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Leonid A. Mirny - Publications

Affiliations: 
Medical Engineering and Sciences Massachusetts Institute of Technology, Cambridge, MA, United States 
Area:
Population genetics and evolutionary theory; Polymer physics theory and simulation; Statistical interpretation of genome-wide data
Website:
http://www.fas.harvard.edu/~biophys/Leonid_Mirny.htm
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Year Citation  Score
2022 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. PMID 35585235 DOI: 10.1038/s41586-022-04730-0  0.311
2020 Banigan EJ, Mirny LA. Loop extrusion: theory meets single-molecule experiments. Current Opinion in Cell Biology. 64: 124-138. PMID 32534241 DOI: 10.1016/J.Ceb.2020.04.011  0.405
2020 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. PMID 32502394 DOI: 10.1016/J.Cell.2020.05.026  0.327
2020 Banigan EJ, van den Berg AA, Brandão HB, Marko JF, Mirny LA. Chromosome organization by one-sided and two-sided loop extrusion. Elife. 9. PMID 32250245 DOI: 10.7554/Elife.53558  0.383
2020 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. Molecular Cell. PMID 32213324 DOI: 10.1016/J.Molcel.2020.03.003  0.381
2020 Feodorova Y, Falk M, Mirny LA, Solovei I. Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals. Trends in Cell Biology. PMID 31980345 DOI: 10.1016/J.Tcb.2019.12.008  0.349
2020 Banigan EJ, Berg AAvd, Brandão HB, Marko JF, Mirny LA. Author response: Chromosome organization by one-sided and two-sided loop extrusion Elife. DOI: 10.7554/Elife.53558.Sa2  0.318
2019 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. Nature Communications. 10: 4485. PMID 31582763 DOI: 10.1038/S41467-019-12208-3  0.73
2019 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, et al. The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nature Communications. 10: 4486. PMID 31582744 DOI: 10.1038/S41467-019-12211-8  0.738
2019 Brandão HB, Paul P, van den Berg AA, Rudner DZ, Wang X, Mirny LA. RNA polymerases as moving barriers to condensin loop extrusion. Proceedings of the National Academy of Sciences of the United States of America. PMID 31548377 DOI: 10.1073/Pnas.1907009116  0.414
2019 Abdennur N, Mirny L. Cooler: scalable storage for Hi-C data and other genomically-labeled arrays. Bioinformatics (Oxford, England). PMID 31290943 DOI: 10.1093/Bioinformatics/Btz540  0.31
2019 Mirny LA, Imakaev M, Abdennur N. Two major mechanisms of chromosome organization. Current Opinion in Cell Biology. 58: 142-152. PMID 31228682 DOI: 10.1016/J.Ceb.2019.05.001  0.382
2019 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. PMID 31168090 DOI: 10.1038/S41586-019-1275-3  0.379
2019 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. PMID 30799036 DOI: 10.1016/J.Cell.2019.01.020  0.367
2018 Nuebler J, Fudenberg G, Imakaev M, Abdennur N, Mirny LA. Chromatin organization by an interplay of loop extrusion and compartmental segregation. Proceedings of the National Academy of Sciences of the United States of America. PMID 29967174 DOI: 10.1016/J.Bpj.2017.11.211  0.388
2018 Fudenberg G, Abdennur N, Imakaev M, Goloborodko A, Mirny LA. Emerging Evidence of Chromosome Folding by Loop Extrusion. Cold Spring Harbor Symposia On Quantitative Biology. PMID 29728444 DOI: 10.1101/Sqb.2017.82.034710  0.75
2018 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 (New York, N.Y.). PMID 29348367 DOI: 10.1126/Science.Aao6135  0.722
2017 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. The Embo Journal. 36: 3600-3618. PMID 29217590 DOI: 10.15252/Embj.201798083  0.387
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. Two independent modes of chromatin organization revealed by cohesin removal. Nature. 551: 51-56. PMID 29094699 DOI: 10.1038/Nature24281  0.74
2017 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. 549: 219-226. PMID 28905911 DOI: 10.1038/Nature23884  0.342
2017 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. Nature Cell Biology. PMID 28825700 DOI: 10.1038/Ncb3594  0.733
