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Volume 40, Number 2, 2001
Deep computing for the life sciences
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Computational challenges in structural and functional genomics - References

by T. Head-Gordon and J. C. Wooley

Cited references and notes

  1. T. Schlick, “Computational Molecular Biophysics Today: A Confluence of Methodological Advances and Complex Biomolecular Applications,” Journal of Computational Physics 151, No. 1, 1–8 (1999).
  2. T. F. Smith and M. S. Waterman, “Identification of Common Molecular Subsequences,” Journal of Molecular Biology 147, 195–197 (1981).
  3. A. Krogh, M. Brown, I. S. Mian, K. Sjölander, and D. Haussler, “Hidden Markov Models in Computational Biology: Applications to Protein Modeling,” Journal of Molecular Biology 235, No. 5, 1501–1531 (1994).
  4. L. Parida, A. Floratos, and I. Rigoutsos, “An Approximation Algorithm for Alignment of Multiple Sequences Using Motif Discovery,” Journal of Combinatorial Optimization 3, 247–275 (1999).
  5. Y. Sakakibara, M. Brown, R. Hughey, I. S. Mian, K. Sjolander, R. C. Underwood, and D. Haussler, “Stochastic Context-Free Grammars for T-RNA Modeling,” Nucleic Acids Research 22, 5112–5120 (1994).
  6. J. S. Liu and C. E. Lawrence, “Bayesian Inference on Biopolymer Models,” Bioinformatics 15, 38–52 (1999).
  7. L. Grate, M. Herbster, R. Hughey, I. S. Mian, H. Noller, and D. Haussler, “RNA Modeling Using Gibbs Sampling and Stochastic Context-Free Grammars,” Proceedings of the 2nd International Conference on Intelligent Systems for Molecular Biology (1994), pp. 138–146.
  8. M. E. J. Newman and G. T. Barkema, Monte Carlo Methods in Statistical Physics, Oxford University Press, London (1999).
  9. D. Fischer, D. Rice, J. U. Bowie, and D. Eisenberg, “Assigning Amino Acid Sequences to 3-Dimensional Protein Folds,” FASEB Journal 10, 126–136 (1996).
  10. J. U. Bowie, R. Luthy, and D. Eisenberg, “A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure,” Science 253, 164–170 (1991).
  11. M. J. Sippl, “Calculation of Conformational Ensembles from Potentials of Mean Force: An Approach to the Knowledge-Based Prediction of Local Structures in Globular Proteins,” Journal of Molecular Biology 213, 859–883 (1990).
  12. N. N. Alexandrov, R. Nussinov, and R. M. Zimmer, “Fast Protein Fold Recognition via Sequence to Structure Alignment and Contact Capacity Potentials,” Pacific Symposium on Biocomputing, L. Hunter and T. E. Klein, Editors (1996), pp. 53–72.
  13. R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, Cambridge (1998).
  14. S. R. Eddy, “Profile Hidden Markov Models,” Bioinformatics 14, 755–763 (1998).
  15. D. Sankoff and J. B. Kruskal, Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, Addison-Wesley Publishing Co., Reading, MA (1983).
  16. A. Sali and T. L. Blundell, “Definition of General Topological Equivalence in Protein Structures: A Procedure Involving Comparison of Properties and Relationships Through Simulated Annealing and Dynamic Programming,” Journal of Molecular Biology 212, 403–428 (1990).
  17. K. Sjölander, K. Karplus, M. P. Brown, R. Hughey, A. Krogh, I. S. Mian, and D. Haussler, “Dirichlet Mixtures: A Method for Improving Detection of Weak but Significant Protein Sequence Homology,” Computer Applications in the Biosciences 12, 327–345 (1996).
  18. A. Martin, M. MacArthur, and J. Thornton, “Assessment of Comparative Modelling in CASP2,” Proteins: Structure, Functions, and Genetics 29, No. S1, 14–28 (1997).
  19. L. Holm and C. Sander, “Fast and Simple Monte Carlo Algorithm for Side Chain Optimization in Proteins: Application to Model Building by Homology,” Proteins: Structure, Functions, and Genetics 14, 213 (1992).
