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An OMICs based meta-analysis to support infection state stratification

Ashleigh C Myall, Simon Perkins, David Rushton, Jonathan David, Phillippa Spencer, Andrew R Jones, Philipp Antczak
2021 Bioinformatics  
To establish a predictive biomarker panel of disease state (viral/bacterial/no-infection) we conducted a meta-analysis of human blood infection studies using Machine Learning (ML).  ...  To ensure an individual receives optimal treatment given their disease state and to reduce over-prescription of antibiotics, the host response can in theory be measured quickly to distinguish between the  ...  We also gratefully acknowledge DSTL (www.gov.uk/dstl) for providing support. The work was in part supported by the University of Liverpool Technology Directorate.  ... 
doi:10.1093/bioinformatics/btab089 pmid:33560295 fatcat:phencvpkcfg6rfhm4qovus6jaq

What is next after the genes for autoimmunity?

John Castiblanco, Mauricio Arcos-Burgos, Juan-Manuel Anaya
2013 BMC Medicine  
Once the currently costly omic-based technologies become universally accessible, the way will be paved for a cleaner picture to risk quantification, prevention, prognosis and diagnosis, allowing us to  ...  Herein, some pitfalls and challenges of the genetics of autoimmune diseases are reviewed, and an approximation to the future of research in this field is presented.  ...  Acknowledgements This work was supported by Universidad del Rosario and Colciencias (122254531722), Bogota, Colombia.  ... 
doi:10.1186/1741-7015-11-197 pmid:24107170 pmcid:PMC3765994 fatcat:tnws3mdqkzet7hpbyageximop4

Biosensor and Lab-on-a-chip Biomarker-identifying Technologies for Oral and Periodontal Diseases

Larissa Steigmann, Shogo Maekawa, Corneliu Sima, Suncica Travan, Chin-Wei Wang, William V. Giannobile
2020 Frontiers in Pharmacology  
Periodontitis is a complex multifactorial disease that can lead to destruction of tooth supporting tissues and subsequent tooth loss.  ...  Advances in biotechnology have led to innovations in lab-on-a-chip and biosensors to interface with oral-based biomarker assessment.  ...  SM was supported by funding from an Osteology Foundation Research Scholarship.  ... 
doi:10.3389/fphar.2020.588480 pmid:33343358 pmcid:PMC7748088 fatcat:j2tvbc4vxfdalktnov23444ilu

Gut Microbiota Dysbiosis as Risk and Premorbid Factors of IBD and IBS Along the Childhood–Adulthood Transition

Lorenza Putignani, Federica Del Chierico, Pamela Vernocchi, Michele Cicala, Salvatore Cucchiara, Bruno Dallapiccola
2016 Inflammatory Bowel Diseases  
In this respect, tracking gut dysbiosis grading may help deciphering host phenotype-genotype associations and microbiota shifts in an integrated top-down omics-based approach within large-scale pediatric  ...  They include (1) high risk or flare-up recurrence -omics-based dysbiosis profiles; (2) microbial and molecular biomarkers of health and disease; (3) -omics-based pipelines for laboratory medicine diagnostics  ...  Predictive IBD and IBS Signatures: An mHealth App Support The integration of meta-omics and phenomics with nutrigenomics (diet) and foodomics (food matrix) profiling is used to create a more comprehensive  ... 
doi:10.1097/mib.0000000000000602 pmid:26588090 fatcat:n2jgz5ya6fakdkt4tzzqexihly

Proteomics and Metabolomics Approaches towards a Functional Insight onto AUTISM Spectrum Disorders: Phenotype Stratification and Biomarker Discovery