2017 McFarland C, Yaglom JA, Wojtkowiak JW, Scott J, Morse DL, Sherman MY, Mirny L. The damaging effect of passenger mutations on cancer progression. Cancer Research. PMID 28536279 DOI: 10.1158/0008-5472.Can-15-3283-T  0.726
2017 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. 169: 930-944.e22. PMID 28525758 DOI: 10.1016/J.Cell.2017.05.004  0.743
2017 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. PMID 28355183 DOI: 10.1038/Nature21711  0.379
2017 Brandao H, Wang X, Rudner D, Mirny L. Elucidating the Role of Transcription in Shaping the 3D Structure of the Bacterial Genome Biophysical Journal. 112: 69a. DOI: 10.1016/J.Bpj.2016.11.417  0.433
2017 Goloborodko A, Imakaev M, Marko JF, Mirny L. Compaction and Segregation of Sister Chromatids by Loop-Extruding Enzymes Biophysical Journal. 112: 373a. DOI: 10.1016/J.Bpj.2016.11.2024  0.743
2016 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. PMID 27986456 DOI: 10.1016/J.Immuni.2016.11.006  0.302
2016 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. PMID 27590115 DOI: 10.1016/J.Immuni.2016.08.007  0.67
2016 Goloborodko A, Marko JF, Mirny LA. Chromosome Compaction by Active Loop Extrusion. Biophysical Journal. 110: 2162-2168. PMID 27224481 DOI: 10.1016/J.Bpj.2016.02.041  0.727
2016 Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA. Formation of Chromosomal Domains by Loop Extrusion. Cell Reports. PMID 27210764 DOI: 10.1016/J.Celrep.2016.04.085  0.737
2016 Goloborodko A, Imakaev MV, Marko JF, Mirny L. Compaction and segregation of sister chromatids via active loop extrusion. Elife. 5. PMID 27192037 DOI: 10.7554/Elife.14864  0.729
2016 Khrameeva EE, Fudenberg G, Gelfand MS, Mirny LA. History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. Journal of Bioinformatics and Computational Biology. 1641002. PMID 27021249 DOI: 10.1142/S021972001641002X  0.399
2016 Dekker J, Mirny L. The 3D Genome as Moderator of Chromosomal Communication. Cell. 164: 1110-1121. PMID 26967279 DOI: 10.1016/J.Cell.2016.02.007  0.345
2016 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. PMID 26760202 DOI: 10.1038/Nature16496  0.363
2016 Goloborodko A, Imakaev MV, Marko JF, Mirny L. Author response: Compaction and segregation of sister chromatids via active loop extrusion Elife. DOI: 10.7554/Elife.14864.018  0.677
2015 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, et al. Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells. Cell. 163: 134-47. PMID 26365489 DOI: 10.1016/J.Cell.2015.08.040  0.36
2015 Imakaev MV, Fudenberg G, Mirny LA. Modeling chromosomes: Beyond pretty pictures. Febs Letters. 589: 3031-6. PMID 26364723 DOI: 10.1016/J.Febslet.2015.09.004  0.345
2014 Doyle B, Fudenberg G, Imakaev M, Mirny LA. Chromatin loops as allosteric modulators of enhancer-promoter interactions. Plos Computational Biology. 10: e1003867. PMID 25340767 DOI: 10.1371/Journal.Pcbi.1003867  0.373
2014 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. 516: 432-5. PMID 25307058 DOI: 10.1038/Nature13833  0.425
2014 McFarland CD, Mirny LA, Korolev KS. Tug-of-war between driver and passenger mutations in cancer and other adaptive processes. Proceedings of the National Academy of Sciences of the United States of America. 111: 15138-43. PMID 25277973 DOI: 10.1073/Pnas.1404341111  0.712
2014 Yaglom JA, McFarland C, Mirny L, Sherman MY. Oncogene-triggered suppression of DNA repair leads to DNA instability in cancer. Oncotarget. 5: 8367-78. PMID 25252808 DOI: 10.18632/Oncotarget.2259  0.739
2013 Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J. Organization of the mitotic chromosome. Science (New York, N.Y.). 342: 948-53. PMID 24200812 DOI: 10.1126/Science.1236083  0.385
2013 Le TB, Imakaev MV, Mirny LA, Laub MT. High-resolution mapping of the spatial organization of a bacterial chromosome. Science (New York, N.Y.). 342: 731-4. PMID 24158908 DOI: 10.1126/Science.1242059  0.408
