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Strategies for dealing with incomplete information in the modeling of molecular interaction networks

H. de Jong, D. Ropers
2006 Briefings in Bioinformatics  
In this article we review two strategies that have been proposed for dealing with incomplete information in the study of molecular interaction networks: parameter sensitivity analysis and model simplification  ...  Modelers of molecular interaction networks encounter the paradoxical situation that while large amounts of data are available, these are often insufficient for the formulation and analysis of mathematical  ...  Acknowledgments The authors acknowledge financial support from the ACI IMPBio initiative of the French Ministry of Research (project BacAttract) and the NEST Adventure program of the European Commission  ... 
doi:10.1093/bib/bbl034 pmid:17003073 fatcat:u6xigzm6cjhglfx6y6xyyhwyaq

The role of protein interaction networks in systems biomedicine

Tuba Sevimoglu, Kazim Yalcin Arga
2014 Computational and Structural Biotechnology Journal  
Acknowledgments The financial support by the Marmara University Research Fund through project FEN-B-090414-0089 is greatly acknowledged.  ...  deal with data about single players (i.e. changes in the expression of individual genes).  ...  The Role of Networks in Medicine Networks provide a systems-level understanding of the mechanisms underlying diseases by serving as a model for data integration and analysis.  ... 
doi:10.1016/j.csbj.2014.08.008 pmid:25379140 pmcid:PMC4212283 fatcat:7ptbsz2vnveizd7uboodqufy3e

Structure-based systems biology: a zoom lens for the cell

Patrick Aloy, Robert B Russell
2005 FEBS Letters  
We suggest a process of zooming on the cell, from global networks through pathways to the precise atomic contacts at the interfaces of interacting proteins.  ...  Systems biology seeks to explain complex biological systems, such as the cell, through the integration of many different types of information.  ...  To reach such an ambitious goal, it will be necessary to develop strategies able to deal with a great variety of biological molecules: small metabolites, proteins, complexes and the sophisticated and dynamic  ... 
doi:10.1016/j.febslet.2005.02.014 pmid:15763563 fatcat:bpqeznkqenahljbg4lte3kwdy4

Network Medicine in the age of biomedical big data [article]

Abhijeet R. Sonawane, Scott T. Weiss, Kimberly Glass, Amitabh Sharma
2019 arXiv   pre-print
Network medicine is an emerging area of research dealing with molecular and genetic interactions, network biomarkers of disease, and therapeutic target discovery.  ...  Marrying the two, network medicine with biomedical data provides a framework to build meaningful models and extract impactful results at a network level.  ...  This information often comes from multiple different data sources, dealing with the various facets of the biological system.  ... 
arXiv:1903.05449v1 fatcat:7v4pvoxezjd55ex5ei2jbteswm

Network Medicine in the Age of Biomedical Big Data

Abhijeet R. Sonawane, Scott T. Weiss, Kimberly Glass, Amitabh Sharma
2019 Frontiers in Genetics  
Network medicine is an emerging area of research dealing with molecular and genetic interactions, network biomarkers of disease, and therapeutic target discovery.  ...  We provide three paradigms, mainly dealing with three major biological network archetypes: protein-protein interaction, expression-based, and gene regulatory networks.  ...  ACKNOWLEDGMENTS AS would like to thank John Quackenbush for inspiration of the three paradigms discussed above, along with Trevor R.  ... 
doi:10.3389/fgene.2019.00294 pmid:31031797 pmcid:PMC6470635 fatcat:qro34cgpuzg6bj72h23yjdylm4

Supporting cognition in systems biology analysis: findings on users' processes and design implications

Barbara Mirel
2009 Journal of Biomedical Discovery and Collaboration  
Researchers interacted with the same proteinprotein interaction tools to discover possible disease mechanisms for further experimentation.  ...  Current usability studies of bioinformatics tools suggest that tools for exploratory analysis support some tasks related to finding relationships of interest but not the deep causal insights necessary  ...  I would like to thank Ben Keller, Fan Meng, Weijian Xuan, and Magesh Jayapandian for their critical reviews of or collaborative contributions to the design implications of findings.  ... 
doi:10.1186/1747-5333-4-2 pmid:19216777 pmcid:PMC2649900 fatcat:zgi75ipuorgstltuxbiph4nshm

Preface: pattern recognition and mining

Pradipta Maji, Sankar K. Pal, Andrzej Skowron
2015 Natural Computing  
This framework can be modeled with principles of neural networks, fuzzy sets and rough sets, both in isolation and integration, among other theories.  ...  The processes occurring in nature can be viewed as different kinds of information processing.  ...  The concept of rough-rule base is used for video tracking to deal with the uncertainties and incompleteness as well as to gain in computation time.  ... 
doi:10.1007/s11047-015-9487-4 fatcat:lxfdyey2ujfbhdyprg7bw63bfu

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

Andrea Califano, Atul J Butte, Stephen Friend, Trey Ideker, Eric Schadt
2012 Nature Genetics  
The context-specific networks of molecular interactions that determine cell behavior provide a particularly relevant framework for the integration of data from multiple 'omics' .  ...  This is not my beautiful pathway An increasing body of evidence suggests that canonical pathways are incomplete and largely inaccurate models for studying the complex  ...  ACknowlEdgmEnTS We would like to acknowledge the generous funding provided by the US National Institutes of Health (NIH) under the following grant awards:  ... 
doi:10.1038/ng.2355 pmid:22836096 pmcid:PMC3593099 fatcat:dya2g4exzzcpfht4du27hfpyiq

