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Probabilistic discovery of overlapping cellular processes and their regulation
2004
Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04
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It provides a unified probabilistic framework of gene regulation for multiple overlapping biological processes. ...
We discuss a probabilistic model of overlapping biological processes, gene membership in those processes, and an addition to that model that identifies regulatory mechanisms controlling process activation ...
CONCLUSIONS AND FUTURE WORK This paper proposes a probabilistic framework for modeling overlapping cellular processes and extracting these models from gene expression data. ...
doi:10.1145/974614.974637
dblp:conf/recomb/BattleSK04
fatcat:5mgljwevsvceboenz3l3psn36m
Probabilistic Discovery of Overlapping Cellular Processes and Their Regulation
2005
Journal of Computational Biology
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It provides a unified probabilistic framework of gene regulation for multiple overlapping biological processes. ...
We discuss a probabilistic model of overlapping biological processes, gene membership in those processes, and an addition to that model that identifies regulatory mechanisms controlling process activation ...
CONCLUSIONS AND FUTURE WORK This paper proposes a probabilistic framework for modeling overlapping cellular processes and extracting these models from gene expression data. ...
doi:10.1089/cmb.2005.12.909
pmid:16201912
fatcat:x3f64k2ebjdgpfwwwp4y4noboa
The globalization of messenger RNA regulation
2014
National Science Review
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These discoveries provided an abundant amount of information, both descriptive and mechanistic, to the rapidly expanding field of RNA biology. ...
Moreover, the cDNA cloning of regulatory RNA-binding proteins (RBPs) and their interactions with a myriad of non-coding RNAs (ncRNAs) as well as coding mRNAs began to accelerate in the second half of the ...
ACKNOWLEDGEMENTS I thank Matt Friedersdorf and Jeff Blackinton for critically reading the manuscript, and I apologize to many colleagues for not being able to cite their valued contributions to this field ...
doi:10.1093/nsr/nwu004
pmid:28078165
pmcid:PMC5222540
fatcat:dbkd6u4vhjaf7f4d3ngou3nq44
Deciphering modular and dynamic behaviors of transcriptional networks
2007
Genomic Medicine
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In silico studies have also been made to mimic the dynamic behavior of regulatory networks, analyzing how disease or cellular phenotypes arise from the connectivity or networks of genes and their products ...
The coordinated and dynamic modulation or interaction of genes or proteins acts as an important mechanism used by a cell in functional regulation. ...
drug discovery, and effective preventive and therapeutic intervention of disease. ...
doi:10.1007/s11568-007-9004-7
pmid:18923925
pmcid:PMC2276884
fatcat:mxdjtxuhk5h6pp46b5ne6um2k4
Identification of competing endogenous RNAs of the tumor suppressor gene PTEN: A probabilistic approach
2017
Scientific Reports
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Regulation by microRNAs (miRNAs) and modulation of miRNA activity are critical components of diverse cellular processes. ...
The approach developed can be applied to map ceRNA networks of critical cellular regulators and to develop novel insights into crosstalk between different pathways involved in cancer. ...
Acknowledgements Authors wish to thank Carl Tony Fakhry for providing help with data processing. ...
doi:10.1038/s41598-017-08209-1
pmid:28798471
pmcid:PMC5552881
fatcat:bxkfkpexsng3jcpwkiqju5bheq
Entropy-Based Graph Clustering of PPI Networks for Predicting Overlapping Functional Modules of Proteins
2021
Entropy
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In this study, the unweighted and weighted GE algorithm is evaluated to prove the validity of predicting function modules. ...
In particular, the detection of overlapping clusters is necessary because a protein is involved in multiple functions under different conditions. graph entropy (GE) is a novel metric to assess the quality ...
In the case of GO:0019054, its function is described as modulation by virus of host cellular process, and the missing element (KPNA6) can be filled in the Karyopherin proteins; this is easy to reveal intuitively ...
doi:10.3390/e23101271
pmid:34681995
pmcid:PMC8534328
fatcat:d5krsgqlkfdc3olnkcnm5ksldi
EXPECTATION-MAXIMIZATION ALGORITHMS FOR FUZZY ASSIGNMENT OF GENES TO CELLULAR PATHWAYS
2006
Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006
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Cellular pathways are composed of multiple reactions and interactions mediated by genes. ...
Our algorithm uses expression data, database annotations and similarity data to infer the most likely assignments, and estimate the affinity of each gene with the known cellular pathways. ...
Moreover, since cellular processes form a complex and highly connected network it is difficult to delineate the boundaries of individual pathways and the same process might be defined differently by different ...
doi:10.1142/18609475730037
fatcat:7tm5jv5fvbdhbedbaax5s4n2qe
EXPECTATION-MAXIMIZATION ALGORITHMS FOR FUZZY ASSIGNMENT OF GENES TO CELLULAR PATHWAYS
2006
Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006
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Cellular pathways are composed of multiple reactions and interactions mediated by genes. ...