2013 Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one Nature. 502: 45-46. PMID 24067607 DOI: 10.1038/Nature12691  0.395
2013 Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nature Reviews. Genetics. 14: 390-403. PMID 23657480 DOI: 10.1038/Nrg3454  0.375
2013 McFarland CD, Korolev KS, Kryukov GV, Sunyaev SR, Mirny LA. Impact of deleterious passenger mutations on cancer progression. Proceedings of the National Academy of Sciences of the United States of America. 110: 2910-5. PMID 23388632 DOI: 10.1073/Pnas.1213968110  0.722
2013 Imakaev M, Fudenberg G, Mirny L. Chromosomal architecture changes upon cell differentiation Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P130  0.323
2013 Goloborodko A, Belton JM, Fudenberg G, Imakaev M, Dekker J, Mirny L. S cerevisiae genome as a confined equilibrium polymer brush Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P129  0.705
2013 Fudenberg G, Belton J, Goloborodko A, Imakaev M, Dekker J, Mirny L. Polymer models of yeast S. cerevisiae genome organization Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P128  0.744
2013 Doyle B, Imakaev M, Fudenberg G, Mirny L. Polymer models of topological insulators Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P127  0.318
2013 Goloborodko A, Fudenberg G, Belton J, Imakaev M, Dekker J, Mirny L. Polymer Models of Yeast S. Cerevisiae Genome Organization Biophysical Journal. 104: 581a-582a. DOI: 10.1016/j.bpj.2012.11.3230  0.677
2012 Engreitz JM, Agarwala V, Mirny LA. Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease. Plos One. 7: e44196. PMID 23028501 DOI: 10.1371/Journal.Pone.0044196  0.394
2012 Leith JS, Tafvizi A, Huang F, Uspal WE, Doyle PS, Fersht AR, Mirny LA, van Oijen AM. Sequence-dependent sliding kinetics of p53. Proceedings of the National Academy of Sciences of the United States of America. 109: 16552-7. PMID 23012405 DOI: 10.1073/Pnas.1120452109  0.782
2012 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. 9: 999-1003. PMID 22941365 DOI: 10.1038/Nmeth.2148  0.728
2012 Fudenberg G, Mirny LA. Higher-order chromatin structure: bridging physics and biology. Current Opinion in Genetics & Development. 22: 115-24. PMID 22360992 DOI: 10.1016/J.Gde.2012.01.006  0.37
2011 Fudenberg G, Getz G, Meyerson M, Mirny LA. High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nature Biotechnology. 29: 1109-13. PMID 22101486 DOI: 10.1038/Nbt.2049  0.367
2011 Marti-Renom MA, Mirny LA. Bridging the resolution gap in structural modeling of 3D genome organization. Plos Computational Biology. 7: e1002125. PMID 21779160 DOI: 10.1371/Journal.Pcbi.1002125  0.369
2011 Tafvizi A, Mirny LA, van Oijen AM. Dancing on DNA: kinetic aspects of search processes on DNA. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 12: 1481-9. PMID 21560221 DOI: 10.1002/Cphc.201100112  0.604
2011 Mirny LA. The fractal globule as a model of chromatin architecture in the cell. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 19: 37-51. PMID 21274616 DOI: 10.1007/S10577-010-9177-0  0.337
2011 Tafvizi A, Huang F, Fersht AR, Mirny LA, van Oijen AM. A single-molecule characterization of p53 search on DNA. Proceedings of the National Academy of Sciences of the United States of America. 108: 563-8. PMID 21178072 DOI: 10.1073/Pnas.1016020107  0.587
2011 McFarland CD, Scott JG, Basanta D, Anderson ARA, Mirny LA. Abstract 24: A genetic model of metastatic evolution: Driver and passenger mutations affect metastatic fitness Cancer Research. 71: 24-24. DOI: 10.1158/1538-7445.Am2011-24  0.71
2011 Fudenberg G, Getz G, Meyerson M, Mirny L. High-order chromatin architecture determines the landscape of chromosomal alterations in cancer Nature Precedings. 6: 1-1. DOI: 10.1038/Npre.2011.6356.1  0.372
2010 Mirny LA. Nucleosome-mediated cooperativity between transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 107: 22534-9. PMID 21149679 DOI: 10.1073/Pnas.0913805107  0.352
2010 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. Journal of Visualized Experiments : Jove. PMID 20461051 DOI: 10.3791/1869  0.442