Maria Vittoria Ristori, Stefano Levi Mortera, Valeria Marzano, Silvia Guerrera, Pamela Vernocchi, Gianluca Ianiro, Simone Gardini, Giuliano Torre, Giovanni Valeri, Stefano Vicari, Antonio Gasbarrini, Lorenza Putignani
2020 International Journal of Molecular Sciences  
Moreover, the way to exploit CDSS, performed by artificial intelligence, is presented as an effective tool to integrate omics data to electronic health/medical records (EHR/EMR), hopefully acting as added  ...  that may vary from patient to patient depending on the specific genomic and other omics findings.  ...  Therefore, an approach to the investigation of ASD based on omics or meta-omics disciplines is becoming crucial for both disease phenotype stratification and biomarker discovery.  ... 
doi:10.3390/ijms21176274 pmid:32872562 fatcat:bg6mmoorl5fblgpurma4kkuygy

Metabolomics technology and bioinformatics for precision medicine

2018 Briefings in Bioinformatics  
Combination of metabolomics with sophisticated bioinformatics analysis and mathematical modeling has an extreme power to provide a metabolic snapshot of the patient over the course of disease and treatment  ...  Precision medicine is rapidly emerging as a strategy to tailor medical treatment to a small group or even individual patients based on their genetics, environment and lifestyle.  ...  The research in the authors' laboratories is financially supported by the grant from NIH NIAID (grant number 5R01AI111962-02) and NIH NIDDK (grant number DK109524-01).  ... 
doi:10.1093/bib/bbx170 pmid:29304189 pmcid:PMC6954408 fatcat:g3uufpuepnfdxo7fzv2cuq5rgu

Shedding metabo'light' on the search for sepsis biomarkers

Claudia C. dos Santos
2015 Critical Care  
The clinical presentation of severe infection with generalized inflammation is similar, if not identical, to systemic inflammation induced by sterile tissue injury.  ...  Here we briefly review the article of Kamisoglu and colleagues in this issue of Critical Care on comparing metabolomics data from different studies to assess whether responses elicited by endotoxin recapitulate  ...  After stratification of sepsis patients based on 28-day survival, the direction of change of 21 of 23 metabolites was the same in endotoxemia and sepsis survivors (compared with non-survivors).  ... 
doi:10.1186/s13054-015-0969-7 pmid:26148483 pmcid:PMC4493818 fatcat:rjuepecfvzaglb3i7i3ngmnheq

Metaproteomics to Decipher CF Host-Microbiota Interactions: Overview, Challenges and Future Perspectives

Pauline Hardouin, Raphael Chiron, Hélène Marchandin, Jean Armengaud, Lucia Grenga
2021 Genes  
In recent years, various omics tools have started to shed new light on microbial communities associated with CF and host–microbiota interactions.  ...  The main cause of morbidity and mortality is chronic infection.  ...  Acknowledgments: P.H. thanks the "Région Occitanie" for supporting her Ph.D. fellowship. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes12060892 pmid:34207804 pmcid:PMC8227082 fatcat:klrkfce7u5audibtlx57qwuyt4

Leveraging implementation science to improve implementation outcomes in precision medicine

John J O Mogaka, San E James, Moses J Chimbari
2020 American journal of translational research  
A generalized PM implementation conceptual framework was developed showing how omics biomarker uptake relates to their evidence base, patient and provider engagement and Big data capabilities of involved  ...  Introduction of omics technologies in clinical practice means increased use of validated biomarkers, through precision medicine (PM).  ...  Acknowledgements We thank Tackling Infections to Benefit Africa-South Africa (TIBA-SA) for general moral and financial support. Disclosure of conflict of interest None.  ... 
pmid:33042394 pmcid:PMC7540127 fatcat:hgr3i7x6afh37oc2lflxqu4hia

Footprints of Sepsis Framed Within Community Acquired Pneumonia in the Blood Transcriptome

Lydia Hopp, Henry Loeffler-Wirth, Lilit Nersisyan, Arsen Arakelyan, Hans Binder
2018 Frontiers in Immunology  
We, hereby, pursue a multi-omics systems-based approach that is expected to enhance our understanding of the biology of sepsis framed within CAP and supports the translation of omics research in terms  ...  novel stratification of caP Based on Functional Dimensions The SOM-analysis of the CAP expression landscape suggests a modified stratification scheme that in addition to high and low levels of sepsis severity  ... 
doi:10.3389/fimmu.2018.01620 pmid:30065722 pmcid:PMC6056630 fatcat:fbtxszf53redxjwanmrp433pki

