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Network-based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

Amanda J. Kedaigle
2017 Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics - ACM-BCB '17  
These two classes of tools are both essential to fully integrate diverse types of high-throughput data. The Omics Integrator Software Package PLOS Computational Biology |  ...  In this work, we introduce Omics Integrator, a software package that takes a variety of 'omic' data as input and identifies putative underlying molecular pathways.  ...  Acknowledgments We thank all the beta testers for running the software, in particular Jonathon Gulliver for his evaluation of the test procedures. Author Contributions  ... 
doi:10.1145/3107411.3107461 dblp:conf/bcb/Kedaigle17 fatcat:vur2d3x6sna33g7ikxe5tutj4e

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

Nurcan Tuncbag, Sara J. C. Gosline, Amanda Kedaigle, Anthony R. Soltis, Anthony Gitter, Ernest Fraenkel, Andreas Prlic
2016 PLoS Computational Biology  
These two classes of tools are both essential to fully integrate diverse types of high-throughput data. The Omics Integrator Software Package PLOS Computational Biology |  ...  In this work, we introduce Omics Integrator, a software package that takes a variety of 'omic' data as input and identifies putative underlying molecular pathways.  ...  Acknowledgments We thank all the beta testers for running the software, in particular Jonathon Gulliver for his evaluation of the test procedures. Author Contributions  ... 
doi:10.1371/journal.pcbi.1004879 pmid:27096930 pmcid:PMC4838263 fatcat:sq7dszd5ifffhckzecrayihcdu

Genomic, Proteomic, and Metabolomic Data Integration Strategies

Kwanjeera Wanichthanarak, Johannes F. Fahrmann, Dmitry Grapov
2015 Biomarker Insights  
This review focuses on select methods and tools for the integration of metabolomic with genomic and proteomic data using a variety of approaches including biochemical pathway-, ontology-, network-, and  ...  Integration of analyses carried out across multiple measurement or omic platforms is an emerging approach to help address these challenges.  ...  Acknowledgements The authors thank Prof Oliver Fiehn for his support. Author contributions  ... 
doi:10.4137/bmi.s29511 pmid:26396492 pmcid:PMC4562606 fatcat:w2kkb25ftjefbfycpu32z3e2qa

Computational Oncology in the Multi-Omics Era: State of the Art

Guillermo de Anda-Jáuregui, Enrique Hernández-Lemus
2020 Frontiers in Oncology  
In this multi-omics context, the use of integrative approaches is mandatory in order to gain further insights on oncological phenomena, and to move forward toward the precision medicine paradigm.  ...  We will discuss the machine learning and network approaches as two of the most promising emerging paradigms, in computational oncology.  ...  With this in mind, the integration of high-throughput data within a network paradigm becomes appealing.  ... 
doi:10.3389/fonc.2020.00423 pmid:32318338 pmcid:PMC7154096 fatcat:lrlg3yyo2ffkdaz2whv2egyklq

Integrated Omics: Tools, Advances, and Future Approaches

Biswapriya B Misra, Carl D Langefeld, Michael Olivier, Laura A Cox
2018 Journal of Molecular Endocrinology  
With the rapid adoption of high-throughput omic approaches to analyze biological samples such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can generate tera- to peta-byte sized  ...  We discuss recent approaches, existing tools, and potential caveats in the integration of omics datasets for development of standardized analytical pipelines that could be adopted by the global omics research  ...  This theory has, since then formed the corner stone of largescale high-throughput and high-dimensional data set oriented omics studies.  ... 
doi:10.1530/jme-18-0055 pmid:30006342 fatcat:62c6xglxcbhhnkxgqo5gt7garq

Community-wide hackathons to identify central themes in single-cell multi-omics

Kim-Anh Lê Cao, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb, Atul Deshpande, Yuzhou Feng, Pratheepa Jeganathan, Melanie Loth, Chen Meng, Wancen Mu (+18 others)
2021 Genome Biology  
Funding We wish to acknowledge the following funding bodies:  ...  The ideal benchmark datasets for multi-omics would be based on the biological reality of molecular and cellular networks, with full capacity to predict the biological impact of perturbations and temporal  ...  An equally important complement to the diverse computational methods used to solve multi-omics analysis problems rests in the biological interpretation of their solutions.  ... 
doi:10.1186/s13059-021-02433-9 pmid:34353350 pmcid:PMC8340473 fatcat:lvcuong62jbdxbfcmyfvsws7si

Databases and tools for constructing signal transduction networks in cancer

Seungyoon Nam
2017 BMB Reports  
Most network generation tools are based on whole transcriptome data. Using statistical models, the integration of other data types into network topology is still challenging.  ...  One of the representative applications of systems biology is to generate a biological network from high-throughput big data, providing a global map of molecular events associated with specific phenotype  ...  HIGH-THROUGHPUT DATA AND ITS REPOSITORIES Currently, there are numerous types of high-throughput data (i.e., "omics"), including genomics, epigenomics, transcriptomics, The diversity of types of high-throughput  ... 
doi:10.5483/bmbrep.2017.50.1.135 pmid:27502015 pmcid:PMC5319659 fatcat:pwjpj6my6bblzj6lcu4urbxxkm

