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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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106 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 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, et al. Rules of engagement for condensins and cohesins guide mitotic chromosome formation. Biorxiv : the Preprint Server For Biology. PMID 38659940 DOI: 10.1101/2024.04.18.590027  0.706
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  0.312
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  0.408
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  0.386
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  0.385
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  0.348
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  0.321
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  0.722
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  0.731
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  0.417
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  0.309
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  0.385
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  0.381
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
2019 Mirny L. Chromosome Organization by Loop Extrusion and Phase Separation Biophysical Journal. 116: 171a. DOI: 10.1016/J.Bpj.2018.11.949  0.302
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  0.39
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  0.745
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  0.715
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  0.388
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  0.733
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  0.341
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  0.727
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  0.714
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  0.737
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  0.38
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  0.436
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  0.738
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  0.66
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  0.72
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  0.73
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  0.723
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  0.402
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  0.347
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  0.668
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  0.361
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  0.348
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  0.374
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  0.427
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  0.698
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  0.728
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  0.388
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  0.412
2013 Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one Nature. 502: 45-46. PMID 24067607 DOI: 10.1038/Nature12691  0.398
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  0.376
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  0.709
2013 Imakaev M, Fudenberg G, Mirny L. Chromosomal architecture changes upon cell differentiation Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P130  0.324
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  0.697
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  0.737
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  0.319
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  0.667
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  0.396
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  0.721
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  0.372
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  0.368
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  0.34
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  0.697
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  0.371
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  0.443
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  0.375
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  0.382
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  0.689
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  0.624
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  0.746
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  0.409
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  0.511
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  0.517
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  0.553
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.  0.398
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  0.51
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  0.544
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  0.529
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  0.524
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