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Items: 1 to 50 of 70

1.

Chromatin organization by an interplay of loop extrusion and compartmental segregation.

Nuebler J, Fudenberg G, Imakaev M, Abdennur N, Mirny LA.

Proc Natl Acad Sci U S A. 2018 Jul 17;115(29):E6697-E6706. doi: 10.1073/pnas.1717730115. Epub 2018 Jul 2.

2.

Emerging Evidence of Chromosome Folding by Loop Extrusion.

Fudenberg G, Abdennur N, Imakaev M, Goloborodko A, Mirny LA.

Cold Spring Harb Symp Quant Biol. 2017;82:45-55. doi: 10.1101/sqb.2017.82.034710. Epub 2018 May 4.

PMID:
29728444
3.

A pathway for mitotic chromosome formation.

Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N, Nuebler J, Kanemaki MT, Xie L, Paulson JR, Earnshaw WC, Mirny LA, Dekker J.

Science. 2018 Feb 9;359(6376). pii: eaao6135. doi: 10.1126/science.aao6135. Epub 2018 Jan 18.

4.

A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture.

Gassler J, Brandão HB, Imakaev M, Flyamer IM, Ladstätter S, Bickmore WA, Peters JM, Mirny LA, Tachibana K.

EMBO J. 2017 Dec 15;36(24):3600-3618. doi: 10.15252/embj.201798083. Epub 2017 Dec 7.

5.

Corrigendum: The 4D nucleome project.

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; 4D Nucleome Network.

Nature. 2017 Dec 14;552(7684):278. doi: 10.1038/nature24667. Epub 2017 Nov 22.

PMID:
29168505
6.

Host proteostasis modulates influenza evolution.

Phillips AM, Gonzalez LO, Nekongo EE, Ponomarenko AI, McHugh SM, Butty VL, Levine SS, Lin YS, Mirny LA, Shoulders MD.

Elife. 2017 Sep 26;6. pii: e28652. doi: 10.7554/eLife.28652.

7.

The 4D nucleome project.

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; 4D Nucleome Network.

Nature. 2017 Sep 13;549(7671):219-226. doi: 10.1038/nature23884. Erratum in: Nature. 2017 Nov 22;:.

8.

The Damaging Effect of Passenger Mutations on Cancer Progression.

McFarland CD, Yaglom JA, Wojtkowiak JW, Scott JG, Morse DL, Sherman MY, Mirny LA.

Cancer Res. 2017 Sep 15;77(18):4763-4772. doi: 10.1158/0008-5472.CAN-15-3283-T. Epub 2017 May 23.

PMID:
28536279
9.

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.

Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG.

Cell. 2017 May 18;169(5):930-944.e22. doi: 10.1016/j.cell.2017.05.004.

10.

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition.

Flyamer IM, Gassler J, Imakaev M, Brandão HB, Ulianov SV, Abdennur N, Razin SV, Mirny LA, Tachibana-Konwalski K.

Nature. 2017 Apr 6;544(7648):110-114. doi: 10.1038/nature21711. Epub 2017 Mar 29.

11.

Isoform-Specific Expression and Feedback Regulation of E Protein TCF4 Control Dendritic Cell Lineage Specification.

Grajkowska LT, Ceribelli M, Lau CM, Warren ME, Tiniakou I, Nakandakari Higa S, Bunin A, Haecker H, Mirny LA, Staudt LM, Reizis B.

Immunity. 2017 Jan 17;46(1):65-77. doi: 10.1016/j.immuni.2016.11.006. Epub 2016 Dec 13.

12.

Hematopoietic Stem Cells Are the Major Source of Multilineage Hematopoiesis in Adult Animals.

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.

Immunity. 2016 Sep 20;45(3):597-609. doi: 10.1016/j.immuni.2016.08.007. Epub 2016 Aug 30.

13.

Chromosome Compaction by Active Loop Extrusion.

Goloborodko A, Marko JF, Mirny LA.

Biophys J. 2016 May 24;110(10):2162-8. doi: 10.1016/j.bpj.2016.02.041.

14.

Formation of Chromosomal Domains by Loop Extrusion.

Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA.

Cell Rep. 2016 May 31;15(9):2038-49. doi: 10.1016/j.celrep.2016.04.085. Epub 2016 May 19.

15.

History of chromosome rearrangements reflects the spatial organization of yeast chromosomes.

Khrameeva EE, Fudenberg G, Gelfand MS, Mirny LA.