2010 Bölinger D, Su?kowska JI, Hsu HP, Mirny LA, Kardar M, Onuchic JN, Virnau P. A Stevedore's protein knot. Plos Computational Biology. 6: e1000731. PMID 20369018 DOI: 10.1371/Journal.Pcbi.1000731  0.348
2009 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, ... ... Mirny LA, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (New York, N.Y.). 326: 289-93. PMID 19815776 DOI: 10.1126/Science.1181369  0.374
2009 Wunderlich Z, Mirny LA. Different gene regulation strategies revealed by analysis of binding motifs. Trends in Genetics : Tig. 25: 434-40. PMID 19815308 DOI: 10.1016/J.Tig.2009.08.003  0.701
2009 Wunderlich Z, Mirny LA. Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Research. 37: 4629-41. PMID 19502496 DOI: 10.1093/Nar/Gkp394  0.685
2009 Kolesov G, Mirny LA. Using evolutionary information to find specificity-determining and co-evolving residues. Methods in Molecular Biology (Clifton, N.J.). 541: 421-48. PMID 19381538 DOI: 10.1007/978-1-59745-243-4_18  0.388
2009 Mirny L, Slutsky M, Wunderlich Z, Tafvizi A, Leith J, Kosmrlj A. How a protein searches for its site on DNA: The mechanism of facilitated diffusion Journal of Physics a: Mathematical and Theoretical. 42. DOI: 10.1088/1751-8113/42/43/434013  0.781
2009 Mirny LA. A Biophysical Model Of Interactions Between Transcription Factors And Chromatin Biophysical Journal. 96: 566a-567a. DOI: 10.1016/J.Bpj.2008.12.3714  0.381
2009 Tafvizi A, Leith JS, Huang F, Fersht AR, Mirny L, van Oijen AM. Single-molecule Studies Of p53 Sliding Along DNA Biophysical Journal. 96: 417a. DOI: 10.1016/J.Bpj.2008.12.2128  0.779
2009 Leith JS, Tafvizi A, Huang F, Fersht AR, Mirny L, van Oijen AM. Sequence-Dependent Kinetics of One-Dimensional Diffusion of p53 on DNA Biophysical Journal. 96: 416a. DOI: 10.1016/J.Bpj.2008.12.2125  0.786
2008 Jamal Rahi S, Virnau P, Mirny LA, Kardar M. Predicting transcription factor specificity with all-atom models. Nucleic Acids Research. 36: 6209-17. PMID 18829719 DOI: 10.1093/Nar/Gkn589  0.384
2008 Wunderlich Z, Mirny LA. Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Research. 36: 3570-8. PMID 18453629 DOI: 10.1093/Nar/Gkn173  0.698
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: L01-3. PMID 18424488 DOI: 10.1529/Biophysj.108.134122  0.777
2008 Wunderlich Z, Mirny L. Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs Nature Precedings. DOI: 10.1038/Npre.2008.2688.2  0.69
2008 Wunderlich Z, Mirny L. An optimized energy potential can predict SH2 domain-peptide interactions Nature Precedings. DOI: 10.1038/Npre.2008.1881.1  0.649
2007 Kolesov G, Wunderlich Z, Laikova ON, Gelfand MS, Mirny LA. How gene order is influenced by the biophysics of transcription regulation. Proceedings of the National Academy of Sciences of the United States of America. 104: 13948-53. PMID 17709750 DOI: 10.1073/Pnas.0700672104  0.701
2007 Kolesov G, Virnau P, Kardar M, Mirny LA. Protein knot server: detection of knots in protein structures. Nucleic Acids Research. 35: W425-8. PMID 17517776 DOI: 10.1093/Nar/Gkm312  0.321
2006 Virnau P, Mirny LA, Kardar M. Intricate knots in proteins: Function and evolution. Plos Computational Biology. 2: e122. PMID 16978047 DOI: 10.1371/Journal.Pcbi.0020122  0.326
2006 Wunderlich Z, Mirny LA. Using the topology of metabolic networks to predict viability of mutant strains. Biophysical Journal. 91: 2304-11. PMID 16782788 DOI: 10.1529/Biophysj.105.080572  0.653
2005 Donald JE, Hubner IA, Rotemberg VM, Shakhnovich EI, Mirny LA. CoC: a database of universally conserved residues in protein folds. Bioinformatics (Oxford, England). 21: 2539-40. PMID 15746286 DOI: 10.1093/Bioinformatics/Bti360  0.747
2005 Wunderlich Z, Mirny L. Genome Biology. 6: P15. DOI: 10.1186/Gb-2005-6-13-P15  0.655
2004 Slutsky M, Mirny LA. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophysical Journal. 87: 4021-35. PMID 15465864 DOI: 10.1529/Biophysj.104.050765  0.413
