Bibliography for MSc Bioinformatics 2006



 In  Bold with *  are simple articles of didactical relevance (or good reviews)!

Cell theory:
Historical Reviews
A unifying concept: the history of cell theory,  P. Mazzarello, Nature Cell Biology, 1, E13-15 (1999)

A Long Twentieth Century of Review the Cell Cycle and BeyondNurse P., Cell 100(1): 71–8 (2000)

The Incredible Life and Times of Biological Cells,  P. Nurse, Science 289: 1711-1716 (2000).
Deterministic Modelling
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory ..., Tyson et al., Curr. Opin. Cell Biol. 15:221 (2003)

Network dynamics and cell physiology., Tyson et al.,, Nat Rev Mol Cell Biol. 2(12):908-16. (2001)
*A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM. Biophys. J. 77:2411-2417.
Quantifying the dynamics of  prion infection: a bifurcation analysis of Laurent's model, Porcher & Gatto, J. Theor. Biol. 205, 283 (2000)
Prion infection dynamics. Nowak MA, DC Krakauer, A Klug, RM May,  Integr Biol 1:3-15, (1998).
Biological switches
How to make a Biological Switch, J. L. Cherry, FR. Adler, J. Theor. Biol., 203, 117--133  (2000).
SWITCHES IN BACTERIOPHAGE LAMBDA DEVELOPMENT, Oppenheim et al. , Annu. Rev. Genet. 39:409-29 (2005)
Building a cellular switch: more lessons from a good egg, Ferrell, J. Bioessays, 21, 866
*Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible, Ferrell, J. Chaos 11(1), 227 (2001)
*Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs, Ferrell, J. TIBS 21, 460 (1996)
*Multistability: a major means of differentiation and evolution in biological systems, Laurent & Kellershohn, TIBS 24, 418 (1999)
*Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems, Smolen et al. AJP -Cell Phys. 274, 531 (1998)
*COMPUTATIONAL STUDIES OF GENE REGULATORY NETWORKS: IN NUMERO MOLECULAR BIOLOGY,
Hasty et al. , Nature Rev. Genetics 2, 268 (2001)
Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Sha, W., Moore, J., Chen, K., Lassaletta, A.D., Yi, C.-S., Tyson, J.J. and Sible, J.C. (2003). Proc. Natl. Acad. Sci. USA 100:975-980.
The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes, Ferrell, Jr., J.E. and Machleder, E.M., (1998), Science 280, pp. 895--898.
Population & Cell Cycle
A model combining cell physiology and population genetics to explain Escherichia coli laboratory evolution, M. Graña & L. Acerenza, BMC Evolutionary Biology , 1:12  (2001)
Noise / Stochasticity in Biological Systems:
models and analysis
Control, exploitation and tolerance of intracellular noise. Rao et al. Nature. 2003 Jan 9;421(6919):190.
It's a noisy business! Genetic regulation at the nanomolar scale. McAdams HH, Arkin A. Trends Genet. 1999 Feb;15(2):65-9.
Noise-based switches and amplifiers for gene expression. Hasty et al. Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2075-80

Noise-induced cooperative behavior in a multicell system. Chen et al. Bioinformatics 2005 21(11):2722-2729
Mechanisms of noise-resistance in genetic oscillators.Vilar et al. PNAS vol. 99 ( 9) 5988 (2002)

Modeling a synthetic multicellular clock: Repressilators coupled ... Garcia-Ojalvo et al. PNAS 101(30), 10955 (2004)

Stochasticity in Transcriptional regulation: origins, consequences, and Mathematical Representations, Kepler & Elston, Bioph. J. 81, 3116 (2001)

Modeling stochastic gene expression: Implications for haploinsufficiency, Cook et al. PNAS 95(26): 15641 (1998)

Going the Distance: A Current View of Enhancer Action, Blackwood & Kadonaga Science 281 (5373), 60 (1998)

Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets, Goss & Peccoud PNAS 95 (12), 6750 (1998)
The Art of the Probable: System Control in the Adaptive Immune System, Germain, R. N. Science 293 (5528), 240 (2001)
Signaling in Small Subcellular Volumes. I. Stochastic and Diffusion Effects on Individual Pathways, Bhalla, Bioph. J. 87(2): 733 (2004)

Stochastic Regulation in Early Immune Response, Lipniacki et al. Bioph. J. 90(3): 725 (2006)

Stochastic mechanisms in gene expression. McAdams &Arkin, PNAS 94(3):814 (1997)

Probabilistic behavior
in Biological Systems: examples
Differentiation in mouse melanoma cells: initial reversibility and an on-off stochastic model. Bennett, D. C. , Cell. 1983 Sep;34(2):445-53.
The expression of liver-specific genes within rat embryonic hepatocytes is a discontinuous process. Dingemanse et al. Differentiation 56(3), 153 (1994)
Enhancers Increase the Probability But not the Level of Gene Expression, Walters et al. PNAS 92, 7125 (1995)

A Binary Mechanism for the Selective Action of a Pancreatic beta -Cell Transcriptional Silencer, Viswnatah et al. J. Biol. Chem. 275(51): 40273 (2002)
Control of Stochasticity in Eukaryotic Gene Expression, Raser & O'Shea, Science 304 (5678),  1811 (2004)

Prediction and measurement of an autoregulatory genetic module
Bibliography for MSc Bioinformatics 2006, Isaacs et al. PNAS 100(13), 7714 (2003)
(Simple) Deterministic Versus Stochastic
Two Examples of Deterministic versus Stochastic Modeling of Chemical Reactions, Mira et al., J. Chem. Education 80(12), 1488 (2003) Abstract

Exact Stochastic Simulation of Coupled Chemical Reactions, D. Gillespie, J. Phys. Chem., 81:2340, 1977.
Stochastic: Gillespie

Stochastic kinetic analysis of developmental pathway bifurcation in phage l-infected Escherichia coli cells, Arkin et al. Genetics 149, 1633 (1998)

Bridging the Gap between Stochastic and Deterministic Regimes in the kinetic simulations of the biochemical reaction networks, Puchalka & Kierzek, Biophysical Journal 86:1357-1372 (2004)

Modeling and simulation of biological systems with stochasticity, Meng et al. In Silico Biology 4, 0024 (2004

Predicting Temporal Fluctuations in an Intracellular Signalling  Pathway, Morton-FIirth & Bray, J. Thoer. Biol. 192, 117 (1998)

Transition from Stochastic to Deterministic Behaviour in Calcium Oscillations , Kummer et al. Biophysical Journal 89:1603-1611 (2005)
Pattern formation: Simple
Spatial pattern formation in chemical and biological systems , Maini et al. J. Chem. Soc. 93 (20), 3601 (1997)
Other reviews:


Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis Grossman AD Annual Review of Genetics 29: 477 (1995)