Observability of the Genome

1. H. Chen et al., “Functional organization of the human 4D Nucleome,” Proceedings of the National Academy of Sciences, vol. 112, no. 26, pp. 8002–8007, Jun. 2015

2. Liu S, Chen H, Ronquist S, Seaman L, Ceglia N, Chen PY, Higgins G, Baldi P, Smale S, Hero A, Muir LA, Rajapakse I. "Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming." iScience (2018)

3. A. Hasnain, S. Balakrishnan, D. M. Joshy, J. Smith, S. B. Haase, and E. Yeung, “Learning perturbation-inducible cell states from observability analysis of transcriptome dynamics,” Nat Commun, vol. 14, no. 1, Art. no. 1, May 2023

4. Liu, Yin, et al. "Transcriptional landscape of the human cell cycle." Proceedings of the National Academy of Sciences 114.13 (2017): 3473-3478. 

5. X. Qiu et al., “Mapping transcriptomic vector fields of single cells,” Cell, Feb. 2022

6. W. Clark, M. Ghaffari, and A. Bloch, “Nonparametric Continuous Sensor Registration.” arXiv, Oct. 18, 2021

7. C. Li, M. C. Virgilio, K. L. Collins, and J. D. Welch, “Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction,” Nat Biotechnol, vol. 41, no. 3, Art. no. 3, Mar. 2023

8. Ali H, Liu S, Yilmaz Y, Couillet R, Rajapakse I, Hero A. "Latent Heterogeneous Multilayer Community Detection." IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (pp. 8142-8146) (2019)

TwinCell Blueprint

1. Böttcher, Lucas, Nino Antulov-Fantulin, and Thomas Asikis. "AI Pontryagin or how artificial neural networks learn to control dynamical systems." Nature communications 13.1 (2022): 333. 

2. Yang, Fan, et al. "scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data." Nature Machine Intelligence 4.10 (2022): 852-866. 

3. Geshkovski, Borjan, et al. "The emergence of clusters in self-attention dynamics." arXiv preprint arXiv:2305.05465 (2023). 

4. Chen, Ricky TQ, et al. "Neural ordinary differential equations." Advances in neural information processing systems 31 (2018). 

Single-cell Pore-C

1. D. Maurya and B. Ravindran, “Hyperedge Prediction using Tensor Eigenvalue Decomposition.” arXiv, Feb. 05, 2021

2. N. Patterson, A. L. Price, and D. Reich, “Population Structure and Eigenanalysis,” PLOS Genetics, vol. 2, no. 12, p. e190, Dec. 2006

3. A. K. Menon and C. Elkan, “Link Prediction via Matrix Factorization”.

4. H. J. Gierman et al., “Domain-wide regulation of gene expression in the human genome,” Genome Res., vol. 17, no. 9, pp. 1286–1295, Sep. 2007

Pore-C Manuscript

Genome Structure and Function 

9. 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. 

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

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

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

13. 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.

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

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

16. Tavares-Cadete, Filipe, et al. "Multi-contact 3C reveals that the human genome during interphase is largely not entangled." Nature structural & molecular biology 27.12 (2020): 1105-1114. 

17. 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. 

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

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

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

21. Stadhouders R, Filion GJ, Graf T. Transcription factors and 3D genome conformation in cell-fate decisions. Nature. 2019 May;569(7756):345-54. 

22. N. Varoquaux, F. Ay, W. S. Noble, and J.-P. Vert, “A statistical approach for inferring the 3D structure of the genome,” Bioinformatics, vol. 30, no. 12, pp. i26–i33, Jun. 2014.

23. Z. Duan et al., “A three-dimensional model of the yeast genome,” Nature, vol. 465, no. 7296, Art. no. 7296, May 2010. Supplemental Material.

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

• 1. Allahyar, Amin, et al. "Enhancer hubs and loop collisions identified from single-allele topologies." Nature genetics 50.8 (2018): 1151-1160.

  2. Ulahannan, Netha, et al. "Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure." bioRxiv (2019): 833590. 

  3. A. S. Deshpande et al., “Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing,” Nat Biotechnol, pp. 1–12, May 2022, doi: 10.1038/s41587-022-01289-z.

  4. W. Li et al., “scNanoHi-C: a single-cell long-read concatemer sequencing method to reveal high-order chromatin structures within individual cells,” Nat Methods, pp. 1–13, Aug. 2023

  5. J.-Y. Zhong et al., “High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding,” Nat Commun, vol. 14, no. 1, Art. no. 1, Mar. 2023

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 

• 1. Dekker, Job. "Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture." Epigenetics & chromatin 7.1 (2014): 1-12. 

  2. Hildebrand, Erica M., and Job Dekker. "Mechanisms and functions of chromosome compartmentalization." Trends in Biochemical Sciences (2020). 

