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Single-cell Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
Flyamer I, Gassler J, Imakaev M, Brandão H, Ulianov S, Abdennur N, Razin S, Mirny M, Tachibana-Konwalski K
Nature: in press

The 4D Nucleome Project
Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Ritland JC, Shendure J, Zhong S and the 4D Nucleome Network
bioRxiv, 2017

Isoform-Specific Expression and Feedback Regulation of E Protein TCF4 Control Dendritic Cell Lineage Specification
Grajkowska LT, MCeribelli M, Lau CM, Warren ME, Tiniakou I, Higa SN, Bunin A, Haecker H, Mirny LA, Staudt LM, Reizis B
Immunity, 2017

Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization
Nora EP, Goloborodko A, Valton A, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny L, Bruneau B
bioRxiv, 2016

Two independent modes of chromosome organization are revealed by cohesin removal
Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering C, Mirny L, Spitz F
bioRxiv, 2016

Hematopoietic stem cells are the major source of multilineage hematopoiesis in adult animals
Sawai CM, Babovic S, Upadhaya S, Knapp DJ, Lavin Y, Lau CM, Goloborodko A, Feng J, Fujisaki J, Ding L, Mirny LA, Merad M, Eaves CJ, Reizis B
Immunity, 2016

Cohesin dependent compaction of mitotic chromosomes
Schalbetter SA, Goloborodko A, Fudenberg G, Belton JM, Miles Catrina, Yu M, Dekker J, Mirny L, Baxter J
bioRxiv, 2016

Goloborodko A, Marko JF, Mirny LA
Chromosome Compaction by Active Loop Extrusion.
Biophys J, 2016
New and Notable: "Extruding Loops to Make Loopy Globules?" by A. Grosberg

Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA
Formation of chromosomal domains by loop extrusion.
Cell Reports, 2016

Goloborodko A, Marko JF, Mirny L
Compaction and segregation of sister chromatids via active loop extrusion
eLife, 2016

Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu C, Zhuang X
Super-resolution imaging reveals distinct chromatin folding for different epigenetic states.
Nature, 2016.

Imakaev MV, Fudenberg G, Mirny LA
Modeling chromosomes: Beyond pretty pictures.
FEBS letters, 2015. 589(20): 3031-3036.

Kind J, Pagie L, Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, Graaf CA, Amendola M, et al.
Genome-wide maps of nuclear lamina interactions in single human cells.
Cell Press, 2015. 163(1): 134-147.

McFarland CD, Yaglom JA, Wojtkowiak JW, Scott JG, Morse DL, Sherman MY, Mirny LA
Passenger DNA alterations reduce cancer fitness in cell culture and mouse models.
bioRxiv, 2015.

Imakaev MV, Tchourine KM, Nechaev SK, Mirny LA
Effects of topological constraints on globular polymers
Soft matter, 2015. 11(4): 665-671.

Mizuguchi T, Fudenberg G, Mehta S, Belton J, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, et al.
Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe
Nature, 2014. 516(7531): 432-435.

Dolmatova E, Tucker NR, Lin H, Cooper RR, Ye J, Sinner MF, Imakaev M, Lubitz SA, Leyton-Mange J, Vlahakes G, et al.
Identification of a functional SNP regulating pRRX1 at the 1q24 locus for atrial fibrillation.
Circulation, 2014.

Doyle B, Fudenberg G, Imakaev M, Mirny LA
Chromatin loops as allosteric modulators of enhancer-promoter interactions
PLoS Comput Biol, 2014. 10(10): e1003867.

McFarland CD, Korolev KS, Mirny LA
A tug-of-war between driver and passenger mutations in cancer and other adaptive processes
PNAS, Oct 2, 2014.

Yaglom JA, McFarland CD, Mirny LA, Sherman MY
Oncogene-triggered suppression of DNA repair leads to DNA instability in cancer
Oncotarget, July 25, 2014.

Weisberg SP, Smith-Raska MR, Esquilin JM, Zhang J, Arenzana TL, Lau CM, Churchill M, Pan H, Klinakis A, Dixon JE, Mirny LA, Mukherjee S, Reizis B.
ZFX Controls Propagation and Prevents Differentiation of Acute T-Lymphoblastic and Myeloid Leukemia

Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J
Organization of the Mitotic Chromosome
Science, 2013 342(6161).

McFarland CD, Korolev KS, Kryukov GV, Sunyaev S, Mirny LA
The impact of deleterious passenger mutations on cancer progression
PNAS 2013 110(7).
Research highlight by Burgess DJ
"Tumor evolution Weighed down by passengers?"
Nature Reviews Cancer (2013).

Leith JS, Tafvizi A, Huang F, Uspal WE, Doyle PS, Fersht AR, Mirny LA, van Oijen AM
Sequence-dependent sliding kinetics of p53.
PNAS 2012;109(41):16652-7.

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.
Nature Methods 2012 Sep 02;

Fudenberg G, Mirny LA
Higher-order chromatin structure: bridging physics and biology.
Curr Opin Genet Dev. 2012 Apr;22(2):115-24.

Fudenberg G, Getz G, Meyerson M, Mirny LA
High order chromatin architecture shapes the landscape of chromosomal alterations in cancer.
Nat Biotechnol. 2011 Nov 20;29(12):1109-13.

Marti-Renom MA, Mirny LA
Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization.
PLoS Comput Biol. 2011 Jul;7(7):e1002125.

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.

Tafvizi A, Huang F, Fersht AR, Mirny LA, van Oijen AM
A single-molecule characterization of p53 search on DNA.
PNAS 2011 108(2), pp563-568

Mirny LA
The fractal globule as a model of chromatin architecture in the cell.
Chromosome Res. 2011 Jan;19(1):37-51.

Mirny LA
Nucleosome-mediated cooperativity between transcription factors.
PNAS 2010 Dec 28;107(52):22534-9

Mirny LA, Needleman DJ. Quantitative characterization of filament dynamics by single-molecule lifetime measurements.
Methods Cell Biol. 2010;95:583-600.

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 May 6;(39).

Bolinger D, Sulkowska JI, Hsu HP, Mirny LA, Kardar M, Onuchic JN, Virnau P. A Stevedore's protein knot. PLoS Comput Biol. 2010 Apr 1;6(4).

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;21(2):323-33.

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.
Data and supplements

Wunderlich Z., Mirny LA Different strategies for transcriptional regulation are revealed by information-theoretical analysis of binding motifs.
Trends Genet. 2009 Oct;25(10):434-40. (2009)

Mirny LA. Nucleosome-mediated cooperativity between transcription factors. 19 Jan (2009)

Leonid Mirny, Michael Slutsky, Zeba Wunderlich, Anahita Tafvizi, Jason Leith and Andrej Kosmrlj How a protein searches for its site on DNA: the mechanism of facilitated diffusion J. Phys. A: Math. Theor. 42 No 43 (30 October 2009) 434013

Kolesov G, Mirny LA Using evolutionary information to find specificity-determining and co-evolving residues. Methods Mol Biol. 541:421-48 (2009)

Wunderlich Z, Mirny LA. An optimized energy potential can predict SH2 domain-peptide interactions. Nucleic Acids Res June 5, 1-13 (2009)

Mirny LA. Cell commuters avoid delays. Nature Physics, 4, 93-95 (2008).

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 36(11):3570 (2008)

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. leith 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).