J Bioinform Comput Biol. 2016 Apr;14(2):1641002. doi: 10.1142/S021972001641002X. Epub 2016 Jan 28.

16.

Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota.

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.

Cell Rep. 2016 Feb 2;14(4):945-955. doi: 10.1016/j.celrep.2015.12.088. Epub 2016 Jan 21.

17.

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states.

Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X.

Nature. 2016 Jan 21;529(7586):418-22. doi: 10.1038/nature16496. Epub 2016 Jan 13.

18.

Genome-wide maps of nuclear lamina interactions in single human cells.

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.

Cell. 2015 Sep 24;163(1):134-47. doi: 10.1016/j.cell.2015.08.040. Epub 2015 Sep 10.

19.

Modeling chromosomes: Beyond pretty pictures.

Imakaev MV, Fudenberg G, Mirny LA.

FEBS Lett. 2015 Oct 7;589(20 Pt A):3031-6. doi: 10.1016/j.febslet.2015.09.004. Epub 2015 Sep 10. Review.

20.

Effects of topological constraints on globular polymers.

Imakaev MV, Tchourine KM, Nechaev SK, Mirny LA.

Soft Matter. 2015 Jan 28;11(4):665-71. doi: 10.1039/c4sm02099e. Epub 2014 Dec 4.

PMID:
25472862
21.

Chromatin loops as allosteric modulators of enhancer-promoter interactions.

Doyle B, Fudenberg G, Imakaev M, Mirny LA.

PLoS Comput Biol. 2014 Oct 23;10(10):e1003867. doi: 10.1371/journal.pcbi.1003867. eCollection 2014 Oct.

22.

Tug-of-war between driver and passenger mutations in cancer and other adaptive processes.

McFarland CD, Mirny LA, Korolev KS.

Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15138-43. doi: 10.1073/pnas.1404341111. Epub 2014 Oct 2.

23.

ZFX controls propagation and prevents differentiation of acute T-lymphoblastic and myeloid leukemia.

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.

Cell Rep. 2014 Feb 13;6(3):528-40. doi: 10.1016/j.celrep.2014.01.007. Epub 2014 Jan 30.

24.

Organization of the mitotic chromosome.

Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J.

Science. 2013 Nov 22;342(6161):948-53. doi: 10.1126/science.1236083. Epub 2013 Nov 7.

25.

High-resolution mapping of the spatial organization of a bacterial chromosome.

Le TB, Imakaev MV, Mirny LA, Laub MT.

Science. 2013 Nov 8;342(6159):731-4. doi: 10.1126/science.1242059. Epub 2013 Oct 24.

26.

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.

Dekker J, Marti-Renom MA, Mirny LA.

Nat Rev Genet. 2013 Jun;14(6):390-403. doi: 10.1038/nrg3454. Epub 2013 May 9. Review.

27.

Impact of deleterious passenger mutations on cancer progression.

McFarland CD, Korolev KS, Kryukov GV, Sunyaev SR, Mirny LA.

Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2910-5. doi: 10.1073/pnas.1213968110. Epub 2013 Feb 6.

28.

Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease.

Engreitz JM, Agarwala V, Mirny LA.

PLoS One. 2012;7(9):e44196. doi: 10.1371/journal.pone.0044196. Epub 2012 Sep 28.

29.

Sequence-dependent sliding kinetics of p53.

Leith JS, Tafvizi A, Huang F, Uspal WE, Doyle PS, Fersht AR, Mirny LA, van Oijen AM.

Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16552-7. doi: 10.1073/pnas.1120452109. Epub 2012 Sep 25.

30.

Iterative correction of Hi-C data reveals hallmarks of chromosome organization.

Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA.

Nat Methods. 2012 Oct;9(10):999-1003. doi: 10.1038/nmeth.2148. Epub 2012 Sep 2.

31.

Higher-order chromatin structure: bridging physics and biology.

Fudenberg G, Mirny LA.

Curr Opin Genet Dev. 2012 Apr;22(2):115-24. doi: 10.1016/j.gde.2012.01.006. Epub 2012 Feb 22. Review.

32.

High order chromatin architecture shapes the landscape of chromosomal alterations in cancer.

Fudenberg G, Getz G, Meyerson M, Mirny LA.

Nat Biotechnol. 2011 Nov 20;29(12):1109-13. doi: 10.1038/nbt.2049.

33.

Bridging the resolution gap in structural modeling of 3D genome organization.

