Publications on Biological Computation

2013

Rafal Bogacz, Optimal decision making in the cortico-basal-ganglia circuit (in press). Chapter in An Introduction to Model-Based Cognitive Neuroscience. March 2013. No electronic version available.

2012

Elizabeth J Coulthard, Rafal Bogacz, Shazia Javed, Lucy K Mooney, Gillian Murphy, Sophie Keeley, Alan L Whone, Distinct roles of dopamine and subthalamic nucleus in learning and probabilistic decision making. Brain, in press, . November 2012. No electronic version available.
Kevin Lloyd, Nadine Becker, Matthew W. Jones, Rafal Bogacz, Learning to use working memory: a reinforcement learning gating model of rule acquisition in rats. Frontiers in Computational Neuroscience, 6, pp. 87–. October 2012. No electronic version available. External information
James Marshall, Rafal Bogacz, Iain Gilchrist, Consistent implementation of decisions in the brain. PLOS One, 7, pp. e43443–. September 2012. No electronic version available. External information
Alexander Pavlides, S. John Hogan, Rafal Bogacz, Improved conditions for the generation of beta oscillations in the subthalamic nucleus-globus pallidus network. European Journal of Neuroscience, 36, pp. 2229–2239. July 2012. No electronic version available.

2011

Tim Kovacs, Andy Wills, Generalization vs. Discrimination in Learning. Chapter in Encyclopedia of the Sciences of Learning. Norbert M. Seel, (eds.). November 2011. PDF, 269 Kbytes.
Michal Kucewicz, Mark Tricklebank, Rafal Bogacz, Matthew W. Jones, Dysfunctional prefrontal cortical network activity and interactions following cannabinoid receptor activation. The Journal of Neuroscience, 31, pp. 15560–15568. October 2011. No electronic version available.
Rafal Bogacz, Tobias Larsen, Integration of reinforcement learning and optimal decision making theories of the basal ganglia. Neural Computation, 23, pp. 817–851. April 2011. No electronic version available. External information
Andrew Lulham, Rafal Bogacz, Simon Vogt, Malcolm W. Brown, An infomax algorithm can perform both familiarity discrimination and feature extraction in a single network. Neural Computation, 23, pp. 909–926. April 2011. No electronic version available.
Paul A. Howard-Jones, Skevi Demetriou, Rafal Bogacz, Jee H. Yoo, Ute Leonards, Towards a Science of Learning Games. Brain, Mind and Education, 5, pp. 33–41. March 2011. No electronic version available. External information
Angela Onslow, Rafal Bogacz, Matthew W. Jones, Quantifying phase-amplitude coupling in neuronal network oscillations. Progress in Biophysics and Molecular Biology, 105, pp. 49–57. February 2011. No electronic version available.

2010

Paul A. Howard-Jones, Rafal Bogacz, Jee H. Yoo, Ute Leonards, Skevi Demetriou, The neural mechanisms of learning from competitors. Neuroimage, 53, pp. 790–799. November 2010. No electronic version available. External information
Birte U. Forstmann, Alfred Anwander, Andreas Schäfer, Jane Neumann, Scott Brown, Eric-Jan Wagenmakers, Rafal Bogacz, Robert Turner, Cortico-Striatal Connections Predict Control over Speed and Accuracy in Perceptual Decision Making. Proceedings of the National Academy of Sciences of the USA, 107, pp. 15916–15920. September 2010. No electronic version available. External information
Jiaxiang Zhang, Rafal Bogacz, Bounded Ornstein-Uhlenbeck models for two-choice time controlled tasks. Journal of Mathematical Psychology, 54, pp. 322–333. May 2010. PDF, 420 Kbytes.
Tobias Larsen, David S. Leslie, Edmund J. Collins, Rafal Bogacz, Posterior weighted reinforcement learning with state uncertainty. Neural Computation, 22, pp. 1149–1179. May 2010. No electronic version available. External information
Jiaxiang Zhang, Rafal Bogacz, Optimal decision making on the basis of evidence represented in spike trains. Neural Computation, 22, pp. 1113–1148. May 2010. No electronic version available. External information
Rafal Bogacz, Peter T. Hu, Philip Holmes, Jonathan D. Cohen, Do humans produce the speed-accuracy tradeoff that maximizes reward rate?. Quarterly Journal of Experimental Psychology, 63, pp. 863–891. May 2010. No electronic version available.
Miriam Zackenhouse, Rafal Bogacz, Philip Holmes, Robust versus optimal strategies for two-alternative forced choice tasks. Journal of Mathematical Psychology, 54, pp. 230–246. April 2010. No electronic version available.
Tobias Larsen, Rafal Bogacz, Initiation and Termination of Integration in a Decision Process. Neural Networks, 23, pp. 322–333. February 2010. No electronic version available.
Rafal Bogacz, Eric-Jan Wagenmakers, Birte U. Forstmann, Sander Nieuwenhuis, The Neural Basis of the Speed-Accuracy Tradeoff. Trends in Neurosciences, 33, pp. 10–16. January 2010. No electronic version available. External information