2004 Slutsky M, Kardar M, Mirny LA. Diffusion in correlated random potentials, with applications to DNA. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 061903. PMID 15244613 DOI: 10.1103/Physreve.69.061903  0.304
2003 Chen W, Mirny L, Shakhnovich EI. Fold recognition with minimal gaps. Proteins. 51: 531-43. PMID 12784212 DOI: 10.1002/Prot.10402  0.625
2003 Li L, Shakhnovich EI, Mirny LA. Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proceedings of the National Academy of Sciences of the United States of America. 100: 4463-8. PMID 12679523 DOI: 10.1073/Pnas.0737647100  0.747
2002 Mirny LA, Gelfand MS. Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. Journal of Molecular Biology. 321: 7-20. PMID 12139929 DOI: 10.1016/S0022-2836(02)00587-9  0.41
2002 Mirny LA, Gelfand MS. Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Research. 30: 1704-11. PMID 11917033 DOI: 10.1093/Nar/30.7.1704  0.398
2002 Mirny LA, Gelfand MS. Using orthologous and paralogous proteins to identify specificity determining residues. Genome Biology. 3: PREPRINT0002. PMID 11897020 DOI: 10.1186/Gb-2002-3-3-Preprint0002  0.408
2002 Dokholyan NV, Mirny LA, Shakhnovich EI. Understanding conserved amino acids in proteins Physica a: Statistical Mechanics and Its Applications. 314: 600-606. DOI: 10.1016/S0378-4371(02)01079-8  0.501
2001 Mirny L, Shakhnovich E. Protein folding theory: From lattice to all-atom models Annual Review of Biophysics and Biomolecular Structure. 30: 361-396. PMID 11340064 DOI: 10.1146/Annurev.Biophys.30.1.361  0.52
2001 Mirny L, Shakhnovich E. Evolutionary conservation of the folding nucleus Journal of Molecular Biology. 308: 123-129. PMID 11327757 DOI: 10.1006/Jmbi.2001.4602  0.512
2000 Vendruscolo M, Mirny LA, Shakhnovich EI, Domany E. Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score. Proteins. 41: 192-201. PMID 10966572 DOI: 10.1002/1097-0134(20001101)41:2<192::Aid-Prot40>3.0.Co;2-3  0.482
2000 Mirny LA, Finkelstein AV, Shakhnovich EI. Statistical significance of protein structure prediction by threading. Proceedings of the National Academy of Sciences of the United States of America. 97: 9978-83. PMID 10954732 DOI: 10.1073/Pnas.160271197  0.519
2000 Li L, Mirny LA, Shakhnovich EI. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nature Structural Biology. 7: 336-42. PMID 10742180 DOI: 10.1038/74111  0.742
1999 Mirny LA, Shakhnovich EI. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. Journal of Molecular Biology. 291: 177-96. PMID 10438614 DOI: 10.1006/Jmbi.1999.2911  0.554
1999 Finkelstein AV, Rykunov DS, Lobanov MY, Badretdinov AY, Reva BA, Skolnick J, Mirny LA, Shakhnovich EI. When and how the homologs can overcome errors in the energy estimates and make the 3D structure prediction possible Biofizika. 44: 990-991.  0.399
1998 Mirny LA, Shakhnovich EI. Protein structure prediction by threading. Why it works and why it does not. Journal of Molecular Biology. 283: 507-26. PMID 9769221 DOI: 10.1006/Jmbi.1998.2092  0.511
1998 Mirny LA, Abkevich VI, Shakhnovich EI. How evolution makes proteins fold quickly. Proceedings of the National Academy of Sciences of the United States of America. 95: 4976-81. PMID 9560213 DOI: 10.1073/Pnas.95.9.4976  0.545
1996 Mirny LA, Abkevich V, Shakhnovich EI. Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model. Folding & Design. 1: 103-16. PMID 9079370 DOI: 10.1016/S1359-0278(96)00019-3  0.53
1996 Mirny LA, Shakhnovich EI. How to derive a protein folding potential? A new approach to an old problem. Journal of Molecular Biology. 264: 1164-79. PMID 9000638 DOI: 10.1006/Jmbi.1996.0704  0.525
1996 Mirny L, Domany E. Protein fold recognition and dynamics in the space of contact maps Proteins: Structure, Function and Genetics. 26: 391-410. PMID 8990495 DOI: 10.1002/(Sici)1097-0134(199612)26:4<391::Aid-Prot3>3.0.Co;2-F  0.334
Low-probability matches (unlikely to be authored by this person)
