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Using Bayesian networks to discover relations between genes, environment, and disease

Chengwei Su, Angeline Andrew, Margaret R Karagas, Mark E Borsuk
2013 BioData Mining  
We review the applicability of Bayesian networks (BNs) for discovering relations between genes, environment, and disease.  ...  We first describe the Bayesian network approach and its applicability to understanding the genetic and environmental basis of disease.  ...  Acknowledgements Research supported by grants from the National Center for Research Resources (5P20RR024474-02) and the National Institute of General Medical Sciences (8 P20 GM103534-02) from the National  ... 
doi:10.1186/1756-0381-6-6 pmid:23514120 pmcid:PMC3614442 fatcat:olxihsfj2jeu7ciwt55rk7xzfm

Big Data Analysis Using Modern Statistical and Machine Learning Methods in Medicine

Changwon Yoo, Luis Ramirez, Juan Liuzzi
2014 International Neurourology Journal  
to the clinical data, gene-gene causal interactions and gene-environment interactions should be also modeled to complete the understanding of the disease progression.  ...  SINGLE NUCLEOTIDE POLYMORPHISMS Recent genome-wide association studies have discovered significant associations between complex diseases and SNPs.  ...  CONFLICT OF INTEREST No potential conflict of interest relevant to this article was reported.  ... 
doi:10.5213/inj.2014.18.2.50 pmid:24987556 pmcid:PMC4076480 fatcat:tcu3oefdtrdn7ijfwc4o7wttaa

Genotype-Environment Interactions Reveal Causal Pathways That Mediate Genetic Effects on Phenotype

Julien Gagneur, Oliver Stegle, Chenchen Zhu, Petra Jakob, Manu M. Tekkedil, Raeka S. Aiyar, Ann-Kathrin Schuon, Dana Pe'er, Lars M. Steinmetz, Justin C. Fay
2013 PLoS Genetics  
Here, we address this challenge using extensive, multi-environment gene expression and fitness profiling of hundreds of genetically diverse yeast strains, in order to identify truly causal intermediate  ...  Unraveling the molecular processes that lead from genotype to phenotype is crucial for the understanding and effective treatment of genetic diseases.  ...  Onge (Stanford Genome Technology Center) for providing us with the yeast deletion collection and support in its usage. Author Contributions  ... 
doi:10.1371/journal.pgen.1003803 pmid:24068968 pmcid:PMC3778020 fatcat:tknovxfexvcc5i77pvsh5cbjxi

Genome-wide association studies and the genetic dissection of complex traits

Paola Sebastiani, Nadia Timofeev, Daniel A. Dworkis, Thomas T. Perls, Martin H. Steinberg
2009 American Journal of Hematology  
(epistasis), and their interaction with environmental factors (gene-environment interaction).  ...  Examples include many of the common age-related diseases such as hypertension [3], diabetes [4, 5] , cardiovascular disease [6], and dementia [7] , which are presumed to be determined by several genes  ...  genes (epistasis), and their interaction with environmental factors (gene-environment interaction).  ... 
doi:10.1002/ajh.21440 pmid:19569043 pmcid:PMC2895326 fatcat:ns7wg3jimjfnbmb2qpwulyphwq

A systems-based framework for understanding complex metabolic and cardiovascular disorders

Sulin Wu, Aldons J. Lusis, Thomas A. Drake
2008 Journal of Lipid Research  
But, it is also important to understand how the genes interact with each other and the environment, and how these interactions change in disease states.  ...  Common forms of metabolic and cardiovascular diseases involve the interplay of numerous genes as well as important environmental factors.  ...  While these approaches continue to be informative, it is also important to address the interactions between genes and the environment (5) .  ... 
doi:10.1194/jlr.r800067-jlr200 pmid:19033210 pmcid:PMC2674684 fatcat:4kwq45wpgbemlkytavad3jrbaq

Extracting biology from high-dimensional biological data

J. Quackenbush
2007 Journal of Experimental Biology  
Modeling pathways and networks Organisms use a combination of cis-and transacting elements to respond to intra-and extracellular environmental stimuli by regulating gene and protein expression.  ...  Using such an approach in an iterative manner, in which a network is first learned, then perturbed and the resulting data used to refine the predicted network structure, may allow us to discover novel  ... 
doi:10.1242/jeb.004432 pmid:17449816 fatcat:f4ve5u7v2fhnjk4lrwxr6kzo6u

Extraction of Conditional Probabilities of the Relationships Between Drugs, Diseases, and Genes from PubMed Guided by Relationships in PharmGKB

Martin Theobald, Nigam Shah, Jeff Shrager
2009 Summit on translational bioinformatics  
Guided by curated associations between genes, treatments (i.e., drugs), and diseases in pharmGKB, we constructed n-way Bayesian networks based on conditional probability tables (cpt's) extracted from co-occurrence  ...  The networks suggest hypotheses regarding drug mechanisms, treatment biomarkers, and/or potential markers of genetic disease.  ...  NS's work was supported by NIH grant U54 HG004028 and a gift from CommerceNet. JS's work was supported by CollabRx, Inc. The comments of several anonymous reviewers helped to improve the final paper.  ... 
pmid:21347183 pmcid:PMC3041559 fatcat:sby6adka7zaplm2akq4x4o2zyu

