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Omics Fusion – A Platform for Integrative Analysis of Omics Data

Benedikt G. Brink, Annica Seidel, Nils Kleinbölting, Tim W. Nattkemper, Stefan P. Albaum
2016 Journal of Integrative Bioinformatics  
We present Omics Fusion, a new web-based platform for integrative analysis of omics data.  ...  Omics Fusion provides a collection of new and established tools and visualization methods to support researchers in exploring omics data, validating results or understanding how to adjust experiments in  ...  Wenzel and Ruben Christian Hamann for their invaluable contributions.  ... 
doi:10.1515/jib-2016-296 fatcat:geiaxflfcrhdrmig2s64eyzkbm

Integrative Network Fusion: a multi-omics approach in molecular profiling [article]

Marco Chierici, Nicole Bussola, Alessia Marcolini, Margherita Francescatto, Alessandro Zandonà, Lucia Trastulla, Claudio Agostinelli, Giuseppe Jurman, Cesare Furlanello
2020 bioRxiv   pre-print
Here we apply the Integrative Network Fusion (INF) pipeline, which combines multiple omics layers exploiting Similarity Network Fusion (SNF) within a machine learning predictive framework.  ...  All the classifiers are run in a 10x5-fold cross- validation schema to warrant reproducibility, following the guidelines for an unbiased Data Analysis Plan by the US FDA-led initiatives MAQC/SEQC.  ...  Our study introduces Integrative Network Fusion (INF), a reproducible network-based framework for high-throughput omics data integration that leverages machine learning models to extract multi-omics predictive  ... 
doi:10.1101/2020.04.01.020685 fatcat:rwm4wuypc5dxvak337jfo25hyq

Integrative Network Fusion: A Multi-Omics Approach in Molecular Profiling

Marco Chierici, Nicole Bussola, Alessia Marcolini, Margherita Francescatto, Alessandro Zandonà, Lucia Trastulla, Claudio Agostinelli, Giuseppe Jurman, Cesare Furlanello
2020 Frontiers in Oncology  
Here we apply the Integrative Network Fusion (INF) pipeline, which combines multiple omics layers exploiting Similarity Network Fusion (SNF) within a machine learning predictive framework.  ...  All the classifiers are run in a 10x5-fold cross-validation schema to warrant reproducibility, following the guidelines for an unbiased Data Analysis Plan by the US FDA-led initiatives MAQC/SEQC.  ...  This study introduces Integrative Network Fusion (INF), a reproducible network-based framework for high-throughput omics data integration that leverages machine learning models to extract multi-omics predictive  ... 
doi:10.3389/fonc.2020.01065 pmid:32714870 pmcid:PMC7340129 fatcat:xewshiydkzcphffw5ocjfmdjli

Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering [article]

Tianle Ma, Aidong Zhang
2017 arXiv   pre-print
Similar to SNF, ANF treats each omic data type as one view of patients and learns a fused affinity (transition) matrix for clustering.  ...  However, it is challenging to integrate heterogeneous omic data types directly.  ...  Since each type of omic data may contain some complementary information about the patients and disease, we can perform integrative network analysis with multi-omic data.  ... 
arXiv:1708.07136v1 fatcat:bbsmf7ehnza3bfwhh5ulipbsyy

Subtypes Identification on Heart Failure with Preserved Ejection Fraction via Network Enhancement Fusion using Multi-omics Data

Yongqing Wu, Huihui Wang, Zhi Li, Jinfang Cheng, Ruiling Fang, Hongyan Cao, Yuehua Cui
2021 Computational and Structural Biotechnology Journal  
The ne-SNF method provides a novel pipeline for subtype identification in integrated analysis of multi-omics data.  ...  Here we proposed to integrate mRNA, DNA methylation and microRNA (miRNA) expression data of HFpEF with a similarity network fusion (SNF) method following a network enhancement (ne-SNF) denoising technique  ...  Acknowledgements We are grateful to the four anonymous reviewers for their insightful comments that helped us greatly improve our manuscript.  ... 
doi:10.1016/j.csbj.2021.03.010 pmid:33868594 pmcid:PMC8039555 fatcat:byb7tif72vggpdpanzqjv3isgm

Multi-Omics Data Fusion via a Joint Kernel Learning Model for Cancer Subtype Discovery and Essential Gene Identification

Jie Feng, Limin Jiang, Shuhao Li, Jijun Tang, Lan Wen
2021 Frontiers in Genetics  
Identification of cancer subtypes is a key part of personalized cancer treatment and provides an important reference for clinical diagnosis and treatment.  ...  fuse these matrices as a global kernel matrix.  ...  Similarity network fusion (SNF) is a network fusion method integrating multicomponent data, which was proposed by Wang et al. (2014) .  ... 
doi:10.3389/fgene.2021.647141 pmid:33747053 pmcid:PMC7969795 fatcat:v7zzdkhltff6nmt4z36ezrz7p4

Cascaded Multi-view Canonical Correlation (CaMCCo) for Early Diagnosis of Alzheimer's Disease via Fusion of Clinical, Imaging and Omic Features

Asha Singanamalli, Haibo Wang, Anant Madabhushi
2017 Scientific Reports  
CaMCCo is evaluated on a data cohort comprising 149 patients for whom neurophysiological, neuroimaging, proteomic and genomic data were available.  ...  sensitivity of 81% and a specificity of 70% for AD diagnosis 4 .  ...  Principal Component Analysis for Data Fusion.  ... 
doi:10.1038/s41598-017-03925-0 pmid:28811553 pmcid:PMC5558022 fatcat:f4zpwwuwezfojgje6tljzloye4

Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation [article]

Martin F. Orth, Didier Surdez, Aruna Marchetto, Sandrine Grossetete, Julia S. Gerke, Sakina Zaidi, Javier Alonso, Ana Sastre, Sylvain Baulande, Martin Sill, Florencia Cidre-Aranaz, Shunya Ohmura (+8 others)
2021 bioRxiv   pre-print
Systematic analysis of these multi-dimensional data illuminated hundreds of new potential EWSR1-ETS target genes, the nature of EWSR1-ETS-preferred GGAA-mSats, and potential indirect modes of EWSR1-ETS-mediated  ...  of heterogeneous gene regulation by dominant fusion oncogenes.  ...  Fabian Metzger for mass spectrometry readouts. We thank Dr. Paul Northcott and Dr. Brian Gudenas for providing R scripts for weighted correlation network analyses and Dr. Carlos  ... 
doi:10.1101/2021.06.08.447518 fatcat:asd6ktad2zfmhnxur7dowzzymy

Integration of multi-omics datasets enables molecular classification of COPD

Chuan-Xing Li, Craig E. Wheelock, C. Magnus Sköld, Åsa M. Wheelock
2018 European Respiratory Journal  
For the first time, a quantitative relationship between multi-omics data integration and accuracy of datadriven classification power has been demonstrated across nine omics data blocks.  ...  Seven different combinations of four to seven omics platforms achieved >95% accuracy.  ...  As a framework for the omics integrations, we used similarity network fusion (SNF) [14] , which represents a new class of integration methods [15] .  ... 
doi:10.1183/13993003.01930-2017 pmid:29545283 fatcat:lf63de7oiref5hdmy7o62bxh3i

Multi-omics Data Integration, Interpretation, and Its Application

Indhupriya Subramanian, Srikant Verma, Shiva Kumar, Abhay Jere, Krishanpal Anamika
2020 Bioinformatics and Biology Insights  
With the advent of high-throughput techniques and availability of multi-omics data generated from a large set of samples, several promising tools and methods have been developed for data integration and  ...  We provide the methodology, use-cases, and limitations of these tools; brief account of multi-omics data repositories and visualization portals; and challenges associated with multi-omics data integration  ...  Priyabrata Panigrahi for initial discussion and participation in the selection of tools and methods. Authors would also like to thank Pratap Sanap for his input on tools categorization.  ... 
doi:10.1177/1177932219899051 pmid:32076369 pmcid:PMC7003173 fatcat:dchnmbmzh5di7jcuc7ilxjsk3e

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  ...  of a biological process.  ...  We also acknowledge a paid artist Ms. Irene Carreras Ribot for generating Figure 1 .  ... 
doi:10.3389/fgene.2020.610798 pmid:33362867 pmcid:PMC7758509 fatcat:vlscnvlybza7fghtxhapg6cfee

Approaches to Integrating Metabolomics and Multi-Omics Data: A Primer

Takoua Jendoubi
2021 Metabolites  
As a result, a vast array of computational tools have been developed to assist with integrative analysis of metabolomics data with different omics.  ...  We will draw particular attention to metabolomics and genomics data to assist those new to this field in the choice of the integrative analysis pipeline.  ...  Chadeau for useful discussions. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/metabo11030184 pmid:33801081 pmcid:PMC8003953 fatcat:tbo2rmowerfclavavtttoczvoa

OmicsAnalyst: a comprehensive web-based platform for visual analytics of multi-omics data

Guangyan Zhou, Jessica Ewald, Jianguo Xia
2021 Nucleic Acids Research  
Here, we introduce OmicsAnalyst, a user-friendly, web-based platform that allows users to perform a wide range of well-established data-driven approaches for multi-omics integration, and visually explore  ...  Data analysis and interpretation remain a critical bottleneck in current multi-omics studies.  ...  Here, we introduce OmicsAnalyst, a web-based visual analytics platform dedicated for data-driven multi-omics integration.  ... 
doi:10.1093/nar/gkab394 pmid:34019646 pmcid:PMC8262745 fatcat:44vygfejmnf2lgh6qkbyrd3ndu

Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science)

Irene Sui Lan Zeng, Thomas Lumley
2018 Bioinformatics and Biology Insights  
Acknowledgements The authors would like to express their gratitude to Ms Vivian Ward who helped to visualize the analytical processes for the review.  ...  It is known that iCluster and similarity network fusion are not designed for the analysis of cross-omics data. 19 iCluster does not scale all measurements and needs preselection of genes.  ...  They use a dimension-reducing technique TUCKER3 for intra-omics analysis and the N-partial least Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science)  ... 
doi:10.1177/1177932218759292 pmid:29497285 pmcid:PMC5824897 fatcat:nbknjl4qq5awrldy7natmg3h6y

Integration of Online Omics-Data Resources for Cancer Research

Tonmoy Das, Geoffroy Andrieux, Musaddeque Ahmed, Sajib Chakraborty
2020 Frontiers in Genetics  
integrate the omics-data in a biologically meaningful manner.  ...  The advantage of multi-omics data integration comes with a trade-off in the form of an added layer of complexity originating from inherently diverse types of omics-datasets that may pose a challenge to  ...  Similarity Network Fusion (SNF) Similarity network fusion is a network-based approach for the integrative multi-omics data sets.  ... 
doi:10.3389/fgene.2020.578345 pmid:33193699 pmcid:PMC7645150 fatcat:adq25boimjbkjgrrdpdwgtmfma
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