Marti-Renom MA, Mirny LA.

PLoS Comput Biol. 2011 Jul;7(7):e1002125. doi: 10.1371/journal.pcbi.1002125. Epub 2011 Jul 14. Review.

34.

Dancing on DNA: kinetic aspects of search processes on DNA.

Tafvizi A, Mirny LA, van Oijen AM.

Chemphyschem. 2011 Jun 6;12(8):1481-9. doi: 10.1002/cphc.201100112. Epub 2011 May 10. Review.

35.

The fractal globule as a model of chromatin architecture in the cell.

Mirny LA.

Chromosome Res. 2011 Jan;19(1):37-51. doi: 10.1007/s10577-010-9177-0.

36.

A single-molecule characterization of p53 search on DNA.

Tafvizi A, Huang F, Fersht AR, Mirny LA, van Oijen AM.

Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):563-8. doi: 10.1073/pnas.1016020107. Epub 2010 Dec 22.

37.

Nucleosome-mediated cooperativity between transcription factors.

Mirny LA.

Proc Natl Acad Sci U S A. 2010 Dec 28;107(52):22534-9. doi: 10.1073/pnas.0913805107. Epub 2010 Dec 13.

38.

Quantitative characterization of filament dynamics by single-molecule lifetime measurements.

Mirny LA, Needleman DJ.

Methods Cell Biol. 2010;95:583-600. doi: 10.1016/S0091-679X(10)95029-2. Review.

PMID:
20466154
39.

Hi-C: a method to study the three-dimensional architecture of genomes.

van Berkum NL, Lieberman-Aiden E, Williams L, Imakaev M, Gnirke A, Mirny LA, Dekker J, Lander ES.

J Vis Exp. 2010 May 6;(39). pii: 1869. doi: 10.3791/1869.

40.

A Stevedore's protein knot.

Bölinger D, Sułkowska JI, Hsu HP, Mirny LA, Kardar M, Onuchic JN, Virnau P.

PLoS Comput Biol. 2010 Apr 1;6(4):e1000731. doi: 10.1371/journal.pcbi.1000731.

41.

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

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.

Science. 2009 Oct 9;326(5950):289-93. doi: 10.1126/science.1181369.

42.

Different gene regulation strategies revealed by analysis of binding motifs.

Wunderlich Z, Mirny LA.

Trends Genet. 2009 Oct;25(10):434-40. doi: 10.1016/j.tig.2009.08.003. Epub 2009 Oct 6.

43.

Using genome-wide measurements for computational prediction of SH2-peptide interactions.

Wunderlich Z, Mirny LA.

Nucleic Acids Res. 2009 Aug;37(14):4629-41. doi: 10.1093/nar/gkp394. Epub 2009 Jun 5.

44.

Using evolutionary information to find specificity-determining and co-evolving residues.

Kolesov G, Mirny LA.

Methods Mol Biol. 2009;541:421-48. doi: 10.1007/978-1-59745-243-4_18. Review.

PMID:
19381538
45.

Predicting transcription factor specificity with all-atom models.

Jamal Rahi S, Virnau P, Mirny LA, Kardar M.

Nucleic Acids Res. 2008 Nov;36(19):6209-17. doi: 10.1093/nar/gkn589. Epub 2008 Oct 1.

46.

Spatial effects on the speed and reliability of protein-DNA search.

Wunderlich Z, Mirny LA.

Nucleic Acids Res. 2008 Jun;36(11):3570-8. doi: 10.1093/nar/gkn173. Epub 2008 May 3.

47.

Tumor suppressor p53 slides on DNA with low friction and high stability.

Tafvizi A, Huang F, Leith JS, Fersht AR, Mirny LA, van Oijen AM.

Biophys J. 2008 Jul;95(1):L01-3. doi: 10.1529/biophysj.108.134122. Epub 2008 Apr 18.

48.

Operating regimes of signaling cycles: statics, dynamics, and noise filtering.

Gomez-Uribe C, Verghese GC, Mirny LA.

PLoS Comput Biol. 2007 Dec;3(12):e246.

49.

How gene order is influenced by the biophysics of transcription regulation.

Kolesov G, Wunderlich Z, Laikova ON, Gelfand MS, Mirny LA.

Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):13948-53. Epub 2007 Aug 20.

50.

Protein knot server: detection of knots in protein structures.

Kolesov G, Virnau P, Kardar M, Mirny LA.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W425-8. Epub 2007 May 21.

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