  20. K. Fidelis, P. Stern, D. Bacon, and J. Moult, “Comparison of Systematic Search and Database Methods for Constructing Segments of Protein Structure,” Protein Engineering 7, 953–960 (1994).
  21. R. Samudrala and J. Moult, “Determinants of Side Chain Conformational Preferences in Protein Structures,” Protein Engineering 11, 991–997 (1998).
  22. M. A. Martí-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, and A. Sali, “Comparative Protein Structure Modeling of Genes and Genomes,” Annual Review of Biophysics and Biomolecular Structure 29, 291–325 (2000).
  23. P. Horton, “A Branch and Bound Algorithm for Local Multiple Alignment,” Proceedings of the Pacific Symposium on Biocomputing, Hawaii, USA, World Scientific Publishing Co., Singapore (1996), pp. 368–383.
  24. R. H. Lathrop and T. F. Smith, “Global Optimum Protein Threading with Gapped Alignment and Empirical Pair Potentials,” Journal of Molecular Biology 255, 641–665 (1996).
  25. R. H. Lathrop, “The Protein Threading Problem with Sequence Amino Acid Interaction Preferences Is NP-Complete,” Protein Engineering 7, 1059–1068 (1994).
  26. H. Flöckner, M. Braxenthaler, P. Lackner, M. Jaritz, M. Ortner, and M. J. Sippl, “Progress in Fold Recognition,” Proteins 23, 376–386 (1995).
  27. Y. Duan and P. A. Kollman, “Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution,” Science 282, 740–744 (1998).
  28. E. Boczko and C. Brooks, “First-Principles Calculation of the Folding Free Energy of a Three-Helix Bundle Protein,” Science 269, 393–396 (1995).
  29. C. Brooks, “Simulations of Protein Folding and Unfolding,” Current Opinion in Structural Biology 8, 222–226 (1998).
  30. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, “A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules,” Journal of the American Chemical Society 117, 5179 (1995).
  31. A. D. MacKerell, Jr., B. Brooks, C. L. Brooks III, L. Nilsson, B. Roux, Y. Won, and M. Karplus, “CHARMM: The Energy Function and Its Parameterization with an Overview of the Program,” The Encyclopedia of Computational Chemistry 1, P. v. R. Schleyer et al., Editors, John Wiley & Sons, Chichester (1998), pp. 271–277.
  32. G. Nemethy, M. S. Pottle, and H. A. Scheraga, “Energy Parameters in Polypeptides, 9. Updating of Geometrical Parameters, Non-Bonding Interactions and Hydrogen Bonding Interactions for Naturally Occurring Amino Acids,” Journal of Physical Chemistry 87, 1883–1887 (1983).
  33. D. M. York, A. Wlodawer, L. G. Pedersen, and T. A. Darden, “Atomic-Level Accuracy in Simulations of Large Protein Crystals,” Proceedings of the National Academy of Sciences (USA) 91, 8715–8718 (1994).
  34. P. Procacci, T. Darden, and M. Marchi, “A Very Fast Molecular Dynamics Method to Simulate Biomolecular Systems with Realistic Electrostatic Interactions,” Journal of Physical Chemistry 100, 10464–10468 (1996).
  35. V. Daggett and M. Levitt, “Protein Folding/Unfolding Dynamics,” Current Opinion in Structural Biology 4, 291–295 (1994).
  36. A. Li and V. Daggett, “Investigation of the Solution Structure of Chymotrypsin Inhibitor 2 Using Molecular Dynamics: Comparison to X-ray Crystallographic and NMR Data,” Protein Engineering 8, 1117–1128 (1995).
  37. J. Moult, “Comparison of Database Potentials and Molecular Mechanics Force Fields,” Current Opinion in Structural Biology 7, 194–199 (1997).
  38. W. Kauzmann, “Some Factors in the Interpretation of Protein Denaturation,” Advances in Protein Chemistry 14, 1–63 (1959).
  39. L. Wesson and D. Eisenberg, “Atomic Solvation Parameters Applied to Molecular Dynamics of Proteins in Solution,” Protein Science 1, 227 (1992).
