Below is a non-exhaustive sample list of papers relevant to the themes in the Complexity and information-theoretic approaches to biology stream ---------------------------------------------------------- at the 3rd Pacific Symposium on BioComputing, Maui, HI, Jan. 1998. ------------------------------------- D L Dowe, L Allison, T I Dix, L Hunter, C S Wallace and T Edgoose (1996): Circular clustering of protein dihedral angles by Minimum Message Length, First Pacific symposium on biocomputing (PSB-1), Hawaii, U.S.A., pp 242-55 (1996). D. L. Dowe, G. E. Farr, A. J. Hurst and K. L. Lentin (1996): "Information-theoretic football tipping", in N. de Mestre (ed.), 3rd Conference on Mathematics and Computers in Sport, Bond University, Qld, Australia, 233-241, 1996. D L Dowe, J J Oliver, T I Dix, L Allison and C S Wallace (1993): A decision graph explanation of protein secondary structure prediction, Proc. 26th Hawaii Int. Conf. on System Sciences (HICSS-26), Hawaii, Vol. 1, pp669-678 (1993). Prank K, Nowlan SJ, Harms HM, Kloppstech M, Brabant G, Hesch RD, Sejnowski TJ. Time series prediction of plasma hormone concentration: Evidence for differences in predictability of parathyroid hormone secretion between osteoporotic patients and normal controls. Journal of Clinical Investigation 95:2910-2919 (1995). Prank K, Kloppstech M, Nowlan SJ, Sejnowski TJ, Brabant G. Self-Organized segmentation of time series: Separating growth hormone secretion in acromegaly from normal controls. Biophysical Journal 70:2540-2547 (1996a). Prank K, Kloppstech M, Nowlan SJ, Sejnowski TJ, Brabant G. Random secretion of growth hormone in humans. Physical Review Letters 77:1909-1911 (1996b). Prank K, Wagner M, Brabant G. Algorithmic complexity of growth hormone release in humans. In: Biocomputing, Proceedings of the 1997 Pacific Symposium, eds. Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein, World Scientifc, Singapore, pp. 352-360 (1996c). Garnier-Osguthorpe-Robson, GOR method of protein secondary structure prediction. K. Yamanishi, Proc. 26th Hawaii Int. Conf. on System Sciences (HICSS-26), Hawaii, Vol. 1, 1993. D. M. Platt and T. I. Dix, A model for comparing genomic restriction maps, Proc. 28th Hawaii Int. Conf. on System Sciences (HICSS-28), Vol 1, pp24-31, 1995. D. M. Platt and T. I. Dix, Stochastic assembly of Contig restriction maps, Proc. 28th Hawaii Int. Conf. on System Sciences (HICSS-28), Vol 1, pp155-164, 1995. L. Allison and C. S. Wallace (e.g., J. Mol. Ev., 1994) on string alignment. Konagaya, A, Kondou, H. Stochastic motif extraction using a genetic algorithm with the MDL principle. HICSS-26, 746-755 (1993). Mainen ZF, Sejnowski TJ. Influence of dentritic structure on firing pattern in model neocortical neurons. Nature 382:363-366 (1996). Malinow R, Mainen ZF. Long-term potentiation in the CA1 hippocampus. Science 271:1604-1605 (1996). Mainen ZF, Joerges J, Huguenard JR, Sejnowski TJ. A model of spike initiation in neocortical pyramidal neurons. Neuron 15:1427-1439 (1995). Mainen ZF, Sejnowski TJ. Reliability of spike timing in neocortical neurons. Science 268:1503-1506 (1995). Gabbiani F, Koch C. Coding of time-varying signals in spike trains of intergrate-and-fire neurons with random threshold. Neural Computation 8:44-66 (1996). Gabbiani F, Metzner W, Wessel R, Koch C. From stimulus encoding to feature extraction in weakly electric fish. Nature 384:564-567 (1996). Mamitsuka, H, Yamanishi, K. Protein alpha-Helix region prediction based on stochastic-rule learning. HICSS-26, 659-668 (1993). Milosavljevic, A. and Jurka, J., "Discovering simple DNA sequences by the algorithmic significance method", Computer Applications in the Biosciences, vol. 9, no. 4, 1993, pp 407-411. Rapp PE, Zimmerman ID, Vining EP, Cohen N, Albano AM, Jimenez-Montano MA. The algorithmic complexity of neural spike trains increases during focal seizures. The Journal of Neurosciences 14:4731-4739 (1994). Rieke F, Warland D, van Steveninck RRD, Bialek W. Spikes: Exploring the neural code, MIT Press, Cambridge, MA (1996). Rivals, E. and Delgrange, O. and Delahaye, J.-P. and Dauchet, M. and Delorme, M.-O. and H{`e}naut, A. and Ollivier, E., "Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in {D}{N}{A} sequences", Computer Applications in the Biosciences, vol. 13, issue 2, pp 131-136, 1997. Solomonoff, R.J., "A formal theory of inductive inference", Information and Control, vol. 7, pp 1-22, 224-254, 1964. Kolmogorov, A.N., "Three approaches to the quantitative definition of information", Problems of Information Transmission, vol. 1, pp 4-7, 1965. Chaitin, G.J., On the Length of Programs for Computing Finite Sequences, Journal of the Association for Computing Machinery, vol. 13, pp 547-549, 1966. Wallace C.S. & Boulton, D.M., `An Information Measure for Classification', Computer Journal, Vol.11, No.2, 1968, pp185-194. Akaike, H., "Information Theory and an extension of the maximum likelihood principle", in Petrov, B.N. and Csaki, F. (ed.), Proceedings of the 2nd International Symposium on Information Theory, 1973, pp 267-281, J. J. Rissanen, "Modeling by shortest data description", Automatica, vol. 14, 1978, pp 465-471. A. Arkin (Stanford), "Computation in genetic networks", ICOBIP '97 (International Conference on Biological Information Processing, http://sun1.rrzn-user.uni-hannover.de/~ndxdendo/ICOBIP97.html). T.J. Sejnowski (San Diego), "Timing in cortical information processing", ICOBIP '97 (International Conference on Biological Information Processing, http://sun1.rrzn-user.uni-hannover.de/~ndxdendo/ICOBIP97.html). As above, this sample list is non-exhaustive. ^^^^^^ ^^^^^^^^^^^^^^ For more information on the "Complexity and information-theoretic approaches to biology" stream, see http://www.cs.monash.edu.au/~dld/PSB-3/PSB-3.Info.CFPs.html (or e-mail Dr. David Dowe, dld@cs.monash.edu.au or Dr. Klaus Prank, ndxdpran@rrzn-user.uni-hannover.de ). For more information on the "3rd Pacific Symposium on BioComputing conference" (PSB-3, 1998), see http://www.cgl.ucsf.edu:80/psb/psb.html .