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Comparative network stratification analysis for identifying functional interpretable network biomarkers

Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen
2017 BMC Bioinformatics  
Results: In this paper, we present a new computational framework based on an integer programming model, named as Comparative Network Stratification (CNS), to extract functional or interpretable network  ...  A major challenge of bioinformatics in the era of precision medicine is to identify the molecular biomarkers for complex diseases.  ...  Consent for publication Not applicable. Ethics approval and consent to participate Not applicable.  ... 
doi:10.1186/s12859-017-1462-x pmid:28361683 pmcid:PMC5374559 fatcat:yx4qkrteezgzromdl5e7hzue7m

The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine

Kivilcim Ozturk, Michelle Dow, Daniel E. Carlin, Rafael Bejar, Hannah Carter
2018 Journal of Molecular Biology  
Here we discuss applications of network analysis to study tumor biology, early methods for N-of-1 tumor genome analysis and the path for such tools to the clinic.  ...  Systems biology and more specifically, network analysis, provides a framework for advancing precision medicine beyond clinical actionability of individual mutations.  ...  biomarkers (therapeutic biomarkers, variant interpretation, subtype biomarkers, survival analysis, prognostic biomarkers) and N-of-1 analysis including transcriptomic analysis and driver prediction.  ... 
doi:10.1016/j.jmb.2018.06.016 pmid:29908887 pmcid:PMC6097914 fatcat:x2jgrae22be4bfzgc4nh46mwni

Challenges and opportunities for oncology biomarker discovery

Avisek Deyati, Erfan Younesi, Martin Hofmann-Apitius, Natalia Novac
2013 Drug Discovery Today  
TeaserCrisis of pharmaceutical industry prompts Research and Development (R&D) focus from blockbusters to niche busters; its clinical success depends on successful prediction of stratification biomarkers  ...  for functional interpretation of OMICs data.  ...  Discover and validate stratification biomarker to a therapy accessing genomic data from cell lines, stem cells, animal models and retrospective analysis of clinical trials NextBio Research: Identifying  ... 
doi:10.1016/j.drudis.2012.12.011 pmid:23280501 fatcat:efrzfpjpxbaa5pon6i4jmq5vg4

Improved Risk Stratification in Pediatric Septic Shock Using Both Protein and mRNA Biomarkers. PERSEVERE-XP

Hector R. Wong, Natalie Z. Cvijanovich, Nick Anas, Geoffrey L. Allen, Neal J. Thomas, Michael T. Bigham, Scott L. Weiss, Julie C. Fitzgerald, Paul A. Checchia, Keith Meyer, Michael Quasney, Mark Hall (+7 others)
2017 American Journal of Respiratory and Critical Care Medicine  
The genes identified through variable reduction were combined with the PERSEVERE-based mortality probability to derive a risk stratification model for 28-day mortality using classification and regression  ...  Conclusions: PERSEVERE-XP combines protein and mRNA biomarkers to provide mortality risk stratification with possible clinical utility.  ...  We proposed a priori to select the highest-scoring pathway or gene network resulting from this analysis for further consideration.  ... 
doi:10.1164/rccm.201701-0066oc pmid:28324661 pmcid:PMC5564676 fatcat:xcjaorhtofg2ffxx4cj6tpzk3a

Integrating Tumor Stroma Biomarkers With Clinical Indicators for Colon Cancer Survival Stratification

Yong Chen, Wenlong Wang, Bo Jiang, Lei Yao, Fada Xia, Xinying Li
2020 Frontiers in Medicine  
Here, we identified tumor stroma biomarkers and evaluated their role in CC prognosis stratification.  ...  prediction and compared.  ...  In this study, we have identified 16 tumor stroma biomarkers for primary CC and created a new indicator for risk stratification and prognosis prediction based on them.  ... 
doi:10.3389/fmed.2020.584747 pmid:33365318 pmcid:PMC7750539 fatcat:wglwqkjcfbamfommj5hr6lhjim