  40. J. Vila, R. L. Williams, M. Velasquez, and H. A. Scheraga, “Empirical Solvation Models Can Be Used to Differentiate Native from Near-Native Conformations of Bovine Pancreatic Trypsin Inhibitor,” Proteins 10, 199 (1991).
  41. W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, “Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics,” Journal of the American Chemical Society 112, 6127 (1990).
  42. B. Honig, K. A. Sharp, and A.-S. Yang, “Macroscopic Models of Aqueous Solutions: Biological and Chemical Applications,” Journal of Physical Chemistry 97, 1101 (1993).
  43. J. M. Sorenson, G. Hura, A. K. Soper, A. Pertsemlidis, and T. Head-Gordon, “Determining the Role of Hydration Forces in Protein Folding,” invited feature article for Journal of Physical Chemistry B 103, 5413–5426 (1999).
  44. A. Rahman and F. H. Stillinger, “Improved Simulation of Liquid Water by Molecular Dynamics,” Journal of the American Chemical Society 95, 7943 (1973).
  45. See J. Sorenson, G. Hura, R. M. Glaeser, and T. Head-Gordon, “What Can X-ray Scattering Tell Us About the Radial Distribution Functions of Water?” submitted to Journal of Chemical Physics (2000) and references therein.
  46. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans, “Interaction Models for Water in Relation to Protein Hydration,” Intermolecular Forces, B. Pullman, Editor, D. Reidel Publishing Company, Dordrecht (1981), p. 331.
  47. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, “Comparison of Simple Potential Functions for Simulating Liquid Water,” Journal of Chemical Physics 79, 926 (1983).
  48. M. W. Mahoney and W. L. Jorgensen, “A Five-Site Model for Liquid Water and the Reproduction of the Density Anomaly by Rigid, Nonpolarizable Potential Functions,” Journal of Chemical Physics 112, 8910 (2000).
  49. Y.-P. Liu, K. Kim, B. J. Berne, R. A. Friesner, and S. W. Rick, “Constructing Ab Initio Force Fields for Molecular Dynamics Simulations,” Journal of Chemical Physics 108, 4739 (1996).
  50. A. A. Chialvo and P. T. Cummings, “Engineering a Simple Polarizable Model for the Molecular Simulation of Water Applicable over Wide Ranges of State Conditions,” Journal of Chemical Physics 105, 8274 (1996).
  51. G. Corongiu and E. Clementi, “Liquid Water with an Ab Initio Potential-X-ray and Neutron Scattering from 238K to 368K,” Journal of Physical Chemistry 97, 2030–2038 (1992).
  52. I. M. Svishchev, P. G. Kusalik, J. Wang, and R. J. Boyd, “Polarizable Point-Charge Model for Water-Results under Normal and Extreme Conditions,” Journal of Chemical Physics 105, 4742 (1996).
  53. B. Chen, J. Xing, and J. I. Siepmann, “Development of Polarizable Water Force Fields for Phase Equilibrium Calculations,” Journal of Physical Chemistry B 104, 2391 (2000).
  54. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford (1987).
  55. M. F. Crowley, T. A. Darden, T. E. Cheatham III, and D. Deerfield, “Fine- and Coarse-Grain Parallel AMBER and Particle Mesh Ewald on MPP's,” Parallel Computing for Industrial and Scientific Applications, J. Jenness, Editor, Morgan Kaufmann Publishers, San Francisco (1998).
  56. T. E. Cheatham III and B. R. Brooks, “Recent Advances in Molecular Dynamics Simulation Towards Realistic Representation of Biomolecules in Solution,” Theoretical Chemistry Accounts 99, 279–288 (1998).
  57. J. Hoye and G. Stell, “Dielectric Theory for Polar Molecules with Fluctuating Polarizability,” Journal of Chemical Physics 73, 461–468 (1980).
  58. L. R. Pratt, “Effective Field of a Dipole in Non-Polar Polarizable Fluids,” Molecular Physics 40, 347–360 (1980).
  59. J. S. Cao and B. J. Berne, “Theory and Simulation of Polar and Nonpolar Polarizable Fluids,” Journal of Chemical Physics 99, 6998 (1993).
  60. S. J. Stuart and B. J. Berne, “Effects of Polarizability on the Hydration of the Chloride Ion,” Journal of Physical Chemistry 100, 11934–11943 (1999).