2009

Ioannis Kaloskampis, Tilo Burghardt, Towards Automated Visual Identification of Great Whites using Biometric Computer Vision. International White Shark Symposium (IWSS), pp. 21–22. December 2009. No electronic version available.
Jiaxiang Zhang, Rafal Bogacz, Philip Holmes, A comparison of bounded diffusion models for choice in time controlled tasks. Journal of Mathematical Psychology, 53, pp. 231–241. August 2009. No electronic version available.
Nigel Franks, Anna Dornhaus, James Marshall, Francois Xavier Dechaume-Moncharmont, The dawn of a golden age in mathematical insect sociobiology. Chapter in Gadau and Fewell (eds.) Organization of Insect Societies. ISBN 978-0-674-03125-8, pp. 437–459. July 2009. No electronic version available.
James Marshall, The donation game with roles played between relatives. Journal of Theoretical Biology, 260(3), pp. 386–391. July 2009. No electronic version available. External information
Rafal Bogacz, Optimal decision-making theories. Chapter in Handbook of Reward and Decision Making. Jean-Claude Dreher, Leon Tremblay, (eds.), pp. 375–397. July 2009. PDF, 300 Kbytes.
James Marshall, Nigel Franks, Colony-level cognition. Current Biology, 19(10), pp. R395–R396. May 2009. No electronic version available. External information
Oliver Ray, Ken Whelan, Ross King, A nonmonotonic logical approach for modelling and revising metabolic networks. 3rd International Conference on Complex, Intelligent and Software Intensive Systems (from 2nd International Workshop on Intelligent Informatics in Biology and Medicine), pp. 825–829. March 2009. PDF, 195 Kbytes.
Dave Cliff, ZIP60: Further Explorations in the Evolutionary Design of Trader Agents and Online Auction-Market Mechanisms. IEEE Transactions on Evolutionary Computation. 13(1):3-18., 13(1), pp. 3–18. January 2009. PDF, 1544 Kbytes.

2008

Peter Trimmer, Alasdair Houston, James Marshall, Rafal Bogacz, Elizabeth Paul, Mike Mendl, John McNamara, Mammalian Choices: combining fast-but-inaccurate and slow-but-accurate decision-making systems. Proceedings of the Royal Society B, 275(1649). ISSN 0962-8452, pp. 2353–2361. October 2008. PDF, 226 Kbytes. External information
Zacharias Androulidakis, Andrew Lulham, Rafal Bogacz, Malcolm W. Brown, Computational models can replicate the capacity of human recognition memory. Network: Computation in Neural System, 19, pp. 161–182. September 2008. No electronic version available. External information

