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. PMID:31266973
LADL: light-activated dynamic looping for endogenous gene expression control
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 […]
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: 10.10.16/j.cels.2019.02.006. Epub 2019 Mar 20. PMID:30904376
5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design
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 […]
Detecting hierarchical genome folding with network modularity
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 […]
Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundaries
Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundaries. 2017 Sept 20. James Sun, Linda Zhou, Daniel J Emerson, Thomas G. Gilgenast, Katelyn Titus, Jonathan A. Beagan, Jennifer E. […]
YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
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 […]
Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming
Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Beagan JA1, Gilgenast TG1, Kim J1, Plona Z1, Norton HK1, Hu G1, Hsu SC2, Shields EJ2, […]