Modeling and Managing Experimental Data Using FuGE
Jones, A.R. , Lister, A.L., Hermida, L. et al.
OMICS: A Journal of Integrative Biology Vol. 13, Issue 3, pp 239-251
Mary Ann Liebert, Inc., 2009

[Abstract]

Saint: A Lightweight Integration Environment for Model Annotation
Lister, A.L., Pocock, M., Taschuk, M. and Wipat, A.
Bioinformatics Vol. 25, Issue 22, pp 3026-3027
Oxford University Press, 2009 ISSN 1460-2059

[Abstract]

The minimum information about a genome sequence (MIGS) specification
Field, D., Garrity, G., Gray, T. et al.
Nature Biotechnology Vol. 26, Issue 5, pp 541 - 547
Nature Publishing Group, 2008
Notes : Newcastle authors are: Allyson Lister, Phillip Lord and Anil Wipat.

[Abstract]

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach
Steggles, L. J., Banks, R., Shaw, O. and Wipat, A.
Bioinformatics Vol. 23, Issue 3, pp 336-343
Oxford University Press, 2007 ISSN 1367-4803

Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models
Lister, A.L., Pocock, M. and Wipat, A.
Journal of Integrative Bioinformatics Vol. 4, Issue 3, pp 1-12
Bielefeld University, Bioinformatics Department, 2007
Notes : Article number 80.

[Abstract]

Exploring Microbial Genome Sequences to Identify Protein Families on the Grid
Sun, Y., Wipat, A., Pocock, M., Lee, P. A., Flanagan, K. and Worthington, J. T.
IEEE Transactions on Information Technology in Biomedicine Vol. 11, Issue 4, pp 435-442
IEEE, 2007

Taverna: lessons in creating a workflow environment for the life sciences
Oinn, T., Greenwood, M., Addis, M., Alpdemir, M.N., Ferris, J., Glover, K., Goble, C., Goderis, A., Hull, D., Marvin, D., Li, P., Lord, P., Pocock, M.R., Senger, M., Stevens, R., Wipat, A. and Wroe, C.
Concurrency and Computation: Practice and Experience Vol. 18, Issue 10, pp 1067-1100
Wiley, 2006
Notes : Special issue: Workflow in Grid Systems.

Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks
Shaw, O., Steggles, J. and Wipat, A.
Electronic Notes in Theoretical Computer Science Vol. 151, Issue 3, pp 111-129
Elsevier B.V., 2006
Notes : Proceedings of the Second International Workshop on the Practical Application of Stochastic Modeling (PASM 2005), Newcastle upon Tyne,UK, 18 July 2005

Taverna: a tool for the composition and enactment of bioinformatics workflows
Oinn, T., Addis, M., Ferris, J., Marvin, D., Senger, M., Greenwood, M., Carver, T., Glover, K., Pocock, M.R., Wipat, A. and Li, P.
Bioinformatics Vol. 20, Issue 17, pp 3045-3054
Oxford University Press, 2004

[Abstract]

SARGE: a tool for creation of putative genetic networks
Shaw, O.J., Harwood, C., Steggles, L.J. and Wipat, A.
Bioinformatics Vol. 20, Issue 18, pp 3638-3640
Oxford University Press, 2004

myGrid and the drug discovery process
Stevens, R., McEntire, R., Goble, C., Greenwood, M., Zhao, J., Wipat, A. and Li, P.
BIOSILICO Vol. 4, Issue 2, pp 140-148
Elsevier Ltd, 2004

Essential Bacillus subtilis genes
Kobayashi, K. et. al.
Proceedings of the National Academy of Sciences of the United States of America (PNAS) Vol. 100, Issue 8, pp 4678-4683
National Academy of Sciences, 2003 ISSN 0027-8424

From genome to function: systematic analysis of the soil bacterium Bacillus subtilis
Harwood, C.R., Crawshaw, S.G. and Wipat, A.
Comparative and Functional Genomics Vol. 2, Issue 1, pp 22-24
John Wiley & Sons, 2001 ISSN 1531-6912

The Bacillus subtilis genome sequence: the molecular blueprint of a soil bacterium
Wipat, A and Harwood, C.R.
FEMS Microbiology Ecology Vol. 28, Issue 1, pp 1-9
Elsevier Science BV, 1999 ISSN 0168-6496