2007

Susanne Hoche, Andreas Nuernberger, Peter Flach, Network Analysis in Natural Sciences and Engineering. AI Communications, 20(4). December 2007. No electronic version available.
Nigel R Franks, James W Hooper, Mike Gumn, Tamsyn H Bridger, James Marshall, Roderich Gross, Anna Dornhaus, Moving targets: collective decision and flexible choices in house-hunting ants. Swarm Intelligence, . ISSN 1935-3812 . December 2007. No electronic version available.
Jiaxiang Zhang, Rafal Bogacz, Superior Colliculus and Basal Ganglia Control the Saccadic Response in Motion Discrimination Tasks. 1st International Conference on Cognitive Neurodynamics, pp. 475–479. November 2007. No electronic version available.
Robert Planqué, Francois-Xavier Dechaume-Moncharmont, Nigel R. Franks, Tim Kovacs, James Marshall, Why do house-hunting ants recruit in both directions?. Naturwissenschaften, 94(11). ISSN 0028-1042, pp. 911–918. November 2007. PDF, 574 Kbytes. External information
James Marshall, Nigel Franks, Computer modelling in behavioural and evolutionary ecology: whys and wherefores. Chapter in Laubichler and Muller (eds.) Modelling Biology - Structures, Behaviors, Evolution. ISBN 978-0-262-12291-7, pp. 335–354. September 2007. No electronic version available.
Rafal Bogacz, Marius Usher, Jiaxiang Zhang, James L. McClelland, Extending a biologically inspired model of choice: multi-alternatives, nonlinearity and value-based multidimensional choice. Philosophical Transactions of the Royal Society, Series B, 362, pp. 1655–1670. August 2007. PDF, 589 Kbytes.
Proceedings of the 2007 Genetic and Evolutionary Compuation Conference (GECCO 2007). Dirk Thierens, Benjamin Doerr, Tim Kovacs, Sanjeev Kumar, Hans-Georg Beyer, Mauro Birattari, Josh Bongard, Jurgen Branke, John Andrew Clark, Dave Cliff, Clare Bates Congdon, Kalyanmoy Deb, (eds.). ACM Press. ISBN 978-1-59593-697-4. July 2007. No electronic version available.
Rafal Bogacz, Optimal decision network with distributed representation. Neural Networks, 20, pp. 564–576. July 2007. No electronic version available.
Rafal Bogacz, Samuel M. McClure, Jian Li, Jonathan D. Cohen, P. Read Montague, Short-term memory traces for action bias in human reinforcement learning. Brain Research, 1153, pp. 111–121. June 2007. PDF, 658 Kbytes.
Rafal Bogacz, Optimal decision making theories: linking neurobiology with behaviour. Trends in Cognitive Sciences, 11(3), pp. 118–125. March 2007. PDF, 768 Kbytes. External information
Rafal Bogacz, Kevin Gurney, The basal ganglia and cortex implement optimal decision making between alternative actions. Neural Computation, 19(2), pp. 442–477. February 2007. PDF, 240 Kbytes.
Mulder N.J., Copley R., Courcelle E., Das U., Daugherty L., Dibley M., Finn R., Fleischmann W., Gough J., Haft D., Hulo N., Apweiler R., Hunter S., Kahn D., Kanapin A., Kejariwal A., Labarga A., Langendijk-Genevaux P.S., Lonsdale D., Lopez R., Letunic I., Madera M., Attwood T.K., Maslen J., McAnulla C., McDowell J., Mistry J., Mitchell A., Nikolskaya A.N., Orchard S., Orengo C., Petryszak R., Selengut J.D., Bairoch A., Sigrist C.J., Thomas P.D., Valentin F., Wilson D., Wu C.H., Yeats C., Bateman A., Binns D., Bork P., Buillard V., Cerutti L., New developments in the InterPro database. Nucl. Acids Res., 35, pp. D224–D228. January 2007. No electronic version available.
Nick Yeung, Rafal Bogacz, Clay B. Holroyd, Sander Nieuwenhuis, Jonathan D. Cohen, Theta phase-resetting and the error-related negativity. Psychophysiology, 44, pp. 39–49. January 2007. PDF, 422 Kbytes.
Robert Planqué, Anna Dornhaus, Nigel R. Franks, Tim Kovacs, James Marshall, Weighting waiting in collective decision-making. Behavioral Ecology and Sociobiology, 61(3). ISBN 0340-5443 print 1432-0762 web, pp. 347–356. January 2007. No electronic version available. External information
Wilson, D., Madera, M., Vogel, C., Chothia, C., Gough J., The SUPERFAMILY database in 2007: families and functions. Nucl. Acids Res., 35, pp. 308–313. January 2007. No electronic version available.

