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Improved statistical model checking methods for pathway analysis

Chuan Hock Koh, Sucheendra K Palaniappan, PS Thiagarajan, Limsoon Wong
2012 BMC Bioinformatics  
In this context, we present two improvements to existing statistical model checking algorithms.  ...  Statistical model checking techniques have been shown to be effective for approximate model checking on large stochastic systems, where explicit representation of the state space is impractical.  ...  This work was supported in part by a Singapore National Research Foundation grant NRF-G-CRP-2007-04-082(d) (for Wong) and National University of Singapore scholarships (for Koh and Palaniappan).  ... 
doi:10.1186/1471-2105-13-s17-s15 pmid:23282174 pmcid:PMC3521229 fatcat:bn4bbrxw7fdkrndbkknss4yx2q

Likelihood-Based Approach to Gene Set Enrichment Analysis with a Finite Mixture Model

Sang Mee Lee, Baolin Wu, John H. Kersey
2012 Statistics in Biosciences  
In this paper, we study a parametric modeling approach to gene set enrichment analysis.  ...  Existing methods have largely relied on nonparametric approaches employing, e.g., categorization, permutation or resampling-based significance analysis methods.  ...  We would like to thank the associate editor and two anonymous referees for their constructive comments, which have dramatically improved the presentation of the paper.  ... 
doi:10.1007/s12561-012-9076-3 pmid:24891922 pmcid:PMC4039382 fatcat:kaw4bzniingvvbdcivku3eb5eu

PathExpand: Extending biological pathways using molecular interaction networks

Enrico Glaab, Anais Baudot, Natalio Krasnogor, Alfonso Valencia
2011 Nature Precedings  
GO-term similarity between pathway-proteins and added proteins compare to random extension model Extension statistics Extension statistics across all databases Statistics on added proteins across  ...  recognize "good" pathway definitions and improve them?  ...  Comparison to previous methods Relation to other network analysis methods  ... 
doi:10.1038/npre.2011.5639.1 fatcat:p6d75ahqnjf5vmmmtm4ozbmpoq

An eClinical trial system for cancer that integrates with clinical pathways and electronic medical records

Keiichi Yamamoto, Kenya Yamanaka, Etsuro Hatano, Eriko Sumi, Takamichi Ishii, Kojiro Taura, Kohta Iguchi, Satoshi Teramukai, Masayuki Yokode, Shinji Uemoto, Masanori Fukushima
2012 Clinical Trials  
At the coordinating centre, the data are checked, integrated, and made available for statistical analysis.  ...  Methods We designed a new clinical trial model that uses EMR data directly in clinical trials and developed a system to follow this model.  ...  We created reports for checking trial data and extracting data for statistical analysis.  ... 
doi:10.1177/1740774512445912 pmid:22605791 fatcat:ixye6ezpk5g6xos7djbh5b3bfe

Evidence for improved prognosis of colorectal cancer diagnosed following the detection of iron deficiency anaemia

Orouba Almilaji, Sally D. Parry, Sharon Docherty, Jonathon Snook
2021 Scientific Reports  
The associations between diagnostic pathway (Bowel Cancer Screening Programme (BCSP), IDA, symptomatic) and tumour side/stage was assessed using logistic regression models in 1138 CRC cases presenting  ...  At any age, the risk of detecting CRC at late-stage was higher in those without a previous blood count check (hazard ratio 1.53, 95% credibility interval 1.08–2.14).  ...  Acknowledgements The authors would like to thank Professor Peter Thomas for his contribution in this study.  ... 
doi:10.1038/s41598-021-92623-z pmid:34158616 fatcat:nlxbt5zhajac7ib3szpl7l56ru

THINK Back: KNowledge-based Interpretation of High Throughput data

Fernando Farfán, Jun Ma, Maureen A Sartor, George Michailidis, Hosagrahar V Jagadish
2012 BMC Bioinformatics  
Our methods perform a thorough and rigorous analysis of biological pathways, using complex factors such as the topology of the pathway graph and the frequency in which genes appear on different pathways  ...  by biological pathways.  ...  Glenn Tarcea for his valuable support and guidance during the development stages of the THINK-Back Web Services suite.  ... 
doi:10.1186/1471-2105-13-s2-s4 pmid:22536867 pmcid:PMC3375631 fatcat:jor24o4a2zb4dng5pi5kx6pfd4

Pathway-Based Analysis Using Genome-wide Association Data from a Korean Non-Small Cell Lung Cancer Study

Donghoon Lee, Geon Kook Lee, Kyong-Ah Yoon, Jin Soo Lee, William C. S. Cho
2013 PLoS ONE  
Pathway statistics were evaluated using Gene Set Enrichment Analysis (GSEA) and Adaptive Rank Truncated Product (ARTP) methods.  ...  the pathway-based analysis.  ...  Acknowledgments We would like to acknowledge the Center for Disease Control in National Institute of Health Korea, who kindly provided the genome-wide SNP data for controls.  ... 
doi:10.1371/journal.pone.0065396 pmid:23762359 pmcid:PMC3675130 fatcat:l23kuuxepvfdligr3p65acchmm

