Banigan EJ, van den Berg AA, Brandão HB, Marko JF, Mirny LA (2020). Chromosome organization by one-sided and two-sided loop extrusion. eLife Brandão HB, Ren Z, Karaboja X, Mirny LA, Wang X (2020). DNA-loop extruding SMC complexes can traverse one another in vivo. bioRxiv Dequeker BJH, Brandão HB, Scherr MJ, Gassler J, Powell S, Gaspar I, Flyamer IM, Tang W, Stocsits R, Davidson IF, et al. (2020). MCM complexes are barriers that restrict cohesin-mediated loop extrusion. bioRxiv Banigan EJ, Mirny LA (2020). The interplay between asymmetric and symmetric DNA loop extrusion. bioRxiv Gurjao C, Tsukrov D, Imakaev M, Luquette LJ, Mirny LA (2020). Limited evidence of tumour mutational burden as a biomarker of response to immunotherapy. bioRxiv Nora EP, Caccianini L, Fudenberg G, So K, Kameswaran V, Nagle A, Uebersohn A, Hajj B, Le Saux A, Coulon A, et al. (2020). Molecular basis of CTCF binding polarity in genome folding. Nature Communications 11(1):1-13 Samata M, Alexiadis A, Richard G, Georgiev P, Nuebler J, Kulkarni T, Renschler G, Basilicata MF, Zenk FL, Shvedunova M, et al. (2020). Intergenerationally maintained histone h4 lysine 16 acetylation is instructive for future gene activation. Cell Banigan EJ, Mirny LA (2020). Loop extrusion: Theory meets single-molecule experiments. Current Opinion in Cell Biology 64 Feodorova Y, Falk M, Mirny LA, Solovei I (2020). Viewing nuclear architecture through the eyes of nocturnal mammals. Trends in Cell Biology 30(4):276-289 Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Parsi KM, Yang L, Maehr R, Mirny LA, et al. (2020). Ultrastructural details of mammalian chromosome architecture. Molecular Cell Abdennur N, Mirny LA (2020). Cooler: Scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics 36(1):311-316 Mirny LA, Imakaev M, Abdennur N (2019). Two major mechanisms of chromosome organization. Current Opinion in Cell Biology 58 Banigan EJ, Mirny LA (2019). Limits of chromosome compaction by loop-extruding motors. Physical Review X 9(3) [bioRxiv (Jan, 2018)] Brandão HB, Paul P, Berg AA, Rudner DZ, Wang X, Mirny LA (2019). RNA polymerases as moving barriers to condensin loop extrusion. Proceedings of the National Academy of Sciences 116(41):20489-20499 Falk M, Feodorova Y, Naumova N, Imakaev M, Lajoie BR, Leonhardt H, Joffe B, Dekker J, Fudenberg G, Solovei I, Mirny LA (2019). Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature 570 [bioRxiv (Jan, 2018)] Finn EH, Pegoraro G, Brandão HB, Valton A, Oomen ME, Dekker J, Mirny L, Misteli T (2019). Extensive heterogeneity and intrinsic variation in spatial genome organization. Cell 176(6):1502-1515.e10 [bioRxiv (Aug, 2017)] Nuebler J, Fudenberg G, Imakaev M, Abdennur N, Mirny LA (2018). Chromatin organization by an interplay of loop extrusion and compartmental segregation. Proceedings of the National Academy of Sciences 115(29):E6697-E6706 [bioRxiv (Oct, 2017)] Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N, Nuebler J, Kanemaki MT, Xie L, Paulson JR, Earnshaw WC, et al. (2018). A pathway for mitotic chromosome formation. Science 359(6376):eaao6135 [bioRxiv (Aug, 2017)] Fudenberg G, Abdennur N, Imakaev M, Goloborodko A, Mirny LA (2017). Emerging evidence of chromosome folding by loop extrusion. Cold Spring Harbor Symposia on Quantitative Biology 82 Gassler J, Brandao HB, Imakaev M, Flyamer IM, Ladstatter S, Bickmore WA, Peters J, Mirny LA, Tachibana-Konwalski K (2017). A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture. The EMBO Journal e201798083 [bioRxiv (Aug, 2017)] Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Ahzir A, Kumar N, Hwang J, Lee S, Alver B, Pfister H, Mirny LA, Park PJ, Gehlenborg N (2018). HiGlass: Web-based visual exploration and