Mirny Lab

Publications

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  1. Dekker J, Mirny LA. The chromosome folding problem and how cells solve it. Cell. 2024 Nov 14;187(23):6424-6450. doi: 10.1016/j.cell.2024.10.026. PMID: 39547207; PMCID: PMC11569382. doi: https://doi.org/10.1016/j.cell.2024.10.026
  2. Viraat Y. Goel, Nicholas G. Aboreden, James M. Jusuf, Haoyue Zhang, Luisa P. Mori, Leonid A. Mirny, Gerd A. Blobel, Edward J. Banigan, Anders S. Hansen
    Dynamics of microcompartment formation at the mitosis-to-G1 transition
    bioRxiv 2024.09.16.611917; doi: https://doi.org/10.1101/2024.09.16.611917
  3. . Karagyozova, A. Gatto, A. Forest, J.-P. Quivy, M. Marti-Renom, L. Mirny, G. Almouzni
    HIRA-dependent provision of histone H3.3 in active chromatin ensures genome compartmentalisation
    Preprint. bioRx 2024.08.27.609896 doi: https://doi.org/10.1101/2024.08.27.609896
  4. T. Karagyozova, A. Gatto, A. Forest, J.-P. Quivy, M. Marti-Renom, L. Mirny, G. Almouzni
    HIRA defines early replication initiation zones independently of their genome compartment
    Preprint.bioRxiv 2024.08.29.610220; doi: https://doi.org/10.1101/2024.08.29.610220
  5. Nicholas M. Adams, Aleksandra Galitsyna, Ioanna Tiniakou, Eduardo Esteva, Colleen M. Lau, Jojo Reyes, Nezar Abdennur, Alexey Shkolikov, George S. Yap, Alireza Khodadadi-Jamayran, Leonid A. Mirny, 
    Boris Reizis. Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells. Preprint. bioRxiv 2024.09.18.613709; doi: https://doi.org/10.1101/2024.09.18.613709  
  6. Solovei I, Mirny L. Spandrels of the cell nucleus. Curr Opin Cell Biol. 2024;90:102421.
  7. Gil J Jr, Navarrete E, Rosin LF, et al. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth. Preprint. Res Sq. 2024;rs.3.rs-4732646. 2024 Jul 31.
  8. Hildebrand EM, Polovnikov K, Dekker B, et al. Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis. Mol Cell. 2024;84(8):1422-1441.e14.
  9. Scelfo A, Barra V, Abdennur N, Spracklin G, Busato F, Salinas-Luypaert C, Bonaiti E, Velasco G, Bonhomme F, Chipont A, Tijhuis AE, Spierings DCJ, Guérin C, Arimondo P, Francastel C, Foijer F, Tost J, Mirny L, Fachinetti D (2024). Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization. Journal of Cell Biology 223(4) [bioRxiv (May, 2023)]
  10. Hildebrand EM, Polovnikov K, Dekker B, Liu Y, Lafontaine DL, Fox AN, Li Y, Venev SV, Mirny LA, Dekker J (2024). Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis. Molecular Cell 84(8):1422-1441.e14 [bioRxiv (January, 2024)]
  11. Samejima K, Gibcus JH, Abraham S, Cisneros-Soberanis F, Samejima I, Beckett AJ, Pučeková N, Abad MA, Medina-Pritchard B, Paulson JR, Xie L, Jeyaprakash AA, Prior IA, Mirny LA, Dekker J, Goloborodko A, Earnshaw WC (2024). Rules of engagement for condensins and cohesins guide mitotic chromosome formation. bioRxiv
  12. Owen JA, Osmanović D, Mirny L (2023). Design principles of 3D epigenetic memory systems. Science 382(6672) [bioRxiv (September, 2022)]
  13. Polovnikov KE, Brandão HB, Belan S, Slavov B, Imakaev M, Mirny LA (2023). Crumpled polymer with loops recapitulates key features of chromosome organization. Physical Review X 13(4) [bioRxiv (May, 2023)]
  14. Gil J, Rosin LF, Navarrete E, Chowdhury N, Abraham S, Cornilleau G, Lei EP, Mozziconacci J, Mirny LA, Muller H, Drinnenberg IA (2023). Unique territorial and sub-chromosomal organization revealed in the holocentric mothBombyx mori. bioRxiv
  15. Liu S, Miné-Hattab J, Villemeur M, Guerois R, Pinholt HD, Mirny LA, Taddei A (2023). In vivo tracking of functionally tagged Rad51 unveils a robust strategy of homology search. Nature Structural & Molecular Biology 30(10):1582-1591
  16. Galitsyna A, Ulianov SV, Bykov NS, Veil M, Gao M, Perevoschikova K, Gelfand M, Razin SV, Mirny L, Onichtchouk D (2023). Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation. bioRxiv
  17. Gurjao C, Tsukrov D, Imakaev M, Luquette LJ, Mirny LA (2023). Is tumor mutational burden predictive of response to immunotherapy?. eLife
  18. Mirny LA (2023). Chromosome and protein folding: In search for unified principles. Current Opinion in Structural Biology 81
  19. Spracklin G, Abdennur N, Imakaev M, Chowdhury N, Pradhan S, Mirny LA, Dekker J (2022). Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. Nature Structural & Molecular Biology [bioRxiv (August, 2021)]
