Filters








5,893 Hits in 4.4 sec

Probabilistic discovery of overlapping cellular processes and their regulation

Alexis Battle, Eran Segal, Daphne Koller
2004 Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04  
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

Alexis Battle, Eran Segal, Daphne Koller
2005 Journal of Computational Biology  
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

Jack D. Keene
2014 National Science Review  
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

Ming Zhan
2007 Genomic Medicine  
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

Kourosh Zarringhalam, Yvonne Tay, Prajna Kulkarni, Assaf C. Bester, Pier Paolo Pandolfi, Rahul V. Kulkarni
2017 Scientific Reports  
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

Hoyeon Jeong, Yoonbee Kim, Yi-Sue Jung, Dae Ryong Kang, Young-Rae Cho
2021 Entropy  
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

Liviu Popescu, Golan Yona
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
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

Liviu Popescu, Golan Yona
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
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

Liviu Popescu, Golan Yona
2006 Computational Systems Bioinformatics  
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]

Samantha Kleinberg, Marco Antoniotti, Satish Tadepalli, Naren Ramakrishnan, Bud Mishra
2010 Unifying Themes in Complex Systems  
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

Chad L Myers, Drew Robson, Adam Wible, Matthew A Hibbs, Camelia Chiriac, Chandra L Theesfeld, Kara Dolinski, Olga G Troyanskaya
2005 Genome Biology  
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

Xun Huang, Xun Huang
2009 Nature Precedings  
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

Xueling Li, Yingxin Zhao, Bing Tian, Mohammad Jamaluddin, Abhishek Mitra, Jun Yang, Maga Rowicka, Allan R. Brasier, Andrzej Kudlicki
2014 Journal of Biological Chemistry  
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?

Joshua Shing Shun Li, Grace Ji-eun Shin, S Sean Millard
2015 Neurogenesis  
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

Edoardo M. Airoldi
2007 PLoS Computational Biology  
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
« Previous Showing results 1 — 15 out of 5,893 results