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Editorial: Systems Biology and Omics Approaches for Understanding Complex Disease Biology
2022
Frontiers in Genetics
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AUTHOR CONTRIBUTIONS All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication. ...
Editorial on the Research Topic Systems Biology and Omics Approaches to Understand Complex Disease Biology High-throughput omics technologies have seamlessly galvanized the fields of big data and systems ...
The genes, proteins or miRNA from multi-omics data are mapped onto the compiled interactome to capture the biological contextspecific interactions, as demonstrated by authors in cervical, breast and ovarian ...
doi:10.3389/fgene.2022.896818
pmid:35495146
pmcid:PMC9039331
fatcat:urffvnvnungefaydfhxm4te3y4
Systems biology of angiogenesis signaling: Computational models and omics
2021
WIREs Mechanisms of Disease
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elucidate and connect the individual molecular and cellular signaling components that function in concert to regulate angiogenesis. ...
Although huge efforts have been devoted to drug development for these diseases by investigation of angiogenesis-targeted therapies, only a few therapeutics and targets have proved effective in humans due ...
DATA AVAILABILITY STATEMENT Data sharing is not applicable to this article as no new data were created or analyzed in this study. ...
doi:10.1002/wsbm.1550
pmid:34970866
pmcid:PMC9243197
fatcat:vqikbkbsa5a6dingizhwfg53bi
Building bridges from 'omics' to cell biology
2009
Genome Biology
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Genome B Bi io ol lo og gy y 2009, 1 10 0: :305 Meeting report B Bu ui il ld di in ng g b br ri id dg ge es s f fr ro om m ' 'o om mi ic cs s' ' t to o c ce el ll l b bi io ol lo og gy y The electronic ...
It is apparent that omics-based technologies have opened up cell biology to a new era of investigation. ...
A recent meeting in the Keystone series focused on the convergence of two fields, large-scale biology 'omics' (defined as anything with an 'omic' ending -genomics, proteomics, metabolomics, and so on) ...
doi:10.1186/gb-2009-10-3-305
pmid:19291275
pmcid:PMC2690995
fatcat:rj63rlakcfhybjg72hcbswdhzq
Systems Biology Approaches to Decipher the Underlying Molecular Mechanisms of Glioblastoma Multiforme
2021
International Journal of Molecular Sciences
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Systems biology approaches have become indispensable in analyzing heterogeneous high-throughput omics data, extracting essential information, and generating new hypotheses from biomedical data. ...
This review provides current knowledge regarding GBM and discusses the multi-omics data and recent systems analysis in GBM to identify key biological functions and genes. ...
Systems biology approaches could comprehensively evaluate the interpretation of multi-omics data derived from wet-lab experiments. ...
doi:10.3390/ijms222413213
pmid:34948010
pmcid:PMC8706582
fatcat:utnzcbyzs5eezpmevm2rgz4vbm
Integration of omics sciences to advance biology and medicine
2014
Clinical Proteomics
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To this end, the National Cancer Institute (NCI) and the National Heart, Lung and Blood Institute (NHLBI) organized a joint workshop in June 2012 with the focus on integration issues related to multi-omics ...
due to a number of factors. ...
Acknowledgement We thank all the workshop participants for their contribution to the discussions and recommendations with regards to the topic of omics integration.
Workshop participant list ...
doi:10.1186/1559-0275-11-45
fatcat:bxyvcnjppzbj7nxuw7emnqfguy
Systems biology analysis for Ewing sarcoma
[chapter]
2020
Zenodo
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and intercellular molecular mechanisms, including regulation of transcription, epigenome and tumoral microenvironment. ...
The situation when the major cancer driver is well known looks like a unique opportunity for applying the systems biology approach in order to understand the EwS mechanisms as well as to uncover some general ...
Some large−scale efforts such as The Cancer Genome Atlas (TCGA) systematically collect multi−level molecular description of adult cancers, and were already subject to multi−omics data analysis (82).Nevertheless ...
doi:10.5281/zenodo.3952243
fatcat:yoknurylgrflleufxgol77qq5e
Nutritional systems biology of type 2 diabetes
2015
Genes & Nutrition
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In this review, we discuss the applications of multi-omics approaches toward a systems-level understanding of how dietary eScholarship provides open access, scholarly publishing services to the University ...
The advent of nutritional systems biology, a field that aims to elucidate the interactions between dietary nutrients and endogenous molecular entities in diseaserelated tissues, offers unique opportunities ...
the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. ...
doi:10.1007/s12263-015-0481-3
pmid:26202330
pmcid:PMC4512958
fatcat:vfoflgpz5nfcvfojkp7ecxjkzi
Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models
2020
Proteomics
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Here, we focus on genome-scale models (GEMs) as one computational systems biology approach for interpreting and integrating multi-omic data. ...
We review a variety of genome-scale modeling methods used to interpret multiple omic data types, including genomics, transcriptomics, proteomics, metabolomics, and meta-omics. ...