2006

Rafal Bogacz, Eric Brown, Jeffrey Moehlis, Phil Holmes, Jonathan D. Cohen, The physics of optimal decision making: A formal analysis of models of performance in two-alternative forced choice tasks. Psychological Review, 113(4), pp. 700–765. October 2006. PDF, 1628 Kbytes.
Tim Kovacs, Xavier LLora, Keiki Takadama, The 9th International Workshop on Learning Classifier Systems (IWLCS-2006 Workshop Summary). SIGEVolution, 1(3). ISSN 1931-8499, pp. 31–33. September 2006. PDF, 2429 Kbytes. External information
Gough, J., Genomic scale sub-family assignment of protein domains. Nucl. Acids Res., 34 (13), pp. 3625–3633. July 2006. No electronic version available.
Tim Kovacs, Manfred Kerber, A study of structural and parametric learning in XCS. Evolutionary Computation, 14(1), pp. 1–19. June 2006. PDF, 359 Kbytes.
Robert Planque, James Marshall, Tim Kovacs, Francois-Xavier Dechaume-Moncharmont, Nigel R. Franks, Ana Sendova-Franks, It takes two to tango: the role of late recruitment in collective decision making. Proceedings of AISB'06: Adaptation in Artificial and Biological Systems. ISSN 1902956975, pp. 207–207. April 2006. PDF, 34 Kbytes. External information
James Marshall, Rafal Bogacz, Anna Dornhaus, Nigel R. Franks, Tim Kovacs, Robert Planque, Similar Models of Optimal Decision Making in Social Insect Colonies and in the Primate Brain. Proceedings of AISB'06: Adaptation in Artificial and Biological Systems. ISSN 1902956975, pp. 205–205. April 2006. PDF, 17 Kbytes. External information
Maeda, N., Beisel, K. W., Bult, C. J., Fletcher, C. F., Forrest, A. R., Furuno, M., Hill, D., Itoh, M., Kanamori-Katayama, M., Katayama, S., Katoh, M., Kasukawa, T., Kawashima, T., Quackenbush, J., Ravasi, T., Ring, B. Z., Shibata, K., Sugiura, K., Takenaka, Y., Teasdale, R. D., Wells, C. A., Zhu, Y., Oyama, R., Kai, C., Kawai, J., Hume, D. A., Carninci, P., Hayashizaki, Y., Gough, J., Frith, M., Engstrom, P. G., Lenhard, B., Aturaliya, R. N., Batalov, S., Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs. PLoS Geneteics, 2 (4), pp. 62–62. April 2006. No electronic version available.
Liu, J., Gough, J., Rost, B., Distinguishing Protein-Coding from Non_coding RNAs through Support Vector Machines. PLoS Genetics, 2 (4), pp. 29–29. April 2006. No electronic version available.
Babu, M. M., Priya, M. L., Selvan, A. T., Madera, M., Gough, J., Sankaran, K., A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. J Bacteriol., 188 (8), pp. 2761–2773. April 2006. No electronic version available.
Vinogradov, S. N., Hoogewijs, D., Bailly, X., Arredondo-Peter, R., Gough, J., Dewilde, S., Moens, L., Vanfleteren, J. R., A phylogenomic profile of globins. BMC Evol Biol., 6, pp. 31–31. April 2006. No electronic version available.

