Advertisement

Modeling and Optimization of Molecular Biosystems to Generate Predictive Models

  • Ankush Bansal
  • Siddhant Kalra
  • Babajan Banaganapalli
  • Tiratha Raj Singh
Chapter

Abstract

With the increase in biological data in online databases, there is a need of optimization techniques to handle data complexity. In the previous decade, theoretical development in computer science opened new windows for system modeling. A growing interest of physicist to solve complex biological processes and regulation mechanism underlying unknown pathway made a significant contribution in optimization techniques. In this chapter, we focused on applications of optimization in systems biology, where optimization plays a vital role to define regulation or inhibition flux for accurate information flow prediction. Optimization methods are used for model building, network construction, and optimization of flux in metabolic and synthetic biology. We believe that a deeper insight of the theory and logic behind the concept of optimization in this chapter will help in the proper implementation of optimization techniques and investigation of complex biological networks including insertion of new ideas to control biosystems in the much effective way.

Keywords

Optimization techniques Bio-models Prediction Flux balance Simulation Networks 

References

  1. Apostolopoulos Y, Lemke MK, Barry AE, Lich KH (2017) Moving alcohol prevention research forward-part II: new directions grounded in community-based system dynamics modeling. Addiction.  https://doi.org/10.1111/add.13953
  2. Athanasiou G, Anastasopoulos GC, Tiritidou E, Lymberopoulos D (2017) A trust model for ubiquitous healthcare environment on the basis of adaptable fuzzy-probabilistic inference system. IEEE J Biomed Health Inform.  https://doi.org/10.1109/JBHI.2017.2733038
  3. Bansal A, Ramana J (2015) TCGDB: a compendium of molecular signatures of thyroid cancer and disorders. J Cancer Sci Ther.  https://doi.org/10.4172/1948-5956.1000350
  4. Bansal A, Srivastava PA (2018) Transcriptomics to metabolomics: a network perspective for big data. http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/978-1-5225-2607-0.ch008:188–206.  https://doi.org/10.4018/978-1-5225-2607-0.ch008
  5. Davis LE, Jeng S, Svalina MN, Huang E, Pittsenbarger J, Cantor EL et al (2017) Integration of genomic, transcriptomic and functional profiles of aggressive osteosarcomas across multiple species. Oncotarget.  https://doi.org/10.18632/oncotarget.19532
  6. Fan D, Lopez Ruiz L, Gong J, Lach J (2017) EHDC: an energy harvesting modeling and profiling platform for body sensor networks. IEEE J Biomed Health Inform.  https://doi.org/10.1109/JBHI.2017.2733549
  7. Giraud S, Brock AM, Macé MJ-M, Jouffrais C (2017) Map learning with a 3D printed interactive small-scale model: improvement of space and text memorization in visually impaired students. Front Psych 8:930.  https://doi.org/10.3389/fpsyg.2017.00930CrossRefGoogle Scholar
  8. Griffen BD, Riley ME, Cannizzo ZJ, Feller IC (2017) Indirect effects of ecosystem engineering combine with consumer behavior to determine the spatial distribution of herbivory. J Anim Ecol.  https://doi.org/10.1111/1365-2656.12730
  9. Huang M, Dissanayake T, Kuechler E, Radak BK, Lee T-S, Giese TJ, York DM (2017) A multi-dimensional B-spline method for accurate modeling sugar puckering in QM/MM simulations. J Chem Theory Comput.  https://doi.org/10.1021/acs.jctc.7b00161
  10. Jindal K, Bansal A (2016) APOEε2 is associated with milder clinical and pathological Alzheimer’s disease. Ann Neurosci 23(2):112.  https://doi.org/10.1159/000443572CrossRefPubMedPubMedCentralGoogle Scholar
  11. Jo S, Cheng X, Lee J, Kim S, Park S-J, Patel DS et al (2017) CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem 38(15):1114–1124.  https://doi.org/10.1002/jcc.24660CrossRefPubMedGoogle Scholar
  12. Kallhovd S, Maleckar MM, Rognes ME (2017) Inverse estimation of cardiac activation times via gradient-based optimisation. Int J Numer Methods Biomed Eng.  https://doi.org/10.1002/cnm.2919
