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1

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

Phillips-Cremins, Jennifer E., Sauria, Michael E.G., Sanyal, Amartya, Gerasimova, Tatiana I., Lajoie, Bryan R., Bell, Joshua S.K., Ong, Chin-Tong, Hookway, Tracy A., Guo, Changying, Sun, Yuhua, Bland,

Journal:

Year:

2013

Language:

english

File:

PDF, 5.56 MB

english, 2013

2

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

Sun, James H., Zhou, Linda, Emerson, Daniel J., Phyo, Sai A., Titus, Katelyn R., Gong, Wanfeng, Gilgenast, Thomas G., Beagan, Jonathan A., Davidson, Beverly L., Tassone, Flora, Phillips-Cremins, Jenni

Journal:

Year:

2018

Language:

english

File:

PDF, 13.39 MB

english, 2018

3

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

Huang, Harvey, Chen, Sunnia T., Titus, Katelyn R., Emerson, Daniel J., Bassett, Danielle S., Phillips-Cremins, Jennifer E.

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 13.29 MB

english, 2019

4

Chromatin Insulators: Linking Genome Organization to Cellular Function

Phillips-Cremins, Jennifer E., Corces, Victor G.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.47 MB

english, 2013

5

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

Sauria, Michael EG, Phillips-Cremins, Jennifer E., Corces, Victor G., Taylor, James

Journal:

Year:

2015

Language:

english

File:

PDF, 1.79 MB

english, 2015

6

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

Beagan, Jonathan A., Phillips-Cremins, Jennifer E.

Journal:

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Year:

2016

Language:

english

File:

PDF, 1.62 MB

english, 2016

7

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

Beagan, Jonathan A., Duong, Michael T., Titus, Katelyn R., Zhou, Linda, Cao, Zhendong, Ma, Jingjing, Lachanski, Caroline V., Gillis, Daniel R., Phillips-Cremins, Jennifer E.

Journal:

Genome Research

Year:

2017

Language:

english

File:

PDF, 1.40 MB

english, 2017

8

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

Rege, Mayuri, Phillips-Cremins, Jennifer E.

Journal:

Year:

2017

Language:

english

File:

PDF, 525 KB

english, 2017

9

Crossed wires: 3D genome misfolding in human disease

Norton, Heidi K., Phillips-Cremins, Jennifer E.

Journal:

The Journal of Cell Biology

Year:

2017

Language:

english

File:

PDF, 1.18 MB

english, 2017

10

Detecting hierarchical genome folding with network modularity

Norton, Heidi K, Emerson, Daniel J, Huang, Harvey, Kim, Jesi, Titus, Katelyn R, Gu, Shi, Bassett, Danielle S, Phillips-Cremins, Jennifer E

Journal:

Year:

2018

Language:

english

File:

PDF, 4.77 MB

english, 2018

11

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

Kim, Ji Hun, Titus, Katelyn R., Gong, Wanfeng, Beagan, Jonathan A., Cao, Zhendong, Phillips-Cremins, Jennifer E.

Journal:

Year:

2018

Language:

english

File:

PDF, 4.82 MB

english, 2018

12

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

Sizemore, Ann E., Phillips-Cremins, Jennifer E., Ghrist, Robert, Bassett, Danielle S.

Journal:

Network Neuroscience

Year:

2018

File:

PDF, 1.04 MB

2018

13

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

Gilgenast, Thomas G., Phillips-Cremins, Jennifer E.

Journal:

Year:

2019

Language:

english

File:

PDF, 8.90 MB

english, 2019

14

Chromatin structure dynamics during the mitosis-to-G1 phase transition

Zhang, Haoyue, Emerson, Daniel J., Gilgenast, Thomas G., Titus, Katelyn R., Lan, Yemin, Huang, Peng, Zhang, Di, Wang, Hongxin, Keller, Cheryl A., Giardine, Belinda, Hardison, Ross C., Phillips-Cremins

Journal:

Year:

2019

File:

PDF, 14.10 MB

2019

15

On the existence and functionality of topologically associating domains

Beagan, Jonathan A., Phillips-Cremins, Jennifer E.

Journal:

Nature Genetics

Year:

2020

Language:

english

File:

PDF, 1.80 MB

english, 2020

16

Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data

Wu, Yang, Qi, Ting, Wang, Huanwei, Zhang, Futao, Zheng, Zhili, Phillips-Cremins, Jennifer E., Deary, Ian J., McRae, Allan F., Wray, Naomi R., Zeng, Jian, Yang, Jian

Journal:

Nature Communications

Year:

2020

File:

PDF, 2.35 MB

2020

17

Alteration of genome folding via contact domain boundary insertion

Zhang, Di, Huang, Peng, Sharma, Malini, Keller, Cheryl A., Giardine, Belinda, Zhang, Haoyue, Gilgenast, Thomas G., Phillips-Cremins, Jennifer E., Hardison, Ross C., Blobel, Gerd A.

Journal:

Nature Genetics

Year:

2020

File:

PDF, 18.17 MB

2020

18

3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data

Fernandez, Lindsey R., Gilgenast, Thomas G., Phillips-Cremins, Jennifer E.

Journal:

Year:

2020

File:

PDF, 5.49 MB

2020

19

Publisher Correction: Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression

Beagan, Jonathan A., Pastuzyn, Elissa D., Fernandez, Lindsey R., Guo, Michael H., Feng, Kelly, Titus, Katelyn R., Chandrashekar, Harshini, Shepherd, Jason D., Phillips-Cremins, Jennifer E.

Journal:

Nature Neuroscience

Year:

2020

File:

PDF, 696 KB

2020