2005

Phil Holmes, Eric Shea-Brown, Jeff Moehlis, Rafal Bogacz, Juan Gao, Gary Aston-Jones, Eric Clayton, Janusz Rajkowski, Jonathan D. Cohen, Optimal decisions: From neural spikes, through stochastic differential equations, to behavior. IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, 88(10), pp. 2496–2503. October 2005. PDF, 500 Kbytes.
Vinogradov, S. N., Hoogewijs, D., Bailly, X., Arrendondo-Peter, R., Guertin, M., Gough, J., Dewilde, S., Moens, L., Vanfleteren, J. R., Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life. Proc Natl Acad Sci USA, 102 (32), pp. 11385–11389. August 2005. No electronic version available.
James Marshall, Collective action selection in social insect colonies. Bryson et al. (eds) Modelling Natural Action Selection: Proceedings of an International Workshop. ISBN 1-902956-40-9, pp. 143–145. July 2005. No electronic version available.
Eric Brown, Juan Gao, Philip Holmes, Rafal Bogacz, Mark Gilzenrat, Jonathan D. Cohen, Simple neural networks that optimize decisions. International Journal of Bifurcation and Chaos, 15(3), pp. 803–826. June 2005. PDF, 605 Kbytes.
Carninci, P., Wells, C., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K. C., Pavan, W. J., Pavesi, G., Pesole, G., Petrovsky, N., Kodzius, R., Piazza, S., Reed, J., Reid, J. F., Ring, B. Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S. L., Sandelin, A., Schneider, C. and, Shimokawa, K., Bajic, V. B., Brenner, S. E., Batalov, S., Forrest, A. R., Zavolan, M., Davis, M. J., Wilming, L. G., Kasukawa, T., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Katayama, S., Bono, H., Chalk, A. M., Chiu, K. P., Choudhary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dalrymple, B. P., de, Bono, B., Gough, J., Della, Gatta, G., di, Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Frith, M. C., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Maeda, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Oyama, R., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P., Kruger, A., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. F., Lazarevic, D., Ravasi, T., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan, Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Lenhard, B., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., The Transcriptional Landscape of the Mammalian Genome. Science, 309 (5740), pp. 1559–1563. April 2005. No electronic version available.
Gough, J., Convergent evolution of domain architectures (is rare). Bioinformatics, 21 (8), pp. 1464–1471. April 2005. No electronic version available.
Mulder, N. J., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Apweiler, R., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J., Mitchell, A., Attwood, T. K., Nikolskaya, A. N., Orchard, S., Pagni, M., Ponting, C. P., Quevillon, E., Selengut, J., Sigrist, C. J., Silventoinen, V., Studholme, D. J., Vaughan, R., Bairoch, A., Wu, C. H., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., InterPro, progress and status in 2005. Nucl. Acids Res., 33. January 2005. No electronic version available.

2004

Rafal Bogacz, Jonathan D. Cohen, Parameterization of connectionist models. Behavior Research Methods, Instruments, & Computers, 36(4), pp. 732–741. December 2004. PDF, 263 Kbytes.
Nick Yeung, Rafal Bogacz, Clay B. Holroyd, Jonathan D. Cohen, Detection of synchronized oscillations in the electroencephalogram: An evaluation of methods. Psychophysiology, 41, pp. 822–832. November 2004. PDF, 1084 Kbytes.
Gough, J., Computational Genomics: Theory and Application. Chapter in . Grant, R., (eds.), pp. 105–124. September 2004. No electronic version available.
Gough, J., Chothia, C., The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins. Structure, 12, pp. 917–925. June 2004. No electronic version available.
Vogel, C., Berzuini, C., Bashton, M., Gough, J., Teichmann, S. A., Supra-domains: Evolutionary units larger than single protein domains. J. Mol. Biol., 336, pp. 809–823. February 2004. No electronic version available.
Madera, M., Vogel, C., Kummerfeld, S.K., Chothia, C., Gough, J., The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res., 32 (10), pp. 235–239. January 2004. No electronic version available.