2018 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, et al. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biology. 19: 125. PMID 30143029 DOI: 10.1186/S13059-018-1486-1  0.3
2019 Mirny L. Chromosome Organization by Loop Extrusion and Phase Separation Biophysical Journal. 116: 171a. DOI: 10.1016/J.Bpj.2018.11.949  0.299
2003 Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proceedings of the National Academy of Sciences of the United States of America. 100: 12123-8. PMID 14517352 DOI: 10.1073/Pnas.2032324100  0.298
2018 Brandão HB, Gassler J, Imakaev M, Flyamer IM, Ladstätter S, Bickmore WA, Peters J, Tachibana-Konwalski K, Mirny LA. A Mechanism of Cohesin-Dependent Loop Extrusion Organizes Mammalian Chromatin Structure in the Developing Embryo Biophysical Journal. 114: 255a. DOI: 10.1016/J.Bpj.2017.11.1417  0.292
2023 Mirny LA. Chromosome and protein folding: In search for unified principles. Current Opinion in Structural Biology. 81: 102610. PMID 37327690 DOI: 10.1016/j.sbi.2023.102610  0.29
2020 Mirny LA, Musacchio A, Marko JF. Decision letter: Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner Elife. DOI: 10.7554/Elife.53885.Sa1  0.29
2006 Spirin V, Gelfand MS, Mironov AA, Mirny LA. A metabolic network in the evolutionary context: multiscale structure and modularity. Proceedings of the National Academy of Sciences of the United States of America. 103: 8774-9. PMID 16731630 DOI: 10.1073/Pnas.0510258103  0.29
2015 Imakaev MV, Tchourine KM, Nechaev SK, Mirny LA. Effects of topological constraints on globular polymers. Soft Matter. 11: 665-71. PMID 25472862 DOI: 10.1039/C4Sm02099E  0.287
1995 Alon RN, Mirny L, Sussman JL, Gutnick DL. Detection of α/β-hydrolase fold in the cell surface esterases of Acinetobacter species using an analysis of 3D profiles Febs Letters. 371: 231-235. PMID 7556598 DOI: 10.1016/0014-5793(95)00861-3  0.286
2022 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. Nature Structural & Molecular Biology. 30: 38-51. PMID 36550219 DOI: 10.1038/s41594-022-00892-7  0.284
2019 Banigan EJ, Mirny LA. Limits of Chromosome Compaction by Loop-Extruding Motors Physical Review X. 9. DOI: 10.1103/Physrevx.9.031007  0.282
2017 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. 6. PMID 28949290 DOI: 10.7554/Elife.28652  0.281
2010 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. Molecular Biology of the Cell. 21: 323-33. PMID 19940016 DOI: 10.1091/Mbc.E09-09-0816  0.276
2021 Brandão HB, Ren Z, Karaboja X, Mirny LA, Wang X. DNA-loop-extruding SMC complexes can traverse one another in vivo. Nature Structural & Molecular Biology. 28: 642-651. PMID 34312537 DOI: 10.1038/s41594-021-00626-1  0.275
2018 Metkar M, Ozadam H, Lajoie BR, Imakaev M, Mirny LA, Dekker J, Moore MJ. Higher-Order Organization Principles of Pre-translational mRNPs. Molecular Cell. 72: 715-726.e3. PMID 30415953 DOI: 10.1016/J.Molcel.2018.09.012  0.274
2004 Slutsky M, Kardar M, Mirny LA. Erratum: Diffusion in correlated random potentials, with applications to DNA [Phys. Rev. E69, 061903 (2004)] Physical Review E. 70. DOI: 10.1103/Physreve.70.049901  0.271
2017 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. The Embo Journal. 36: 3600-3618. PMID 29217590 DOI: 10.15252/embj.201798083  0.266
2023 Galitsyna A, Ulianov SV, Bykov NS, Veil M, Gao M, Perevoschikova K, Gelfand M, Razin SV, Mirny L, Onichtchouk D. Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation. Biorxiv : the Preprint Server For Biology. PMID 37503128 DOI: 10.1101/2023.07.15.549120  0.266
2011 Reith D, Mirny L, Virnau P. GPU based molecular dynamics simulations of polymer rings in concentrated solution: Structure and scaling Progress of Theoretical Physics Supplement. 135-145. DOI: 10.1143/Ptps.191.135  0.259
2021 Mirny L, Dekker J. Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. Cold Spring Harbor Perspectives in Biology. PMID 34518339 DOI: 10.1101/cshperspect.a040147  0.256
