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SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance
2017
BMC Systems Biology
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Network querying algorithms provide computational means to identify conserved network modules in large-scale biological networks that are similar to known functional modules, such as pathways or molecular ...
Results: In this paper, we propose SEQUOIA, a novel network querying algorithm that effectively addresses these issues by utilizing a context-sensitive random walk (CSRW) model for network comparison and ...
Acknowledgements This work was supported in part by the National Science Foundation through the NSF Award CCF-1149544. ...
doi:10.1186/s12918-017-0404-6
pmid:28361708
pmcid:PMC5374659
fatcat:6a5ir3bir5cqznm7lvljy4klqu
SEQUOIA
2016
Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16
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Network querying algorithms provide computational means to identify conserved network modules in large-scale biological networks that are similar to known functional modules, such as pathways or molecular ...
Results: In this paper, we propose SEQUOIA, a novel network querying algorithm that effectively addresses these issues by utilizing a context-sensitive random walk (CSRW) model for network comparison and ...
Acknowledgements This work was supported in part by the National Science Foundation through the NSF Award CCF-1149544. ...
doi:10.1145/2975167.2985676
dblp:conf/bcb/JeongY16
fatcat:arggxqnbgrbt3eb6pptym6cvr4
CUFID-query: accurate network querying through random walk based network flow estimation
2017
BMC Bioinformatics
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As a result, such conserved functional modules can be identified through comparative analysis of biological networks. ...
Conclusions: Through extensive performance evaluation based on biological networks with known functional modules, we show that CUFID-query outperforms the existing state-of-the-art algorithms in terms ...
Acknowledgements This work was supported in part by the National Science Foundation through the NSF Award CCF-1149544 and NSF Award CCF-1447235. ...
doi:10.1186/s12859-017-1899-y
pmid:29297279
pmcid:PMC5751815
fatcat:foqreqkwmnf55i6xjapuwwpb2y
Discovery of biological networks from diverse functional genomic data
2005
Genome Biology
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We have developed a general probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data. ...
This framework was validated by accurately recovering known networks for 31 biological processes in Saccharomyces cerevisiae and experimentally verifying predictions for the process of chromosomal segregation ...
the network search algorithm toward the specific biological context represented in the query set. ...
doi:10.1186/gb-2005-6-13-r114
pmid:16420673
pmcid:PMC1414113
fatcat:zbwq3u3eufebrdbwqlikgteljq
ChiBE: interactive visualization and manipulation of BioPAX pathway models
2009
Computer applications in the biosciences : CABIOS
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Users can easily query and visualize pathways through an integrated Pathway Commons query tool and analyze molecular profiles in pathway context. ...
and molecular complexes. ...
, to discovering graph-theoretic properties in biological networks. ...
doi:10.1093/bioinformatics/btp665
pmid:20007251
pmcid:PMC2815657
fatcat:2iaoiahmgfccxewyjguyph4clq
Integrating biological pathways and genomic profiles with ChiBE 2
2014
BMC Genomics
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Results: ChiBE is a free, open-source software tool for visualizing, querying, and analyzing human biological pathways in BioPAX format. ...
as well as in local BioPAX models. ...
ChiBE identifies an altered complex in breast cancer In this example, we start with a list of frequently mutated genes in breast cancer. ...
doi:10.1186/1471-2164-15-642
pmid:25086704
pmcid:PMC4131037
fatcat:o72jriywrzfzhgg5l5m56jxqoq
Genetic studies of diseases
2007
Cellular and Molecular Life Sciences (CMLS)
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The biological system is a complex physicochemical system consisting of numerous dynamic networks of biochemical reactions and signaling interactions between cellular components. ...
The numerous online pathway databases vary widely in coverage and representation of biological processes. ...
Discussion: networks analysis of biological system In this current stage of information explosion, massive scale experimental datasets are only meaningful when scrupulously interpreted in the context of ...
doi:10.1007/s00018-007-7053-7
pmid:17415520
fatcat:xv7my5xo3jdkbbdmvhsbawo7li
Reactome: An integrated expert model of human molecular processes and access toolkit
2007
Journal of Integrative Bioinformatics
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SummaryThe behaviour of pervasive molecular processes in human biology can be studied through the large-scale modeling of the molecular events that define them. ...
