| | Book Review Review of "Systems Biology in Practice" by Edda Klipp, Ralf Hertwig, Axel Kowald, Christoph Wierling and Hans Lehrach Paul S Agutter Theor Biol Med Model. 2005; 2: 34. Published online 2005 August 26. doi: 10.1186/1742-4682-2-34.PMCID: PMC1215524 Commentaries The complexity of anatomical systems Fabio Grizzi and Maurizio Chiriva-Internati Theor Biol Med Model. 2005; 2: 26. Published online 2005 July 19. doi: 10.1186/1742-4682-2-26.PMCID: PMC1180857 Uncertainty principle of genetic information in a living cell Pierluigi Strippoli, Silvia Canaider, Francesco Noferini, Pietro D'Addabbo, Lorenza Vitale, Federica Facchin, Luca Lenzi, Raffaella Casadei, Paolo Carinci, Maria Zannotti, and Flavia Frabetti Theor Biol Med Model. 2005; 2: 40. Published online 2005 September 30. doi: 10.1186/1742-4682-2-40.PMCID: PMC1262781 Comment on and reply to "Analysis of variation of amplitudes in cell cycle gene expression" by Liu, Gaido and Wolfinger: On the analysis of gene expression during the normal, eukaryotic, cell cycle Stephen Cooper Theor Biol Med Model. 2005; 2: 47. Published online 2005 November 18. doi: 10.1186/1742-4682-2-47.PMCID: PMC1298338 Editorial A new journal – "Theoretical Biology and Medical Modelling" Denys N Wheatley Theor Biol Med Model. 2005; 2: 21. Published online 2005 June 12. doi: 10.1186/1742-4682-2-21.PMCID: PMC1156957 Research Human embryonal epithelial cells of the developing small intestinal crypts can express the Hodgkin-cell associated antigen Ki-1 (CD30) in spontaneous abortions during the first trimester of gestation Demetrio Tamiolakis, John Venizelos, Maria Lambropoulou, Silva Nikolaidou, Sophia Bolioti, Maria Tsiapali, Dionysios Verettas, Panagiotis Tsikouras, Athanasios Chatzimichail, and Nikolas Papadopoulos Theor Biol Med Model. 2005; 2: 1. Published online 2005 January 11. doi: 10.1186/1742-4682-2-1.PMCID: PMC546234 Construction of predictive promoter models on the example of antibacterial response of human epithelial cells Ekaterina Shelest and Edgar Wingender Theor Biol Med Model. 2005; 2: 2. Published online 2005 January 12. doi: 10.1186/1742-4682-2-2.PMCID: PMC546226 In vitro bioassay as a predictor of in vivo response Ross Barnard and Konstantin G Gurevich Theor Biol Med Model. 2005; 2: 3. Published online 2005 February 7. doi: 10.1186/1742-4682-2-3.PMCID: PMC549212 Single cell studies of the cell cycle and some models JM Mitchison Theor Biol Med Model. 2005; 2: 4. Published online 2005 February 9. doi: 10.1186/1742-4682-2-4.PMCID: PMC550673 Propagated repolarization of simulated action potentials in cardiac muscle and smooth muscle Nicholas Sperelakis, Lakshminarayanan Ramasamy, and Bijoy Kalloor Theor Biol Med Model. 2005; 2: 5. Published online 2005 February 14. doi: 10.1186/1742-4682-2-5.PMCID: PMC550671 Volume-based non-continuum modeling of bone functional adaptation Zhengyuan Wang and Adrian Mondry Theor Biol Med Model. 2005; 2: 6. Published online 2005 February 28. doi: 10.1186/1742-4682-2-6.PMCID: PMC553991 High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study Aswin Sai Narain Seshasayee Theor Biol Med Model. 2005; 2: 7. Published online 2005 March 11. doi: 10.1186/1742-4682-2-7.PMCID: PMC555740 The quantitation of buffering action I. A formal & general approach Bernhard M Schmitt Theor Biol Med Model. 2005; 2: 8. Published online 2005 March 15. doi: 10.1186/1742-4682-2-8.PMCID: PMC1079953 The quantitation of buffering action II. Applications of the formal & general approach Bernhard M Schmitt Theor Biol Med Model. 2005; 2: 9. Published online 2005 March 16. doi: 10.1186/1742-4682-2-9.PMCID: PMC1079954 The Estradiol-Dihydrotestosterone model of prostate cancer A Edward Friedman Theor Biol Med Model. 2005; 2: 10. Published online 2005 March 18. doi: 10.1186/1742-4682-2-10.PMCID: PMC1079949 A topological model of biofeedback based on catecholamine interactions Tapas K Basak, Suman Halder, Madona Kumar, Renu Sharma, and Bijoylaxmi Midya Theor Biol Med Model. 2005; 2: 11. Published online 2005 March 21. doi: 10.1186/1742-4682-2-11.PMCID: PMC1079950 Tyrosine phosphorylation of myosin heavy chain during skeletal muscle differentiation: an integrated bioinformatics approach DF Harney, RK Butler, and RJ Edwards Theor Biol Med Model. 