  20. Keizer VIP, Grosse-Holz S, Woringer M, Zambon L, Aizel K, Bongaerts M, Delille F, Kolar-Znika L, Scolari VF, Hoffmann S, Banigan EJ, Mirny LA, Dahan M, Fachinetti D, Coulon A (2022). Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics. Science 377(6605):489-495 [bioRxiv (Apr, 2021)]
  21. Nagano M, Hu B, Yokobayashi S, Yamamura A, Umemura F, Coradin M, Ohta H, Yabuta Y, Ishikura Y, Okamoto I, Ikeda H, Kawahira N, Nosaka Y, Shimizu S, Kojima Y, Mizuta K, Kasahara T, Imoto Y, Meehan K, Stocsits R, Wutz G, Hiraoka Y, Murakawa Y, Yamamoto T, Tachibana K, Peters J, Mirny LA, Garcia BA, Majewski J, Saitou M (2022). Nucleome programming is required for the foundation of totipotency in mammalian germline development. The EMBO Journal 41(13)
  22. Dequeker BJH, Scherr MJ, Brandão HB, Gassler J, Powell S, Gaspar I, Flyamer IM, Lalic A, Tang W, Stocsits R, Davidson IF, Peters J, Duderstadt KE, Mirny LA, Tachibana K (2022). MCM complexes are barriers that restrict cohesin-mediated loop extrusion. Nature 606(7912):197-203 [bioRxiv (Oct, 2020)]
  23. Reiff SB, Schroeder AJ, Kırlı K, Cosolo A, Bakker C, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, Öztürk SU, Çamoğlu U, Mirny LA, Gehlenborg N, Alver BH, Park PJ (2022). The 4D nucleome data portal as a resource for searching and visualizing curated nucleomics data. Nature Communications 13(1) [bioRxiv (Oct, 2021)]
  24. Deforzh E, Uhlmann EJ, Das E, Galitsyna A, Arora R, Saravanan H, Rabinovsky R, Wirawan AD, Teplyuk NM, El Fatimy R, Perumalla S, Jairam A, Wei Z, Mirny L, Krichevsky AM (2022). Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus, and neoplastic transformation in glioma. Molecular Cell 82(10):1894-1908.e5
  25. Gabriele M, Brandão HB, Grosse-Holz S, Jha A, Dailey GM, Cattoglio C, Hsieh TS, Mirny L, Zechner C, Hansen AS (2022). Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Science 376(6592):496-501 [bioRxiv (Dec, 2021)]
  26. Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Galitsyna A, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny L, Solovei I (2022). Spatial organization of transcribed eukaryotic genes. Nature Cell Biology 24(3):327-339 [bioRxiv (Apr, 2021)]
  27. Polovnikov K, Belan S, Imakaev M, Brandão HB, Mirny LA (2022). Fractal polymer with loops recapitulates key features of chromosome organization. bioRxiv
  28. Banigan EJ, Tang W, Berg AA, Stocsits RR, Wutz G, Brandão HB, Busslinger GA, Peters J, Mirny LA (2022). Transcription shapes 3D chromatin organization by interacting with loop extrusion. bioRxiv
  29. Mirny L, Dekker J (2021). Mechanisms of chromosome folding and nuclear organization: Their interplay and open questions. Cold Spring Harbor Perspectives in Biology 14(7):a040147
  30. Akgol Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RMJ, Maehr R, Rando OJ, Mirny LA, Gibcus JH, Dekker J (2021). Systematic evaluation of chromosome conformation capture assays. Nature Methods 18(9):1046-1055 [bioRxiv (Dec, 2020)]
  31. Spracklin G, Abdennur N, Imakaev M, Chowdhury N, Pradhan S, Mirny L, Dekker J (2021). Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers. bioRxiv
  32. Brandão HB, Ren Z, Karaboja X, Mirny LA, Wang X (2021). DNA-loop-extruding SMC complexes can traverse one another in vivo. Nature Structural & Molecular Biology 28(8):642-651 [bioRxiv (Oct, 2020)]
  33. Mirny LA (2021). Cells use loop extrusion to weave and tie the genome. Nature 590(7847):554-555
  34. Mirny LA, Solovei I (2021). Keeping chromatin in the loop(s). Nature Reviews Molecular Cell Biology 22(7):439-440
  35. Banigan EJ, Mirny LA (2020). The interplay between asymmetric and symmetric DNA loop extrusion. eLife 9 [bioRxiv (Sep, 2020)]
  36. 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 [bioRxiv (Dec, 2019)]
  37. 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
  38. 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
  39. Abdennur N, Mirny LA (2020). Cooler: Scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics 36(1):311-316 [bioRxiv (Feb, 2019)]
  40. Banigan EJ, Mirny LA (2020). Loop extrusion: Theory meets single-molecule experiments. Current Opinion in Cell Biology 64
  41. 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 [bioRxiv (May, 2019)]
  42. Banigan EJ, van den Berg AA, Brandão HB, Marko JF, Mirny LA (2020). Chromosome organization by one-sided and two-sided loop extrusion. eLife [bioRxiv (Apr, 2020)]
