Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

Leonid Alex Mirny, Ph.D.

Title
Institution
Department
Address
Phone

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

Research
research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
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  1. UM1HG011536 (DEKKER, JOB) Sep 18, 2020 - Jun 30, 2025
    NIH
    Center for 3D Structure and Physics of the Genome
    Role: Co-Principal Investigator
  2. U54DK107980 (DEKKER, JOB) Sep 30, 2015 - Jan 31, 2021
    NIH
    Center for 3D Structure and Physics of the Genome
    Role: Co-Principal Investigator
  3. R01GM114190 (MIRNY, LEONID A) Jun 1, 2015 - Aug 31, 2024
    NIH
    Polymer models of mitotic and interphase chromosomes
    Role: Principal Investigator
  4. U54CA143874 (MANALIS, SCOTT R) Sep 23, 2009 - Jul 31, 2014
    NIH/NCI
    The MIT Center for Single-Cell Dynamics in Cancer (SCDC)
    Role: Co-Principal Investigator
  5. P41RR006009 (LEVINE, MICHAEL J) Sep 1, 1990 - Jul 31, 2013
    NIH/NCRR
    High Performance Computing for Biomedical Research
    Role: Co-Principal Investigator

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.
Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Spracklin G, Abdennur N, Imakaev M, Chowdhury N, Pradhan S, Mirny LA, Dekker J. Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. Nat Struct Mol Biol. 2023 Jan; 30(1):38-51. PMID: 36550219; PMCID: PMC9851908.
    Citations:    Fields:    Translation:Cells
  2. Reiff SB, Schroeder AJ, Kirli K, Cosolo A, Bakker C, Mercado L, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, Öztürk SU, Çamoglu U, Mirny LA, Gehlenborg N, Alver BH, Park PJ. Author Correction: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nat Commun. 2022 Nov 02; 13(1):6561. PMID: 36323678; PMCID: PMC9630381.
    Citations:    Fields:    
  3. 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. Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics. Science. 2022 07 29; 377(6605):489-495. PMID: 35901134.
    Citations:    Fields:    
  4. Mirny L, Dekker J. Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. Cold Spring Harb Perspect Biol. 2022 07 01; 14(7). PMID: 34518339; PMCID: PMC9248823.
    Citations: 5     Fields:    Translation:Cells
  5. 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 JM, Mirny LA, Garcia BA, Majewski J, Saitou M. Nucleome programming is required for the foundation of totipotency in mammalian germline development. EMBO J. 2022 07 04; 41(13):e110600. PMID: 35703121; PMCID: PMC9251848.
    Citations: 1     Fields:    Translation:AnimalsCells
  6. Dequeker BJH, Scherr MJ, Brandão HB, Gassler J, Powell S, Gaspar I, Flyamer IM, Lalic A, Tang W, Stocsits R, Davidson IF, Peters JM, Duderstadt KE, Mirny LA, Tachibana K. MCM complexes are barriers that restrict cohesin-mediated loop extrusion. Nature. 2022 06; 606(7912):197-203. PMID: 35585235; PMCID: PMC9159944.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  7. Reiff SB, Schroeder AJ, Kirli K, Cosolo A, Bakker C, Mercado L, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, Öztürk SU, Çamoglu U, Mirny LA, Gehlenborg N, Alver BH, Park PJ. The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nat Commun. 2022 05 02; 13(1):2365. PMID: 35501320; PMCID: PMC9061818.
    Citations:    Fields:    Translation:Cells
  8. Gabriele M, Brandão HB, Grosse-Holz S, Jha A, Dailey GM, Cattoglio C, Hsieh TS, Mirny L, Zechner C, Hansen AS. Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Science. 2022 04 29; 376(6592):496-501. PMID: 35420890; PMCID: PMC9069445.
    Citations: 4     Fields:    Translation:AnimalsCells
  9. 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. Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus, and neoplastic transformation in glioma. Mol Cell. 2022 05 19; 82(10):1894-1908.e5. PMID: 35390275; PMCID: PMC9271318.
    Citations:    Fields:    Translation:HumansCells
  10. 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. Spatial organization of transcribed eukaryotic genes. Nat Cell Biol. 2022 03; 24(3):327-339. PMID: 35177821; PMCID: PMC9380065.