2005; 2: 12. Published online 2005 March 25. doi: 10.1186/1742-4682-2-12.PMCID: PMC1079951 Mathematical model of blunt injury to the vascular wall via formation of rouleaux and changes in local hemodynamic and rheological factors. Implications for the mechanism of traumatic myocardial infarction Rovshan M Ismailov Theor Biol Med Model. 2005; 2: 13. Published online 2005 March 30. doi: 10.1186/1742-4682-2-13.PMCID: PMC1079952 Hyperbolastic growth models: theory and application Mohammad Tabatabai, David Keith Williams, and Zoran Bursac Theor Biol Med Model. 2005; 2: 14. Published online 2005 March 30. doi: 10.1186/1742-4682-2-14.PMCID: PMC1084364 Location of DNA damage by charge exchanging repair enzymes: effects of cooperativity on location time Kasper Astrup Eriksen Theor Biol Med Model. 2005; 2: 15. Published online 2005 April 8. doi: 10.1186/1742-4682-2-15.PMCID: PMC1142343 Breakdown of accommodation in nerve: a possible role for persistent sodium current Kristian Hennings, Lars Arendt-Nielsen, and Ole K Andersen Theor Biol Med Model. 2005; 2: 16. Published online 2005 April 12. doi: 10.1186/1742-4682-2-16.PMCID: PMC1090618 An ETP model (exclusion-tolerance-progression) for multi drug resistance Subburaj Kannan Theor Biol Med Model. 2005; 2: 17. Published online 2005 April 27. doi: 10.1186/1742-4682-2-17.PMCID: PMC1131929 Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition Yoichi Nakayama, Ayako Kinoshita, and Masaru Tomita Theor Biol Med Model. 2005; 2: 18. Published online 2005 May 9. doi: 10.1186/1742-4682-2-18.PMCID: PMC1142344 Quantification of the glycogen cascade system: the ultrasensitive responses of liver glycogen synthase and muscle phosphorylase are due to distinctive regulatory designs Vivek K Mutalik and KV Venkatesh Theor Biol Med Model. 2005; 2: 19. Published online 2005 May 20. doi: 10.1186/1742-4682-2-19.PMCID: PMC1180476 Promoter addresses: revelations from oligonucleotide profiling applied to the Escherichia coli genome Karthikeyan Sivaraman, Aswin Sai Narain Seshasayee, Krishnakumar Swaminathan, Geetha Muthukumaran, and Gautam Pennathur Theor Biol Med Model. 2005; 2: 20. Published online 2005 May 31. doi: 10.1186/1742-4682-2-20.PMCID: PMC1166578 The ups and downs of biological timers Noa Rappaport, Shay Winter, and Naama Barkai Theor Biol Med Model. 2005; 2: 22. Published online 2005 June 20. doi: 10.1186/1742-4682-2-22.PMCID: PMC1208956 Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach Anne-Laure Boulesteix and Korbinian Strimmer Theor Biol Med Model. 2005; 2: 23. Published online 2005 June 24. doi: 10.1186/1742-4682-2-23.PMCID: PMC1182396 Identification and isolation of embryonic stem cells in reproductive endocrinology: theoretical protocols for conservation of human embryos derived from in vitro fertilization Eric Scott Sills, Takumi Takeuchi, Noriko Tanaka, Queenie V Neri, and Gianpiero D Palermo Theor Biol Med Model. 2005; 2: 25. Published online 2005 July 18. doi: 10.1186/1742-4682-2-25.PMCID: PMC1185568 Statistical distribution of blood serotonin as a predictor of early autistic brain abnormalities Skirmantas Janušonis Theor Biol Med Model. 2005; 2: 27. Published online 2005 July 19. doi: 10.1186/1742-4682-2-27.PMCID: PMC1199627 Modelling of oedemous limbs and venous ulcers using partial differential equations Hassan Ugail and Michael J Wilson Theor Biol Med Model. 2005; 2: 28. Published online 2005 August 3. doi: 10.1186/1742-4682-2-28.PMCID: PMC1198260 The fractal geometry of nutrient exchange surfaces does not provide an explanation for 3/4-power metabolic scaling Page R Painter Theor Biol Med Model. 2005; 2: 30. Published online 2005 August 11. doi: 10.1186/1742-4682-2-30.PMCID: PMC1226149 Allometric scaling of the maximum metabolic rate of mammals: oxygen transport from the lungs to the heart is a limiting step Page R Painter Theor Biol Med Model. 2005; 2: 31. Published online 2005 August 11. doi: 10.1186/1742-4682-2-31.PMCID: PMC1236962 On the number of founding germ cells in humans Chang-Jiang Zheng, E Georg Luebeck, Breck Byers, and Suresh H Moolgavkar Theor Biol Med Model. 2005; 2: 32. Published online 2005 August 24. doi: 10.1186/1742-4682-2-32.PMCID: PMC1215522 Possible Cis-acting signal that could be involved in the localization of different mRNAs in neuronal axons Gonzalo E Aranda-Abreu, Ma Elena Hernández, Abraham Soto, and Jorge Manzo Theor Biol Med Model. 