Publications for Alistair Rust

Journal Papers

• The Innate Immune Database (IIDB)
  Korb M, Rust A G, Thorsson V, Battail C, Li B, Hwang D, Kennedy K, Roach J C, Rosenberger C M, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H.
  BMC Immunology, In press, 2008
• Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources
  Lähdesmäki H, Rust A G and Shmulevich I.
  PLoS ONE, In press, 2008
• Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Motif Dynamics
  Ramsey S A, Klemm S L, Zak D E, Kennedy K A, Thorsson V, Li B, Gilchrist M, Gold E, Johnson C D, Litvak V, Navarro G, Roach J C, Rosenberger C M, Rust A G, Yudkovsky N, Aderem A and Shmulevich I.
  PLoS Computational Biology, In press, 2008
• Systems Biology Approaches Identify ATF3 as a Negative Regulator of Toll-like Receptor 4
  Gilchrist M, Thorsson V, Li B, Rust A G, Korb B, Kennedy K, Hai T, Bolouri H and Aderem A.
  Nature, 441(7090), 173-178, 2006
  [PMID:16688168]
• Transcription Binding Site Prediction Using Markov Models
  Abnizova I, Rust A G, Robinson M, te Boekhorst R, Gilks W R.
  J Bioinform Comput Biol, 4(2), 425-441, 2006
  [PMID:16819793]
• A Data Integration Methodology for Systems Biology
  Hwang D, Rust A G, Ramsey S, Smith J J, Leslie D M, Weston A D, de Atauri P, Aitchison J D, Hood L, Siegel A F and Bolouri H.
  PNAS, 102(48), 17296-17301, 2005
  [PMID:16301537]
• A Data Integration Methodology for Systems Biology: Experimental Verification
  Hwang D, Smith J J, Leslie D M, Weston A D, Rust A G, Ramsey S, de Atauri P, Siegel A F, Bolouri H, Aitchison J D and Hood L.
  PNAS, 102(48), 17302-17307, 2005
  [PMID:16301536]
• Ensembl 2002: Accommodating Comparative Genomics
  Clamp M, Andrews D et al.
  Nucleic Acids, Jan 1;31(1), 38-42, 2003
  [PMID:12519943]
• Initial Sequencing and Comparative Analysis of the Mouse Genome
  Mouse Genome Sequencing Consortium.
  Nature, Dec 5;420(6915), 520-562, 2002
  [PMID:12466850]
• Genome Annotation Techniques: New Approaches and Challenges
  Rust A G, Mongin E, and Birney, E.
  Drug Discovery Today, May 6;Vol.7, No.11, S70-76, 2002
  [PMID:12047883]
• A Provisional Regulatory Gene Network for Specification of Endomesoderm in the Sea Urchin Embryo
  Davidson E H, Rast J P, Oliveri P, Ransick A, Calestani C, Yuh C-H, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown C T, Livi C B, Lee P Y, Revilla R, Schilstra M J, Clarke P J C, Rust A G, Pan Z, Arnone M I, Rowen L, Cameron R A, McClay D R, Hood L and Bolouri H.
  Developmental Biology, Jun 1;246(1), 162-90, 2002
  [PMID:12027441]
• New Computational Approaches for Analysis of cis-Regulatory Networks
  Brown C T, Rust A G, Clarke P J C, Pan Z, Schilstra M J, De Buysscher T, Griffin G, Wold B J, Cameron R A, Davidson E H and Bolouri H.
  Developmental Biology, Jun 1;246(1), 86-102, 2002
  [PMID:12027436]
• A Genomic Regulatory Network for Development
  Davidson E H, Rast J P, Oliveri P, Ransick A, Calestani C, Yuh C-H, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown C T, Livi C B, Lee P Y, Revilla R, Rust A G, Pan Z, Schilstra M J, Clarke P J C, Arnone M I, Rowen L, Cameron R A, McClay D R, Hood L and Bolouri H.
  Science, Mar 1;Vol.295(5560), 1669-1678, 2002
  [PMID:11872831]
• The Ensembl Genome Database Project
  Hubbard T, Barker D et al.
  Nucleic Acids Research, Jan 1;Vol.30, No.1, 38-41, 2002
  [PMID:11752248]
• A Finite State Automaton Model for Multi-Neuron Simulations
  Schilstra, M J, Rust A G, Adams R, and Bolouri H.
  Neurocomputing, 44-46, 1141-1148, 2002