The yvsA-yvqA (293 degrees-289 degrees) region of the Bacillus subtilis chromosome containing genes involved in metal ion uptake and a putative sigma factor
Wipat, A., Brignell, C. and Guy, J. et. al.
Microbiology Vol. 144, Issue 6, pp 1593-1600
Society for General Microbiology, 1998 ISSN 1350-0872

An internal FK506-binding domain is the catalytic core of the prolyl isomerase activity associated with the Bacillus subtilis trigger factor
Gothel, S.F., Schmid, R. and Wipat, A. et. al.
European Journal of Biochemistry Vol. 244, pp 59-65
Blackwell Science, 1997 ISSN 0014-2956

A putative DNA repair operon in B. subtilis comprising a gene encoding a DNA repair polymerase, a mutS homolog and an unidentified ORF
Emmerson, P.T., Brignell, C. and Wipat, A. et. al.
The FASEB Journal Vol. 11, Issue 9, pp 2994
Federation of American Societies for Experimental Biology, 1997 ISSN 0892-6638

The complete genome sequence of the Gram-positive model organism Bacillus subtilis
Kunst, F. et. al.
Nature Vol. 390, Issue 6657, pp 249-256
Nature Publishing Group, 1997 ISSN 0028-0836

Sequencing and functional analysis of the genome of Bacillus subtilis strain 168
Harwood, C.R. and Wipat, A.
FEBS Letters Vol. 389, Issue 1, pp 84-87
Elsevier Science BV, 1996 ISSN 0014-5793

Sequence and transcriptional analysis of clpX, a class-III heat shock gene of Bacillus subtilis
Gerth, U., Wipat, A. and Harwood, C.R. et. al.
Gene Vol. 181, Issue 1-2, pp 77-83
Elsevier Science BV, 1996 ISSN 0378-1119

The dnaB-pheA (256 degrees-240 degrees) region of the Bacillus subtilis chromosome containing genes responsible for stress responses, the utilization of plant cell walls and primary metabolism
Wipat, A., Carter, N. and Brignell, S.C. et. al.
Microbiology Vol. 142, Issue 11, pp 3067-3078
Society for General Microbiology, 1996 ISSN 1350-0872

Monoclonal antibodies for Streptomyces lividans and their use for immunomagnetic capture of spores from soil
Wipat, A., Wellington, E.M.H. and Saunders, V.A.
Microbiology Vol. 140, Issue 8, pp 2067-2076
Society for General Microbiology, 1994 ISSN 1350-0872

Streptomyces marker plasmids for monitoring survival and spread of streptomycetes in soil
Wipat, A., Wellington, E.M.H. and Saunders, V.A.
Applied and Environmental Microbiology Vol. 57, Issue 11, pp 3322-3330
American Society for Microbiology, 1991 ISSN 0099-2240

Functional analysis of the Bacillus subtilis genome
Harwood, C.R., Wipat, A. and Prágai, Z.
In Functional Microbial Genomics,
Wren, B. and Dorrell, N. (eds.), pp 337-367
Methods in Microbiology, 33
Academic Press, 2003, ISBN 0-12-521533-9

Bacterial protein synthesis
Harwood, C.R. and Wipat, A.
In Molecular Medical Microbiology,
Sussman, M. (ed), pp 321-388
Academic Press, 2002, ISBN 0-12-677530-3

Genome management and analysis: prokaryotes
Harwood, C.R. and Wipat, A.
In Basic Biotechnology (2nd edition),
Ratledge, C. and Kristiansen, B. (eds.), Cambridge University Press, 2001, ISBN 0-521-77917-0

Molecular biology and genetics of Bacillus species
Bron, S., Meima, R., and van Dijl, J.-M. et. al.
In Manual of Industrial Microbiology and Biotechnology (2nd Edition),
Demain, A.L. and Davids, J.E. (eds.), pp 392-416
American Society for Microbiology (ASM) Press, 1999, ISBN 1-55581-128-0

Detection systems for streptomycetes
Wipat, A., Wellington, E.M. and Saunders, V.A.
In Genetic Interactions Among Microorganisms in the Natural Environment,
Wellington, E.M.H. and van Elsas, J.D. (eds.), pp 83-90
Pergamon Press, 1992, ISBN 0-08-042000-1

