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A Hybrid Knowledge Discovery Approach for Mining Predictive Biomarkers in Metabolomic Data [chapter]

Dhouha Grissa, Blandine Comte, Estelle Pujos-Guillot, Amedeo Napoli
2016 Lecture Notes in Computer Science  
Accordingly, in this paper, we propose a new hybrid knowledge discovery approach for discovering meaningful predictive biological patterns.  ...  The analysis of complex and massive biological data issued from metabolomic analytical platforms is a challenge of high importance.  ...  The design of a Hybrid Knowledge Discovery Approach for Metabolomic Data In this section, we explain how to design a hybrid knowledge discovery process in agreement with experts in biology and in combining  ... 
doi:10.1007/978-3-319-46128-1_36 fatcat:asnrd6vnr5cgbgly3iz3cipxx4

Recent Advances in Discovery of Lead Structures from Microbial Natural Products: Genomics- and Metabolomics-Guided Acceleration

Linda Sukmarini
2021 Molecules  
Due to traditional discovery approaches' limitations relying on untargeted screening methods, there is a growing trend to employ unconventional secondary metabolomics techniques.  ...  They offer major opportunities for finding novel lead structures that are active against a broad spectrum of assay targets, particularly those from secondary metabolites of microbial origin.  ...  Acknowledgments: The author would like to thank the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) for their support through the Returning Experts-Migration and Diaspora Programme.  ... 
doi:10.3390/molecules26092542 pmid:33925414 fatcat:nbn4sda5b5dujd37evfv5tcqbq

Elements About Exploratory, Knowledge-Based, Hybrid, and Explainable Knowledge Discovery [chapter]

Miguel Couceiro, Amedeo Napoli
2019 Lecture Notes in Computer Science  
For illustrating these dimensions and objectives, we analyze a concrete case about the mining of biological data, where we characterize these dimensions and their connections.  ...  This calls for hybridization, combining numerical and symbolic mining methods to improve the applicability and interpretability of KDD.  ...  In particular, the pattern mining procedure involves FCA and the design of a concept lattice Fig. 3 : A hybrid and exploratory approach to metabolomic data mining, with a classification process based  ... 
doi:10.1007/978-3-030-21462-3_1 fatcat:diskhipnbjc73banfdegh6rxqa

Omics based approach for biodiscovery of microbial natural products in antibiotic resistance era

N. Chandra Mohana, H.C. Yashavantha Rao, D. Rakshith, P.R. Mithun, B.R. Nuthan, S. Satish
2018 Journal of Genetic Engineering and Biotechnology  
The need for a new antibiotic pipeline to confront threat imposed by resistant pathogens has become a major global concern for human health.  ...  To confront the challenge there is a need for discovery and development of new class of antibiotics.  ...  Acknowledgements The authors would like to thank Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore, Karnataka, India for providing facilities.  ... 
doi:10.1016/j.jgeb.2018.01.006 pmid:30647697 pmcid:PMC6296576 fatcat:5pqjwtcbfrh2pcnptb32wmzwpy

A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries

Kalpana Raja, Matthew Patrick, Yilin Gao, Desmond Madu, Yuyang Yang, Lam C. Tsoi
2017 International Journal of Genomics  
The managing, storing, and analyzing of this big data have been a great challenge for the researchers, especially when moving towards the goal of generating testable data-driven hypotheses, which has been  ...  Text mining (also known as literature mining) is one of the commonly used approaches for automated generation of biological knowledge from the huge number of published articles.  ...  Transcriptomics, Metabolomics, and Text Mining. Text mining approaches for transcriptomics and metabolomics are limited.  ... 
doi:10.1155/2017/6213474 pmid:28331849 pmcid:PMC5346376 fatcat:7yhwtsgyqndabcrhpx7uxsx7da

Metabolomics: A Tool for Cultivar Phenotyping and Investigation of Grain Crops

Claude Y. Hamany Djande, Chanel Pretorius, Fidele Tugizimana, Lizelle A. Piater, Ian A. Dubery
2020 Agronomy  
Moreover, the value of metabolomics has been redefined from simple biomarker identification to a tool for discovering active drivers involved in biological processes.  ...  We illustrate and conclude that the rapid advances in metabolomics are driving an explosion of information that will advance modern breeding approaches for grain crops and address problems associated with  ...  Data mining, a crucial step in metabolomic workflows, can be carried out in two different approaches.  ... 
doi:10.3390/agronomy10060831 fatcat:dg2xtl4df5fbxkptnwxooclvv4

Metabolites Associated with Adaptation of Microorganisms to an Acidophilic, Metal-Rich Environment Identified by Stable-Isotope-Enabled Metabolomics

A. C. Mosier, N. B. Justice, B. P. Bowen, R. Baran, B. C. Thomas, T. R. Northen, J. F. Banfield
2013 mBio  
Community genomic, transcriptomic, and proteomic data implicate fungi in taurine metabolism.  ...  However, metabolites directly linked to their physiology are less well defined because metabolomics methods lag behind other omics technologies due to a wide range of experimental complexities often associated  ...  For metabolomic analyses presented here, biofilm samples were collected from the air-AMD solution interface of the AB-muck site within the Richmond Mine on 15 July 2011 (here referred to as the mine biofilm  ... 
doi:10.1128/mbio.00484-12 pmid:23481603 pmcid:PMC3604775 fatcat:atvg6jtk5jdoxa5duvg2v7ouhq