  61. G. J. Martyna, “Adiabatic Path Integral Molecular Dynamics Methods. I. Theory,” Journal of Chemical Physics 104, 2018 (1996).
  62. J. S. Cao and G. J. Martyna, “Adiabatic Path Integral Molecular Dynamics Methods. II. Algorithms,” Journal of Chemical Physics 104, 2028 (1996).
  63. H. C. Andersen, “Molecular Dynamics Simulations at Constant Pressure and/or Temperature,” Journal of Chemical Physics 72, 2384–2393 (1980).
  64. R. Car and M. Parrinello, “Unified Approach for Molecular Dynamics and Density-Functional Theory,” Physical Review Letters 55, 2471 (1985).
  65. G. J. Martyna, D. J. Tobias, and M. L. Klein, “Constant Pressure Molecular Dynamics Algorithms,” Journal of Chemical Physics 101, 4177 (1994).
  66. M. E. Tuckerman, G. Martyna, D. J. Tobias, and M. L. Klein, “Explicit Reversible Integrators for Extended Systems Dynamics,” Molecular Physics 87, 1117 (1996).
  67. S. Samuelson, D. J. Tobias, and G. Martyna, “Modern Computational Methodology Applied to the Simulation of Blocked Trialanine Peptide in Vacuo, Water Clusters, and Bulk Water,” Journal of Physical Chemistry 101, 7592 (1997).
  68. M. E. Tuckerman, G. J. Martyna, and B. J. Berne, “Reversible Multiple Time Scale Molecular Dynamics,” Journal of Chemical Physics 97, 1990–2001 (1992).
  69. T. Schlick, E. Barth, and M. Mandziuk, “Biomolecular Dynamics at Long Timesteps: Bridging the Timescale Gap Between Simulation and Experimentation,” Annual Review of Biophysics and Biomolecular Structure 26, 179–220 (1997).
  70. E. Barth and T. Schlick, “Overcoming Stability Limitations in Biomolecular Dynamics: I. Combining Force Splitting via Extrapolation with Langevin Dynamics in LN,” Journal of Chemical Physics 109, 1617–1632 (1998).
  71. E. Barth and T. Schlick, “Extrapolation Versus Impulse in Multiple-Timestepping Schemes: II. Linear Analysis and Applications to Newtonian and Langevin Dynamics,” Journal of Chemical Physics 109, 1632–1642 (1998).
  72. C. Bartels and M. Karplus, “Multidimensional Adaptive Umbrella Sampling: Applications to Main Chain and Side Chain Peptide Conformations,” Journal of Computational Chemistry 18, 1450–1462 (1997).
  73. S. O. Samuelson and G. J. Martyna, “Two Dimensional Umbrella Sampling Techniques for the Computer Simulation Study of Helical Peptides at Thermal Equilibrium: The 3k (i) Peptide in Vacuo and Solution,” Journal of Chemical Physics 109, 11061–11073 (1998).
  74. S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, “Multidimensional Free-Energy Calculations Using the Weighted Histogram Analysis Method,” Journal of Computational Chemistry 16, 1339–1350 (1995).
  75. M. E. Tuckerman and G. J. Martyna, “Understanding Modern Molecular Dynamics: Techniques and Applications,” Journal of Physical Chemistry B 104, 159–178 (2000).
  76. M. Head-Gordon, “Quantum Chemistry and Molecular Processes,” Journal of Physical Chemistry 100, 13213–13225 (1999).
  77. P. M. W. Gill, “Molecular Integrals over Gaussian Basis Functions,” Advances in Quantum Chemistry 25, 141–163 (1994).
  78. C. A. White, B. G. Johnson, P. M. W. Gill, and M. Head-Gordon, “Linear Scaling Density Functional Calculations via the Continuous Fast Multipole Method,” Chemical Physics Letters 253, 268–278 (1996).
  79. L. Greengard and V. Rokhlin, “A Fast Algorithm for Particle Simulations,” Journal of Computational Physics 135, 280–292 (1997).
  80. X.-P. Li, R. W. Nunes, and D. Vanderbilt, “Density-Matrix Electronic-Structure Method with Linear System-Size Scaling,” Physical Review B 47, 10891 (1993).