  3. Ji, Xiong, et al. "3D chromosome regulatory landscape of human pluripotent cells." Cell stem cell 18.2 (2016): 262-275. 

  4. Lieberman-Aiden, Erez, et al. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." science 326.5950 (2009): 289-293. 

  5. Yardımcı, Galip Gürkan, et al. "Measuring the reproducibility and quality of Hi-C data." Genome biology 20.1 (2019): 1-19. 

Single Cell Hi-C

• 1. Nagano, Takashi, et al. "Single-cell Hi-C reveals cell-to-cell variability in chromosome structure." Nature 502.7469 (2013): 59-64. 

  2.  Nagano T, Lubling Y, Várnai C, Dudley C, Leung W, Baran Y, et al. "Cell-cycle dynamics of chromosomal organization at single-cell resolution." Nature. 2017 Jul;547(7661):61–7.

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

  4. Tan, Longzhi, et al. "Three-dimensional genome structures of single diploid human cells." Science 361.6405 (2018): 924-928. 

  5. Zhou, Jingtian, et al. "Robust single-cell Hi-C clustering by convolution-and random-walk–based imputation." Proceedings of the National Academy of Sciences 116.28 (2019): 14011-14018. 

  6. Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J. Massively multiplex single-cell Hi-C. Nature methods. 2017 Mar;14(3):263-6. 

  7. Chen, Chongyi, Dong Xing, Longzhi Tan, Heng Li, Guangyu Zhou, Lei Huang, and X. Sunney Xie. "Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)." Science 356, no. 6334 (2017): 189-194.

Other Resources

Transcription factories 

Observability of Hypergraphs Project

1. Baggio, Giacomo, Danielle S. Bassett, and Fabio Pasqualetti. "Data-driven control of complex networks." Nature communications 12.1 (2021): 1-13. 

2. Mullari, Tanel, et al. "The concepts of Lie derivative for discrete-time systems." Proceedings of the Estonian Academy of Sciences 61.4 (2012): 253. 

3. Kawano, Yu, and Toshiyuki Ohtsuka. "Global observability of discrete-time polynomial systems." IFAC Proceedings Volumes 43.14 (2010): 203-207. 

4. Liu, Yang-Yu, Jean-Jacques Slotine, and Albert-László Barabási. "Observability of complex systems." Proceedings of the National Academy of Sciences 110.7 (2013): 2460-2465.

5. Zeng, Shen, et al. "Ensemble observability of linear systems." IEEE Transactions on Automatic Control 61.6 (2015): 1452-1465. 

6. Chen, Xudong. "Ensemble observability of Bloch equations with unknown population density." Automatica 119 (2020): 109057. 

7. Zhang, Wei, and Jr-Shin Li. "Ensemble Control on Lie Groups." SIAM Journal on Control and Optimization 59.5 (2021): 3805-3827. 

8. Sedoglavic, Alexandre. "A probabilistic algorithm to test local algebraic observability in polynomial time." Proceedings of the 2001 international symposium on Symbolic and algebraic computation. 2001. 

9. Jurdjevic, Velimir, and I7996670554 Kupka. "Polynomial control systems." Mathematische Annalen 272.3 (1985): 361-368. 

10. Jurdjevic, Velimir, and Ivan Kupka. "Control systems on semi-simple Lie groups and their homogeneous spaces." Annales de L'institut Fourier. Vol. 31. No. 4. 1981. 

11. Baillieul, John. "Controllability and observability of polynomial dynamical systems." Nonlinear Analysis: Theory, Methods & Applications 5.5 (1981): 543-552. 

12. Dal Cengio, Sara, Vivien Lecomte, and Matteo Polettini. "Geometry of nonequilibrium reaction networks." (2022). 

13. Chen, Can, et al. "Controllability of hypergraphs." IEEE Transactions on Network Science and Engineering 8.2 (2021): 1646-1657. 

14. Gerbet, Daniel, and Klaus Röbenack. "On global and local observability of nonlinear polynomial systems: A decidable criterion." at-Automatisierungstechnik 68.6 (2020): 395-409. 

15. Anguelova, Milena. Nonlinear Observability and Identi ability: General Theory and a Case Study of a Kinetic Model for S. cerevisiae. Chalmers Tekniska Hogskola (Sweden), 2004. 

Inferring Multiway Interactions Project

1. Benson, Austin R., David F. Gleich, and Jure Leskovec. "Higher-order organization of complex networks." Science 353, no. 6295 (2016): 163-166.

2. Sarker, Arnab, Jean-Baptiste Seby, Austin R. Benson, and Ali Jadbabaie. "Higher order information identifies tie strength." arXiv preprint arXiv:2108.02091 (2021).

3. Lee, Geon, Jihoon Ko, and Kijung Shin. "Hypergraph motifs: Concepts, algorithms, and discoveries." arXiv preprint arXiv:2003.01853 (2020).