    Citations: 4     Fields:    Translation:AnimalsCells
  11. 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. Systematic evaluation of chromosome conformation capture assays. Nat Methods. 2021 09; 18(9):1046-1055. PMID: 34480151; PMCID: PMC8446342.
    Citations: 11     Fields:    Translation:HumansCells
  12. Brandão HB, Ren Z, Karaboja X, Mirny LA, Wang X. DNA-loop-extruding SMC complexes can traverse one another in vivo. Nat Struct Mol Biol. 2021 08; 28(8):642-651. PMID: 34312537; PMCID: PMC8878250.
    Citations: 6     Fields:    Translation:Cells
  13. Mirny LA. Cells use loop extrusion to weave and tie the genome. Nature. 2021 02; 590(7847):554-555. PMID: 33597775.
    Citations: 1     Fields:    Translation:Cells
  14. Mirny LA, Solovei I. Keeping chromatin in the loop(s). Nat Rev Mol Cell Biol. 2021 07; 22(7):439-440. PMID: 33504981.
    Citations: 2     Fields:    Translation:Cells
  15. Banigan EJ, Mirny LA. The interplay between asymmetric and symmetric DNA loop extrusion. Elife. 2020 12 09; 9. PMID: 33295869; PMCID: PMC7793625.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  16. Nora EP, Caccianini L, Fudenberg G, So K, Kameswaran V, Nagle A, Uebersohn A, Hajj B, Saux AL, Coulon A, Mirny LA, Pollard KS, Dahan M, Bruneau BG. Molecular basis of CTCF binding polarity in genome folding. Nat Commun. 2020 11 05; 11(1):5612. PMID: 33154377.
    Citations: 27     Fields:    Translation:AnimalsCells
  17. Banigan EJ, Mirny LA. Loop extrusion: theory meets single-molecule experiments. Curr Opin Cell Biol. 2020 06; 64:124-138. PMID: 32534241.
    Citations: 28     Fields:    Translation:HumansAnimalsCells
  18. Samata M, Alexiadis A, Richard G, Georgiev P, Nuebler J, Kulkarni T, Renschler G, Basilicata MF, Zenk FL, Shvedunova M, Semplicio G, Mirny L, Iovino N, Akhtar A. Intergenerationally Maintained Histone H4 Lysine 16 Acetylation Is Instructive for Future Gene Activation. Cell. 2020 07 09; 182(1):127-144.e23. PMID: 32502394.
    Citations: 16     Fields:    Translation:AnimalsCells
  19. Banigan EJ, van den Berg AA, Brandão HB, Marko JF, Mirny LA. Chromosome organization by one-sided and two-sided loop extrusion. Elife. 2020 04 06; 9. PMID: 32250245; PMCID: PMC7295573.
    Citations: 33     Fields:    Translation:Cells
  20. Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ. Ultrastructural Details of Mammalian Chromosome Architecture. Mol Cell. 2020 05 07; 78(3):554-565.e7. PMID: 32213324.
    Citations: 97     Fields:    Translation:HumansAnimalsCells
  21. Feodorova Y, Falk M, Mirny LA, Solovei I. Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals. Trends Cell Biol. 2020 04; 30(4):276-289. PMID: 31980345.
    Citations: 14     Fields:    Translation:HumansAnimalsCells
  22. Abdennur N, Mirny LA. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020 01 01; 36(1):311-316. PMID: 31290943; PMCID: PMC8205516.
    Citations: 93     Fields:    
  23. AlHaj Abed J, Erceg J, Goloborodko A, Nguyen SC, McCole RB, Saylor W, Fudenberg G, Lajoie BR, Dekker J, Mirny LA, Wu CT. Highly structured homolog pairing reflects functional organization of the Drosophila genome. Nat Commun. 2019 10 03; 10(1):4485. PMID: 31582763.
    Citations: 14     Fields:    Translation:AnimalsCells
  24. Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, Mirny LA, Wu CT. The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nat Commun. 2019 10 03; 10(1):4486. PMID: 31582744.
    Citations: 11     Fields:    Translation:AnimalsCells
  25. Brandão HB, Paul P, van den Berg AA, Rudner DZ, Wang X, Mirny LA. RNA polymerases as moving barriers to condensin loop extrusion. Proc Natl Acad Sci U S A. 2019 10 08; 116(41):20489-20499. PMID: 31548377.
