IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v626y2023ics0378437123005988.html
   My bibliography  Save this article

DNA visibility graphs

Author

Listed:
  • Kosmidis, Kosmas
  • Hütt, Marc-Thorsten

Abstract

DNA walks are mathematical representations of DNA sequences that have been used to study the long-range organization of DNA. Visibility graphs are network representations of time series that give access to features usually difficult to analyze on the time series level alone. Here we combine the two approaches and introduce the concept of DNA visibility graphs. The main goal of our investigation is to calibrate this new tool by analyzing DNA visibility graphs for various random DNA sequences.

Suggested Citation

  • Kosmidis, Kosmas & Hütt, Marc-Thorsten, 2023. "DNA visibility graphs," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 626(C).
    • Handle: RePEc:eee:phsmap:v:626:y:2023:i:c:s0378437123005988
    DOI: 10.1016/j.physa.2023.129043
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437123005988
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000
    File URL: https://libkey.io/10.1016/j.physa.2023.129043?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Dorogovtsev, S.N. & Mendes, J.F.F., 2003. "Evolution of Networks: From Biological Nets to the Internet and WWW," OUP Catalogue, Oxford University Press, number 9780198515906.
    2. Tanja Woyke & Hanno Teeling & Natalia N. Ivanova & Marcel Huntemann & Michael Richter & Frank Oliver Gloeckner & Dario Boffelli & Iain J. Anderson & Kerrie W. Barry & Harris J. Shapiro & Ernest Szeto , 2006. "Symbiosis insights through metagenomic analysis of a microbial consortium," Nature, Nature, vol. 443(7114), pages 950-955, October.
    3. Gutiérrez, J.M. & Rodrı́guez, M.A. & Abramson, G., 2001. "Multifractal analysis of DNA sequences using a novel chaos-game representation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 300(1), pages 271-284.
    4. P. A. Jacobs & P. A. W. Lewis, 1983. "Stationary Discrete Autoregressive‐Moving Average Time Series Generated By Mixtures," Journal of Time Series Analysis, Wiley Blackwell, vol. 4(1), pages 19-36, January.
    5. Möller, Simon & Hameister, Heike & Hütt, Marc-Thorsten, 2014. "A genome signature derived from the interplay of word frequencies and symbol correlations," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 414(C), pages 216-226.
    6. Anshul Kundaje & Wouter Meuleman & Jason Ernst & Misha Bilenky & Angela Yen & Alireza Heravi-Moussavi & Pouya Kheradpour & Zhizhuo Zhang & Jianrong Wang & Michael J. Ziller & Viren Amin & John W. Whit, 2015. "Integrative analysis of 111 reference human epigenomes," Nature, Nature, vol. 518(7539), pages 317-330, February.
    7. Jill E. Moore & Michael J. Purcaro & Henry E. Pratt & Charles B. Epstein & Noam Shoresh & Jessika Adrian & Trupti Kawli & Carrie A. Davis & Alexander Dobin & Rajinder Kaul & Jessica Halow & Eric L. No, 2020. "Expanded encyclopaedias of DNA elements in the human and mouse genomes," Nature, Nature, vol. 583(7818), pages 699-710, July.
    8. Peng, C.-K. & Buldyrev, S.V. & Goldberger, A.L. & Havlin, S. & Mantegna, R.N. & Simons, M. & Stanley, H.E., 1995. "Statistical properties of DNA sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 221(1), pages 180-192.
    9. Dehnert, M. & Helm, W.E. & Hütt, M.-Th., 2003. "A discrete autoregressive process as a model for short-range correlations in DNA sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 327(3), pages 535-553.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Möller, Simon & Hameister, Heike & Hütt, Marc-Thorsten, 2014. "A genome signature derived from the interplay of word frequencies and symbol correlations," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 414(C), pages 216-226.
    2. Ya-Chun Gao & Zong-Wen Wei & Bing-Hong Wang, 2013. "Dynamic Evolution Of Financial Network And Its Relation To Economic Crises," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 24(02), pages 1-10.