analysis of genome interaction maps. Genome Biology 19(1) [bioRxiv (Mar, 2017)] Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, H. Haering C, Mirny L, Spitz F (2017). Two independent modes of chromatin organization revealed by cohesin removal. Nature 551(7678):51-56 [bioRxiv (Dec, 2016)] Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O’Shea CC, Park PJ, Ren B, et al. (2017). The 4D nucleome project. Nature 549(7671):219-226 Phillips AM, Gonzalez LO, Nekongo EE, Ponomarenko AI, McHugh SM, Butty VL, Levine SS, Lin Y, Mirny LA, Shoulders MD (2017). Host proteostasis modulates influenza evolution. eLife 6 Schalbetter SA, Goloborodko A, Fudenberg G, Belton J, Miles C, Yu M, Dekker J, Mirny L, Baxter J (2017). SMC complexes differentially compact mitotic chromosomes according to genomic context. Nature Cell Biology 19(9):1071-1080 [bioRxiv (Dec, 2016)] Nora EP, Goloborodko A, Valton A, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG (2017). Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169(5):930-944.e22 [bioRxiv (Dec, 2016)] McFarland CD, Yaglom JA, Wojtkowiak JW, Scott JG, Morse DL, Sherman MY, Mirny LA (2017). The damaging effect of passenger mutations on cancer progression. Cancer Research [bioRxiv (Sep, 2015)] Flyamer IM, Gassler J, Imakaev M, Brandão HB, Ulianov SV, Abdennur N, Razin SV, Mirny LA, Tachibana-Konwalski K (2017). Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature 544(7648):110-114 Grajkowska LT, Ceribelli M, Lau CM, Warren ME, Tiniakou I, Nakandakari Higa S, Bunin A, Haecker H, Mirny LA, Staudt LM, Reizis B (2017). Isoform-specific expression and feedback regulation of E protein TCF4 control dendritic cell lineage specification. Immunity 46(1):65-77 Sawai CM, Babovic S, Upadhaya S, Knapp DJ, Lavin Y, Lau CM, Goloborodko A, Feng J, Fujisaki J, Ding L, Mirny L, Merad M, Eaves CJ, Reizis B (2016). Hematopoietic stem cells are the major source of multilineage hematopoiesis in adult animals. Immunity 45(3):597-609 Goloborodko A, Marko JF, Mirny LA (2016). Chromosome compaction by active loop extrusion. Biophysical Journal 110(10):2162-2168 [bioRxiv (Jun, 2015)] Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA (2016). Formation of chromosomal domains by loop extrusion. Cell Reports 15(9):2038-2049 [bioRxiv (Aug, 2015)] Goloborodko A, Imakaev MV, Marko JF, Mirny L (2016). Compaction and segregation of sister chromatids via active loop extrusion. eLife 5 [bioRxiv (Jan, 2016)] Dekker J, Mirny L (2016). The 3D genome as moderator of chromosomal communication. Cell 164(6):1110-1121 Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu C, Zhuang X (2016). Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529(7586):418-422 Imakaev MV, Fudenberg G, Mirny LA (2015). Modeling chromosomes: Beyond pretty pictures. FEBS Letters 589(20PartA):3031-3036 Kind J, Pagie L, Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny L, Jalink K, Dekker J, van Oudenaarden A, van Steensel B (2015). Genome-wide maps of nuclear lamina interactions in single human cells. Cell 163(1):134-147 Imakaev MV, Tchourine KM, Nechaev SK, Mirny LA (2015). Effects of topological constraints on globular polymers. Soft Matter 11(4):665-671 Mizuguchi T, Fudenberg G, Mehta S, Belton J, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewal S (2014). Cohesin-dependent globules and heterochromatin shape 3D genome architecture in s. pombe. Nature 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. (2014). Identification of a functional SNP regulating pRRX1 at the 1q24 locus for atrial fibrillation. Circulation 130(Suppl 2):A18865-A18865 Doyle B, Fudenberg G, Imakaev M, Mirny LA (2014). Chromatin loops as allosteric modulators of enhancer-promoter