Categorizing Molecular Features of NOTCH4 Involved in Breast Cancer

Vinod P. Sinoorkar, Shrutika S. Pagul
2019 International Journal of Scientific Research in Science and Technology  
The major signaling pathways involved in the breast cancer are Estrogen pathway, MAPK signaling pathway, PI3K/AKT signaling pathway, Notch signaling pathway, Wnt signaling pathway and P53 signaling pathway  ...  interactions, it can be considered as one of the potent drug target in breast cancer and can contribute to a novel alternate and promising treatment strategy for breast cancer through computer aided drug  ...  It includes PROCHECK-NMR for checking the quality of structures solved by NMR. The build 3D model quality was checked using PROCHECK.  ... 
doi:10.32628/ijsrst196161 fatcat:w5en64qlajfmrdm5grsm2qymqy

Variance analysis and handling of Clinical Pathway: An overview of the state of knowledge

Gang Du, Liyuan Huang, Mengwei Zhou
2020 IEEE Access  
Clinical pathway is a multi-disciplinary treatment plan and work mode, which is favorable for improving healthcare service quality and reducing medical costs.  ...  In this study, methods of clinical pathway variance analysis and handling are illustrated. In addition, this paper points out the limitations of each method.  ...  Her research interests include clinical pathway variance modeling and business analysis. VOLUME 8, 2020  ... 
doi:10.1109/access.2020.3020151 fatcat:pe54rtkionfopgz6awtkx7kuzu

FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods

Fatemeh Mansoori, Maseud Rahgozar, Kaveh Kavousi
2019 BMC Bioinformatics  
We have developed a tool named Formal model checking based pathway analysis (FoPA) based on this approach.  ...  Signaling pathways are formally modeled, and then model checking tools are applied to find the likelihood of perturbation for each pathway in a given condition.  ...  Authors' contributions Authors conceived jointly the idea of using formal methods for pathway analysis.  ... 
doi:10.1186/s12859-019-2635-6 fatcat:afylvjdogbgtvknc5oyuanit5a

MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis

J. Xia, R. Mandal, I. V. Sinelnikov, D. Broadhurst, D. S. Wishart
2012 Nucleic Acids Research  
and visualization for 15 different model organisms.  ...  module that allows users to identify biologically meaningful patterns using metabolite set enrichment analysis and (iii) a metabolic pathway analysis module that allows users to perform pathway analysis  ...  On the other hand, the pathway analysis function (option iv) currently contains pathway information from 16 different model organisms.  ... 
doi:10.1093/nar/gks374 pmid:22553367 pmcid:PMC3394314 fatcat:odculz427bhmtgakdurckxdg2a

Methods to Expand Cell Signaling Models Using Automated Reading and Model Checking [chapter]

Kai-Wen Liang, Qinsi Wang, Cheryl Telmer, Divyaa Ravichandran, Peter Spirtes, Natasa Miskov-Zivanov
2017 Lecture Notes in Computer Science  
We present here a framework that utilizes the results from state-of-theart biomedical literature mining, biological system modeling and analysis techniques, and provides means to scientists to assemble  ...  Our framework described here allows for rapidly conducting thousands of in silico experiments that are designed as part of this process.  ...  Acknowledgement We would like to thank Mihai Surdeanu (REACH team) and Hans Chalupsky (RUBICON team) for providing output of their reading and assembly engines, and Michael Lotze for his guidance in studying  ... 
doi:10.1007/978-3-319-67471-1_9 fatcat:slmt4silujcpzfcsv3l4z23xce

Taming the complexity of biological pathways through parallel computing

P. Ballarini, R. Guido, T. Mazza, D. Prandi
2008 Briefings in Bioinformatics  
His research interests are in formal techniques for systems' verification/ specification, probabilistic model-checking, stochastic Petri nets and temporal logic reasoning.  ...  Mathematical methods for modelling biological systems are mostly based on a centralised solution approach: the modelled system is described as a whole and the solution technique, normally the integration  ...  For instance, extreme pathways [23] are an algorithm for the analysis of metabolic networks.  ... 
doi:10.1093/bib/bbp020 pmid:19339382 fatcat:5yzyzsjbjvd2hb5rxufpg6hube

MetaboAnalyst 3.0—making metabolomics more meaningful

Jianguo Xia, Igor V. Sinelnikov, Beomsoo Han, David S. Wishart
2015 Nucleic Acids Research  
power analysis for improved planning of metabolomics studies and (iii) a module to support integrative pathway analysis for both genes and metabolites.  ...  Three new modules have also been added including: (i) a module for biomarker analysis based on the calculation of receiver operating characteristic curves; (ii) a module for sample size estimation and  ...  functional analysis (Enrichment Analysis, Pathway Analysis and Integrated Pathway Analysis) and Category 3: advanced methods for translational studies (Biomarker Analysis and Power Analysis).  ... 
doi:10.1093/nar/gkv380 pmid:25897128 pmcid:PMC4489235 fatcat:qte6o34sazay5otag3ntflhcvu

Identification and characterisation of midbrain nuclei using optimised functional magnetic resonance imaging

Eve H. Limbrick-Oldfield, Jonathan C.W. Brooks, Richard J.S. Wise, Francesco Padormo, Jo V. Hajnal, Christian F. Beckmann, Mark A. Ungless
2012 NeuroImage  
This pathway was compared to conventional registration pathways, and was shown to significantly improve midbrain registration.  ...  Here we present a replicable and automated method to improve the detection and localisation of midbrain fMRI signals.  ...  Acknowledgments We thank the volunteers for taking part in this study, and Emer Hughes and Amy McGuinness for assistance with the data collection.  ... 
doi:10.1016/j.neuroimage.2011.08.016 pmid:21867762 pmcid:PMC3236997 fatcat:od3r7w2f7bfprbrf6fqbcfb7iu
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