Comparative Analysis of Modularity in Biological Systems

Xin Li, Sinan Erten, Gurkan Bebek, Mehmet Koyuturk, Jing Li
2009 2009 Ohio Collaborative Conference on Bioinformatics  
In systems biology, comparative analysis of molecular interactions across diverse species indicates that conservation and divergence of networks can be used to understand functional evolution from a systems  ...  In the context of phylogeny reconstruction, our experiments on a comprehensive collection of simulated and real networks show that comparison of networks based on module trajectories is more informative  ...  Although the network sizes in this database vary dramatically for different species, MOPHY can effectively deal with such incompleteness by considering modules from each pair of species.  ... 
doi:10.1109/occbio.2009.29 fatcat:rtufkqv6n5bvnmkcgjx24id3rq

Identification of aberrant pathways and network activities from high-throughput data

J. Wang, Y. Zhang, C. Marian, H. W. Ressom
2012 Briefings in Bioinformatics  
A major challenge in the diagnosis and treatment of such diseases is to identify characteristic aberrancies in the biological pathways and molecular network activities and elucidate their relationship  ...  Many complex diseases such as cancer are associated with changes in biological pathways and molecular networks rather than being caused by single gene alterations.  ...  We appreciate the organizers and participants of the Workshop on Identification of Aberrant Pathway and Network Activity from High-Throughput Data at the 2011 Pacific Biocomputing Symposium for providing  ... 
doi:10.1093/bib/bbs001 pmid:22287794 pmcid:PMC3404398 fatcat:woielqwwtbc6bhdoub3hycnu6a

Soft Set Theory for Decision Making in Computational Biology under Incomplete Information

Beatriz Santos-Buitrago, Adrian Riesco, Merrill Knapp, Jose Carlos R. Alcantud, Gustavo Santos-Garcia, Carolyn Talcott
2019 IEEE Access  
Using this new strategy, we propose an extension in the biological symbolic models of Pathway Logic.  ...  In this paper, we define an application of logic modeling with rewriting logic and soft set theory.  ...  ACKNOWLEDGMENT The authors would like to thank the valuable suggestions of the editor and the anonymous reviewers that allowed us to improve the original manuscript.  ... 
doi:10.1109/access.2019.2896947 pmid:31788396 pmcid:PMC6884365 fatcat:4gta66xe2be2jgx6f2gu3ukagi

Models and computational strategies linking physiological response to molecular networks from large-scale data

F. Ortega, K. Sameith, N. Turan, R. Compton, V. Trevino, M. Vannucci, F. Falciani
2008 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
Here, we review some of the most widely used methodologies and report new results in support of the usefulness of modularization and other modelling techniques in identifying components of the molecular  ...  levels of the organizational complexity of the molecular network.  ...  The work described in this paper has been partially supported by the European Commission (BIOBRIDGE project).  ... 
doi:10.1098/rsta.2008.0085 pmid:18559319 fatcat:4yl6bjgxibeanmidtn7fdis2ru

Systems Biology as a Comparative Approach to Understand Complex Gene Expression in Neurological Diseases

Leticia Diaz-Beltran, Carlos Cano, Dennis Wall, Francisco Esteban
2013 Behavioral Sciences  
the role of systems approaches in the design of classifiers that can shorten the time for behavioral diagnosis of autism.  ...  Here, we present a review of integrative approaches that help to understand the underlying biological processes involved in the etiopathogenesis of neurological diseases, for example, those related to  ...  These works show how Boolean Networks join the complexity of network analysis with the simplicity of logic models and are able to provide a good connection between molecular interactions and cell phenotype  ... 
doi:10.3390/bs3020253 pmid:25379238 pmcid:PMC4217627 fatcat:ky4wdfmworcmlesh7ejhppt6le

Virus–host interactions: from systems biology to translational research

Xinxia Peng, Eric Y Chan, Yu Li, Deborah L Diamond, Marcus J Korth, Michael G Katze
2009 Current Opinion in Microbiology  
In this review, we highlight new high-throughput technologies, a new philosophy for studying virushost interactions, and discuss the potential of systems biology to facilitate bench-to-bedside research  ...  Together with advances in data integration, systems biology approaches now have the potential to provide profound impacts on translational research, leading to the more rapid development of new therapeutics  ...  We thank Matt Dyer for insightful suggestions and assistance with the preparation of the manuscript.  ... 
doi:10.1016/j.mib.2009.06.003 pmid:19576841 pmcid:PMC2742299 fatcat:ylka32m3ezdypov3gcem2q2gde

Next challenges in protein-protein docking: from proteome to interactome and beyond

Adrien S.J. Melquiond, Ezgi Karaca, Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin
2011 Wiley Interdisciplinary Reviews. Computational Molecular Science  
Interactomes are huge, intricate and highly dynamic molecular networks that determine the fate of the cell.  ...  The quest for the elucidation of such networks is usually followed by the thirst of understanding, and lastly by the fantasy of predicting.  ...  Acknowledgments This work was supported by the Netherlands Organization for Scientific Research (VICI grant #700.56.442 to AMJJB) and by the European Community FP7 e--Infrastructure WeNMR project (grant  ... 
doi:10.1002/wcms.91 fatcat:45rmtmlypnduljiw4ukqr7nqvu
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