Transcriptional Instability during Evolving Sepsis May Limit Biomarker Based Risk Stratification

Antonia Kwan, Mike Hubank, Asrar Rashid, Nigel Klein, Mark J. Peters, Ioannis P. Androulakis
2013 PLoS ONE  
" that have been proposed for diagnostic and risk stratification functions.  ...  Serial estimations or more comprehensive network approaches may be required to optimize risk stratification in complex, time-critical conditions such as evolving sepsis.  ...  Contributed reagents/materials/analysis tools: AR. Wrote the paper: AK MP NK.  ... 
doi:10.1371/journal.pone.0060501 pmid:23544148 pmcid:PMC3609793 fatcat:n7hsu42ltzeixgalxl4vttaeym

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery

Alvin Leung, Gary D. Bader, Jüri Reimand
2014 Computer applications in the biosciences : CABIOS  
HyperModules is a network search algorithm that finds frequently mutated gene modules with significant clinical or phenotypic signatures from biomolecular interaction networks.  ...  Correlating disease mutations with clinical and phenotypic information such as drug response or patient survival is an important goal of personalized cancer genomics and a first step in biomarker discovery  ...  ACKNOWLEDGEMENTS The authors thank Jason Montojo and Harold Rodriguez for Cytoscape help. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btu172 pmid:24713437 pmcid:PMC4103591 fatcat:howfy3q5x5blrnd6pmdmjefzyq

Patient Stratification of Clear Cell Renal Cell Carcinoma Using the Global Transcription Factor Activity Landscape Derived From RNA-Seq Data

Yanyan Zhu, Shundong Cang, Bowang Chen, Yue Gu, Miaomiao Jiang, Junya Yan, Fengmin Shao, Xiaoyun Huang
2020 Frontiers in Oncology  
Using the TCGA cohort dataset, we identified different subtypes that have distinct up-regulated biomarkers and altered biological pathways.  ...  However, no comprehensive analysis of transcription factor activity has been proposed so far to realize patient stratification.  ...  Network nodes are also displayed as pies. Color code for pie sector represents a gene list. Survival Analysis Kaplan-Meier analysis was used for survival curve analysis.  ... 
doi:10.3389/fonc.2020.526577 pmid:33344220 pmcid:PMC7746882 fatcat:4zgt4xmr3nda5fdip4udl3mkay

Proteomics and phosphoproteomics in precision medicine: applications and challenges

Girolamo Giudice, Evangelia Petsalaki
2017 Briefings in Bioinformatics  
molecular mechanism and discover personalized biomarkers, networks and treatments.  ...  Therefore, for the first time, we have the opportunity to measure the proteomic profiles of thousands of patient samples or disease model cell lines in a systematic way, to identify the precise underlying  ...  NBS, network-based stratification; RW, random walk.  ... 
doi:10.1093/bib/bbx141 pmid:29077858 fatcat:mpep67sbybbydpdcpvjqdf5joe

Computational systems biology approaches for Parkinson's disease

Enrico Glaab
2017 Cell and Tissue Research  
Identifying and interpreting the combinatorial effects of multiple PD-associated molecular changes may pave the way towards an earlier and reliable diagnosis and more effective therapeutic interventions  ...  Strengths and weaknesses of different cellular pathway and network analyses, and multivariate machine learning techniques for investigating PD-related omics data are discussed, and strategies proposed  ...  Acknowledgements Acknowledgement is made for support by the  ... 
doi:10.1007/s00441-017-2734-5 pmid:29185073 pmcid:PMC6015628 fatcat:bjbg57j5mfe4jkhrq2pfbs7qge