  81. G. Galli and M. Parrinello, “Large-scale Electronic Structure Calculations,” Physical Review Letters 69, 3547 (1992).
  82. A. D. Becke, “Density-Functional Exchange-Energy Approximation with Correct Asymptotic-Behavior,” Physical Review A 38, 3098–3100 (1988).
  83. J. P. Perdew, J. A. Chaevary, S. H. Vosko, K. A. Jackson, M. R. Pederson, D. J. Singh, and C. Fiolhais, “Atoms, Molecules, Solids, and Surfaces—Applications of the Generalized Gradient Approximation for Exchange and Correlation,” Physical Review B 46, 6671 (1992).
  84. C. Lee, W. Yang, and R. G. Parr, “Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density,” Physical Review B 37, 785–789 (1988).
  85. S. Saeb and P. Pulay, “Local Treatment of Electron Correlation,” Annual Review of Physical Chemistry 44, 213 (1993).
  86. R. J. Bartlett, “Coupled-Cluster Approach to Molecular Structure and Spectra: A Step Toward Predictive Quantum Chemistry,” Journal of Physical Chemistry 93, 1697 (1989).
  87. R. Car and M. Parrinello, “Unified Approach for Molecular Dynamics and Density-Functional Theory,” Physical Review Letters 55, 2471–2474 (1985).
  88. K. Laasonen and M. L. Klein, “Ab Initio Molecular Dynamics Study of Hydrochloric Acid in Water,” Journal of the American Chemical Society 116, 11620 (1994).
  89. K. Laasonen, M. Sprik, M. Parrinello, and R. Car, “Ab Initio Liquid Water,” Journal of Chemical Physics 99, 9080 (1993).
  90. A. Monge, E. J. P. Lathrop, J. R. Gunn, P. S. Shenkin, and R. A. Friesner, “Computer Modeling of Protein Folding: Conformational and Energetic Analysis of Reduced and Detailed Protein Models,” Journal of Molecular Biology 239, 995–1012 (1995).
  91. K. Yue, K. M. Fiebig, P. D. Thomas, H. S. Chan, E. I. Shakhnovich, and K. A. Dill, “A Test of Lattice Protein Folding Algorithms,” Proceedings of the National Academy of Sciences (USA) 92, 325–329 (1995).
  92. F. H. Stillinger, “Diffusion Smoothing,” Physical Review B 32, 3134–3141 (1985).
  93. J. Kostrowicki and H. A. Scheraga, “Application of the Diffusion Equation for Global Optimization to Oligopeptides,” Journal of Physical Chemistry 96, 7442–7449 (1992).
  94. D. Shalloway, “Application of the Renormalization Group to Deterministic Global Minimization of Molecular Conformation Energy Functions,” Journal of Global Optimization 2, 281–311 (1992).
  95. A. Roitberg and R. Elber, “Modeling Sidechains in Peptides and Proteins: Application of the Locally Enhanced Sampling and the Simulated Annealing Methods to Find Minimum Energy Conformations,” Journal of Chemical Physics 95, 9277–9287 (1991).
  96. C. A. Laughton, “A Study of Simulated Annealing Protocols for Use with Molecular Dynamics in Protein Structure Prediction,” Protein Engineering 7, 235–241 (1994).
  97. S. M. Legrand and K. M. Merz, “The Genetic Algorithm and the Conformational Search of Polypeptides and Proteins,” Molecular Simulation 13, 299–320 (1994).
  98. Z. Li and H. A. Scheraga, “Monte-Carlo-Minimization Approach to the Multiple Minima Problem in Protein Folding,” Proceedings of the National Academy of Sciences (USA) 84, 6611–6615 (1987).
  99. R. E. Bruccoleri, “Application of Systematic Conformational Search to Protein Modeling,” Molecular Simulations 10, 151–174 (1993).
  100. R. Abagyan and M. Totrov, “Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins,” Journal of Molecular Biology 235, 938–1002 (1994).
  101. T. Head-Gordon, J. Arrecis, and F. H. Stillinger, “A Strategy for Finding Classes of Minima on a Hypersurface: Implications for Approaches to the Protein Folding Problem,” Proceedings of the National Academy of Sciences (USA) 88, 11076–11080 (1991).
