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Editorial: Systems Biology and Omics Approaches for Understanding Complex Disease Biology

Amit Kumar Yadav, Sanjay Kumar Banerjee, Bhabatosh Das, Kumardeep Chaudhary
2022 Frontiers in Genetics  
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

Yu Zhang, Hanwen Wang, Rebeca Hannah M. Oliveira, Chen Zhao, Aleksander S. Popel
2021 WIREs Mechanisms of Disease  
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

Brian Cox
2009 Genome Biology  
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

Ali Kaynar, Ozlem Altay, Xiangyu Li, Cheng Zhang, Hasan Turkez, Mathias Uhlén, Saeed Shoaie, Adil Mardinoglu
2021 International Journal of Molecular Sciences  
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

Emily S Boja, Christopher R Kinsinger, Henry Rodriguez, Pothur Srinivas
2014 Clinical Proteomics  
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]

Marianyela Petrizzelli, Jane Merlevede, Andrei Zinovyev
2020 Zenodo  
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 multiomics data analysis (82).Nevertheless  ... 
doi:10.5281/zenodo.3952243 fatcat:yoknurylgrflleufxgol77qq5e

Nutritional systems biology of type 2 diabetes

Yuqi Zhao, Rio Elizabeth Barrere-Cain, Xia Yang
2015 Genes & Nutrition  
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

Sanjeev Dahal, James T. Yurkovich, Hao Xu, Bernhard O. Palsson, Laurence Yang
2020 Proteomics  
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]

Marco Fernandes, Holger Husi
2019 Systems Biology [Working Title]  
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

Ho-Youn Kim, Hae-Rim Kim, Sang-Heon Lee
2014 Immune Network  
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

Bhavjinder K. Dhillon, Maren Smith, Arjun Baghela, Amy H. Y. Lee, Robert E. W. Hancock
2020 Frontiers in Immunology  
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]

Alysson H. Urbanski, Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil, José D. Araujo, Rachel Creighton, Helder I. Nakaya, Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil, Department of Bioengineering, University of Washington, Seattle, WA, USA, Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil, Scientific Platform Pasteur/USP, University of Sao Paulo, Sao Paulo, Brazil
2019 Computational Biology  
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

Kerrie B Bouker, Yue Wang, Jianhua Xuan, Robert Clarke
2012 Drug Discovery Today : Disease Mechanisms  
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

E. L. Leung, Z.-W. Cao, Z.-H. Jiang, H. Zhou, L. Liu
2012 Briefings in Bioinformatics  
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

Henry A. Adeola, Silvana Papagerakis, Petros Papagerakis
2019 Frontiers in Physiology  
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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