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Items: 10

1.

Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations.

Fulco CP, Nasser J, Jones TR, Munson G, Bergman DT, Subramanian V, Grossman SR, Anyoha R, Doughty BR, Patwardhan TA, Nguyen TH, Kane M, Perez EM, Durand NC, Lareau CA, Stamenova EK, Aiden EL, Lander ES, Engreitz JM.

Nat Genet. 2019 Dec;51(12):1664-1669. doi: 10.1038/s41588-019-0538-0. Epub 2019 Nov 29.

PMID:
31784727
2.

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL.

Pastore A, Gaiti F, Lu SX, Brand RM, Kulm S, Chaligne R, Gu H, Huang KY, Stamenova EK, Béguelin W, Jiang Y, Schulman RC, Kim KT, Alonso A, Allan JN, Furman RR, Gnirke A, Wu CJ, Melnick AM, Meissner A, Bernstein BE, Abdel-Wahab O, Landau DA.

Nat Commun. 2019 Apr 23;10(1):1874. doi: 10.1038/s41467-019-09645-5.

3.

The Energetics and Physiological Impact of Cohesin Extrusion.

Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk AL, Tang Z, Nelson S, Di Pierro M, Cheng RR, Machol I, St Hilaire BG, Durand NC, Shamim MS, Stamenova EK, Onuchic JN, Ruan Y, Nussenzweig A, Levens D, Aiden EL, Casellas R.

Cell. 2018 Sep 20;175(1):292-294. doi: 10.1016/j.cell.2018.09.002. No abstract available.

4.

The Energetics and Physiological Impact of Cohesin Extrusion.

Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk AL, Tang Z, Nelson S, Di Pierro M, Cheng RR, Machol I, St Hilaire BG, Durand NC, Shamim MS, Stamenova EK, Onuchic JN, Ruan Y, Nussenzweig A, Levens D, Aiden EL, Casellas R.

Cell. 2018 May 17;173(5):1165-1178.e20. doi: 10.1016/j.cell.2018.03.072. Epub 2018 Apr 26. Erratum in: Cell. 2018 Sep 20;175(1):292-294.

5.

Genome-wide tracking of dCas9-methyltransferase footprints.

Galonska C, Charlton J, Mattei AL, Donaghey J, Clement K, Gu H, Mohammad AW, Stamenova EK, Cacchiarelli D, Klages S, Timmermann B, Cantz T, Schöler HR, Gnirke A, Ziller MJ, Meissner A.

Nat Commun. 2018 Feb 9;9(1):597. doi: 10.1038/s41467-017-02708-5.

6.

Genetic determinants and epigenetic effects of pioneer-factor occupancy.

Donaghey J, Thakurela S, Charlton J, Chen JS, Smith ZD, Gu H, Pop R, Clement K, Stamenova EK, Karnik R, Kelley DR, Gifford CA, Cacchiarelli D, Rinn JL, Gnirke A, Ziller MJ, Meissner A.

Nat Genet. 2018 Feb;50(2):250-258. doi: 10.1038/s41588-017-0034-3. Epub 2018 Jan 22.

7.

Targeted bisulfite sequencing of the dynamic DNA methylome.

Ziller MJ, Stamenova EK, Gu H, Gnirke A, Meissner A.

Epigenetics Chromatin. 2016 Dec 3;9:55. eCollection 2016.

8.

Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture.

Darrow EM, Huntley MH, Dudchenko O, Stamenova EK, Durand NC, Sun Z, Huang SC, Sanborn AL, Machol I, Shamim M, Seberg AP, Lander ES, Chadwick BP, Aiden EL.

Proc Natl Acad Sci U S A. 2016 Aug 2;113(31):E4504-12. doi: 10.1073/pnas.1609643113. Epub 2016 Jul 18.

9.

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.

Sanborn AL, Rao SS, Huang SC, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6456-65. doi: 10.1073/pnas.1518552112. Epub 2015 Oct 23.

10.

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL.

Cell. 2014 Dec 18;159(7):1665-80. doi: 10.1016/j.cell.2014.11.021. Epub 2014 Dec 11. Erratum in: Cell. 2015 Jul 30;162(3):687-8.

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