Leonid Mirny, PhD
Massachusetts Institute of Technology
Massachusetts Institute of Technology
Phone: (617) 452-4862
Leonid Mirny, PhD
Massachusetts Institute of Technology
EDUCATIONAL TITLES
DF/HCC PROGRAM AFFILIATION
Publications from Harvard Catalyst Profiles
- 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; 28:642-651. PubMed
- Banigan EJ, Mirny LA. Loop extrusion: theory meets single-molecule experiments. Curr Opin Cell Biol 2020; 64:124-138. PubMed
- 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. PubMed
- Banigan EJ, van den Berg AA, Brandão HB, Marko JF, Mirny LA. Chromosome organization by one-sided and two-sided loop extrusion. Elife 2020. PubMed
- 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. PubMed
- 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; 11:5612. PubMed
- Banigan EJ, Mirny LA. The interplay between asymmetric and symmetric DNA loop extrusion. Elife 2020. PubMed
- 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. PubMed
- Abdennur N, Mirny L. Cooler: scalable storage for Hi-C data and other genomically-labeled arrays. Bioinformatics 2019. PubMed
- Mirny LA, Imakaev M, Abdennur N. Two major mechanisms of chromosome organization. Curr Opin Cell Biol 2019; 58:142-152. PubMed
- 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; 570:395-399. PubMed
- 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; 176:1502-1515.e10. PubMed
- 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; 10:4485. PubMed
- 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; 10:4486. PubMed
- 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; 72:715-726.e3. PubMed
- 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. PubMed
- Fudenberg G, Abdennur N, Imakaev M, Goloborodko A, Mirny LA. Emerging Evidence of Chromosome Folding by Loop Extrusion. Cold Spring Harb Symp Quant Biol 2018. PubMed
- 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; 19:125. PubMed
- 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. PubMed
- Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, H Haering C, Mirny L, Spitz F. Two independent modes of chromatin organization revealed by cohesin removal. Nature 2017; 551:51-56. PubMed
- 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; 549:219-226. PubMed
- 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; 19:1071-1080. PubMed
- McFarland C, Yaglom JA, Wojtkowiak JW, Scott J, Morse DL, Sherman MY, Mirny L. The damaging effect of passenger mutations on cancer progression. Cancer Res 2017. PubMed
- 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; 169:930-944.e22. PubMed
- 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; 544:110-114. PubMed
- 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; 46:65-77. PubMed
- 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. Hematopoietic Stem Cells Are the Major Source of Multilineage Hematopoiesis in Adult Animals. Immunity 2016; 45:597-609. PubMed
- Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA. Formation of Chromosomal Domains by Loop Extrusion. Cell Rep 2016; 15:2038-49. PubMed
- Goloborodko A, Marko JF, Mirny LA. Chromosome Compaction by Active Loop Extrusion. Biophys J 2016; 110:2162-8. PubMed
- Khrameeva EE, Fudenberg G, Gelfand MS, Mirny LA. History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. J Bioinform Comput Biol 2016; 14:1641002. PubMed
- 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; 529:418-22. PubMed
- Goloborodko A, Imakaev MV, Marko JF, Mirny L. Compaction and segregation of sister chromatids via active loop extrusion. Elife 2016. PubMed
- 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; 163:134-47. PubMed
- Imakaev MV, Tchourine KM, Nechaev SK, Mirny LA. Effects of topological constraints on globular polymers. Soft Matter 2015; 11:665-71. PubMed
- Mizuguchi T, Fudenberg G, Mehta S, Belton JM, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewal SI. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature 2014. PubMed
- 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; 111:15138-43. PubMed
- Doyle B, Fudenberg G, Imakaev M, Mirny LA. Chromatin loops as allosteric modulators of enhancer-promoter interactions. PLoS Comput. Biol. 2014; 10:e1003867. PubMed
- Yaglom JA, McFarland C, Mirny L, Sherman MY. Oncogene-triggered suppression of DNA repair leads to DNA instability in cancer. 2014; 5:8367-78. PubMed
- Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J. Organization of the mitotic chromosome. Science 2013; 342:948-53. PubMed
- Le TB, Imakaev MV, Mirny LA, Laub MT. High-resolution mapping of the spatial organization of a bacterial chromosome. Science 2013; 342:731-4. PubMed
- Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 2013. PubMed
- 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; 110:2910-5. PubMed
- 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; 9:999-1003. PubMed