Gene transfer between streptomycetes in soil
Wellington, E.M.H., Cresswell, N. and Herron, P.R. et. al.
In Bacterial Genetics in Natural Environments,
Fry, J.C. and Day, M.J. (eds.), pp 216-230
Kluwer Academic Publishers, Dordrecht/Chapman and Hall, 1990, ISBN 0-412-35630-9

Annotation of SBML Models Through Rule-Based Semantic Integration
Lister, A. L., Lord, P., Pocock, M. and Wipat, A.
In The 12th Annual Bio-Ontologies Meeting, June 28, 2009, colocated with ISMB 2009, Stockholm, Sweden
Lord, P., Shah, N., Sansone, S.-A. et al. (eds.)
pp 49-52
ISCB, 2009

[Abstract]

Annotation of SBML Models Through Rule-Based Semantic Integration
Lister, A.L., Lord, P., Pocock, M. et al.
In The 12th Annual Bio-Ontologies Meeting, June 28, 2009. Colocated with ISMB 2009, Stockholm, Sweden
Lord, P., Shah, N., Sansone, S.-A. et al. (eds.)
pp 49-52
2009
Notes : The full conference proceedings are available here: http://bio-ontologies.org.uk/download/Bio-Ontologies2009.pdf

[Abstract]

Integration of full-coverage probabilistic functional networks with relevance to specific biological processes
James, K., Wipat, A. and Hallinan, J.
In Data Integration in the Life Sciences: 6th International Workshop, DILS 2009, Manchester, UK, July 20-22, 2009
Paton, N.W., Missier, P. and Hedeler, C. (eds.)
Lecture Notes in Computer Science, 5647, pp 31-46
Springer, 2009

Motifs and modules in fractured functional yeast networks
Hallinan, J. and Wipat, A.
In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology ( CIBCB 2007 ), 1-5 April 2007
pp 189-196
IEEE, 2007

Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets
Steggles, L.J., Banks, R. and Wipat, A.
In Computational Methods in Systems Biology. International Conference, CMSB 2006, Trento, Italy, October 18-19, 2006
Priami, C. (ed.)
Lecture Notes in Bioinformatics, 4210, pp 127-141
Springer-Verlag, 2006

e-Science Tools for the Genomic Scale Characterisation of Bacterial Secreted Proteins
Craddock, T., Lord, P., Harwood, C. and Wipat, A.
In Proceedings of the UK e-Science All Hands Meeting 2006, Nottingham, UK, 18th-21st September
Cox , S.J. (ed.)
pp 788-795
National e-Science Centre, 2006
Notes : Proceedings on CD-ROM.

Clustering and cross-talk in a yeast functional interaction network
Hallinan, J. and Wipat, A.
In Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06, ... Toronto, Ontario, Canada, September 28 & 29, 2006
pp 140-147
IEEE , 2006

A Grid-based System for Microbial Genome Comparison and Analysis
Sun, Y., Wipat, A., Pocock, M., Lee, P.A., Watson, P., Flanagan, K. and Worthington, J.T.
In 2005 IEEE International Symposium on Cluster Computing and the Grid , Cardiff, Wales, May 9-12 2005
2, pp 977-984
IEEE, 2005
Notes : CCGrid 2005

[Abstract]

Applying Petri Nets to Systems Biology using XMLTechnologies
Shaw, O., Koelmans, A., Steggles, J. and Wipat, A.
In Workshop on the Definition, Implementation and Application of a Standard Interchange Format for Petri Nets. Satellite event of ATPN : 25th International Conference on Application and Theory of Petri Nets, Bologna, Italy, June 26, 2004
Kindler, E. (ed)
pp 11-25
2004

Association of variations in I kappa B-epsilon with Graves’ disease using classical and myGrid methodologies
Li, P., Hayward, K., Jennings, C., Owen, K., Oinn, T., Stevens, R., Pearce, S. and Wipat, A.
In 2004 UK e-Science All Hands Meeting
Cox S.J.
Proceedings of the UK e-Science All Hands Meeting 2004,
2004

[Abstract]

Developing Grid-based Systems for Microbial Genome
Wipat, A., Sun, Y., Pocock, M., Lee, P., Watson, P. and Flanagan, K.
In UK e-Science All Hands Meeting 2004, Nottingham UK
Cox, S.J. (ed)
pp 532-538
EPSRC, 2004