2005; 2: 33. Published online 2005 August 24. doi: 10.1186/1742-4682-2-33.PMCID: PMC1215523 Nucleic acid chaperons: a theory of an RNA-assisted protein folding Jan C Biro Theor Biol Med Model. 2005; 2: 35. Published online 2005 September 1. doi: 10.1186/1742-4682-2-35.PMCID: PMC1232867 Boundary effects influence velocity of transverse propagation of simulated cardiac action potentials Nicholas Sperelakis, Bijoy Kalloor, and Lakshminarayanan Ramasamy Theor Biol Med Model. 2005; 2: 36. Published online 2005 September 6. doi: 10.1186/1742-4682-2-36.PMCID: PMC1236963 A comparative study of a theoretical neural net model with MEG data from epileptic patients and normal individuals A Kotini, P Anninos, AN Anastasiadis, and D Tamiolakis Theor Biol Med Model. 2005; 2: 37. Published online 2005 September 7. doi: 10.1186/1742-4682-2-37.PMCID: PMC1236964 Targeting MDM2 by the small molecule RITA: towards the development of new multi-target drugs against cancer L Michel Espinoza-Fonseca Theor Biol Med Model. 2005; 2: 38. Published online 2005 September 20. doi: 10.1186/1742-4682-2-38.PMCID: PMC1243243 Volume of the effect compartment in simulations of neuromuscular block Vladimir Nigrovic, Johannes H Proost, Anton Amann, and Shashi B Bhatt Theor Biol Med Model. 2005; 2: 41. Published online 2005 October 3. doi: 10.1186/1742-4682-2-41.PMCID: PMC1262782 Hybrid dynamic/static method for large-scale simulation of metabolism Katsuyuki Yugi, Yoichi Nakayama, Ayako Kinoshita, and Masaru Tomita Theor Biol Med Model. 2005; 2: 42. Published online 2005 October 4. doi: 10.1186/1742-4682-2-42.PMCID: PMC1262783 Modeling the signaling endosome hypothesis: Why a drive to the nucleus is better than a (random) walk Charles L Howe Theor Biol Med Model. 2005; 2: 43. Published online 2005 October 19. doi: 10.1186/1742-4682-2-43.PMCID: PMC1276819 A mathematical model of the euglycemic hyperinsulinemic clamp Umberto Picchini, Andrea De Gaetano, Simona Panunzi, Susanne Ditlevsen, and Geltrude Mingrone Theor Biol Med Model. 2005; 2: 44. Published online 2005 November 3. doi: 10.1186/1742-4682-2-44.PMCID: PMC1291408 Supply-demand balance in outward-directed networks and Kleiber's law Page R Painter Theor Biol Med Model. 2005; 2: 45. Published online 2005 November 10. doi: 10.1186/1742-4682-2-45.PMCID: PMC1325050 Analysis of variation of amplitudes in cell cycle gene expression Delong Liu, Kevin W Gaido, and Russ Wolfinger Theor Biol Med Model. 2005; 2: 46. Published online 2005 November 11. doi: 10.1186/1742-4682-2-46.PMCID: PMC1315354 Repolarization of the action potential enabled by Na+ channel deactivation in PSpice simulation of cardiac muscle propagation Lakshminarayanan Ramasamy and Nicholas Sperelakis Theor Biol Med Model. 2005; 2: 48. Published online 2005 December 12. doi: 10.1186/1742-4682-2-48.PMCID: PMC1326226 A Global Workspace perspective on mental disorders Rodrick Wallace Theor Biol Med Model. 2005; 2: 49. Published online 2005 December 21. doi: 10.1186/1742-4682-2-49.PMCID: PMC1343591 Reviews Vasculature deprivation – induced osteonecrosis of the rat femoral head as a model for therapeutic trials Jacob Bejar, Eli Peled, and Jochanan H Boss Theor Biol Med Model. 2005; 2: 24. Published online 2005 July 5. doi: 10.1186/1742-4682-2-24.PMCID: PMC1208957 Three subsets of sequence complexity and their relevance to biopolymeric information David L Abel and Jack T Trevors Theor Biol Med Model. 2005; 2: 29. Published online 2005 August 11. doi: 10.1186/1742-4682-2-29.PMCID: PMC1208958 Data from necropsy studies and in vitro tissue studies lead to a model for allometric scaling of basal metabolic rate Page R Painter Theor Biol Med Model. 2005; 2: 39. Published online 2005 September 27. doi: 10.1186/1742-4682-2-39.PMCID: PMC1262780 Neurogenetic interactions and aberrant behavioral co-morbidity of attention deficit hyperactivity disorder (ADHD): dispelling myths David E Comings, Thomas JH Chen, Kenneth Blum, Julie F Mengucci, Seth H Blum, and Brian Meshkin Theor Biol Med Model. 2005; 2: 50. Published online 2005 December 23. doi: 10.1186/1742-4682-2-50.PMCID: PMC1352384 |