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Items: 21

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 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.

4.

Diminished PRRX1 Expression Is Associated With Increased Risk of Atrial Fibrillation and Shortening of the Cardiac Action Potential.

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.

Circ Cardiovasc Genet. 2017 Oct;10(5). pii: e001902. doi: 10.1161/CIRCGENETICS.117.001902.

5.

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure.

Ulianov SV, Galitsyna AA, Flyamer IM, Golov AK, Khrameeva EE, Imakaev MV, Abdennur NA, Gelfand MS, Gavrilov AA, Razin SV.

Epigenetics Chromatin. 2017 Jul 11;10(1):35. doi: 10.1186/s13072-017-0142-4.

6.

FISH-ing for captured contacts: towards reconciling FISH and 3C.

Fudenberg G, Imakaev M.

Nat Methods. 2017 Jul;14(7):673-678. doi: 10.1038/nmeth.4329. Epub 2017 Jun 12.

7.

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.

8.

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.

9.

Compaction and segregation of sister chromatids via active loop extrusion.

Goloborodko A, Imakaev MV, Marko JF, Mirny L.

Elife. 2016 May 18;5. pii: e14864. doi: 10.7554/eLife.14864.

10.

Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation.

Čuklina J, Hahn J, Imakaev M, Omasits U, Förstner KU, Ljubimov N, Goebel M, Pessi G, Fischer HM, Ahrens CH, Gelfand MS, Evguenieva-Hackenberg E.

BMC Genomics. 2016 Apr 23;17:302. doi: 10.1186/s12864-016-2602-9.

11.

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.

12.

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains.

Ulianov SV, Khrameeva EE, Gavrilov AA, Flyamer IM, Kos P, Mikhaleva EA, Penin AA, Logacheva MD, Imakaev MV, Chertovich A, Gelfand MS, Shevelyov YY, Razin SV.

Genome Res. 2016 Jan;26(1):70-84. doi: 10.1101/gr.196006.115. Epub 2015 Oct 30.

13.

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.

14.

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.

15.

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
16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

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