A roadmap towards personalized immunology

Sylvie Delhalle, Sebastian F. N. Bode, Rudi Balling, Markus Ollert, Feng Q. He
2018 npj Systems Biology and Applications  
There is still a long way ahead on translating our capability to identify potentially targetable personalized biomarkers into effective personalized therapy in immune-centralized diseases.  ...  strategies towards personalized stratification and treatment for infectious or non-communicable inflammatory diseases such as autoimmune diseases or allergies.  ...  critical for discovering various types of biomarkers. a Longitudinal followup of individual patients with multilayer "Omics" analysis is essential for identifying different types of biomarkers.  ... 
doi:10.1038/s41540-017-0045-9 pmid:29423275 pmcid:PMC5802799 fatcat:mrh4gptkrbemxf3ykewsa5b3j4

Patient stratification of clear cell renal cell carcinoma using the global transcription factor activity landscape derived from RNA-seq data [article]

Yanyan Zhu, Shundong Cang, Bowang Chen, Yue Gu, Miaomiao Jiang, Junya Yan, Fengmin Shao, Xiaoyun Huang
2019 bioRxiv   pre-print
Using the TCGA cohort dataset, we identified different subtypes that have distinct upregulated biomarkers and altered biological pathways.  ...  However, no comprehensive analysis of transcription factor activity has been proposed so far to realize patient stratification.  ...  Network nodes are also displayed as pies. Color code for pie sector represents a gene list. Survival analysis Kaplan Meier analysis was used for survival curve analysis.  ... 
doi:10.1101/829796 fatcat:6dwiljkmtjf6dceqx2usogq7pu

Time to Recurrence and Survival in Serous Ovarian Tumors Predicted from Integrated Genomic Profiles

Parminder K. Mankoo, Ronglai Shen, Nikolaus Schultz, Douglas A. Levine, Chris Sander, Sumitra Deb
2011 PLoS ONE  
Using integrated genomic profiles resulted in information gain for prediction of outcomes. Pathway analysis provided potential insights into functional changes affecting disease progression.  ...  The prognostic signatures, if prospectively validated, may be useful for interpreting therapeutic outcomes for clinical trials that aim to improve the therapy for SeOvCa patients.  ...  We thank Venkatraman Seshan for help with time prediction calculations and other useful discussions; Glenn Heller for discussions regarding regression analysis; Meeyoung Park for CoxPath discussions; Lewyn  ... 
doi:10.1371/journal.pone.0024709 pmid:22073136 pmcid:PMC3207809 fatcat:yet4n3hub5erzed7sv474g4vhq

Network Based Consensus Gene Signatures for Biomarker Discovery in Breast Cancer

Holger Fröhlich, Wanjin Hong
2011 PLoS ONE  
for highly stable and interpretable predictive biomarkers.  ...  Common upstream proteins of close gene products, which we identified via our developed algorithm, show a very clear and significant functional interpretation in terms of overrepresented KEGG pathways,  ...  Acknowledgments The idea for this work came to me due to the results of Amit Kawalia's Masters thesis. I therefore like to thank him for his commitment here.  ... 
doi:10.1371/journal.pone.0025364 pmid:22046239 pmcid:PMC3201953 fatcat:5u3jd7cifjejnph5zy5kjl3xua

An unsupervised learning approach to identify novel signatures of health and disease from multimodal data

Ilan Shomorony, Elizabeth T. Cirulli, Lei Huang, Lori A. Napier, Robyn R. Heister, Michael Hicks, Isaac V. Cohen, Hung-Chun Yu, Christine Leon Swisher, Natalie M. Schenker-Ahmed, Weizhong Li, Karen E. Nelson (+8 others)
2020 Genome Medicine  
Stratification of individuals based on the signatures of these biomarkers identified distinct subsets of individuals with similar health statuses.  ...  Another metabolite, cinnamoylglycine, was identified as a potential biomarker for both gut microbiome health and lean mass percentage.  ...  IS, ETC, LH, RRH, MH, IVC, HCY, AMK, CTC, EFK, and NS supported the interpretations. IS, ETC, and NS wrote the paper. TDS is responsible for the TwinUK study.  ... 
doi:10.1186/s13073-019-0705-z pmid:31924279 pmcid:PMC6953286 fatcat:2r7bgha4a5at5cabr42adndmty
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