L Mirny:

Tafvizi A, Huang F, Leith JS, Fersht AR, Mirny LA, van Oijen AM. Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability. Biophysical Journal, 95, L01-L03 (2008).

Rahi SJ, Virnau P, Mirny LA, Kardar M. Predicting Transcription Factor Specificity with All-Atom Models. Nucleic Acids Res, 36, 6209-17 (2008).

Wunderlich Z, Mirny LA. Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Res (2008) (in press).

Kolesov G*, Wunderlich Z*, Laikova ON, Gelfand MS, Mirny LA. How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci. 104,13948-53 (2007).

Kolesov G, Virnau P, Kardar M, Mirny LA. Protein knot server: detection of knots in protein structures. Nucleic Acids Res (2007).

Galan-Caridad JM, Harel S, Arenzana TL, Hou ZE, Doetsch FK, Mirny LA, Reizis B. Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Cell 129, 345-57 (2007).

Levine, J., H. Y. Kueh, L. A. Mirny. Instrinsic Flutuations, Robustness, and Tunability in Signaling Cascades. Biophys J 92, 4473-81 (2007).

Gomez-Uribe, C., G. C. Verghese, L. A. Mirny. Operating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering. PLoS Computational Biology . (2007). Supplementary Information

Virnau, P., Mirny, L. A. & Kardar, M. Intricate knots in proteins: function and evolution. PLoS Comput Biol 2, e122 (2006).

Wunderlich, Z., Mirny L.A. Using Topology of the Metabolic Network to Predict Viability of Mutant Strains. Biophysical Journal 91, 2304-11 (2006).

Spirin, V., Gelfand, M.S., Mironov, A.A, Mirny LA. A metabolic network in the evolutionary context: Multiscale structure and modularity. Proc Natl Acad Sci 23, 8774-9 (2006).

Donald, J. E., Hubner, I. A., Rotemberg, V. M., Shakhnovich, E. I. & Mirny, L. A. CoC: a database of universally conserved residues in protein folds. Bioinformatics 21, 2539-2540 (2005).

Slutsky, M. & Mirny, L. A. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys J 87, 4021-4035 (2004).

Slutsky, M., Kardar, M. & Mirny, L. A. Diffusion in correlated random potentials, with applications to DNA. Phys Rev E 69, 061903 (2004).

Lidmar, J., Mirny, L. & Nelson, D. R. Virus shapes and buckling transitions in spherical shells. Phys Rev E 68, 051910 (2003).

Spirin, V., Gelfand, M. S. & Mirny, L. A. Computational analysis of metabolic modules and pathways in E.coli metabolic network. International Conference in Systems Biology (2003).

Spirin, V. & Mirny, L. A. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 100, 12123-12128 (2003).

Chen, W., Mirny, L. & Shakhnovich, E. I. Fold recognition with minimal gaps. Proteins 51, 531-543 (2003).

Li, L., Shakhnovich, E. I. & Mirny, L. A. Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proc Natl Acad Sci U S A 100, 4463-4468 (2003).

Dokholyan, N. V., Mirny, L. A. & Shakhnovich, E. I. Understanding conserved amino acids in proteins. Physica A 314, 600-606 (2002).

Ekins, S., Mirny, L. & Schuetz, E. G. A ligand-based approach to understanding selectivity of nuclear hormone receptors PXR, CAR, FXR, LXRalpha, and LXRbeta. Pharm Res 19, 1788-1800 (2002).

Mirny, L. A. & Gelfand, M. S. Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. J Mol Biol 321, 7-20 (2002).

Mirny, L. A. & Gelfand, M. S. Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Res 30, 1704-1711 (2002).

Mirny, L. & Shakhnovich, E. Protein folding theory: from lattice to all-atom models. Annu Rev Biophys Biomol Struct 30, 361-396 (2001).

Mirny, L. & Shakhnovich, E. Evolutionary conservation of the folding nucleus. J Mol Biol 308, 123-129 (2001).

Mirny, L. A. & Gelfand, M. S. What evolution can tell us about protein-DNA interactions? International School of Physics "Enrico Fermi" (2000).

Vendruscolo, M., Mirny, L. A., Shakhnovich, E. I. & Domany, E. Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score. Proteins 41, 192-201 (2000).

Mirny, L. A., Finkelstein, A. V. & Shakhnovich, E. I. Statistical significance of protein structure prediction by threading. Proc Natl Acad Sci U S A 97, 9978-9983 (2000).

Li, L., Mirny, L. A. & Shakhnovich, E. I. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat Struct Biol 7, 336-342 (2000).

