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Items: 17


The importance of the whole: Topological data analysis for the network neuroscientist.

Sizemore AE, Phillips-Cremins JE, Ghrist R, Bassett DS.

Netw Neurosci. 2019 Jul 1;3(3):656-673. doi: 10.1162/netn_a_00073. eCollection 2019.


A subset of topologically associating domains fold into mesoscale core-periphery networks.

Huang H, Chen ST, Titus KR, Emerson DJ, Bassett DS, Phillips-Cremins JE.

Sci Rep. 2019 Jul 2;9(1):9526. doi: 10.1038/s41598-019-45457-9.


LADL: light-activated dynamic looping for endogenous gene expression control.

Kim JH, Rege M, Valeri J, Dunagin MC, Metzger A, Titus KR, Gilgenast TG, Gong W, Beagan JA, Raj A, Phillips-Cremins JE.

Nat Methods. 2019 Jul;16(7):633-639. doi: 10.1038/s41592-019-0436-5. Epub 2019 Jun 24.


Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data.

Gilgenast TG, Phillips-Cremins JE.

Cell Syst. 2019 Mar 27;8(3):197-211.e13. doi: 10.1016/j.cels.2019.02.006. Epub 2019 Mar 20.


Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries.

Sun JH, Zhou L, Emerson DJ, Phyo SA, Titus KR, Gong W, Gilgenast TG, Beagan JA, Davidson BL, Tassone F, Phillips-Cremins JE.

Cell. 2018 Sep 20;175(1):224-238.e15. doi: 10.1016/j.cell.2018.08.005. Epub 2018 Aug 30.


5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design.

Kim JH, Titus KR, Gong W, Beagan JA, Cao Z, Phillips-Cremins JE.

Methods. 2018 Jun 1;142:39-46. doi: 10.1016/j.ymeth.2018.05.005. Epub 2018 May 24.


Detecting hierarchical genome folding with network modularity.

Norton HK, Emerson DJ, Huang H, Kim J, Titus KR, Gu S, Bassett DS, Phillips-Cremins JE.

Nat Methods. 2018 Feb;15(2):119-122. doi: 10.1038/nmeth.4560. Epub 2018 Jan 15.


Dynamic Looping Interactions: Setting the 3D Stage for the Macrophage.

Rege M, Phillips-Cremins JE.

Mol Cell. 2017 Sep 21;67(6):901-903. doi: 10.1016/j.molcel.2017.09.011.


Crossed wires: 3D genome misfolding in human disease.

Norton HK, Phillips-Cremins JE.

J Cell Biol. 2017 Nov 6;216(11):3441-3452. doi: 10.1083/jcb.201611001. Epub 2017 Aug 30. Review.


YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment.

Beagan JA, Duong MT, Titus KR, Zhou L, Cao Z, Ma J, Lachanski CV, Gillis DR, Phillips-Cremins JE.

Genome Res. 2017 Jul;27(7):1139-1152. doi: 10.1101/gr.215160.116. Epub 2017 May 23.


The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries.

Hsu SC, Gilgenast TG, Bartman CR, Edwards CR, Stonestrom AJ, Huang P, Emerson DJ, Evans P, Werner MT, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremins JE, Blobel GA.

Mol Cell. 2017 Apr 6;66(1):102-116.e7. doi: 10.1016/j.molcel.2017.02.027.


CRISPR/Cas9 genome editing throws descriptive 3-D genome folding studies for a loop.

Beagan JA, Phillips-Cremins JE.

Wiley Interdiscip Rev Syst Biol Med. 2016 Jul;8(4):286-99. doi: 10.1002/wsbm.1338. Epub 2016 Jun 6. Review.


Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming.

Beagan JA, Gilgenast TG, Kim J, Plona Z, Norton HK, Hu G, Hsu SC, Shields EJ, Lyu X, Apostolou E, Hochedlinger K, Corces VG, Dekker J, Phillips-Cremins JE.

Cell Stem Cell. 2016 May 5;18(5):611-24. doi: 10.1016/j.stem.2016.04.004.


HiFive: a tool suite for easy and efficient HiC and 5C data analysis.

Sauria ME, Phillips-Cremins JE, Corces VG, Taylor J.

Genome Biol. 2015 Oct 24;16:237. doi: 10.1186/s13059-015-0806-y.


Unraveling architecture of the pluripotent genome.

Phillips-Cremins JE.

Curr Opin Cell Biol. 2014 Jun;28:96-104. doi: 10.1016/ Epub 2014 Jun 2. Review.


Chromatin insulators: linking genome organization to cellular function.

Phillips-Cremins JE, Corces VG.

Mol Cell. 2013 May 23;50(4):461-74. doi: 10.1016/j.molcel.2013.04.018. Review.


Architectural protein subclasses shape 3D organization of genomes during lineage commitment.

Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, Bland MJ, Wagstaff W, Dalton S, McDevitt TC, Sen R, Dekker J, Taylor J, Corces VG.

Cell. 2013 Jun 6;153(6):1281-95. doi: 10.1016/j.cell.2013.04.053. Epub 2013 May 23.

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