2017 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, ... ... Mirny L, et al. Diminished PRRX1 Expression Is Associated With Increased Risk of Atrial Fibrillation and Shortening of the Cardiac Action Potential. Circulation. Cardiovascular Genetics. 10. PMID 28974514 DOI: 10.1161/Circgenetics.117.001902  0.255
2002 Ekins S, Mirny L, Schuetz EG. A ligand-based approach to understanding selectivity of nuclear hormone receptors PXR, CAR, FXR, LXRα, and LXRβ Pharmaceutical Research. 19: 1788-1800. PMID 12523656 DOI: 10.1023/A:1021429105173  0.255
2007 Levine J, Kueh HY, Mirny L. Intrinsic fluctuations, robustness, and tunability in signaling cycles. Biophysical Journal. 92: 4473-81. PMID 17400695 DOI: 10.1529/Biophysj.106.088856  0.254
2020 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. Nature Communications. 11: 5612. PMID 33154377 DOI: 10.1038/s41467-020-19283-x  0.254
2014 Doyle B, Fudenberg G, Imakaev M, Mirny LA. Enhancer-promoter pairs in the context of other interactions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1003867.G001  0.253
2017 Falk MJ, Naumova NM, Fudenberg G, Feodorova YN, Dekker J, Mirny LA, Solovei I. Polymer Models Integrate Inverted Nuclear Geometry with Conventional HI-C Compartmentalization Biophysical Journal. 112: 373a. DOI: 10.1016/J.Bpj.2016.11.2025  0.252
1996 Shlyakhter A, Mirny L, Vlasov A, Wilson R. Monte Carlo modeling of epidemiological studies Human and Ecological Risk Assessment (Hera). 2: 920-938. DOI: 10.1080/10807039609383656  0.252
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. Cell Reports. 6: 528-40. PMID 24485662 DOI: 10.1016/J.Celrep.2014.01.007  0.25
2020 Banigan EJ, Mirny LA. The interplay between asymmetric and symmetric DNA loop extrusion. Elife. 9. PMID 33295869 DOI: 10.7554/eLife.63528  0.249
2019 Caccianini L, Nora EP, Nuebler J, LesSaux A, Heard E, Mirny L, Bruneau B, Dahan M. Single Molecule Imaging of CTCF and Cohesin. Dissecting the Dynamic Interplay between Chromatin Loop Regulators Biophysical Journal. 116: 22a. DOI: 10.1016/J.Bpj.2018.11.160  0.248
2023 Liu S, Miné-Hattab J, Villemeur M, Guerois R, Pinholt HD, Mirny LA, Taddei A. In vivo tracking of functionally tagged Rad51 unveils a robust strategy of homology search. Nature Structural & Molecular Biology. PMID 37605042 DOI: 10.1038/s41594-023-01065-w  0.248
2003 Lidmar J, Mirny L, Nelson DR. Virus shapes and buckling transitions in spherical shells. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 68: 051910. PMID 14682823 DOI: 10.1103/Physreve.68.051910  0.246
2010 Mirny LA, Needleman DJ. Quantitative characterization of filament dynamics by single-molecule lifetime measurements. Methods in Cell Biology. 95: 583-600. PMID 20466154 DOI: 10.1016/S0091-679X(10)95029-2  0.242
2023 Banigan EJ, Tang W, van den Berg AA, Stocsits RR, Wutz G, Brandão HB, Busslinger GA, Peters JM, Mirny LA. Transcription shapes 3D chromatin organization by interacting with loop extrusion. Proceedings of the National Academy of Sciences of the United States of America. 120: e2210480120. PMID 36897969 DOI: 10.1073/pnas.2210480120  0.24
1994 Chepel Yu. V, Khvostunov IK, Mirny LA, Talyzina TA, Andreev SG. 3-D computer modelling of chromatin fibres for radiation damage simulation Radiation Protection Dosimetry. 52: 259-263. DOI: 10.1093/Oxfordjournals.Rpd.A082197  0.239
2022 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 (New York, N.Y.). 377: 489-495. PMID 35901134 DOI: 10.1126/science.abi9810  0.237
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. PMID 17448993 DOI: 10.1016/J.Cell.2007.03.014  0.236
2019 van den Berg AA, Wutz G, Stocsits RR, Brandao H, Busslinger G, Peters J, Mirny L. RNAP as a Moving Barrier to Loop Extrusion Biophysical Journal. 116: 22a. DOI: 10.1016/J.Bpj.2018.11.159  0.232
2014 Doyle B, Fudenberg G, Imakaev M, Mirny LA. Insulation and facilitation strength depends on enhancer-promoter positions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1003867.G003  0.231
2007 Gomez-Uribe C, Verghese GC, Mirny LA. Operating regimes of signaling cycles: statics, dynamics, and noise filtering. Plos Computational Biology. 3: e246. PMID 18159939 DOI: 10.1371/Journal.Pcbi.0030246  0.23