2003

Gherardi, E., Youles, M. E., Miguel, R. N., Blundell, T. L., Iamele, L., Gough, J., Bandyopadhyay, A., Hartmann, G., Butler, P. J., Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor. Proc. Natl. Acad. Sci. U.S.A., 100 (21), pp. 12039–12044. October 2003. No electronic version available.
Kanapin, A., Teasdale, R. D., Yuan, Z., Batalov, S., Davis, M. J., Gough, J., Grimmond, S., Kawaji, H., Magrane, M., Matsuda, H., Schonbach, C., Mouse Proteome Analysis. Genome Res., 13, pp. 1335–1344. June 2003. No electronic version available.
Kasukawa, T., Kanapin, A., Matsuda, H., Schriml, L. M., Hayashizaki, Y., Okazaki, Y., Quackenbush, J., Furuno, M., Nikaido, I., Bono, H., Hume, D. A., Bult, C., Hill, D. P., Baldarelli, R., Gough, J., Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System. Genome Res., 13, pp. 1542–1551. June 2003. No electronic version available.
Chothia, C., Gough, J., Vogel, C., Teichmann, S. A., Evolution of the protein repertoire. Science, 300 (5626), pp. 1701–1703. June 2003. No electronic version available.
Rafal Bogacz, Malcolm W. Brown, Comparison of computational models of familiarity discrimination in the perirhinal cortex. Hippocampus, 13, pp. 494–524. March 2003. PDF, 612 Kbytes.

2002

Okazaki, Y., Suzuki, H., Yanagisawa, M., Yang, I., Yang, L., Yuan, Z., Zavolan, M., Zhu, Y., Zimmer, A., Carninci, P., Hayatsu, N., Hirozane-Kishikawa, T., Yamanaka, I., Konno, H., Nakamura, M., Sakazume, N., Sato, K., Shiraki, T., Waki, K., Kawai, J., Aizawa, K., Arakawa, T., Fukuda, S., Kiyosawa, H., Hara, A., Hashizume, W., Imotani, K., Ishii, Y., Yagi, K., Tomaru, Y., Hasegawa, Y., Nogami, A., Schonbach, C., Gojobori, T., Baldarelli, R., Furuno, M., Hill, D. P., Bult, C., Hume, D. A., Quackenbush, J., Schriml, L. M., Kanapin, A., Matsuda, H., Batalov, S., Beisel, K. W., Blake, J. A., Kasukawa, T., Bradt, D., Brusic, V., Chothia, C., Corbani, L. E., Cousins, S., Dalla, E., Dragani, T. A., Fletcher, C. F., Forrest, A., Frazer, K. S., Adachi, J., Gaasterland T., Gariboldi, M., Gissi, C., Godzik, A., Gough, J., Grimmond, S., Gustincich, S., Hirokawa, N., Jackson, I. J., Jarvis, E. D., Bono, H., Kanai, A., Kawaji, H., Kawasawa, Y., Kedzierski, R. M., King, B. L., Konagaya, A., Kurochkin, I. V., Lee, Y., Lenhard, B., Lyons, P. A., Kondo, S., Maglott, D. R., Maltais, L., Marchionni, L., McKenzie, L., Miki, H., Nagashima, T., Numata, K., Okido, T., Pavan, W. J., Pertea, G., Nikaido, I., Pesole, G., Petrovsky, N., Pillai, R., Pontius, J. U., Qi, D., Ramachandran, S., Ravasi, T., Reed, J. C., Reed, D. J., Reid, J., Osato, N., Ring, B. Z., Ringwald, M., Sandelin, A., Schneider, C., Semple, C. A., Setou, M., Shimada, K., Sultana, R., Takenaka, Y., Taylor, M. S., Saito, R., Teasdale, R. D., Tomita, M., Verardo, R., Wagner, L., Wahlestedt, C., Wang, Y., Watanabe, Y., Wells, C., Wilming, L. G., Wynshaw-Boris, A., Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420 (6915), pp. 563–573. December 2002. No electronic version available.
Rafal Bogacz, Malcolm W. Brown, The restricted influence of sparseness of coding on the capacity of familiarity discrimination networks. Network: Computation in Neural System, 13, pp. 457–485. November 2002. PDF, 285 Kbytes.
Gough, J., The SUPERFAMILY database in structural genomics.. Acta Cryst., In press. November 2002. No electronic version available.
Madera, M., Gough, J., A comparison of profile hidden Markov model procedures for remote homology detection . Nucl. Acids. Res., 30 (19), pp. 4321–4328. October 2002. No electronic version available.
Gough, J., Hidden Markov models and their application to genome analysis in the context of protein structure. PhD thesis. University of Cambridge. October 2002. No electronic version available.
Hua, S. J., Guo, T., Gough, J., Sun, Z. R., Proteins with alpha/beta Fold Class Have High Participation in Fusion Events. J. Mol. Biol., 320 (4), pp. 713–719. July 2002. No electronic version available.
Jardine, O., Gough, J., Chothia, C., Teichmann, T., Comparison of the Small Molecule Metabolic Pathways of Escherichia coli and Saccharomyces cerevisiae. Genome Res., 12 (6), pp. 916–929. June 2002. No electronic version available.
Rafal Bogacz, Malcolm W. Brown, Capacity of perirhinal cortex network for recognising frequently repeating stimuli. Neurocomputing, 44-46, pp. 337–342. February 2002. PDF, 48 Kbytes.
Gough, J., Chothia, C., SUPERFAMILY:HMMs representing all proteins of known structure.. Nucl. Acids Res., 30 (1), pp. 268–272. January 2002. No electronic version available.

