, and Neil Davey Improving accuracy of binding site predictions by use of non-linear integration of multiple algorithmic predictions In Proceedings of ECCB/JBI Computational Biology, Madrid, 2005 url: http://www.eccb05.org/PostersDetail.php?s_Topic=&s_Surname=robinson&s_Title=&poster_id=218
Y. Sun, M. Robinson, A. Rust, R. Adams, P. Kaye, and N. Davey Using real-valued meta classifiers to integrate binding site predictions In Proceedings of IEEE International Joint Conference on Neural Networks IJCNN05, Montreal, Canada, 2005, pp 481-486 ISBN: 0-7803-9049-0
Yi Sun, Mark Robinson, Alistair G. Rust, Rod Adams, Paul Kaye, and Neil Davey Integrating binding site predictions using meta classification methods In Proceedings of ICANNGA2005, Coimbra, Portugal, 2005, pp 321-324 ISBN: 3-211-24934
S. M. Keating, B. Bornstein, M. Hucka, and A. Finney SBMLToolbox: a MATLAB toolbox for SBML users In Proceedings of International Conference on Systems Biology (ICSB 2004), Heidelberg, Germany, 2004
Benjamin Bornstein, Sarah M. Keating, Michael Hucka, and Andrew Finney libSBML: a software library for the Systems Biology Markup Language (SBM) In Proceedings of International Conference on Systems Biology (ICSB), Heidelberg, Germany, 2004
Yi Sun, Rod Adams, Mark Robinson, Alistair G. Rust, and Neil Davey Integrating binding site predictions using non-linear classification methods In Proceedings of Sheffield Machine Learning Workshop, 2004
Rod Adams, Neil Davey, Paul Kaye, and Wanida Pensuwon Optimising a Hierarchical Neural Clusterer Applied to Large Gene Sequence Data Sets In Proceedings of IEEE Conference on Intelligent Systems (IS04), Varna, Bulgaria, 2004 ISBN: 0-7803-8278-1
T. Nutsch, W. Marwan, D. Oesterhelt, and E.-D. Gilles A coherent kinetic model of sensing and response in Halobacterium salinarium phototaxis based on the mechanims of flagellar motor switching In Proceedings of Fourth International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russian Academy of Sciences, 2004
Andrew Finney and Michael Hucka Developing SBML beyond Level 2: Proposals for Development In Proceedings of International Conference CMSB, Paris, France, 2004 ISBN: 3-540-25375-0
Rod Adams, René te Boekhorst, Alistair G. Rust, Paul. Kaye, and Maria J. Schilstra Design of Spatially Extended Neural Networks for Specific Applications In Proceedings of IEEE International Joint Conference on Neural Networks (IJCNN04), Budapest, Hungary, 2004 ISBN: 0-7803-8360-5
Maria J. Schilstra and Hamid Bolouri The logic of gene regulation In Proceedings of 3rd International Conference on Systems Biology (ICSB): The Logic of Life, Karolinska Institutet, Stockholm, Sweden, 2002 ISBN: 91-85910-63-5
Maria J. Schilstra and Hamid Bolouri Logical modelling of developmental genetic regulatory networks with NetBuilder In Proceedings of 2nd Int. Conf. Systems Biology (ICSB 2001), Los Angeles, CA, 2001
Maria J. Schilstra and Hamid Bolouri NetBuilder: a graphical tool for modelling genetic regulatory networks In Proceedings of 2nd Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg, Germany, 2001
Other conference and workshop presentationsMaria J. Schilstra The logic of gene regulation Presented at Systems Modelling in Plants and Microbes, University of East Anglia, Norwich, UK, 2005. url: http://www2.cmp.uea.ac.uk/~vlm/symposium/schilstra.html
Maria J. Schilstra SBML and CellML: XML-based markup languages for models of biochemical systems Presented at 3th International Symposium on Networks in Bioinformatics, University of Amsterdam, Amsterdam, The Netherlands, 2005. url: http://isnb.amc.uva.nl/isnb2005/index.html
Maria J. Schilstra A closer look at gene transcription Presented at Workshop Microbial Systems Biology, University of Surrey, Guildford, 2005. url: http://www.soc.surrey.ac.uk/ias/reports/bsb.htm
M. Hucka, A. Finney, B. J. Bornstein, B. Shapiro, S. M. Keating, A. Funahashi, M. J. Schilstra, B. Kovitz, and J. Matthews SBML Software and Services Presented at Intelligent Systems for Molecular Biology (ISMB 2004), Glasgow, UK, 2004. url: http://sbml.org/documents/
Maria J. Schilstra Transient Force Relaxation in a Processive Molecular Motor Presented at XIth Workshop of the BioThermoKinetics Study Group: Developing concepts for systems biology (BTK 2004), Oxford University, Oxford, UK, 2004. url: http://btk2004.brookes.ac.uk:8080/BTK2004/Abstracts/Accepted%20Abstracts
Maria J. Schilstra, Alistair G. Rust, Rod Adams, and Hamid Bolouri A finite state automaton model for multi-neuron simulations Presented at 10th Annual Computational Neuroscience Meeting, Pacific Grove, CA, USA, 2001.
Book chapters
Andrew Finney, Michael Hucka, Benjamin Bornstein, Sarah M. Keating, Bruce E. Shapiro, Joanne Matthews, Ben L. Kovitz, Maria J. Schilstra, Akira Funahashi, John C. Doyle, and Hiroaki Kitano Software infrastructure for effective communication and reuse of computational models In: System modeling in cellular biology, 'Vol., eds. Z Szallasi, S Jörg, and V Periwal, pp 355-378 The MIT Press: Cambridge, MA, 2006. ISBN: 0-262-19548-8
Hamid Bolouri and Maria J. Schilstra Models of genetic regulatory networks In: Computation in Cells. Perspectives and Tools of Thought, eds. Paton, R, Bolouri, H, Holcombe, M, Parish, JH, and Tateson, R Springer-Verlag: Berlin. pp 149-160, 2004 ISBN: 3-540-00358-4
Alistair G. Rust, Rod Adams, Maria J. Schilstra, and Hamid Bolouri Evolving computational neural systems using synthetic developmental mechanisms In: On growth, form, and computers, eds. Bentley, P and Kumar, S Elsevier: Oxford, UK. pp 353-376, 2003 ISBN: 0-12-428765-4
Technical reports
Johannes F. Knabe, Chrystopher L. Nehaniv, Maria J. Schilstra, and Tom Quick University of Hertfordshire Technical Report nr 438
|