This resource dataset is systematically cross-referenced to major molecular and literature databases, and is accessible to the community in a number of well-established formats. ...
: The formation of molecular complexes is a mainstay in representing a number of biological scenarios. ...
doi:10.1515/jib-2007-84
fatcat:a2bb4t4pfrduvnavqzmmwioykq
Integration of omics data: how well does it work for bacteria?
2006
Molecular Microbiology
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However, because of the complexity of biological systems and the specificities of the data-generating technologies (noisiness, heterogeneity, etc.), integrating omics data in an attempt to reconstruct ...
signalling networks is not trivial. ...
Acknowledgements We apologize to those colleagues whose work we have been forced to omit through considerations of space. This work is partially supported by: (i) ...
doi:10.1111/j.1365-2958.2006.05453.x
pmid:17040488
fatcat:jsstbyt3cbf3le3upkrstfi6vy
Systems Proteomics for Translational Network Medicine
2012
Circulation: Cardiovascular Genetics
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biological contexts. ...
Network medicine/biology Analysis of molecular (eg, protein, gene, metabolite) interaction networks through complex network theory, comprising topological features characterizing symmetric or asymmetric ...
doi:10.1161/circgenetics.110.958991
pmid:22896016
pmcid:PMC3466103
fatcat:hudrukaw5je4bfanb4hlcyjege
Protein–glycosaminoglycan interaction networks: Focus on heparan sulfate
2017
Perspectives in Science
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situations such as angiogenesis and host-pathogen interactions, (iv) to build, contextualize and analyze the corresponding protein-heparan sulfate interaction networks to identify molecular connections ...
The aim of our work is (i) to identify and characterize protein-GAG interactions occurring at the cell surface and in the ECM, (ii) to study the assembly of multimolecular complexes formed at the cell ...
to their binding to proteins in a biologically relevant context. ...
doi:10.1016/j.pisc.2016.10.004
fatcat:pwxcs3smezg3ddhmls4ce6nh24
Comparative analysis of protein networks
2012
Communications of the ACM
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In the context of comparative network analysis, color coding was mainly used to tackle network querying problems, where typically the query subnetwork is small (5-15 proteins), motivating the use of this ...
For instance, in Sharan et al., 31 a cross-species analysis is used to identify yeast-bacterial conserved complexes. ...
doi:10.1145/2160718.2160738
fatcat:garjqtjvanhgrk5ns5tijtijam
Bioinformatics in the post-sequence era
2003
Nature Genetics
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the identification of clusters of related genes and networks of interacting proteins. ...
In the past decade, bioinformatics has become an integral part of research and development in the biomedical sciences. ...
in gene context analysisand these expression clusters can identify potential members of gene groups responsible for specific physiological processes. ...
doi:10.1038/ng1109
pmid:12610540
fatcat:xaa5e6mikrdwdhk6gjzsc33hxe
Data integration and visualization system for enabling conceptual biology
2005
Bioinformatics
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The system implementation is based on a multi-tier architecture using a native XML database and a software tool for querying and visualizing complex biological networks. ...
Results: Our integration approach is based on the premise that relationships between biological entities can be represented as a complex network. ...
in a specific context. ...
doi:10.1093/bioinformatics/bti1015
pmid:15961455
fatcat:ozhwui4ynvanvll3fc2bsna23e
Network representations of immune system complexity
2015
Wiley Interdisciplinary Reviews: Systems Biology and Medicine
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These networks range from those involving gene regulatory and proteinprotein interactions underlying intracellular signaling pathways and single cell responses to increasingly complex networks of in vivo ...
The mammalian immune system is a dynamic multi-scale system composed of a hierarchically organized set of molecular, cellular and organismal networks that act in concert to promote effective host defense ...
Recent technological advances have enabled us to query these many levels through acquisition of large-scale 'omics' datasets that have facilitated network biology research in the context of innate immune ...
doi:10.1002/wsbm.1288
pmid:25625853
pmcid:PMC4339634
fatcat:pe7eqjaqijhgrhhz5wtfep42ju
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