Submitted Papers

• Using Pre and Post-processing Methods to Improve Binding Site Predictions
  Sun Y, Gonzalez C C, Adams R, te Boekhorst R, Rust A G, Davey N and Robinson M
  [Submitted]

PhD Thesis

• Developmental Self-Organisation in Artificial Neural Networks
  Rust A G.
  Dept. of Computer Science, University of Hertfordshire, July 1998

Book Chapters

• Evolving Computational Neural Systems Using Synthetic Developmental Mechanisms
  Rust A G, Adams R, Schilstra M and Bolouri H.
  On Growth, Form and Computers,
  Kumar S and Bentley, P J (eds), Academic Press, London, UK, 2003
• Towards Computational Neural Systems Through Developmental Evolution
  Rust A G, Adams R, George S and Bolouri H.
  Emergent Neural Computation Architectures based on Neuroscience,
  Wermter S, Austin J and Willshaw D J (eds), Lecture Notes in Artificial Intelligence (LNAI2036), 188-202, Springer-Verlag, 2001

Conference Papers

• Predicting Binding Sites in the Mouse Genome
  Sun Y, Robinson M, Adams R, Davey N and Rust A G,
  Proc.6th International Conference on Machine Learning and Applications, 476-481, 2007
• Using Pre-processing Methods to Improve Binding Site Predictions
  Adams R, Robinson M, Sun Y, Adams R, te Boekhorst R, Rust A G and Davey N.
  Proc. 4th International Joint Conference on Computer Science and Software Engineering (JCSSE2007), 822-829, 2007
• Using Real-valued Meta Classifiers to Integrate and Contextualize Binding Site Predictions
  Robinson M, Sharabi O, Sun Y, Adams R, te Boekhorst R, Rust A G and Davey N.
  Proc. 8th International Conference on Adaptive and Natural Computing Algorithms (ICANNGA'07), 822-829, 2007
• Using Feature Selection Methods for Binding Site Predictions
  Sun Y, Robinson M, Adams R, te Boekhorst R, Rust A G and Davey N.
  Proc. 5th IEEE International Conference on Cognitive Informatics (ICCI'06), 566-571, 2006
• Using Sampling Methods to Improve Binding Site Predictions
  Sun Y, Robinson M, Adams R, te Boekhorst R, Rust A G and Davey N.
  Proc. European Symposium on Artificial Neural Networks, Advances in Computational Intelligence and Learning (ESANN06), 533-538, 2006
• Improving Computational Predictions of Cis-regulatory Binding Sites
  Robinson M, Sun Y, te Boekhorst R, Kaye P, Adams R, Davey N and Rust A G.
  Proc. Pacific Symposium on Biocomputing 11 (PSB2006), 391-402, 2006
  [PMID:17094255]
• Using a Hybrid Adaboost Algorithm to Integrate Binding Site Predictions
  Sun Y, Robinson M, Adams R, Kaye P, Rust A G, and Davey N.
  Proc. Int. Conference on Machine Intelligence (ICMI2005), 2005
• Integrating Binding Site Predictions Using Meta Classification Methods
  Sun Y, Robinson M, Adams R, Rust A G, Kaye P and Davey N.
  Proc. Int. Conference on Artificial Neural Networks and Genetic Algorithms (ICANNGA2005), 321-324, 2005
• Using Real-valued Meta Classifiers to Integrate Binding Site Predictions
  Sun Y, Robinson M, Adams R, Kaye P, Rust A G and Davey N.
  Proc. Int. Joint Conference on Neural Networks (IJCNN2005), 481-486, 2005
• Integrating Binding Site Predictions Using Non-Linear Classification Methods
  Sun Y, Robinson M, Adams R, Kaye P, Rust A G and Davey N.
  Proc. Sheffield University Machine Learning Workshop, Springer-Verlag Lecture Notes in Computer Science, 2005
• Design of Spatially Extended Neural Networks for Specific Applications
  Adams R, te Boekhorst R, Rust A G, Kaye P and Schilstra M.
  Proc. of the Int. Joint Conf. on Neural Networks (IJCNN 2004), 3101-3106, 2004
• Evolutionary Neural Topiary: Growing and Sculpting Artificial Neurons to Order
  Rust A G, Adams R and Bolouri H.
  In Bedau M A, McCaskill J S, Packard N H and Rasmussen S (eds), Proceedings of the 7th International Conference on the Simulation and Synthesis of Living Systems (AlifeVII), 146-150, 2000
• Image Redundancy Reduction for Neural Network Classification using Discrete Cosine Transforms
  Pan Z, Rust A G, and Bolouri H.
  Proceedings of the IEEE-INNS-ENNS International Joint Conference on Neural Networks (IJCNN'2000), Vol III, 149-154, 2000
• Developmental Evolution of Dendritic Morphology in a Multi-Compartmental Neuron Model
  Rust A G and Adams R.
  In Proceedings of the 9th International Conference on Artificial Neural Networks (ICANN'99), Vol 1, 383-388, IEE, London, 1999
  Poster from the conference.

