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Leonid Alex Mirny, PH.D.

TitleMember of the Faculty of the Harvard-MIT Division of Health Sciences and Technology
InstitutionMassachusetts Institute of Technology
DepartmentHealth Sciences and Technology
AddressMass Institute of Technology
Mit E25-526
77 Massachusetts Ave
Cambridge MA 02139
Phone617/452-4862

 Overview 
 overview
biophysics
chromatin
protein-DNA interactions
transcription regulation
structural biology
biological networks


 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
List All   |   Timeline
  1. Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J. Organization of the mitotic chromosome. Science. 2013 Nov 22; 342(6161):948-53.
    View in: PubMed
  2. Le TB, Imakaev MV, Mirny LA, Laub MT. High-resolution mapping of the spatial organization of a bacterial chromosome. Science. 2013 Nov 8; 342(6159):731-4.
    View in: PubMed
  3. Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one. Nature. 2013 Oct 3; 502(7469):45-6.
    View in: PubMed
  4. Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013 Jun; 14(6):390-403.
    View in: PubMed
  5. McFarland CD, Korolev KS, Kryukov GV, Sunyaev SR, Mirny LA. Impact of deleterious passenger mutations on cancer progression. Proc Natl Acad Sci U S A. 2013 Feb 19; 110(8):2910-5.
    View in: PubMed
  6. Engreitz JM, Agarwala V, Mirny LA. Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease. PLoS One. 2012; 7(9):e44196.
    View in: PubMed
  7. Leith JS, Tafvizi A, Huang F, Uspal WE, Doyle PS, Fersht AR, Mirny LA, van Oijen AM. Sequence-dependent sliding kinetics of p53. Proc Natl Acad Sci U S A. 2012 Oct 9; 109(41):16552-7.
    View in: PubMed
  8. Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods. 2012 Oct; 9(10):999-1003.
    View in: PubMed
  9. Fudenberg G, Mirny LA. Higher-order chromatin structure: bridging physics and biology. Curr Opin Genet Dev. 2012 Apr; 22(2):115-24.
    View in: PubMed
  10. Fudenberg G, Getz G, Meyerson M, Mirny LA. High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat Biotechnol. 2011 Dec; 29(12):1109-13.
    View in: PubMed
  11. Marti-Renom MA, Mirny LA. Bridging the resolution gap in structural modeling of 3D genome organization. PLoS Comput Biol. 2011 Jul; 7(7):e1002125.
    View in: PubMed
  12. Tafvizi A, Mirny LA, van Oijen AM. Dancing on DNA: kinetic aspects of search processes on DNA. Chemphyschem. 2011 Jun 6; 12(8):1481-9.
    View in: PubMed
  13. Mirny LA. The fractal globule as a model of chromatin architecture in the cell. Chromosome Res. 2011 Jan; 19(1):37-51.
    View in: PubMed
  14. Tafvizi A, Huang F, Fersht AR, Mirny LA, van Oijen AM. A single-molecule characterization of p53 search on DNA. Proc Natl Acad Sci U S A. 2011 Jan 11; 108(2):563-8.
    View in: PubMed
  15. Mirny LA. Nucleosome-mediated cooperativity between transcription factors. Proc Natl Acad Sci U S A. 2010 Dec 28; 107(52):22534-9.
    View in: PubMed
  16. van Berkum NL, Lieberman-Aiden E, Williams L, Imakaev M, Gnirke A, Mirny LA, Dekker J, Lander ES. Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp. 2010; (39).
    View in: PubMed
  17. Bölinger D, Sulkowska JI, Hsu HP, Mirny LA, Kardar M, Onuchic JN, Virnau P. A Stevedore's protein knot. PLoS Comput Biol. 2010 Apr; 6(4):e1000731.
    View in: PubMed
  18. Mirny LA, Needleman DJ. Quantitative characterization of filament dynamics by single-molecule lifetime measurements. Methods Cell Biol. 2010; 95:583-600.
    View in: PubMed
  19. Mirny LA. Nucleosome-mediated cooperativity between transcription factors. 2009.
  20. Needleman DJ, Groen A, Ohi R, Maresca T, Mirny L, Mitchison T. Fast microtubule dynamics in meiotic spindles measured by single molecule imaging: evidence that the spindle environment does not stabilize microtubules. Mol Biol Cell. 2010 Jan 15; 21(2):323-33.
    View in: PubMed
  21. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009 Oct 9; 326(5950):289-93.
    View in: PubMed
  22. Wunderlich Z, Mirny LA. Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet. 2009 Oct; 25(10):434-40.
    View in: PubMed
  23. Wunderlich Z, Mirny LA. Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Res. 2009 Aug; 37(14):4629-41.
    View in: PubMed
  24. Kolesov G, Mirny LA. Using evolutionary information to find specificity-determining and co-evolving residues. Methods Mol Biol. 2009; 541:421-48.
    View in: PubMed
  25. Wunderlich Z, Mirny LA. Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Res. 2008 Jun; 36(11):3570-8.
    View in: PubMed
  26. 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. Biophys J. 2008 Jul; 95(1):L01-3.
    View in: PubMed
  27. Gomez-Uribe C, Verghese GC, Mirny LA. Operating regimes of signaling cycles: statics, dynamics, and noise filtering. PLoS Comput Biol. 2007 Dec; 3(12):e246.
    View in: PubMed
  28. 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 U S A. 2007 Aug 28; 104(35):13948-53.
    View in: PubMed
  29. Kolesov G, Virnau P, Kardar M, Mirny LA. Protein knot server: detection of knots in protein structures. Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W425-8.
    View in: PubMed
  30. 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. 2007 Apr 20; 129(2):345-57.
    View in: PubMed
  31. Virnau P, Mirny LA, Kardar M. Intricate knots in proteins: Function and evolution. PLoS Comput Biol. 2006 Sep 15; 2(9):e122.
    View in: PubMed
  32. Spirin V, Gelfand MS, Mironov AA, Mirny LA. A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci U S A. 2006 Jun 6; 103(23):8774-9.
    View in: PubMed
  33. Slutsky M, Mirny LA. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys J. 2004 Dec; 87(6):4021-35.
    View in: PubMed
  34. Lidmar J, Mirny L, Nelson DR. Virus shapes and buckling transitions in spherical shells. Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Nov; 68(5 Pt 1):051910.
    View in: PubMed
  35. Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A. 2003 Oct 14; 100(21):12123-8.
    View in: PubMed
  36. Alon RN, Mirny L, Sussman JL, Gutnick DL. Detection of alpha/beta-hydrolase fold in the cell surface esterases of Acinetobacter species using an analysis of 3D profiles. FEBS Lett. 1995 Sep 11; 371(3):231-5.
    View in: PubMed
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