    Citations: 31     Fields:    Translation:Cells
  26. Falk M, Feodorova Y, Naumova N, Imakaev M, Lajoie BR, Leonhardt H, Joffe B, Dekker J, Fudenberg G, Solovei I, Mirny LA. Publisher Correction: Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature. 2019 Aug; 572(7771):E22. PMID: 31375785.
    Citations:    Fields:    
  27. Mirny LA, Imakaev M, Abdennur N. Two major mechanisms of chromosome organization. Curr Opin Cell Biol. 2019 06; 58:142-152. PMID: 31228682; PMCID: PMC6800258.
    Citations: 58     Fields:    Translation:HumansAnimalsCells
  28. Falk M, Feodorova Y, Naumova N, Imakaev M, Lajoie BR, Leonhardt H, Joffe B, Dekker J, Fudenberg G, Solovei I, Mirny LA. Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature. 2019 06; 570(7761):395-399. PMID: 31168090; PMCID: PMC7206897.
    Citations: 154     Fields:    Translation:AnimalsCells
  29. Finn EH, Pegoraro G, Brandão HB, Valton AL, Oomen ME, Dekker J, Mirny L, Misteli T. Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Cell. 2019 03 07; 176(6):1502-1515.e10. PMID: 30799036.
    Citations: 137     Fields:    Translation:HumansCells
  30. Metkar M, Ozadam H, Lajoie BR, Imakaev M, Mirny LA, Dekker J, Moore MJ. Higher-Order Organization Principles of Pre-translational mRNPs. Mol Cell. 2018 11 15; 72(4):715-726.e3. PMID: 30415953; PMCID: PMC6239896.
    Citations: 22     Fields:    Translation:HumansCells
  31. Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, Hwang J, Lee S, Alver BH, Pfister H, Mirny LA, Park PJ, Gehlenborg N. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018 08 24; 19(1):125. PMID: 30143029; PMCID: PMC6109259.
    Citations: 136     Fields:    
  32. Nuebler J, Fudenberg G, Imakaev M, Abdennur N, Mirny LA. Chromatin organization by an interplay of loop extrusion and compartmental segregation. Proc Natl Acad Sci U S A. 2018 07 17; 115(29):E6697-E6706. PMID: 29967174; PMCID: PMC6055145.
    Citations: 191     Fields:    Translation:AnimalsCells
  33. Fudenberg G, Abdennur N, Imakaev M, Goloborodko A, Mirny LA. Emerging Evidence of Chromosome Folding by Loop Extrusion. Cold Spring Harb Symp Quant Biol. 2017; 82:45-55. PMID: 29728444; PMCID: PMC6512960.
    Citations: 82     Fields:    
  34. Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N, Nuebler J, Kanemaki MT, Xie L, Paulson JR, Earnshaw WC, Mirny LA, Dekker J. A pathway for mitotic chromosome formation. Science. 2018 02 09; 359(6376). PMID: 29348367.
    Citations: 218     Fields:    Translation:AnimalsCells
  35. Gassler J, Brandão HB, Imakaev M, Flyamer IM, Ladstätter S, Bickmore WA, Peters JM, Mirny LA, Tachibana K. A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture. EMBO J. 2017 12 15; 36(24):3600-3618. PMID: 29217590; PMCID: PMC5730859.
    Citations: 111     Fields:    Translation:AnimalsCells
  36. Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. Corrigendum: The 4D nucleome project. Nature. 2017 12 14; 552(7684):278. PMID: 29168505.
    Citations: 1     Fields:    
  37. Tucker NR, Dolmatova EV, Lin H, Cooper RR, Ye J, Hucker WJ, Jameson HS, Parsons VA, Weng LC, Mills RW, Sinner MF, Imakaev M, Leyton-Mange J, Vlahakes G, Benjamin EJ, Lunetta KL, Lubitz SA, Mirny L, Milan DJ, Ellinor PT. Diminished PRRX1 Expression Is Associated With Increased Risk of Atrial Fibrillation and Shortening of the Cardiac Action Potential. Circ Cardiovasc Genet. 2017 Oct; 10(5). PMID: 28974514.
    Citations: 15     Fields:    Translation:HumansAnimalsCells
  38. Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, Spitz F. Two independent modes of chromatin organization revealed by cohesin removal. Nature. 2017 11 02; 551(7678):51-56. PMID: 29094699; PMCID: PMC5687303.