Integrating multi-omic data with genome-scale models Studies are now combining multi-omic platforms with GEMs to study complex interactions that occur at the molecular level within organisms. ...
doi:10.1002/pmic.201900282
pmid:32579720
fatcat:h3euvl3j5vggjmbh5buaspz4uy
Integrative Systems Biology Resources and Approaches in Disease Analytics
[chapter]
2019
Systems Biology [Working Title]
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Here, we will describe several database resources, standalone and web-based tools applied in disease analytics workflows based in data-driven integration of outputs of multi-omic detection platforms. ...
Currently, our analytical competences are struggling to keep-up the pace of in-deep analysis of all generated large-scale data resultant of high-throughput omics platforms. ...
Acknowledgements The research leading to these results has received funding from the European Union's Seventh Framework Programme FP7/2007-2013 under grant agreement FP7-PEOPLE-2013-ITN-608332. ...
doi:10.5772/intechopen.84834
fatcat:szdavjmg2jbwpnjl2irao6ehty
Advances in Systems Biology Approaches for Autoimmune Diseases
2014
Immune Network
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Systems biology approaches for AIDs in combination with multi-OMICs and network analysis. ...
The chromatin immunoprecipitation (ChIP) method is used to investigate the interaction between transcription factors and genomic DNA and to identify genes putatively regulated by these factors. markers ...
doi:10.4110/in.2014.14.2.73
pmid:24851096
pmcid:PMC4022781
fatcat:gz3gnu2kejcyzcot6ll6wdg474
Systems Biology Approaches to Understanding the Human Immune System
2020
Frontiers in Immunology
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Changes in molecular pathways can be detected using high-throughput omics datasets (e.g., transcriptomics, proteomics, and metabolomics) by using methods such as pathway enrichment, network analysis, machine ...
In this perspective article, we highlight the use of protein-protein interaction (PPI) networks as a multi-omics integration approach to unravel information flow and mechanisms during complex biological ...
ACKNOWLEDGMENTS The authors wish to acknowledge collaborators Fiona Brinkman, David Lynn, Jeff Xia, Tamara Munzner, and previous lab members Erin Gill, Chris Fjell, and Jennifer Gardy as well as the InnateDB ...
doi:10.3389/fimmu.2020.01683
pmid:32849587
pmcid:PMC7406790
fatcat:znyhac4tgfeg5gr6t3xiaczz7q
Integrative Biology Approaches Applied to Human Diseases
[chapter]
2019
Computational Biology
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However, extracting meaningful information from this "sea of data" remains a major challenge. The field of integrative biology utilizes a holistic approach to integrate multilayer biological data. ...
In this chapter, we introduce concepts and techniques for the analysis of single-layer omics data and for integrating multilayer omics datasets to extract meaningful and relevant biological insights. ...
The central dogma of molecular biology states that the information is transferred sequentially from mRNA to proteins (67) . ...
doi:10.15586/computationalbiology.2019.ch2
fatcat:pyr5zig3vvdvxlcv3qgncage5a
Antiestrogen resistance and the application of systems biology
2012
Drug Discovery Today : Disease Mechanisms
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Recent systems biology approaches allow for the integration of data from high throughput "-omics" technologies. ...
Understanding the molecular changes that drive an acquired antiestrogen resistance phenotype is of major clinical relevance. ...
Acknowledgments This work was supported in part by awards from the US Department of Health and Human Services to Robert Clarke: R01-CA131465 and U54-CA149147. ...
doi:10.1016/j.ddmec.2012.10.003
pmid:23539064
pmcid:PMC3607389
fatcat:5bht4r4ocfdblhjeyeoen35qj4
Network-based drug discovery by integrating systems biology and computational technologies
2012
Briefings in Bioinformatics
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Recently, robustness of multiple systems biology platforms shows powerful to uncover molecular mechanisms and connections between the drugs and their targeting dynamic network. ...
to develop into new wave of network-based multi-target drugs. ...
Overall, better integration of the data derived from multiple '-omics' technologies can lead to optimization of the treatment by taking advantage of molecular synergy [56] . ...
doi:10.1093/bib/bbs043
pmid:22877768
pmcid:PMC3713711
fatcat:t3wp24cgyff6zechfsm5hagfji
Systems Biology Approaches and Precision Oral Health: A Circadian Clock Perspective
2019
Frontiers in Physiology
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Emerging omics technologies permits largescale multi-dimensional investigations of the molecular landscape of a given disease and the comprehensive characterization of its underlying cellular components ...
have investigated the implications of circadian disruption in oral, head and neck pathologies using multi-omics approaches and linking the omics data to patient-specific circadian profiles. ...
Multi-omics and system biology approaches are becoming the golden standards to pave the road for precision health. ...
doi:10.3389/fphys.2019.00399
pmid:31040792
pmcid:PMC6476986
fatcat:3huihdxfkzctvmzbcaoliepwmu
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