Our algorithm uses expression data, database annotations and similarity data to infer the most likely assignments, and estimate the affinity of each gene with the known cellular pathways. ...
Moreover, since cellular processes form a complex and highly connected network it is difficult to delineate the boundaries of individual pathways and the same process might be defined differently by different ...
doi:10.1142/1860947573_0037
fatcat:bfmjsb5a6jh6bms7fmi47r6nwa
EXPECTATION-MAXIMIZATION ALGORITHMS FOR FUZZY ASSIGNMENT OF GENES TO CELLULAR PATHWAYS
2006
Computational Systems Bioinformatics
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Cellular pathways are composed of multiple reactions and interactions mediated by genes. ...
Our algorithm uses expression data, database annotations and similarity data to infer the most likely assignments, and estimate the affinity of each gene with the known cellular pathways. ...
Moreover, since cellular processes form a complex and highly connected network it is difficult to delineate the boundaries of individual pathways and the same process might be defined differently by different ...
doi:10.1142/9781860947575_0034
fatcat:qcff7z2ac5e2jikdwpr5ny5fte
Systems Biology via Redescription and Ontologies (II): A Tool for Discovery in Complex Systems
[chapter]
2010
Unifying Themes in Complex Systems
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Such perspectives are important in order to obtain a process-level understanding of the underlying cellular machinery; especially how cells react, respond, and recover from environmental changes. ...
Yet, each of these processes is difficult to decipher as their visible signatures are only seen in a syntactic background, devoid of the context. ...
This cluster then separates into two groups, which overlap with genes from 4:5. 5:9 and 5:15 As The Mphase ends and G1 begins, 5:9 contains down regulated processes such as post replication repair and ...
doi:10.1007/978-3-540-85081-6_24
fatcat:ujk23frurbe57n7cnyhgc2lk6m
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 ...
on limited types of interaction data and their use of binary, rather than probabilistic networks. ...
doi:10.1186/gb-2005-6-13-r114
pmid:16420673
pmcid:PMC1414113
fatcat:zbwq3u3eufebrdbwqlikgteljq
PTOMSM: A modified version of Topological Overlap Measure used for predicting Protein-Protein Interaction Network
2009
Nature Precedings
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Furthermore, we examined the influence of the sizes of training and test datasets on prediction, and further demonstrated the effectiveness of PTOMSM in predicting PPI. ...
Therefore, we propose a modified version of Topological Overlap Measure to identify not only extant direct PPIs links, but also novel protein interactions that can be indirectly inferred from various relationships ...
related research and Weixiang Liu for discussion of Mathematics. ...
doi:10.1038/npre.2009.4107.1
fatcat:wow6ptasana3jf5dnqxkdqudzm
Modulation of Gene Expression Regulated by the Transcription Factor NF-κB/RelA
2014
Journal of Biological Chemistry
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We used a probabilistic model to infer 8349 (M, NF-B/RelA, TG) triplets and their modes of modulatory action from our combined LC-MS/MS and ChIP-Seq (ChIP followed by next generation sequencing) data, ...
Significance: We provide new insight into the activity of NF-B/RelA. Our inference model can be applied to other processes and pathways. ...
For C-II-1b, the enriched GO categories are regulation of apoptosis, multiorganism process, positive regulation of apoptosis, regulation of cell cycle, and regulation of cellular protein metabolic process ...
doi:10.1074/jbc.m113.539965
pmid:24523406
pmcid:PMC4002100
fatcat:w7gkxzxmingfljozwiwgavuudi
Neuronal cell-type-specific alternative splicing: A mechanism for specifying connections in the brain?
2015
Neurogenesis
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Proteome diversity is much needed in the nervous system where multifaceted cellular processes, such as neurotransmission and synaptic plasticity, are coordinated with only a modest number of genes. ...
was validated by the discovery that both a secreted and a membrane-bound form of an antibody were being produced from a single gene. 2-5 Since then, more examples of the same phenomena have emerged and ...
Proteome diversity is much needed in the nervous system where multifaceted cellular processes, such as neurotransmission and synaptic plasticity, are coordinated with only a modest number of genes. ...
doi:10.1080/23262133.2015.1122699
pmid:27606331
pmcid:PMC4973604
fatcat:i5hy3unhorcwrllyu52gf2x7ga
Getting Started in Probabilistic Graphical Models
2007
PLoS Computational Biology
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Probabilistic graphical models (PGMs) have become a popular tool for computational analysis of biological data in a variety of domains. But, what exactly are they and how do they work? ...
This note sketches out some answers and illustrates the main ideas behind the statistical approach to biological pattern discovery. ...
, and by National Institutes of Health grant R01 GM071966. ...
doi:10.1371/journal.pcbi.0030252
pmid:18069887
pmcid:PMC2134967
fatcat:ja62f3h3tnbpfmmelkntaqr624
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