From biophysics to ‘omics and systems biology

Djordjevic, M.; Rodic, Andjela; Graovac, Stefan

doi:10.1007/s00249-019-01366-3

Cited by 11 publications

(7 citation statements)

References 63 publications

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“…Solutions toward the effectual survey of such molecules and finding of their universal laws include the application of informatics, which allows the comparison of items represented by sequences, although frequently at the exclusion of physicochemical properties. Therefore, combinations of computational biophysics and bioinformatics (including multi-omics analyses) will be powerful tools for the analysis of biomolecular dynamics [ 211 ].…”

Section: Summary and Future Perspectivesmentioning

confidence: 99%

Molecular dynamics analysis of biomolecular systems including nucleic acids

2022

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Section: Summary and Future Perspectivesmentioning

confidence: 99%

Molecular dynamics analysis of biomolecular systems including nucleic acids

2022

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“…Currently, mathematical models have been extensively used to understand biological processes in life sciences, including but not restricted to the analysis of genomics, proteomics, metabolomics, and epigenomics of a broad range of taxa (Zhao and Li, 2017;Cheng and Leung, 2018;Djordjevic et al, 2019).…”

Section: Systems Biology: Concepts and Applicationsmentioning

confidence: 99%

Perspectives From Systems Biology to Improve Knowledge of Leishmania Drug Resistance

Horácio

Hickson

Murta

et al. 2021

Front. Cell. Infect. Microbiol.

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Neglected Tropical Diseases include a broad range of pathogens, hosts, and vectors, which represent evolving complex systems. Leishmaniasis, caused by different Leishmania species and transmitted to humans by sandflies, are among such diseases. Leishmania and other Trypanosomatidae display some peculiar features, which make them a complex system to study. Leishmaniasis chemotherapy is limited due to high toxicity of available drugs, long-term treatment protocols, and occurrence of drug resistant parasite strains. Systems biology studies the interactions and behavior of complex biological processes and may improve knowledge of Leishmania drug resistance. System-level studies to understand Leishmania biology have been challenging mainly because of its unusual molecular features. Networks integrating the biochemical and biological pathways involved in drug resistance have been reported in literature. Antioxidant defense enzymes have been identified as potential drug targets against leishmaniasis. These and other biomarkers might be studied from the perspective of systems biology and systems parasitology opening new frontiers for drug development and treatment of leishmaniasis and other diseases. Our main goals include: 1) Summarize current advances in Leishmania research focused on chemotherapy and drug resistance. 2) Share our viewpoint on the application of systems biology to Leishmania studies. 3) Provide insights and directions for future investigation.

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“…Data-driven statistical models describe the relationship between the elements of a signalling network that most accurately reflect available experimental data. This is a relatively recent approach in the field of systems biology that has quickly risen in popularity due to its applicability in the analysis of large datasets generated by high throughput experimental techniques (Djordjevic, Rodic, & Graovac, 2019). By employing an integrated statistical analysis on high-volume, multidimensional "-omics" data, it is possible to create a comparison between the signalling events in normal, healthy cells and the aberrant signalling that occurs in diseased-state cells, thereby identifying the network structures that may promote this diseased phenotype, rather than having to focus on genes individually (Blair, Trichler, & Gaille, 2012), or infer the activity of signalling pathways based on gene expression (Schubert, et al, 2018).…”

Section: Statistical Modellingmentioning

confidence: 99%