2022 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, ... ... Mirny LA, et al. The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nature Communications. 13: 2365. PMID 35501320 DOI: 10.1038/s41467-022-29697-4  0.226
2016 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, ... ... Mirny LA, et al. Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota. Cell Reports. PMID 26804920 DOI: 10.1016/J.Celrep.2015.12.088  0.224
2008 Mirny L. Biophysics: Cell commuters avoid delays Nature Physics. 4: 93-95. DOI: 10.1038/Nphys848  0.221
2019 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. PMID 31375785 DOI: 10.1038/S41586-019-1454-2  0.221
2021 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, et al. Systematic evaluation of chromosome conformation capture assays. Nature Methods. PMID 34480151 DOI: 10.1038/s41592-021-01248-7  0.218
2017 Phillips AM, Gonzalez LO, Nekongo EE, Ponomarenko AI, McHugh SM, Butty VL, Levine SS, Lin Y, Mirny LA, Shoulders MD. Author response: Host proteostasis modulates influenza evolution Elife. DOI: 10.7554/Elife.28652.022  0.188
2017 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. PMID 29168505 DOI: 10.1038/Nature24667  0.188
2022 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, ... ... Mirny LA, et al. Nucleome programming is required for the foundation of totipotency in mammalian germline development. The Embo Journal. e110600. PMID 35703121 DOI: 10.15252/embj.2022110600  0.181
2016 Dekker J, Mirny L. The 3D Genome as Moderator of Chromosomal Communication Cell. 164: 1110-1121. DOI: 10.1016/j.cell.2016.02.007  0.175
2015 Kind J, Pagie L, deVries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, deGraaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, et al. Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells Cell. DOI: 10.1016/j.cell.2015.08.040  0.175
2022 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 (New York, N.Y.). 376: 496-501. PMID 35420890 DOI: 10.1126/science.abn6583  0.175
2022 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. Nature Cell Biology. PMID 35177821 DOI: 10.1038/s41556-022-00847-6  0.167
2023 Owen JA, Osmanović D, Mirny L. Design principles of 3D epigenetic memory systems. Science (New York, N.Y.). 382: eadg3053. PMID 37972190 DOI: 10.1126/science.adg3053  0.163
2021 Mirny LA. Cells use loop extrusion to weave and tie the genome. Nature. 590: 554-555. PMID 33597775 DOI: 10.1038/d41586-021-00351-1  0.159
2024 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, ... ... Mirny L, et al. Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization. The Journal of Cell Biology. 223. PMID 38376465 DOI: 10.1083/jcb.202307026  0.12
2023 Liu S, Miné-Hattab J, Villemeur M, Guerois R, Pinholt HD, Mirny LA, Taddei A. Publisher Correction: In vivo tracking of functionally tagged Rad51 unveils a robust strategy of homology search. Nature Structural & Molecular Biology. 30: 1607. PMID 37679566 DOI: 10.1038/s41594-023-01114-4  0.111
2023 Liu S, Miné-Hattab J, Villemeur M, Guerois R, Pinholt HD, Mirny LA, Taddei A. Author Correction: In vivo tracking of functionally tagged Rad51 unveils a robust strategy of homology search. Nature Structural & Molecular Biology. PMID 37993685 DOI: 10.1038/s41594-023-01180-8  0.111
2021 Mirny LA, Solovei I. Keeping chromatin in the loop(s). Nature Reviews. Molecular Cell Biology. PMID 33504981 DOI: 10.1038/s41580-021-00337-x  0.103
2022 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. Molecular Cell. PMID 35390275 DOI: 10.1016/j.molcel.2022.03.018  0.09
2022 Reiff SB, Schroeder AJ, Kırlı 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, ... ... Mirny LA, et al. Author Correction: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nature Communications. 13: 6561. PMID 36323678 DOI: 10.1038/s41467-022-34458-4  0.055
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