Mirny, L. A. & Shakhnovich, E. I. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J Mol Biol 291, 177-196 (1999).

Mirny, L. A. & Shakhnovich, E. I. Protein structure prediction by threading. Why it works and why it does not. J Mol Biol 283, 507-526 (1998).

Mirny, L. A., Abkevich, V. I. & Shakhnovich, E. I. How evolution makes proteins fold quickly. Proc Natl Acad Sci U S A 95, 4976-4981 (1998).

Mirny, L. A. From Lattice Models to Real Proteins. Ph.D. Thesis. (Harvard University, 1996).

Mirny, L. A. & Shakhnovich, E. I. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol 264, 1164-1179 (1996).

Mirny, L. & Domany, E. Protein fold recognition and dynamics in the space of contact maps. Proteins 26, 391-410 (1996).

Mirny, L. A., Abkevich, V. & Shakhnovich, E. I. Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model. Fold Des 1, 103-116 (1996).

Shlyakhter, A., Mirny, L., Vlasov, A. & Wilson, R. Monte Carlo modeling of epidemiological studies. Human and Ecological Risk Assessment 2, 920-938 (1996).

Alon, R. N., Mirny, L., Sussman, J. L. & Gutnick, D. L. Detection of alpha/beta-hydrolase fold in the cell surface esterases of Acinetobacter species using an analysis of 3D profiles. FEBS Lett 371, 231-235 (1995).

Chepel, V. Y., Khvostunov, I. K., Mirny, L. A., Talyzina, T. A. & Andreev, S. G. 3-D Computer Modeling Of Chromatin Fibers For Radiation-Damage Simulation. Radiation Protection Dosimetry 52, 259-263 (1994).

C Gomez-Uribe:

Gomez-Uribe, C., G. C. Verghese, L. A. Mirny. Operating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering. PLoS Computational Biology . (2007). Supplementary Information

G Kolesov:

Kolesov G*, Wunderlich Z*, Laikova ON, Gelfand MS, Mirny LA. How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci. 104,13948-53 (2007).

Kolesov G, Virnau P, Kardar M, Mirny LA. Protein knot server: detection of knots in protein structures. Nucleic Acids Res (2007).

J Levine:

Levine, J., H. Y. Kueh, L. A. Mirny. Instrinsic Flutuations, Robustness, and Tunability in Signaling Cascades. Biophys J 92, 4473-81 (2007).

L Li:

Li, L., Shakhnovich, E. I. & Mirny, L. A. Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proc Natl Acad Sci U S A 100, 4463-4468 (2003).

Li, L., Mirny, L. A. & Shakhnovich, E. I. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat Struct Biol 7, 336-342 (2000).

M Slutsky:

Slutsky, M., Zandi, R., Kantor, Y. & Kardar, M. Apex exponents for polymer-probe interactions. Physical Review Letters 94 (2005).

Slutsky, M. Diffusion in a half-space: From Lord Kelvin to path integrals. American Journal of Physics 73, 308-314 (2005).

Slutsky, M. Protein-DNA Interaction, Random Walks and Polymer Statistics. Ph.D. Thesis. (MIT, 2005).

Slutsky, M. & Mirny, L. A. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys J 87, 4021-4035 (2004).

Slutsky, M., Kardar, M. & Mirny, L. A. Diffusion in correlated random potentials, with applications to DNA. Phys Rev E 69, 061903 (2004).

V Spirin:

Spirin, V., Gelfand, M.S., Mironov, A.A, Mirny LA. A metabolic network in the evolutionary context: Multiscale structure and modularity. Proc Natl Acad Sci 23, 8774-9 (2006).

Spirin, V., Gelfand, M. S. & Mirny, L. A. Computational analysis of metabolic modules and pathways in E. coli metabolic network. International Conference in Systems Biology (2003).

Spirin, V. & Mirny, L. A. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 100, 12123-12128 (2003).

A Tafvizi:

Tafvizi A, Huang F, Leith JS, Fersht AR, Mirny LA, van Oijen AM. Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability. Biophysical Journal, 95, L01-L03 (2008).

Z Wunderlich:

Wunderlich Z, Mirny LA. Spatial effects on the speed an\d reliability of protein-DNA search. Nucleic Acids Res (2008) (in \press).

Kolesov G*, Wunderlich Z*, Laikova ON, Gelfand MS, Mirny LA. How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci. 104,13948-53 (2007).

Wunderlich, Z., Mirny L.A. Using Topology of the Metabolic Network to Predict Viability of Mutant Strains. Biophysical Journal 91, 2304-11 (2006).