    3. Zhou, Wei-Xing & Jiang, Zhi-Qiang & Sornette, Didier, 2007. "Exploring self-similarity of complex cellular networks: The edge-covering method with simulated annealing and log-periodic sampling," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 375(2), pages 741-752.
    4. Bezsudnov, I.V. & Snarskii, A.A., 2014. "From the time series to the complex networks: The parametric natural visibility graph," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 414(C), pages 53-60.
    5. Mark S. Handcock & Adrian E. Raftery & Jeremy M. Tantrum, 2007. "Model‐based clustering for social networks," Journal of the Royal Statistical Society Series A, Royal Statistical Society, vol. 170(2), pages 301-354, March.
    6. Wang, Qingyun & Duan, Zhisheng & Chen, Guanrong & Feng, Zhaosheng, 2008. "Synchronization in a class of weighted complex networks with coupling delays," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 387(22), pages 5616-5622.
    7. F. W. S. Lima, 2015. "Evolution of egoism on semi-directed and undirected Barabási-Albert networks," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 26(12), pages 1-9.
    8. Matthias Wielscher & Pooja R. Mandaviya & Brigitte Kuehnel & Roby Joehanes & Rima Mustafa & Oliver Robinson & Yan Zhang & Barbara Bodinier & Esther Walton & Pashupati P. Mishra & Pascal Schlosser & Ro, 2022. "DNA methylation signature of chronic low-grade inflammation and its role in cardio-respiratory diseases," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    9. G. Ghoshal & M. E.J. Newman, 2007. "Growing distributed networks with arbitrary degree distributions," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 58(2), pages 175-184, July.
    10. Chang, Y.F. & Han, S.K. & Wang, X.D., 2018. "The way to uncover community structure with core and diversity," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 501(C), pages 111-119.
    11. Chakrabarti, Anindya S., 2015. "Stochastic Lotka-Volterra equations: A model of lagged diffusion of technology in an interconnected world," IIMA Working Papers WP2015-08-05, Indian Institute of Management Ahmedabad, Research and Publication Department.
    12. A. M. M. Shahiduzzaman Quoreshi & Reaz Uddin & Naushad Mamode Khan, 2019. "Quasi-Maximum Likelihood Estimation for Long Memory Stock Transaction Data—Under Conditional Heteroskedasticity Framework," JRFM, MDPI, vol. 12(2), pages 1-13, April.
    13. Roth, Camille, 2007. "Empiricism for descriptive social network models," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 378(1), pages 53-58.
    14. Douglas R. White & Jason Owen-Smith & James Moody & Walter W. Powell, 2004. "Networks, Fields and Organizations: Micro-Dynamics, Scale and Cohesive Embeddings," Computational and Mathematical Organization Theory, Springer, vol. 10(1), pages 95-117, May.
    15. Marc A. Scott & Kaushik Mohan & Jacques‐Antoine Gauthier, 2020. "Model‐based clustering and analysis of life history data," Journal of the Royal Statistical Society Series A, Royal Statistical Society, vol. 183(3), pages 1231-1251, June.
    16. L. da F. Costa & L. E.C. da Rocha, 2006. "A generalized approach to complex networks," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 50(1), pages 237-242, March.
    17. Perc, Matjaž, 2010. "Zipf’s law and log-normal distributions in measures of scientific output across fields and institutions: 40 years of Slovenia’s research as an example," Journal of Informetrics, Elsevier, vol. 4(3), pages 358-364.
    18. Florian Blöchl & Fabian J. Theis & Fernando Vega-Redondo & Eric O'N. Fisher, 2010. "Which Sectors of a Modern Economy are most Central?," CESifo Working Paper Series 3175, CESifo.
    19. M. C. González & A. O. Sousa & H. J. Herrmann, 2004. "Opinion Formation On A Deterministic Pseudo-Fractal Network," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 15(01), pages 45-57.
    20. A. Chatterjee, 2009. "Kinetic models for wealth exchange on directed networks," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 67(4), pages 593-598, February.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:626:y:2023:i:c:s0378437123005988. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.