  102. T. Head-Gordon and F. H. Stillinger, “Predicting Polypeptide and Protein Structures from Amino Acid Sequence: Antlion Method Applied to Melittin,” Biopolymers 33, 293–303 (1993).
  103. S. Crivelli, T. M. Philip, R. Byrd, E. Eskow, R. Schnabe, R. C. Yu, and T. Head-Gordon, “A Global Optimization Strategy for Predicting alpha-Helical Protein Tertiary Structure,” Computers & Chemistry 24, Nos. 3–4, 489–497 (2000).
  104. J. M. Blaney and J. S. Dixon, “A Good Ligand Is Hard to Find: Automated Docking Method,” Perspectives in Drug Discovery and Design 1, 301–319 (1993).
  105. I. D. Kuntz, E. C. Meng, and B. K. Shoichet, “Structure-Based Molecular Design,” Accounts of Chemical Research 27, 117–123 (1994).
  106. T. P. Lybrand, “Ligand-Protein Docking and Rational Drug Design,” Current Opinion in Structural Biology 5, 224–228 (1995).
  107. M. Totrov and R. Abagyan, “Flexible Protein-Ligand Docking by Global Energy Optimization in Internal Coordinates,” Proteins: Structure, Function, and Genetics, Supplement 1, 215–220 (1997).
  108. T. J. A. Ewing and I. D. Kuntz, “Critical Evaluation of Search Algorithms for Automated Molecular Docking and Database Screening,” Journal of Computational Chemistry 18, 1175–1189 (1997).
  109. D. M. Lorber and B. K. Shoichet, “Flexible Ligand Docking Using Conformational Ensembles,” Protein Science 7, 938–950 (1998).
  110. A. Canning, A. De Vita, G. Galli, F. Gygi, F. Mauri, and R. Car, “Quantum Molecular Dynamics on Massively Parallel Computers,” Cray User Group Fall Proceedings, Tours, France (1994), p. 18.
  111. NWChem: A Computational Chemistry Package for Parallel Computers, Version 3.3.1, High Performance Computational Chemistry Group, Pacific Northwest National Laboratory, Richland, WA (1998).
  112. G. Kresse and J. Furthmüller, “Efficiency of Ab-Initio Total Energy Calculations for Metals and Semiconductors Using a Plane-Wave Basis Set,” Computational Material Science 6, 15–50 (1996).
  113. G. Kresse and J. Furthmüller, “Efficient Iterative Schemes for Ab Initio Total-Energy Calculations Using a Plane-Wave Basis Set,” Physical Review B 54, 11169–11186 (1996).
  114. A. Arkin, J. Ross, and H. H. McAdams, “Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage-Infected Escherichia Coli Cells,” Genetics 149, 1633–1648 (1998).
  115. H. H. McAdams and A. Arkin, “It's a Noisy Business! Genetic Regulation at the Nanomolar Scale,” Trends in Genetics 15, 65–69 (1999).
  116. H. H. McAdams and A. Arkin, “Towards a Circuit Engineering Discipline,” Current Biology 10, 318–320 (2000).
  117. H. H. McAdams and A. Arkin, “Simulation of Prokaryotic Genetic Circuits,” Annual Review of Biophysics and Biomolecular Structure 27, 199–224 (1998).
  118. M. Ehlde and G. Zacchi, “Mist: A User-Friendly Metabolic Simulator,” Computer Applications in the Biosciences (1995).
  119. P. Mendes, “GEPASI: A Software Package for Modelling the Dynamics, Steady States and Control of Biochemical and Other Systems,” Computer Applications in the Biosciences 9, 563–571 (1993).
  120. H. H. McAdams and L. Shapiro, “Circuit Simulation of Genetic Networks,” Science 269, 650–656 (1995).
  121. R. Somogyi and C. A. Sniegoski, “Modeling the Complexity of Genetic Networks: Understanding Multigenic and Pleiotropic Regulation,” Complexity 1, 45–63 (1996).
  122. T. Gaasterland, “Structural Genomics: Bioinformatics in the Driver's Seat,” Nature Biotechnology 16, 625–627 (1998).