    Citations: 362     Fields:    Translation:AnimalsCells
  39. Phillips AM, Gonzalez LO, Nekongo EE, Ponomarenko AI, McHugh SM, Butty VL, Levine SS, Lin YS, Mirny LA, Shoulders MD. Host proteostasis modulates influenza evolution. Elife. 2017 09 26; 6. PMID: 28949290.
    Citations: 16     Fields:    Translation:AnimalsCells
  40. Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. The 4D nucleome project. Nature. 2017 09 13; 549(7671):219-226. PMID: 28905911; PMCID: PMC5617335.
    Citations: 201     Fields:    Translation:HumansAnimalsCells
  41. Schalbetter SA, Goloborodko A, Fudenberg G, Belton JM, Miles C, Yu M, Dekker J, Mirny L, Baxter J. SMC complexes differentially compact mitotic chromosomes according to genomic context. Nat Cell Biol. 2017 Sep; 19(9):1071-1080. PMID: 28825700; PMCID: PMC5640152.
    Citations: 54     Fields:    Translation:AnimalsCells
  42. McFarland CD, Yaglom JA, Wojtkowiak JW, Scott JG, Morse DL, Sherman MY, Mirny LA. The Damaging Effect of Passenger Mutations on Cancer Progression. Cancer Res. 2017 09 15; 77(18):4763-4772. PMID: 28536279; PMCID: PMC5639691.
    Citations: 33     Fields:    Translation:HumansAnimalsCells
  43. Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell. 2017 May 18; 169(5):930-944.e22. PMID: 28525758; PMCID: PMC5538188.
    Citations: 520     Fields:    Translation:AnimalsCells
  44. Flyamer IM, Gassler J, Imakaev M, Brandão HB, Ulianov SV, Abdennur N, Razin SV, Mirny LA, Tachibana-Konwalski K. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature. 2017 04 06; 544(7648):110-114. PMID: 28355183; PMCID: PMC5639698.
    Citations: 244     Fields:    Translation:AnimalsCells
  45. Grajkowska LT, Ceribelli M, Lau CM, Warren ME, Tiniakou I, Nakandakari Higa S, Bunin A, Haecker H, Mirny LA, Staudt LM, Reizis B. Isoform-Specific Expression and Feedback Regulation of E Protein TCF4 Control Dendritic Cell Lineage Specification. Immunity. 2017 01 17; 46(1):65-77. PMID: 27986456.
    Citations: 36     Fields:    Translation:AnimalsCells
  46. Sawai CM, Babovic S, Upadhaya S, Knapp DJHF, Lavin Y, Lau CM, Goloborodko A, Feng J, Fujisaki J, Ding L, Mirny LA, Merad M, Eaves CJ, Reizis B. Hematopoietic Stem Cells Are the Major Source of Multilineage Hematopoiesis in Adult Animals. Immunity. 2016 09 20; 45(3):597-609. PMID: 27590115.
    Citations: 151     Fields:    Translation:AnimalsCells
  47. Goloborodko A, Marko JF, Mirny LA. Chromosome Compaction by Active Loop Extrusion. Biophys J. 2016 05 24; 110(10):2162-8. PMID: 27224481.
    Citations: 92     Fields:    Translation:HumansCells
  48. Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA. Formation of Chromosomal Domains by Loop Extrusion. Cell Rep. 2016 05 31; 15(9):2038-49. PMID: 27210764.
    Citations: 600     Fields:    Translation:Cells
  49. Goloborodko A, Imakaev MV, Marko JF, Mirny L. Compaction and segregation of sister chromatids via active loop extrusion. Elife. 2016 05 18; 5. PMID: 27192037.
    Citations: 116     Fields:    Translation:Cells
  50. Dekker J, Mirny L. The 3D Genome as Moderator of Chromosomal Communication. Cell. 2016 Mar 10; 164(6):1110-1121. PMID: 26967279; PMCID: PMC4788811.
    Citations: 363     Fields:    Translation:HumansAnimalsCells
  51. Khrameeva EE, Fudenberg G, Gelfand MS, Mirny LA. History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. J Bioinform Comput Biol. 2016 04; 14(2):1641002. PMID: 27021249.