Clinical implications of omics and systems medicine: focus on predictive and individualized treatment

M. Benson
2015 Journal of Internal Medicine  
Systems medicine is an emerging discipline, which may contribute to such developments by combining omics with 2 computational, functional and clinical studies.  ...  High-throughput techniques (omics) allow identification of such subgroups.  ...  An important concept to address this problem is targeted omics, which refers to limiting the analysis based on other sources of information.  ... 
doi:10.1111/joim.12412 pmid:26891944 fatcat:44uuvfucdjgshadvi6cekxttzi

Systems Biology of Gastric Cancer: Perspectives on the Omics-Based Diagnosis and Treatment

Xiao-Jing Shi, Yongjun Wei, Boyang Ji
2020 Frontiers in Molecular Biosciences  
Here, we review recent progress in application of omics technologies in gastric cancer research, with special focus on the utilization of systems biology approaches to integrate multi-omics data.  ...  Finally, the application of data-driven systems biology and machine learning approaches could provide a predictive understanding of gastric cancer, and pave the way to the development of novel biomarkers  ...  ACKNOWLEDGMENTS The authors would like to thank Dr. Xin Chen for insightful discussions and the help in preparing the manuscript.  ... 
doi:10.3389/fmolb.2020.00203 pmid:33005629 pmcid:PMC7479200 fatcat:bvnf53arpbfovo2w2dllwaayru

Big data and stratified medicine: what does it mean for children?

Wen Y Ding, Michael W Beresford, Moin A Saleem, Athimalaipet V Ramanan
2018 Archives of Disease in Childhood  
With the increased speed and decreased cost of processing and analysing data from rare disease registries, we are increasingly able to use a systems biology approach (including '-omics') to screen across  ...  Improving our understanding of the molecular mechanisms underlying disease, and how to classify patients according to these will lead the way for targeted therapies for individual patients.  ...  [34] This 'personalised immunomonitoring' revealed seven distinct patient groups according to disease activity, supported by genotypes.  ... 
doi:10.1136/archdischild-2018-315125 pmid:30266876 fatcat:ze5kowpuufh47k6wcwqwra5szi

Leveraging Multilayered "Omics" Data for Atopic Dermatitis: A Road Map to Precision Medicine

Debajyoti Ghosh, Jonathan A. Bernstein, Gurjit K. Khurana Hershey, Marc E. Rothenberg, Tesfaye B. Mersha
2018 Frontiers in Immunology  
Though the roles of high-throughput "omics" integrations in defining endotypes are recognized, current analyses are primarily based on individual omics data and using binary clinical outcomes.  ...  Although individual omics analysis, such as genome-wide association studies (GWAS), can effectively map variants correlated with AD, the majority of the heritability and the functional relevance of discovered  ...  B/D-HPP) supports state-of-the-art assessments of human proteome in health and disease (76) .  ... 
doi:10.3389/fimmu.2018.02727 pmid:30631320 pmcid:PMC6315155 fatcat:pt73lpuyengbhpknq3ghwhzk74

Exhaled biomarkers in childhood asthma: old and new approaches

Valentina Ferraro, Silvia Carraro, Sara Bozzetto, Stefania Zanconato, Eugenio Baraldi
2018 Asthma Research and Practice  
Conclusion: Among non-invasive methods to study asthma, exhaled breath analysis remains one of the most interesting approaches, feNO and "-omic" sciences seem promising for the purpose of characterizing  ...  non-invasive methods for the study of airway inflammation in children, focusing on the measure of the fractional exhaled nitric oxide (feNO), on the measure of the exhaled breath temperature (EBT) and on the analysis  ...  So, even if there is no clear evidence to support the use of feNO in addition to standard symptom-based management for day-to-day asthma control [38, 39] , it may be that a therapy based on feNO levels  ... 
doi:10.1186/s40733-018-0045-6 pmid:30094051 pmcid:PMC6081883 fatcat:audzdtbjmjbixi5iuuv5wmnzwm
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