Editorial: Peptide/Polyketide Molecules From Marine Macro and/or Microorganisms

Valeria Costantino, Marie-Lise Bourguet-Kondracki, Efstathia Ioannou
2020 Frontiers in Chemistry  
to the innovative "genome mining" approach yielding exciting data worthy of dissemination to academic and public fora.  ...  of complex metabolome based on tandem mass spectrometry data (MS/MS).  ... 
doi:10.3389/fchem.2020.00490 pmid:32760692 pmcid:PMC7372131 fatcat:gacz6hujjbcabkiicxggzszoei

Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities

Shaman Narayanasamy, Emilie E. L. Muller, Abdul R. Sheik, Paul Wilmes
2015 Microbial Biotechnology  
Such knowledge will form the foundation for discovering novel genes on a  ...  The integration of information from genome to metabolome allows the establishment of associations between genetic potential and final phenotype, a feature not realizable by only considering single 'omes  ...  Data mining, machine learning and/or modelling approaches will be useful for extracting features of interest, e.g. known and unknown populations/genes, and also to derive associations (or links) between  ... 
doi:10.1111/1751-7915.12255 pmid:25678254 pmcid:PMC4408170 fatcat:2d73nyweanae5fgtewmdxniga4

Pathomx: an interactive workflow-based tool for the analysis of metabolomic data

Martin A Fitzpatrick, Catherine M McGrath, Stephen P Young
2014 BMC Bioinformatics  
However, the development of robust methods for the analysis of metabolomic data is a work-in-progress.  ...  Metabolomics is a systems approach to the analysis of cellular processes through small-molecule metabolite profiling.  ...  data.  ... 
doi:10.1186/s12859-014-0396-9 pmid:25490956 pmcid:PMC4271363 fatcat:66rlqvvxbzbvvnagjfcuaeb4fu

Genome and metabolome mining of marine obligate Salinispora strains to discover new natural products

Süleyman ÖZAKIN
2019 Turkish Journal of Biology  
Metabolic profiling was performed by a nontargeted LC-MS/MS approach combined with spectral networking using Global Natural Product Social Molecular Networking (GNPS).  ...  Dereplication and tentative identification of natural products were evaluated for common chemical properties and their associated pathways.  ...  This work was supported by a fellowship awarded to Süleyman Özakın by the Scientific and Technological Research Council of Turkey (TÜBİTAK 2214/A Fellowship Program).  ... 
doi:10.3906/biy-1807-136 pmid:30930633 pmcid:PMC6426641 fatcat:thyaclp6pbc4zolazsd3ve7nxa

An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria

Maria Maansson, Nikolaj G. Vynne, Andreas Klitgaard, Jane L. Nybo, Jette Melchiorsen, Don D. Nguyen, Laura M. Sanchez, Nadine Ziemert, Pieter C. Dorrestein, Mikael R. Andersen, Lone Gram, Peter J. Turnbaugh
2016 mSystems  
Here, we present an integrated approach to evaluate the biosynthetic richness in bacteria and mine the associated chemical diversity.  ...  Combining chemical analysis and genetics is an efficient "mining" workflow for identifying diverse pharmaceutical candidates in a broad range of microorganisms and therefore of great use in bioprospecting  ...  To explore the diversity within the pan-metabolome and prioritize chemical features for more detailed structural analysis, a two-pronged approach was used: multivariate analysis based on machine learning  ... 
doi:10.1128/msystems.00028-15 pmid:27822535 pmcid:PMC5069768 fatcat:lsv654wbafez7luxdgzthspppa

Application of ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) metabolomic fingerprinting to characterise GM and conventional maize varieties

L. Václavík, J. Ovesná, L. Kučera, J. Hodek, K. Demnerová, J. Hajšlová
2013 Czech Journal of Food Sciences  
Typical metabolomic fingerprints were established for individual plants. The plants representing two varieties formed well separated clusters.  ...  The feasibility of metabolomic fingerprinting approach based on ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UHPLC-QTOFMS) was studied to assess its ability  ...  The presented approach allows largescale evaluation of leaf metabolome and can provide extensive data for GMO safety assessment.  ... 
doi:10.17221/177/2013-cjfs fatcat:hwbzm4dqubb3deuzvvhcfkdrzu

Functional Genomics, Proteomics, Metabolomics and Bioinformatics for Systems Biology [chapter]

Stéphane Ballereau, Enrico Glaab, Alexei Kolodkin, Amphun Chaiboonchoe, Maria Biryukov, Nikos Vlassis, Hassan Ahmed, Johann Pellet, Nitin Baliga, Leroy Hood, Reinhard Schneider, Rudi Balling (+1 others)
2013 Systems Biology  
Methods for clustering, feature selection, prediction analysis, text mining and pathway analysis used to analyse and integrate the data produced are then presented.  ...  This chapter introduces Systems Biology, its context, aims, concepts and strategies, then describes approaches used in genomics, epigenomics, transcriptomics, proteomics, metabolomics and lipidomics, and  ...  , and in part by the EU grants to CA in the context of the MeDALL consortium (Mechanisms of the Development of Allergy, Grant Agreement FP7 N°264357) and the U-BIOPRED consortium (Unbiased Biomarkers for  ... 
doi:10.1007/978-94-007-6803-1_1 fatcat:toqji65vxzbejo6wdfxuncwnmq

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

Ivana Blaženović, Tobias Kind, Jian Ji, Oliver Fiehn
2018 Metabolites  
The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics.  ...  It is recommended to integrate the level of annotation for each compound into metabolomic profiling reports.  ...  Another approach showed the combined use of high-resolution MS/MS data and use of the metabolic in-silico network expansion database (MINE) for the discovery of novel methylated epi-metabolites including  ... 
doi:10.3390/metabo8020031 pmid:29748461 pmcid:PMC6027441 fatcat:lozwgydywrhvrctkxmemdmanxm
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