  43. 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
  44. 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 [bioRxiv (Apr, 2019)]
  45. Banigan EJ, Mirny LA (2019). Limits of chromosome compaction by loop-extruding motors. Physical Review X 9(3) [bioRxiv (Jan, 2018)]
  46. Mirny LA, Imakaev M, Abdennur N (2019). Two major mechanisms of chromosome organization. Current Opinion in Cell Biology 58
  47. 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)]
  48. 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)]
  49. 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)]
  50. 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)]
  51. 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
  52. 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)]
  53. 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)]
  54. 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)]
  55. 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
  56. 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
  57. 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)]
  58. 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)]
  59. 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)]
  60. 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
  61. 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
  62. 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
  63. Goloborodko A, Marko JF, Mirny LA (2016). Chromosome compaction by active loop extrusion. Biophysical Journal 110(10):2162-2168 [bioRxiv (Jun, 2015)]
  64. 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)]
  65. Goloborodko A, Imakaev MV, Marko JF, Mirny L (2016). Compaction and segregation of sister chromatids via active loop extrusion. eLife 5 [bioRxiv (Jan, 2016)]
  66. Dekker J, Mirny L (2016). The 3D genome as moderator of chromosomal communication. Cell 164(6):1110-1121
  67. 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
  68. Imakaev MV, Fudenberg G, Mirny LA (2015). Modeling chromosomes: Beyond pretty pictures. FEBS Letters 589(20PartA):3031-3036
  69. 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
  70. Imakaev MV, Tchourine KM, Nechaev SK, Mirny LA (2015). Effects of topological constraints on globular polymers. Soft Matter 11(4):665-671
  71. 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
  72. 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
  73. 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)]
  74. 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)]
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. Dekker J, Mirny L (2013). Biological techniques: Chromosomes captured one by one. Nature 502(7469):45-46
  81. 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
  82. 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
  83. 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
  84. 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
  85. Fudenberg G, Mirny LA (2012). Higher-order chromatin structure: Bridging physics and biology. Current Opinion in Genetics & Development 22(2):115-124
  86. 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
  87. Marti-Renom MA, Mirny LA (2011). Bridging the resolution gap in structural modeling of 3D genome organization. PLoS Computational Biology 7(7):e1002125
  88. Tafvizi A, Mirny LA, Oijen AM (2011). Dancing on DNA: Kinetic aspects of search processes on DNA. ChemPhysChem 12(8):1481-1489
  89. 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
  90. Mirny LA (2011). The fractal globule as a model of chromatin architecture in the cell. Chromosome Research 19(1):37-51
  91. Mirny LA (2010). Nucleosome-mediated cooperativity between transcription factors. Proceedings of the National Academy of Sciences 107(52):22534-22539
  92. Mirny LA, Needleman DJ (2010). Quantitative characterization of filament dynamics by single-molecule lifetime measurements. Microtubules, in vitro
  93. 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
  94. 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
  95. 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
  96. Wunderlich Z, Mirny LA (2009). Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Research 37(14):4629-4641
  97. 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
  98. Wunderlich Z, Mirny LA (2009). Different gene regulation strategies revealed by analysis of binding motifs. Trends in Genetics 25(10):434-440