Single-platform 'multi-omic' profiling: unified mass spectrometry and computational workflows for integrative proteomics–metabolomics analysis

Benjamin C. Blum, Fatemeh Mousavi, Andrew Emili
2018 Molecular Omics  
Advances in instrumentation and analysis tools are permitting evermore comprehensive interrogation of diverse biomolecules and allowing investigators to move from linear signaling cascades to network models  ...  , which more accurately reflect the molecular basis of biological systems and processes.  ...  Acknowledgements The authors acknowledge constructive input from members of the Emili Lab (University of Toronto and Boston University) for their assistance in compiling supporting information.  ... 
doi:10.1039/c8mo00136g pmid:30211418 fatcat:a7zh2wdz3jcu3bb6qwvumgxmfi

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  
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.  ...  We also highlight some current challenges in the field, such as the need for more specialized and interpretable methods, while increasing the accessibility of integrative analysis for the scientific community  ...  TOOLS FOR THE ANALYSIS OF SINGLE-LAYER HIGH-THROUGHPUT DATA Ensuring data quality is an essential step in the analysis and integration of omics data.  ... 
doi:10.15586/computationalbiology.2019.ch2 fatcat:pyr5zig3vvdvxlcv3qgncage5a

Integrating -Omics: Systems Biology as Explored Through C. elegans Research

Roel Van Assche, Valérie Broeckx, Kurt Boonen, Evelyne Maes, Wouter De Haes, Liliane Schoofs, Liesbet Temmerman
2015 Journal of Molecular Biology  
Now, individual techniques and methods for integration are maturing to the point that researchers can focus on network-based integration rather than simply interpreting single -ome studies.  ...  From the large volumes of -omics data that have been gathered over the years, it is clear that the information derived from one -ome is usually far from complete.  ...  An even more elaborate integrating method relies on network-based integration (Fig. 2c) , in which the simple one-to-one comparison of datasets is replaced by mapping all data onto molecular networks  ... 
doi:10.1016/j.jmb.2015.03.015 pmid:25839106 fatcat:i76lnn323jgijabhmswciwyboi

Applications of Multi-Omics Technologies for Crop Improvement

Yaodong Yang, Mumtaz Ali Saand, Liyun Huang, Walid Badawy Abdelaal, Jun Zhang, Yi Wu, Jing Li, Muzafar Hussain Sirohi, Fuyou Wang
2021 Frontiers in Plant Science  
Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement.  ...  Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement  ...  Whereas, the diversity arrays technology (DArT) a high-throughput technique which is based on microarray hybridization involving genotyping of numerous polymorphic loci spread over the genome (Jaccoud  ... 
doi:10.3389/fpls.2021.563953 pmid:34539683 pmcid:PMC8446515 fatcat:dk4kvn6qxfe4xoz266tquokway

Integrative Systems Biology Resources and Approaches in Disease Analytics [chapter]

Marco Fernandes, Holger Husi
2019 Systems Biology [Working Title]  
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.  ...  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.  ...  Conflict of interest The authors declare that there is no conflict of interest regarding the publication of this manuscript.  ... 
doi:10.5772/intechopen.84834 fatcat:szdavjmg2jbwpnjl2irao6ehty

Decoding plant-environment interactions that influence crop agronomic traits

Keiichi Mochida, Ryuei Nishii, Takashi Hirayama
2020 Plant and Cell Physiology  
We review recent advances in analytical technologies for monitoring health status in plants based on multi-omics analyses and strategies for integrating heterogeneous datasets from multiple omics areas  ...  overall throughput of gene discovery and crop breeding.  ...  For example, mixOmix is an integrated package providing a framework for multi-omics data integration for the identification of biomarkers and molecular signatures with such multivariate analysis-based  ... 
doi:10.1093/pcp/pcaa064 pmid:32392328 pmcid:PMC7434589 fatcat:nyevejd6anc7nj7n763s5j42ca

Explainable Machine Learning for Longitudinal Multi-Omic Microbiome

Paula Laccourreye, Concha Bielza, Pedro Larrañaga
2022 Mathematics  
Our study aims to extend the current knowledge of associations between the human microbiome and health and disease through the application of dynamic Bayesian networks to describe the temporal variation  ...  We develop a set of preprocessing steps to clean, filter, select, integrate, and model informative metagenomics, metatranscriptomics, and metabolomics longitudinal data from the Human Microbiome Project  ...  of this manuscript.  ... 
doi:10.3390/math10121994 fatcat:vd7hkogsinaitebzjk4inegvhe

State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing

Michal Krassowski, Vivek Das, Sangram K. Sahu, Biswapriya B. Misra
2020 Frontiers in Genetics  
Multi-omics, variously called integrated omics, pan-omics, and trans-omics, aims to combine two or more omics data sets to aid in data analysis, visualization and interpretation to determine the mechanism  ...  However, the mushrooming of a myriad of tools, datasets, and approaches tends to inundate the literature and overwhelm researchers new to the field.  ...  We would like to thank the developers and researchers of the multi-omics community who drive the field forward with their code, packages, tools, and resources, whether their work was discussed or not included  ... 
doi:10.3389/fgene.2020.610798 pmid:33362867 pmcid:PMC7758509 fatcat:vlscnvlybza7fghtxhapg6cfee
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