• Molecular Self-Organisation in a Developmental Model for the Evolution of Large-Scale Artificial Neural Networks
  Bolouri H, Adams R, George S and Rust A G.
  Proceedings of the 1998 International Conference on Neural Information Processing and Intelligent Information Systems (ICONIP'98), Kitakyushu, Japan, 21-23 October, Vol 2, 797-800, 1998

• Developmental Evolution of an Edge Detecting Retina
  Rust A G, Adams R, George S and Bolouri H.
  In Niklasson L, Boden M and Ziemke T (eds), Proceedings of the 8th International Conference on Artificial Neural Networks (ICANN'98), Vol 2, pp 561-566, Springer Verlag, 1998
  Letter sized version of ps.

• Molecular Self-Organisation in a Developmental Model for the Evolution of Large-Scale Artificial Neural Networks
  Bolouri H, Adams R, George S and Rust A G.
  Presented at The Right Stuff: Appropriate Mathematics for Evolutionary and Developmental Biology
  a Full-Day Workshop at the 6th International Conference on Artificial Life and Computation: the Boundaries are Changing (ALIFE'VI), Los Angeles, USA, 26-29 June, 1998
  Workshop papers are collected in University of Hertfordshire Computer Science Technical Report TR315, June 1998

• Activity-Based Pruning in Developmental Artificial Neural Networks
  Rust A G, Adams R, George S and Bolouri H.
  In Husbands P and Harvey I (eds), Proceedings of the 4th European Conference on Artificial Life (ECAL'97), Cambridge, MA, MIT Press, 224-233, 1997

• Designing Development Rules for Artificial Evolution
  Rust A G, Adams R, George S and Bolouri H.
  In Smith G D, Steele N C and Albrecht R F (eds), Proceedings of the 4th International Conference on Artificial Neural Networks and Genetic Algorithms (ICANNGA'97), Vienna, Springer-Verlag, 508-511, 1997

• Applications of AI Techniques to Aid Paths Towards Concurrent Engineering
  Parkinson B, Hinder S, Rohr U, Rust A and Shwartzberg D.
  In Case K and Newman S (eds), Proceedings of the 10th National Conference on Manufacturing Research, Taylor and Francis, 472-476, 1994

Workshop Presentations

• Harnessing Developmental Self-Organisation to Design Artificial Neural Systems
  Rust A G, Adams R and Bolouri H.
  Presented at Self-Organising Systems - Future Prospects for Computing, an EPSRC funded, 2 day workshop held at UMIST, Manchester, 28/29 October 1999

• Towards Computational Neural Systems Through Developmental Evolution
  Rust A G, Adams R and Bolouri H.
  Presented at EmerNet: International Workshop on Emergent Neural Computation Architectures Based on Neuroscience, post-conference workshop at ICANN'99, Edinburgh, Scotland, 11 September 1999

Technical Reports

• Artificial Evolution: Modelling the Development of the Retina
  Rust A G, Adams R, George S and Bolouri H.
  Technical Memorandum ERDC/1996/0015 and Computer Science Technical Report TR255, September 1996