    Citations: 1     Fields:    Translation:AnimalsCells
  52. Wang F, Kaplan JL, Gold BD, Bhasin MK, Ward NL, Kellermayer R, Kirschner BS, Heyman MB, Dowd SE, Cox SB, Dogan H, Steven B, Ferry GD, Cohen SA, Baldassano RN, Moran CJ, Garnett EA, Drake L, Otu HH, Mirny LA, Libermann TA, Winter HS, Korolev KS. Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota. Cell Rep. 2016 Feb 02; 14(4):945-955. PMID: 26804920; PMCID: PMC4740235.
    Citations: 25     Fields:    Translation:Humans
  53. Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature. 2016 Jan 21; 529(7586):418-22. PMID: 26760202.
    Citations: 311     Fields:    Translation:AnimalsCells
  54. Imakaev MV, Fudenberg G, Mirny LA. Modeling chromosomes: Beyond pretty pictures. FEBS Lett. 2015 Oct 07; 589(20 Pt A):3031-6. PMID: 26364723; PMCID: PMC4722799.
    Citations: 36     Fields:    Translation:HumansAnimalsCells
  55. Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B. Genome-wide maps of nuclear lamina interactions in single human cells. Cell. 2015 Sep 24; 163(1):134-47. PMID: 26365489; PMCID: PMC4583798.
    Citations: 179     Fields:    Translation:HumansCells
  56. Imakaev MV, Tchourine KM, Nechaev SK, Mirny LA. Effects of topological constraints on globular polymers. Soft Matter. 2015 Jan 28; 11(4):665-71. PMID: 25472862.
    Citations: 12     Fields:    
  57. Doyle B, Fudenberg G, Imakaev M, Mirny LA. Chromatin loops as allosteric modulators of enhancer-promoter interactions. PLoS Comput Biol. 2014 Oct; 10(10):e1003867. PMID: 25340767.
    Citations: 51     Fields:    Translation:Cells
  58. Mizuguchi T, Fudenberg G, Mehta S, Belton JM, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewal SIS. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature. 2014 Dec 18; 516(7531):432-435. PMID: 25307058.
    Citations: 124     Fields:    Translation:AnimalsCells
  59. McFarland CD, Mirny LA, Korolev KS. Tug-of-war between driver and passenger mutations in cancer and other adaptive processes. Proc Natl Acad Sci U S A. 2014 Oct 21; 111(42):15138-43. PMID: 25277973.
    Citations: 62     Fields:    Translation:Humans
  60. Yaglom JA, McFarland C, Mirny L, Sherman MY. Oncogene-triggered suppression of DNA repair leads to DNA instability in cancer. Oncotarget. 2014 Sep 30; 5(18):8367-78. PMID: 25252808.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  61. 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. Cell Rep. 2014 Feb 13; 6(3):528-40. PMID: 24485662.
    Citations: 15     Fields:    Translation:AnimalsCells
  62. 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. PMID: 24200812.
    Citations: 397     Fields:    Translation:HumansCells
  63. Le TB, Imakaev MV, Mirny LA, Laub MT. High-resolution mapping of the spatial organization of a bacterial chromosome. Science. 2013 Nov 08; 342(6159):731-4. PMID: 24158908.
    Citations: 227     Fields:    Translation:Cells
  64. Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one. Nature. 2013 Oct 03; 502(7469):45-6. PMID: 24067607.
    Citations: 6     Fields:    Translation:AnimalsCells
  65. 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. PMID: 23657480.
    Citations: 485     Fields:    Translation:HumansAnimalsCells
  66. 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. PMID: 23388632.
    Citations: 139     Fields:    Translation:Humans
  67. 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. PMID: 23028501.
    Citations: 55     Fields:    Translation:HumansCells
  68. 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 09; 109(41):16552-7. PMID: 23012405.
    Citations: 45     Fields:    Translation:HumansAnimalsCells
  69. 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. PMID: 22941365.
    Citations: 541     Fields:    Translation:HumansCells
  70. Fudenberg G, Mirny LA. Higher-order chromatin structure: bridging physics and biology. Curr Opin Genet Dev. 2012 Apr; 22(2):115-24. PMID: 22360992.
    Citations: 74     Fields:    Translation:HumansAnimalsCells
  71. 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. PMID: 22101486.
