Manuscript References

Pore-C Manuscript

Genome Structure and Function

  1. Chen H, Chen J, Muir LA, Ronquist S, Meixner W, Ljungman M, Ried T, Smale S, Rajapakse I. "Functional Organization of the Human 4D Nucleome. " Proceedings of the National Academy of Sciences 112.26 (2015): 8002-8007.

  2. Dixon, Jesse R., et al. "Chromatin architecture reorganization during stem cell differentiation." Nature 518.7539 (2015): 331-336.

  3. Dixon, Jesse R., David U. Gorkin, and Bing Ren. "Chromatin domains: the unit of chromosome organization." Molecular cell 62.5 (2016): 668-680.

  4. Dixon, Jesse R., et al. "Topological domains in mammalian genomes identified by analysis of chromatin interactions." Nature 485.7398 (2012): 376-380.

  5. Maass, Philipp G., A. Rasim Barutcu, and John L. Rinn. "Interchromosomal interactions: a genomic love story of kissing chromosomes." Journal of Cell Biology 218.1 (2019): 27-38.

  6. Neph, Shane, et al. "Circuitry and dynamics of human transcription factor regulatory networks." Cell 150.6 (2012): 1274-1286.

  7. Olivares-Chauvet, Pedro, et al. "Capturing pairwise and multi-way chromosomal conformations using chromosomal walks." Nature 540.7632 (2016): 296-300.

  8. Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping." Cell 159.7 (2014): 1665-1680.

  9. Stevens, Tim J., et al. "3D structures of individual mammalian genomes studied by single-cell Hi-C." Nature 544.7648 (2017): 59-64.

  10. Xiong, Kyle, and Jian Ma. "Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions." Nature communications 10.1 (2019): 1-12.

  11. Zhang, Ruochi, Tianming Zhou, and Jian Ma. "Multiscale and integrative single-cell Hi-C analysis with Higashi." bioRxiv (2020).

Hypergraphs

  1. Benson, Austin R., David F. Gleich, and Jure Leskovec. "Higher-order organization of complex networks." Science 353.6295 (2016): 163-166.

  2. Valdivia, Paola, et al. "Analyzing Dynamic Hypergraphs with Parallel Aggregated Ordered Hypergraph Visualization." IEEE Transactions on Visualization and Computer Graphics (2019).

  3. Zhang, Ruochi, and Jian Ma. "MATCHA: Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning." Cell Systems 10.5 (2020): 397-407.

Pore-C

Transcription Factories

  1. Cook, Peter R. "Predicting three-dimensional genome structure from transcriptional activity." Nature genetics 32.3 (2002): 347-352.

  2. Cook, Peter R. "The organization of replication and transcription." Science 284.5421 (1999): 1790-1795.

  3. Cook, Peter R., and Davide Marenduzzo. "Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations." Nucleic acids research 46.19 (2018): 9895-9906.

  4. Dai, Chao, et al. "Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities." Nature communications 7.1 (2016): 1-11.

  5. Gheorghe, Marius, et al. "A map of direct TF–DNA interactions in the human genome." Nucleic acids research 47.4 (2019): e21-e21.

  6. Ghirlando, Rodolfo, and Gary Felsenfeld. "CTCF: making the right connections." Genes & development 30.8 (2016): 881-891.

  7. Marenduzzo, Davide, Cristian Micheletti, and Peter R. Cook. "Entropy-driven genome organization." Biophysical journal 90.10 (2006): 3712-3721.

  8. Narlikar, Geeta J., et al. "Is transcriptional regulation just going through a phase?." Molecular Cell 81.8 (2021): 1579-1585.

  9. Osborne, Cameron S., et al. "Active genes dynamically colocalize to shared sites of ongoing transcription." Nature genetics 36.10 (2004): 1065-1071.

  10. Osborne, Cameron S., et al. "Myc dynamically and preferentially relocates to a transcription factory occupied by Igh." PLoS Biol 5.8 (2007): e192.

  11. Papantonis, Argyris, and Peter R. Cook. "Transcription factories: genome organization and gene regulation." Chemical reviews 113.11 (2013): 8683-8705.

  12. Plys, Aaron J., and Robert E. Kingston. "Dynamic condensates activate transcription." Science 361.6400 (2018): 329-330.

  13. Rieder, Dietmar, Zlatko Trajanoski, and James McNally. "Transcription factories." Frontiers in genetics 3 (2012): 221.

  14. Sutherland, Heidi, and Wendy A. Bickmore. "Transcription factories: gene expression in unions?." Nature Reviews Genetics 10.7 (2009): 457-466.

  15. Xu, Meng, and Peter R. Cook. "Similar active genes cluster in specialized transcription factories." Journal of Cell Biology 181.4 (2008): 615-623.

Chromosome Conformation Capture

Single Cell Hi-C


Other Resources