  13. Kim SY, Kawaguchi T, Yan L, Young J, Qi Q, Takabe K (2017) Clinical relevance of microRNA expressions in breast cancer validated using the cancer genome atlas (TCGA). Ann Surg Oncol.  https://doi.org/10.1245/s10434-017-5984-2
  14. Kitano H (2002) Systems biology: a brief overview. Science 295(5560):1662–1664.  https://doi.org/10.1126/science.1069492CrossRefPubMedGoogle Scholar
  15. Kumar A, Singh TR (2017) A new decision tree to solve the puzzle of Alzheimer’s disease pathogenesis through standard diagnosis scoring system. Interdiscip Sci Comput Life Sci 9(1):107–115.  https://doi.org/10.1007/s12539-016-0144-0CrossRefGoogle Scholar
  16. Kumar V, Bansal A, Chauhan RS (2017) Modular design of picroside-II biosynthesis deciphered through NGS transcriptomes and metabolic intermediates analysis in naturally variant chemotypes of a medicinal herb, Picrorhiza kurroa. Front Plant Sci 8:564.  https://doi.org/10.3389/fpls.2017.00564CrossRefPubMedPubMedCentralGoogle Scholar
  17. Nordholt N, van Heerden J, Kort R, Bruggeman FJ (2017) Effects of growth rate and promoter activity on single-cell protein expression. Sci Rep 7(1):6299.  https://doi.org/10.1038/s41598-017-05871-3CrossRefPubMedPubMedCentralGoogle Scholar
  18. Qing Y, Gerson SL (2017) Mismatch repair deficient hematopoietic stem cells are preleukemic stem cells. PLoS One 12(8):e0182175.  https://doi.org/10.1371/journal.pone.0182175CrossRefPubMedPubMedCentralGoogle Scholar
  19. Romero AH, López SE (2017) In silico molecular docking studies of new potential 4-phthalazinyl-hydrazones on selected Trypanosoma cruzi and Leishmania enzyme targets. J Mol Graph Model 76:313–329.  https://doi.org/10.1016/j.jmgm.2017.07.013CrossRefPubMedGoogle Scholar
  20. Sehgal M, Gupta R, Moussa A, Singh TR (2015) An integrative approach for mapping differentially expressed genes and network components using novel parameters to elucidate key regulatory genes in colorectal cancer. PLoS One 10(7):e0133901.  https://doi.org/10.1371/journal.pone.0133901CrossRefPubMedPubMedCentralGoogle Scholar
  21. Sun L, Sang M, Zheng C, Wang D, Shi H, Liu K et al (2017) The genetic architecture of heterochronsy as a quantitative trait: lessons from a computational model. Brief Bioinform.  https://doi.org/10.1093/bib/bbx056
  22. Teku GN, Vihinen M (2017) Simulation of the dynamics of primary immunodeficiencies in CD4+ T-cells. PLoS One 12(4):e0176500.  https://doi.org/10.1371/journal.pone.0176500CrossRefPubMedPubMedCentralGoogle Scholar
  23. Vreven T, Pierce BG, Borrman TM, Weng Z (2017) Performance of ZDOCK and IRAD in CAPRI rounds 28-34. Proteins 85(3):408–416.  https://doi.org/10.1002/prot.25186CrossRefPubMedGoogle Scholar
  24. Webb K, White T (2005) UML as a cell and biochemistry modeling language. Biosystems 80(3):283–302.  https://doi.org/10.1016/j.biosystems.2004.12.003CrossRefPubMedGoogle Scholar
  25. Winter A, Schmid R, Bayliss R (2015) Structural insights into Separase architecture and substrate recognition through computational modelling of Caspase-like and death domains. PLoS Comput Biol 11(10):e1004548.  https://doi.org/10.1371/journal.pcbi.1004548CrossRefPubMedPubMedCentralGoogle Scholar
  26. Xie X, Liu Z, Xu C, Zhang Y (2017) A multiple sensors platform method for power line inspection based on a large unmanned helicopter. Sensors (Basel) 17(6).  https://doi.org/10.3390/s17061222
  27. Yalçın B, Zhao L, Stofanko M, O’Sullivan NC, Kang ZH, Roost A et al (2017) Modeling of axonal endoplasmic reticulum network by spastic paraplegia proteins. Elife 6.  https://doi.org/10.7554/eLife.23882
  28. Zheng J, Fessler JA, Chan H-P (2017) Detector blur and correlated noise modeling for digital breast tomosynthesis reconstruction. IEEE Trans Med Imaging.  https://doi.org/10.1109/TMI.2017.2732824

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Ankush Bansal
    • 1
  • Siddhant Kalra
    • 1
  • Babajan Banaganapalli
    • 2
  • Tiratha Raj Singh
    • 1
  1. 1.Department of Biotechnology and BioinformaticsJaypee University of Information TechnologySolanIndia
  2. 2.Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Department of Genetic Medicine, Faculty of MedicineKing Abdulaziz UniversityJeddahSaudi Arabia

Personalised recommendations