    Citations: 114     Fields:    Translation:HumansCells
  72. Marti-Renom MA, Mirny LA. Bridging the resolution gap in structural modeling of 3D genome organization. PLoS Comput Biol. 2011 Jul; 7(7):e1002125. PMID: 21779160.
    Citations: 43     Fields:    Translation:HumansCells
  73. Tafvizi A, Mirny LA, van Oijen AM. Dancing on DNA: kinetic aspects of search processes on DNA. Chemphyschem. 2011 Jun 06; 12(8):1481-9. PMID: 21560221.
    Citations: 69     Fields:    Translation:Cells
  74. Mirny LA. The fractal globule as a model of chromatin architecture in the cell. Chromosome Res. 2011 Jan; 19(1):37-51. PMID: 21274616.
    Citations: 172     Fields:    Translation:HumansCells
  75. 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. PMID: 21178072; PMCID: PMC3021058.
    Citations: 111     Fields:    Translation:HumansCells
  76. Mirny LA. Nucleosome-mediated cooperativity between transcription factors. Proc Natl Acad Sci U S A. 2010 Dec 28; 107(52):22534-9. PMID: 21149679.
    Citations: 145     Fields:    Translation:Cells
  77. 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 06; (39). PMID: 20461051.
    Citations: 168     Fields:    Translation:Cells
  78. Bölinger D, Sulkowska JI, Hsu HP, Mirny LA, Kardar M, Onuchic JN, Virnau P. A Stevedore's protein knot. PLoS Comput Biol. 2010 Apr 01; 6(4):e1000731. PMID: 20369018.
    Citations: 63     Fields:    Translation:Cells
  79. Mirny LA, Needleman DJ. Quantitative characterization of filament dynamics by single-molecule lifetime measurements. Methods Cell Biol. 2010; 95:583-600. PMID: 20466154.
    Citations: 5     Fields:    Translation:AnimalsCells
  80. Mirny LA. Nucleosome-mediated cooperativity between transcription factors. 2009. View Publication.
  81. 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. PMID: 19940016.
    Citations: 40     Fields:    Translation:AnimalsCells
  82. 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 09; 326(5950):289-93. PMID: 19815776.
    Citations: 3082     Fields:    Translation:HumansCells
  83. Wunderlich Z, Mirny LA. Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet. 2009 Oct; 25(10):434-40. PMID: 19815308.
    Citations: 111     Fields:    Translation:Cells
  84. Wunderlich Z, Mirny LA. Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Res. 2009 Aug; 37(14):4629-41. PMID: 19502496.
    Citations: 10     Fields:    Translation:Cells
  85. Kolesov G, Mirny LA. Using evolutionary information to find specificity-determining and co-evolving residues. Methods Mol Biol. 2009; 541:421-48. PMID: 19381538.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  86. Wunderlich Z, Mirny LA. Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Res. 2008 Jun; 36(11):3570-8. PMID: 18453629.
    Citations: 43     Fields:    Translation:Cells
  87. 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. PMID: 18424488.
    Citations: 79     Fields:    
  88. 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. PMID: 18159939; PMCID: PMC2230677.
    Citations: 46     Fields:    Translation:HumansAnimalsCells
  89. 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. PMID: 17709750; PMCID: PMC1955771.
    Citations: 58     Fields:    Translation:Cells
  90. 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. PMID: 17517776; PMCID: PMC1933242.
    Citations: 37     Fields:    Translation:Cells
  91. 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. PMID: 17448993; PMCID: PMC1899089.
    Citations: 113     Fields:    Translation:AnimalsCells
  92. Virnau P, Mirny LA, Kardar M. Intricate knots in proteins: Function and evolution. PLoS Comput Biol. 2006 Sep 15; 2(9):e122. PMID: 16978047; PMCID: PMC1570178.
    Citations: 96     Fields:    Translation:HumansCells
  93. 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 06; 103(23):8774-9. PMID: 16731630; PMCID: PMC1482654.
    Citations: 43     Fields:    Translation:Cells
  94. Slutsky M, Mirny LA. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys J. 2004 Dec; 87(6):4021-35. PMID: 15465864; PMCID: PMC1304911.
    Citations: 191     Fields:    Translation:Cells
  95. 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. PMID: 14682823.
    Citations: 86     Fields:    Translation:Cells
  96. 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. PMID: 14517352; PMCID: PMC218723.
    Citations: 389     Fields:    
  97. 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. PMID: 7556598.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.