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Items: 21

1.

Publisher Correction: Heterochromatin drives compartmentalization of inverted and conventional nuclei.

Falk M, Feodorova Y, Naumova N, Imakaev M, Lajoie BR, Leonhardt H, Joffe B, Dekker J, Fudenberg G, Solovei I, Mirny LA.

Nature. 2019 Aug;572(7771):E22. doi: 10.1038/s41586-019-1454-2.

PMID:
31375785
2.

Heterochromatin drives compartmentalization of inverted and conventional nuclei.

Falk M, Feodorova Y, Naumova N, Imakaev M, Lajoie BR, Leonhardt H, Joffe B, Dekker J, Fudenberg G, Solovei I, Mirny LA.

Nature. 2019 Jun;570(7761):395-399. doi: 10.1038/s41586-019-1275-3. Epub 2019 Jun 5. Erratum in: Nature. 2019 Aug;572(7771):E22.

PMID:
31168090
3.

Chromatin features constrain structural variation across evolutionary timescales.

Fudenberg G, Pollard KS.

Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2175-2180. doi: 10.1073/pnas.1808631116. Epub 2019 Jan 18.

4.

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.

5.

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.

6.

Two independent modes of chromatin organization revealed by cohesin removal.

Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, Spitz F.

Nature. 2017 Nov 2;551(7678):51-56. doi: 10.1038/nature24281. Epub 2017 Sep 27.

7.

SMC complexes differentially compact mitotic chromosomes according to genomic context.

Schalbetter SA, Goloborodko A, Fudenberg G, Belton JM, Miles C, Yu M, Dekker J, Mirny L, Baxter J.

Nat Cell Biol. 2017 Sep;19(9):1071-1080. doi: 10.1038/ncb3594. Epub 2017 Aug 21.

8.

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.

9.

Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome.

Hsieh TS, Fudenberg G, Goloborodko A, Rando OJ.

Nat Methods. 2016 Dec;13(12):1009-1011. doi: 10.1038/nmeth.4025. Epub 2016 Oct 10.

PMID:
27723753
10.

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.

11.

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.

12.

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.

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.

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.

16.

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe.

Mizuguchi T, Fudenberg G, Mehta S, Belton JM, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewal SIS.

Nature. 2014 Dec 18;516(7531):432-435. doi: 10.1038/nature13833. Epub 2014 Oct 12.

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.

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.

19.

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.

20.

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.

21.

Bayesian image recovery for dendritic structures under low signal-to-noise conditions.

Fudenberg G, Paninski L.

IEEE Trans Image Process. 2009 Mar;18(3):471-82. doi: 10.1109/TIP.2008.2010212.

PMID:
19211329

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