Delivering Web service coordination capability to users
Oinn, T., Addis, M. J., Ferris, J., Marvin, D. J., Greenwood, M., Goble, C., Wipat, A., Li, P. and Carver, T.
In Thirteenth World Wide Web Conference (WWW2004), May 17-22, 2004, New York, USA.
pp 438-439
ACM, 2004

[Abstract]

Experiences with e-Science workflow specification and enactment in bioinformatics
Addis, M., Ferris, J., Greenwood, M., Li, P. , Marvin, D., Oinn, T. and Wipat, A.
In UK e-Science All Hands Meeting 2003, Nottingham, UK.
Cox, S. J. (ed)
pp 459-466
EPSRC, 2003

[Abstract]

Performing in silico experiments on the Grid: a users perspective.
Stevens, R., Glover, K., Greenhalgh, C., Jennings, C., Pearce, S., Li, P. et al.
In UK e-Science All Hands Meeting 2003, Nottingham, UK
Cox, S. J. (ed)
pp 43-50
EPSRC, 2003

[Abstract]

On the Use of Agents in a BioInformatics Grid
Moreau, L., Miles, S. and Goble, C. et. al.
In 3rd IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGRID '03): Workshop on Agent Based Cluster and Grid Computing, Tokyo, Japan, 12-15 May 2003
Lee, S., Sekguchi, S., Matsuoka, S. and Sato, M. (eds.)
pp 653-661
IEEE Computer Society Press, 2003

Detection of Streptomyces marker plasmids in soil
Saunders, V.A., Wellington, E.M.H. and Wipat, A.
In 2nd International Conference on the Release of Genetically-engineered Micro-organisms (REGEM 2): Release of Genetically Modified Microorganisms, Nottingham, England, 29-31 August 1991
Stewart-Tull, D.E.S. and Sussman, M. (eds.)
FEMS Symposium Series, 63,
Kluwer Academic/Plenum Publishers, 1992ISBN 0-306-44302-3

Plasmid transfer between streptomycetes in soil
Wellington, E.M.H., Saunders, V.A., Cresswell, N. and Wipat, A.
In 7th International Symposium on Biology of Actinomycetes (ISBA 88), Tokyo, Japan, May 1988
Okami, Y., Beppu, T. and Ogwara, H. (eds.)
pp 300-305
Japan Scientific Societies Press, Tokyo, 1988ISBN 4-7622-1552-X

CS-TR N^o 1043 Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models
Lister, A. L., Pocock, M., Wipat, A.
School of Computing Science, Newcastle University, Aug 2007

[Abstract]

CS-TR N^o 1016 Implementing the FuGE Object Model: a Systems Biology Data Portal and Integrator
Lister, A. L., Jones, A. R., Pocock, M., Shaw, O., Wipat, A.
School of Computing Science, Newcastle University, Apr 2007

[Abstract]

CS-TR N^o 962 Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets
Steggles, L. J., Banks, R., Wipat, A.
School of Computing Science, Newcastle University, May 2006

[Abstract]

CS-TR N^o 942 A data model for the representation of a gel electrophoresis experiment
Gibson, F., Wipat, A., Pocock, M., Morris, N.
School of Computing Science, Newcastle University, Jan 2006

[Abstract]

CS-TR N^o 931 Exploring Microbial Genome Sequences to Identify Protein Families on the Grid
Sun, Y., Wipat, A., Pocock, M., Lee, P., Flanagan, K., Worthington, J.
School of Computing Science, Newcastle University, Oct 2005

[Abstract]

CS-TR N^o 909 Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks
Shaw, O.J., Steggles, L.J., Wipat, A.
School of Computing Science, Newcastle University, May 2005

[Abstract]

CS-TR N^o 881 A Grid-based System for Microbial Genome Comparison and Analysis
Sun Y., Wipat A., Pocock M., Lee P., Watson P., Flanagan K. and Worthington J.
School of Computing Science, Newcastle University, Dec 2004

[Abstract]

CS-TR N^o 827 Applying Petri Nets to Systems Biology using XML Technologies
Shaw, O., Koelmans, A., Steggles, J. and Wipat, A.
School of Computing Science, Newcastle University, Mar 2004

[Abstract]