interactions. PLoS Computational Biology 10(10):e1003867 [bioRxiv (Nov, 2014)] McFarland CD, Mirny LA, Korolev KS (2014). Tug-of-war between driver and passenger mutations in cancer and other adaptive processes. Proceedings of the National Academy of Sciences 111(42):15138-15143 [bioRxiv (Feb, 2014)] Yaglom JA, McFarland C, Mirny L, Sherman MY (2014). Oncogene-triggered suppression of DNA repair leads to DNA instability in cancer. Oncotarget 5(18):8367-8378 Weisberg SP, Smith-Raska MR, Esquilin JM, Zhang J, Arenzana TL, Lau CM, Churchill M, Pan H, Klinakis A, Dixon JE, et al. (2014). ZFX controls propagation and prevents differentiation of acute t-lymphoblastic and myeloid leukemia. Cell Reports 6(3):528-540 Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J (2013). Organization of the mitotic chromosome. Science 342(6161):948-953 McFarland CD, Korolev KS, Kryukov GV, Sunyaev SR, Mirny LA (2013). Impact of deleterious passenger mutations on cancer progression. Proceedings of the National Academy of Sciences 110(8):2910-2915 Le TBK, Imakaev MV, Mirny LA, Laub MT (2013). High-resolution mapping of the spatial organization of a bacterial chromosome. Science 342(6159):731-734 Dekker J, Mirny L (2013). Biological techniques: Chromosomes captured one by one. Nature 502(7469):45-46 Dekker J, Marti-Renom MA, Mirny LA (2013). Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data. Nature Reviews Genetics 14(6):390-403 Leith JS, Tafvizi A, Huang F, Uspal WE, Doyle PS, Fersht AR, Mirny LA, Oijen AM (2012). Sequence-dependent sliding kinetics of p53. Proceedings of the National Academy of Sciences 109(41):16552-16557 Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA (2012). Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature Methods 9(10):999-1003 Engreitz JM, Agarwala V, Mirny LA (2012). Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease. PLoS ONE 7(9):e44196 Fudenberg G, Mirny LA (2012). Higher-order chromatin structure: Bridging physics and biology. Current Opinion in Genetics & Development 22(2):115-124 Fudenberg G, Getz G, Meyerson M, Mirny LA (2011). High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nature Biotechnology 29(12):1109-1113 Marti-Renom MA, Mirny LA (2011). Bridging the resolution gap in structural modeling of 3D genome organization. PLoS Computational Biology 7(7):e1002125 Tafvizi A, Mirny LA, Oijen AM (2011). Dancing on DNA: Kinetic aspects of search processes on DNA. ChemPhysChem 12(8):1481-1489 Tafvizi A, Huang F, Fersht AR, Mirny LA, Oijen AM (2011). A single-molecule characterization of p53 search on DNA. Proceedings of the National Academy of Sciences 108(2):563-568 Mirny LA (2011). The fractal globule as a model of chromatin architecture in the cell. Chromosome Research 19(1):37-51 Mirny LA (2010). Nucleosome-mediated cooperativity between transcription factors. Proceedings of the National Academy of Sciences 107(52):22534-22539 Mirny LA, Needleman DJ (2010). Quantitative characterization of filament dynamics by single-molecule lifetime measurements. Microtubules, in vitro Berkum NL, Lieberman-Aiden E, Williams L, Imakaev M, Gnirke A, Mirny LA, Dekker J, Lander ES (2010). Hi-C: A method to study the three-dimensional architecture of genomes.. Journal of Visualized Experiments Bölinger D, Sułkowska JI, Hsu H, Mirny LA, Kardar M, Onuchic JN, Virnau P (2010). A stevedore’s protein knot. PLoS Computational Biology 6(4):e1000731 Needleman DJ, Groen A, Ohi R, Maresca T, Mirny L, Mitchison T (2009). Fast microtubule dynamics in meiotic spindles measured by single molecule imaging: Evidence that the spindle environment does not stabilize microtubules. Molecular Biology of the Cell 21(2):323-333 Wunderlich Z, Mirny LA (2009). Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Research 37(14):4629-4641 Lieberman-Aiden E, Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950):289-293 Wunderlich Z, Mirny LA (2009). Different gene regulation strategies revealed by analysis of binding motifs. Trends in Genetics 25(10):434-440 Mirny L, Slutsky M, Wunderlich Z, Tafvizi A, Leith J, Kosmrlj A (2009). How a protein searches for its site on DNA: The mechanism of facilitated diffusion. Journal of Physics A: Mathematical and Theoretical 42(43):434013 Leith JS, Tafvizi A, Huang F, Fersht AR, Mirny LA, Oijen AM (2009). Sequence-dependent kinetics of one-dimensional diffusion of p53 on DNA. Biophysical Journal 96(3):416a Kolesov G, Mirny LA (2009). Using evolutionary information to find specificity-determining and co-evolving residues. Computational Systems Biology Jamal Rahi S, Virnau P, Mirny LA, Kardar M (2008). Predicting transcription factor specificity with all-atom models. Nucleic Acids Research 36(19):6209-6217 Tafvizi A, Huang F, Leith JS, Fersht AR, Mirny LA, Oijen AM (2008). Tumor suppressor p53 slides on DNA with low friction and high stability. Biophysical Journal 95(1):L01-L03 Wunderlich Z, Mirny LA (2008). Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Research 36(11):3570-3578 Mirny L (2008). Biophysics: Cell commuters avoid delays. Nature Physics 4(2):93-95 Gomez-Uribe C, Verghese GC, Mirny LA (2007). Operating regimes of signaling cycles: Statics, dynamics, and noise filtering. PLoS Computational Biology 3(12):e246 Kolesov G, Wunderlich Z, Laikova ON, Gelfand MS, Mirny LA (2007). How gene order is influenced by the biophysics of transcription regulation. Proceedings of the National Academy of Sciences 104(35):13948-13953 Kolesov G, Virnau P, Kardar M, Mirny LA (2007). Protein knot server: Detection of knots in protein structures. Nucleic Acids Research 35(Web Server):W425-W428 Levine J, Kueh HY, Mirny L (2007). Intrinsic fluctuations, robustness, and tunability in signaling cycles. Biophysical Journal 92(12):4473-4481 Galan-Caridad JM, Harel S, Arenzana TL, Hou ZE, Doetsch FK, Mirny LA, Reizis B (2007). Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Cell 129(2):345-357 Wunderlich Z, Mirny LA (2006). Using the topology of metabolic networks to predict viability of mutant strains. Biophysical Journal 91(6):2304-2311 Virnau P, Mirny LA, Kardar M (2006). Intricate knots in proteins: Function and evolution. PLoS Computational Biology 2(9):e122 Spirin V, Gelfand MS, Mironov AA, Mirny LA (2006). A metabolic network in the evolutionary context: Multiscale structure and modularity. Proceedings of the National Academy of Sciences 103(23):8774-8779 Donald JE, Hubner IA, Rotemberg VM, Shakhnovich EI, Mirny LA (2005). CoC: A database of universally conserved residues in protein folds. Bioinformatics 21(10):2539-2540 Slutsky M, Mirny LA (2004). Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential. Biophysical Journal 87(6):4021-4035 Slutsky M, Kardar M, Mirny L (2004). Diffusion in correlated random potentials, with applications to DNA. Physical Review E 69(6) Lidmar J, Mirny L, Nelson DR (2003). Virus shapes and buckling transitions in spherical shells. Physical Review E 68(5) Spirin V, Mirny LA (2003). Protein complexes and functional modules in molecular networks. Proceedings of the National Academy of Sciences 100(21):12123-12128 Spirin V, Gelfand M, Mirny L (2003). Computational analysis of metabolic modules and pathways in E. coli metabolic network. ISCB 4 Chen W, Mirny L, Shakhnovich EI (2003). Fold recognition with minimal gaps. Proteins: Structure, Function, and Bioinformatics 51(4):531-543 Li L, Shakhnovich EI, Mirny LA (2003). Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proceedings of the National Academy of Sciences 100(8):4463-4468 Ekins S, Mirny L, Schuetz EG (2002). A Ligand-Based Approach to Understanding Selectivity of Nuclear Hormone Receptors PXR, CAR, FXR, LXRα, and LXRβ. Pharmaceutical Research 19(12):1788-1800 Dokholyan NV, Mirny LA, Shakhnovich EI (2002). Understanding conserved amino acids in proteins. Physica A: Statistical Mechanics and its Applications 314(1-4):600-606 Mirny LA, Gelfand MS (2002). Using orthologous and paralogous proteins to identify specificity determining residues. Genome Biology 3(3):preprint0002.1 Mirny LA (2002). Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Research 30(7):1704-1711 Mirny L, Shakhnovich E (2001). Protein folding theory: From lattice to all-atom models. Annual Review of Biophysics and Biomolecular Structure 30(1):361-396 Mirny L, Shakhnovich E (2001). Evolutionary conservation of the folding nucleus. Journal of Molecular Biology 308(2):123-129 Mirny L, Gelfand M (2001). What evolution can tell us about protein-DNA interactions. Proceedings of the International School of Physics "Enrico Fermi" 145 Mirny L, Shakhnovich E (2001). Protein folding: Matching theory and experiment. Proceedings of the International School of Physics "Enrico Fermi" 145 Vendruscolo M, Mirny LA, Shakhnovich EI, Domany E (2000). Comparison of two optimization methods to derive energy parameters for protein folding: Perceptron and Z score. 3.0.CO;2-3>Proteins: Structure, Function, and Genetics 41(2):192-201 Mirny LA, Finkelstein AV, Shakhnovich EI (2000). Statistical significance of protein structure prediction by threading. Proceedings of the National Academy of Sciences 97(18):9978-9983 Li L, Mirny LA, Shakhnovich EI (2000). Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nature Structural Biology 7(4):336-342 Mirny LA, Shakhnovich EI (1999). Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function. Journal of Molecular Biology 291(1):177-196 Finkelstein A, Rykunov D, Lobanov MY, Badretdinov AY, Reva B, Skolnick J, Mirny L, Shakhnovich E (1999). Molecular biophysics-overcoming the crudeness of energy estimates in protein 3D structure prediction by homologs: The when and the how.. Biophysics 44(6):946-956 Mirny LA, Shakhnovich EI (1998). Protein structure prediction by threading. Why it works and why it does not.. Journal of Molecular Biology 283(2):507-526 Mirny LA, Abkevich VI, Shakhnovich EI (1998). How evolution makes proteins fold quickly. Proceedings of the National Academy of Sciences 95(9):4976-4981 Mirny LA (1998). Protein folding: From lattice models to real proteins. Harvard University, Ph.D. Thesis. Mirny LA, Shakhnovich EI (1996). How to derive a protein folding potential? A new approach to an old problem. Journal of Molecular Biology 264(5):1164-1179 Shlyakhter A, Mirny L, Vlasov A, Wilson R (1996). Monte carlo modeling of epidemiological studies. Human and Ecological Risk Assessment: An International Journal 2(4):920-938 Mirny L, Domany E (1996). Protein fold recognition and dynamics in the space of contact maps. Proteins: Structure, Function, and Genetics 26(4):391-410 Mirny LA, Abkevich V, Shakhnovich EI (1996). Universality and diversity of the protein folding scenarios:a comprehensive analysis with the aid of a lattice model. Folding and Design 1(2):103-116 Alon RN, Mirny L, Sussman JL, Gutnick DL (1995). Detection of alpha/beta-hydrolase fold in the cell surface esterases of acinetobacter species using an analysis of 3D profiles. FEBS letters 371(3):231-235 Chepel VY, Khvostunov I, Mirny L, Talyzina T, Andreev S (1994). 3-D computer modelling of chromatin fibres for radiation damage simulation. Radiation Protection Dosimetry 52(1):259-264