2001

Teichmann, S.A., Rison, S. C. G., Thornton, J. M., Riley, M., Gough, J., Chothia, C., Small Molecule Metabolism: An Enzyme Mosaic. Trends Biotechnol., 19 (12), pp. 482–486. December 2001. No electronic version available.
Gough, J., Karplus, K., Hughey, R., Chothia, C., Assignment of Homology to Genome Sequences Using a Library of Hidden Markov Models That Represent All Protein of Known Structure. J. Mol. Biol., 313 (4), pp. 903–919. November 2001. No electronic version available.
Rafal Bogacz, Computational models of familiarity discrimination in the perirhinal cortex. PhD thesis. Department of Computer Science, University of Bristol. October 2001. PDF, 926 Kbytes.
Teichmann, S. A., Rison, S. C., Thornton, J. M., Riley, M., Gough, J., Chothia, C., The Evolution and Structural Anatomy of the Small Molecule Metabolic Pathways in Escherichia coli. J Mol Biol, 311 (4), pp. 693–708. August 2001. No electronic version available.
Apic, G., Gough, J., Teichmann, S. A., Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol., 310 (2), pp. 311–325. July 2001. No electronic version available.
Rafal Bogacz, Malcolm W. Brown, Christophe Giraud-Carrier, Emergence of Motion-sensitive Neurons Properties by Learning Sparse Code for Natural Moving Images. Chapter in Advances in Neural Information Processing Systems. Todd K. Leen, Thomas G. Dietterich, Volker Tresp, (eds.). ISBN 0-262-12241-3, pp. 838–844. June 2001. PDF, 153 Kbytes.
Apic, G., Gough, J., Teichmann, S. A., An insight into domain combinations. Bioinformatics, 17 Suppl 1, pp. 83–89. April 2001. No electronic version available.
Rafal Bogacz, Malcolm W, Brown, Christophe Giraud-Carrier, Model of co-operation between recency, familiarity and novelty neurons in the perirhinal cortex. Neurocomputing, 38, pp. 1121–1126. February 2001. PDF, 126 Kbytes.
Rafal Bogacz, Malcolm W. Brown, Christophe Giraud-Carrier, Model of Familiarity Discrimination in the Perirhinal Cortex. Journal of Computational Neuroscience, 10 (1). ISSN 0929-5313, pp. 5–23. January 2001. PDF, 174 Kbytes.

2000

Gough, J., Chothia, C., Karplus, K., Barrett, C., Hughey, R., Currents in Computational Molecular Biology. Chapter in . Miyano, S., Shamir, R., Takagi, T., (eds.), pp. 124–125. December 2000. No electronic version available.
R Bogacz, MW Brown, C Giraud-Carrier, Frequency-based Error Back-propagation in a Cortical Network. Proceedings of the IEEE-INNS-ENNS International Joint Conference on Neural Networks, Vol. II. ISBN 0-7695-0619-4, pp. 211–216. July 2000. PDF, 57 Kbytes.

1999

R. Bogacz, M. W. Brown, C. Giraud-Carrier, High Capacity Neural Networks for Familiarity Discrimination. Proceedings of the Ninth International Conference on Artificial Neural Networks (ICANN99), pp. 773–778. September 1999. PDF, 64 Kbytes.