Peer-Reviewed Publications
2011
An analytical approach differentiates between individual and
collective cancer invasion
Katz E, Verleyen W, Blackmore CG, Edward M, Smith VA, Harrison DJ (2011) Analytical Cellular Pathology 34: 35-48.
2010
Revealing ecological networks using Bayesian
network inference algorithms
Milns I, Beale CM, Smith VA (2010) Ecology 91: 1892-1899.
Revealing structure of complex biological systems using Bayesian networks
Smith VA (2010) In: Network Science: Complexity in Nature and Technology
(Estrada E, Fox M, Higham DJ , Oppo G-L, eds; Springer) pp 185-204.
Some useful mathematical tools to transform microarray data into interactive molecular networks
Matthäus F, Smith VA, Gebicke-Haerter PJ (2010) In:
Systems Biology in Psychiatric Research: From High-Throughput Data to Mathematical Modeling
(Tretter F, Gebicke-Haerter PJ, Winterer G, Mendoza E, eds;
John Wiley and Sons) pp 277-300.
Cancer systems biology
Faratian D, Bown JL, Smith VA, Langdon SP, Harrison DJ (2010) In:
Systems Biology in Drug Discovery and Development: Methods and Protocols (Yan Q, ed;
Springer) pp 245-263.
Causal pattern recovery from neural
spike train data using the Snap Shot Score
Echtermeyer C, Smulders TV, Smith VA (2010)
Journal of Computational Neuroscience 29: 231-252
Also published as: Echtermeyer et al (2009) Journal of Computational Neuroscience Online First: 31 July 2009.
2009
Interactive molecular networks
obtained by computer-aided conversion of microarray
data from brains of alcohol-drinking rats
Matthäus F, Smith VA, Fogtman A, Sommer WH, Leonardi-Essmann F, Lourdusamy A,
Reimers MA, Spanagel R, Gebicke-Haerter PJ (2009)
Pharmacopsychiatry 42: S118-S128.
2008
Evolving
an agent-based model to probe behavioral rules in flocks of cowbirds
Smith VA (2008)
Proceedings of the Eleventh International Conference on Artificial Life
MIT Press, Cambridge, MA, pp 561-568.
[Version with noted errata corrected]
2007
Testing measures of animal
social association by computer simulation
White DJ, Smith VA (2007)
Behaviour 144: 1447-1468.
The CARMEN e-Science pilot project:
Neuroinformatics work packages
Smith LS, Austin J, Baker S, Borisyuk R, Eglen S, Feng J, Gurney K, Jackson T,
Kaiser M, Overton P, Panzeri S, Quian Quiroga R, Schultz SR, Sernagor E, Smith VA, Smulders TV,
Stuart L, Whittington M, Ingram C (2007) In:
Proceediings of the UK e-Science Programme All Hands Meeting 2007
(SJ Cox, ed), National e-Science Centre, pp 591-598.
2006
Computational inference of neural information flow networks
Smith VA, Yu J, Smulders TV, Hartemink AJ, Jarvis ED (2006)
PLoS Computational Biology 2: e161.
[Supporting Protocol, Figures, Tables (PDF)]
[Supporting Video (PowerPoint)]
2004
Advances to Bayesian network inference for generating causal networks from observational biological data
Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED (2004) Bioinformatics 20: 3594-3603.
2003
Influence of network topology and data collection on network inference
Smith VA, Jarvis ED, Hartemink AJ (2003) Pacific Symposium on Biocomputing 8: 164-175.
2002
Using Bayesian network inference algorithms to recover molecular genetic regulatory networks
Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED (2002) International Conference on Systems Biology 2002 (ICSB02), December 2002.
A framework for integrating the songbird brain
Jarvis ED, Smith VA, Wada K, Rivas MV, McElroy M, Smulders TV, Carninci P, Hayashizaki Y, Dietrich F,
Wu X, McConnell P, Yu J, Wang PP, Hartemink AJ, Lin S (2002) Journal of Comparative Physiology A 188: 961-980.
Evaluating functional network inference using simulations of complex biological systems
Smith VA, Jarvis ED, Hartemink AJ (2002) Bioinformatics 18: S216-S224.
The context of social learning: association patterns in a captive flock of brown-headed cowbirds
Smith VA, King AP, West MJ (2002) Animal Behaviour 63: 23-35.
2000
A role of her own: female cowbirds, Molothrus ater, influence the development and outcome of song learning
Smith VA, King AP, West MJ (2000) Animal Behaviour 60: 599-609.
Other Publications
2008
1st Year Practicals: Their Role in Developing Future Bioscientists
Adams D, Arkle S, Bevan R, Boachie-Ansah G, Bradshaw T, Cameron G,
Campbell A-M, Chamberlain M, Gibson A, Gowers D, Hayes M, Heritage J,
Hollingsworth M, Hooper H, Hudson K, Hughes I, Lindsey N, Meskin S, Park J,
Podesta T, Rattray J, Scott G, Shearer MC, Smalley H, Smith VA, Smith D, Tierney A,
Todd M, Verran J, Wakeford C, Wilbraham J, Wilson J (2008) HEA Centre for Bioscience Report.
2007
The scientific method: teaching the how of science and not just the what
Shearer MC, Smith VA (2007) Centre for Bioscience Bulletin 21: 8.
(Note authorship correction in Centre for Bioscience Bulletin 22: 2)