  99. 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
  100. 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
  101. Kolesov G, Mirny LA (2009). Using evolutionary information to find specificity-determining and co-evolving residues. Computational Systems Biology
  102. 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
  103. 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
  104. Wunderlich Z, Mirny LA (2008). Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Research 36(11):3570-3578
  105. Mirny L (2008). Biophysics: Cell commuters avoid delays. Nature Physics 4(2):93-95
  106. Gomez-Uribe C, Verghese GC, Mirny LA (2007). Operating regimes of signaling cycles: Statics, dynamics, and noise filtering. PLoS Computational Biology 3(12):e246
  107. 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
  108. 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
  109. Levine J, Kueh HY, Mirny L (2007). Intrinsic fluctuations, robustness, and tunability in signaling cycles. Biophysical Journal 92(12):4473-4481
  110. 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
  111. Wunderlich Z, Mirny LA (2006). Using the topology of metabolic networks to predict viability of mutant strains. Biophysical Journal 91(6):2304-2311
  112. Virnau P, Mirny LA, Kardar M (2006). Intricate knots in proteins: Function and evolution. PLoS Computational Biology 2(9):e122
  113. 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
  114. 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
  115. Slutsky M, Mirny LA (2004). Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential. Biophysical Journal 87(6):4021-4035
  116. Slutsky M, Kardar M, Mirny L (2004). Diffusion in correlated random potentials, with applications to DNA. Physical Review E 69(6)
  117. Lidmar J, Mirny L, Nelson DR (2003). Virus shapes and buckling transitions in spherical shells. Physical Review E 68(5)
  118. Spirin V, Mirny LA (2003). Protein complexes and functional modules in molecular networks. Proceedings of the National Academy of Sciences 100(21):12123-12128
  119. Spirin V, Gelfand M, Mirny L (2003). Computational analysis of metabolic modules and pathways in E. coli metabolic network. ISCB 4
  120. Chen W, Mirny L, Shakhnovich EI (2003). Fold recognition with minimal gaps. Proteins: Structure, Function, and Bioinformatics 51(4):531-543
  121. 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
  122. 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
  123. 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
  124. Mirny LA, Gelfand MS (2002). Using orthologous and paralogous proteins to identify specificity determining residues. Genome Biology 3(3):preprint0002.1
  125. Mirny LA (2002). Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Research 30(7):1704-1711
  126. 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
  127. Mirny L, Shakhnovich E (2001). Evolutionary conservation of the folding nucleus. Journal of Molecular Biology 308(2):123-129
  128. Mirny L, Gelfand M (2001). What evolution can tell us about protein-DNA interactions. Proceedings of the International School of Physics “Enrico Fermi” 145
  129. Mirny L, Shakhnovich E (2001). Protein folding: Matching theory and experiment. Proceedings of the International School of Physics “Enrico Fermi” 145
  130. 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
  131. 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
  132. 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
  133. 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
  134. 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
  135. 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
  136. Mirny LA, Abkevich VI, Shakhnovich EI (1998). How evolution makes proteins fold quickly. Proceedings of the National Academy of Sciences 95(9):4976-4981
  137. Mirny LA (1998). Protein folding: From lattice models to real proteins. Harvard University, Ph.D. Thesis.
  138. 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
  139. 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
  140. 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
  141. 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
  142. 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
  143. 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