An Efficient Model for Medical Data Classification using Gene Features

Kosaraju Chaitanya, Rachakonda Venkatesh, Thulasi Bikku
2019 International Journal of Advanced Computer Science and Applications  
In the medical field to solve the new issues, the novel approaches for managing relevant features by using genomes are considered; using the sub-sequence of genes the outcome of interest is analyzed.  ...  The primary point of the proposed ensemble learning models is to characterize the high dimensional information for gene/proteinbased disease expectation in light of substantial biomedical databases.  ...  An extension of parallel semantic mining model is used to find the relationship between two semantic entities (e.g. genedisease1, gene--disease2, etc.) and to check the existence of the disease patterns  ... 
doi:10.14569/ijacsa.2019.0101160 fatcat:j34saznehjdkhdw4m4doej76ae

Different Types of Curvature and Their Vanishing Conditions

Manisha Maheshkumar Kankarej
2021 Academic Journal of Applied Mathematical Sciences  
Some necessary properties of the Hessian operator are discussed with respect to all curvatures as well.  ...  In the present paper, I studied different types of Curvature like Riemannian Curvature, Concircular Curvature, Weyl Curvature, and Projective Curvature in Quarter Symmetric non-Metric Connection in P-Sasakian  ...  Acknowledgments The author would like to thank Mr.  ... 
doi:10.32861/ajams.73.143.148 fatcat:4cymftqmtbckhpkjyotlx3aubi

Network Medicine: New Paradigm in the -Omics Era

Nancy Lan Guo
2011 Anatomy & Physiology  
[160, 161] used scatter plots of the expression between two genes to derive the implication relations in the whole genome.  ...  Molecular network analysis has led to promising applications in identifying new disease genes [72-89] and disease-related subnetworks [90-99] mapping cause-and-effect genetic perturbations [100-106] and  ... 
doi:10.4172/2161-0940.1000e106 pmid:24634802 pmcid:PMC3951174 fatcat:q5zyxa4rizchzpxe7i6kzlfj5e

An instance-specific causal framework for learning intercellular communication networks that define microenvironments of individual tumors [article]

Xueer Chen, Lujia Chen, Cornelius H.L. Kurten, Fattaneh Jabbari, Lazar Vujanovic, Ying Ding, Aditi Kulkarni, Tracy Tabib, Robert Lafyatis, Gregory F. Cooper, Robert Ferris, Xinghua Lu
2021 bioRxiv   pre-print
Using head and neck squamous cell carcinoma (HNSCC) tumors as a testbed, we first mined single-cell RNA-sequencing data to discover gene expression modules (GEMs) that reflect the states of transcriptomic  ...  Finally, we applied instance-specific causal network learning to discover an ICN within each tumor.  ...  Survival analyses showed significant differences in patient outcomes between the clusters, supporting the impact of the modeled immune environment on disease progression.  ... 
doi:10.1101/2021.11.11.467838 fatcat:oyxwc5gyavgflogef5vitasfhe

The inference of breast cancer metastasis through gene regulatory networks

F.K. Ahmad, S. Deris, N.H. Othman
2012 Journal of Biomedical Informatics  
Given this complexity, a computational study using the Bayesian network technique has been employed to construct a gene regulatory network from microarray data.  ...  Although the Bayesian network has been notified as a prominent method to infer gene regulatory processes, learning the Bayesian network structure is NP hard and computationally intricate.  ...  Hassane Bouzahir and Dr. Nor Idayu Mahat for useful suggestions and discussions.  ... 
doi:10.1016/j.jbi.2011.11.015 pmid:22179053 fatcat:s4qrirjx5nfm7fzafl6xkkncwe

Exploring the human genome with functional maps

C. Huttenhower, E. M. Haley, M. A. Hibbs, V. Dumeaux, D. R. Barrett, H. A. Coller, O. G. Troyanskaya
2009 Genome Research  
Acknowledgments We thank Florian Markowetz, Edo Airoldi, Chad Myers, Aster Legesse-Miller, Josh Forman, Eric Suh, Sarah Pfau, Leonid Kruglyak, and  ...  and GeNIe modeling environment (Druzdzel 1999) from the University of Pittsburgh Decision Systems Library for Bayesian network manipulation.  ...  To generate functional maps, these networks are mined for functional associations between groups of genes, which might represent individual genes, pathways, processes, or diseases.  ... 
doi:10.1101/gr.082214.108 pmid:19246570 pmcid:PMC2694471 fatcat:my3d3id4ebfzropnkp35og6awe

Computational methods for Traditional Chinese Medicine: A survey

Suryani Lukman, Yulan He, Siu-Cheung Hui
2007 Computer Methods and Programs in Biomedicine  
Various approaches on exploring relationships among TCM components and finding genes/proteins relating to TCM symptom complex are also studied.  ...  A review on basic elements of TCM is provided to illuminate various challenges and progresses in its study using computational methods.  ...  Bayesian networks were also used to establish the relationship between quantitative chromatictextural features and diseases [28] .  ... 
doi:10.1016/j.cmpb.2007.09.008 pmid:17983685 fatcat:pladmfn4mrd7pg7zuw5mhbqreq

Network medicine approaches to the genetics of complex diseases

Edwin K Silverman, Joseph Loscalzo
2012 Discovery Medicine  
Network medicine, which applies systems biology and network science to complex molecular networks underlying human disease, focuses on identifying the interacting genes and proteins which lead to disease  ...  The long biological path between a genetic risk variant and development of a complex disease involves a range of biochemical intermediates, including coding and non-coding RNA, proteins, and metabolites  ...  Acknowledgments This work was supported by NIH grants HL113264, HL075478, HL105339, and HL083069 (EKS) and by NIH grants HL061795, HL048743, HL107192, HL070819, and HL108630 (JL).  ... 
pmid:22935211 pmcid:PMC3545396 fatcat:4oz3k2n2gbefzjkaffap2hzgz4
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