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An Efficient Feature Extraction Technique Based on Local Coding PSSM and Multifeatures Fusion for Predicting Protein-Protein Interactions
2019
Evolutionary Bioinformatics
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Increasing evidence has indicated that protein-protein interactions (PPIs) play important roles in various aspects of the structural and functional organization of a cell. ...
Result: To evaluate the performance of the proposed feature extraction approach, we employed support vector machine (SVM) as a prediction classifier and applied this method to yeast and human PPI datasets ...
Acknowledgements The authors would like to thank all the guest editors and anonymous reviewers for their constructive advice. ...
doi:10.1177/1176934319879920
pmid:31619921
pmcid:PMC6777060
fatcat:3nhhnkwt2zeahnhiftt23yzlma
Frequent gene fissions associated with human pathogenic bacteria
2014
Genomics
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Gene fusion and fission events are important for evolutionary studies and for predicting protein-protein interactions. ...
In this project, the role of fusion and fission events in the genome evolution of 104 human bacterial pathogens was studied. 141 protein pairs were identified to be involved in gene fusion or fission events ...
contribution to the preliminary analysis of the bacterial sequences; Georgia Tsiliki for her technical support and her contribution to the statistical evaluation of the results; and George Diallinas for ...
doi:10.1016/j.ygeno.2014.02.001
pmid:24530517
fatcat:s45iprqjyjgzhfhkaywq6tgxjm
Large-scale identification of yeast integral membrane protein interactions
2005
Proceedings of the National Academy of Sciences of the United States of America
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The results identify potential previously undescribed components of established biological processes and roles for integral membrane proteins of ascribed functions. ...
To ascribe confidence levels to the interactions, we used a support vector machine algorithm to classify interactions based on the assay results and protein data derived from the literature. ...
Merz for critical reading of the manuscript; J. Hesselberth for assistance in the computational analysis; S. Thaminy for unpublished reagents; and T. Hazbun and S. McCraith for helpful discussions. ...
doi:10.1073/pnas.0505482102
pmid:16093310
pmcid:PMC1189342
fatcat:rpfigtb56vevrirky2usg455da
ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins
2019
PLoS Computational Biology
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This process resulted in a set of 358 fusion proteins and their corresponding protein interactions, as a training set for a Naïve Bayes classifier, to identify predicted fusion proteins that have reliable ...
Given that the two parental proteins for predicted fusion proteins are known, we used our previously developed method for identifying chimeric protein-protein interactions (ChiPPIs) associated with the ...
Dorith Raviv-Shay for proofreading the manuscript. We would like to thank Prof.Alfonso Valencia for his expertise and valuable discussions. We would also like to thank Dr. ...
doi:10.1371/journal.pcbi.1007239
pmid:31437145
pmcid:PMC6705771
fatcat:khvc73jyljdvjpjkkdbkyedgxa
A Comprehensive Approach Characterizing Fusion Proteins and Their Interactions Using Biomedical Literature
[article]
2018
bioRxiv
pre-print
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We classified 1817 unique fusion proteins and their corresponding 2908 protein-protein interactions for 18 cancer types. ...
The extracted fusion proteins and their protein-protein interactions are used as a training set for a Naive Bayes classifier that is further used for final identification of testing dataset, consisting ...
Dorith Raviv-Shay for proofreading the manuscript. Prof. Alfonso Valencia, Dr. ...
doi:10.1101/371088
fatcat:ce3wb4scovbeth5wl4yavqcsam
The comparative genomics of protein interactions
2007
Genome Informatics Series
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The detection of gene fusion events across genomes can be used for the prediction of functional associations of proteins, including physical interactions or complex formation. ...
In addition, we provide a set of predictions for functionally associated proteins across seven species using experimental information and demonstrate the applicability of fusion analysis for the comparative ...
Acknowledgments We thank members of the former Computational Genomics Group for discussions. ...
pmid:18546511
fatcat:bdsw4iv665dvzlnjuwpzqs2zfa
Computational epitope mapping of class I fusion proteins using Bayes classification
[article]
2022
bioRxiv
pre-print
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We introduce a novel method Accelerated class I fusion protein Epitope Mapping (AxIEM) that accounts for fusion protein flexibility to significantly improve out-of-sample prediction of discontinuous antibody ...
Harnessing data from previous experimental epitope mapping efforts of several class I fusion proteins, we demonstrate that accuracy of epitope prediction depends on residue environment and allows for the ...
J.M and J.C. contributed to the review of the manuscript. ...
doi:10.1101/2022.05.23.493016
fatcat:4yg6u25gqvgvvojiq2pgjcuoee
THE COMPARATIVE GENOMICS OF PROTEIN INTERACTIONS
2007
Genome Informatics 2007
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The detection of gene fusion events across genomes can be used for the prediction of functional associations of proteins, including physical interactions or complex formation. ...
In addition, we provide a set of predictions for functionally associated proteins across seven species using experimental information and demonstrate the applicability of fusion analysis for the comparative ...
Acknowledgments We thank members of the former Computational Genomics Group for discussions. ...
doi:10.1142/9781860949852_0012
fatcat:3qstibpgtjbgrf6v3atfqdqsii
Inference of Functional Relations in Predicted Protein Networks with a Machine Learning Approach
2010
PLoS ONE
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Methodology/Principal Findings: We have studied the possibility of constructing a classifier in order to combine the output of the several protein interaction prediction methods. ...
The large number of possible protein-protein interactions and complexes, the variety of environmental conditions and cellular states in which these interactions can be reorganized, and the multiple ways ...
Krallinger for critical reading of the manuscript.
Author Contributions ...
doi:10.1371/journal.pone.0009969
pmid:20376314
pmcid:PMC2848617
fatcat:m2mhfnsykbfdra3vgkudgrkgxi
THE COMPARATIVE GENOMICS OF PROTEIN INTERACTIONS
2007
Genome Informatics Series
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Acknowledgments We thank members of the former Computational Genomics Group for discussions. ...
O. thanks the UK Medical Research Council and IBM Research for additional support. ...
overlap, allows us to assess the extent of the conservation of interacting proteins and generate predictions of protein interactions for distantly related species. ...
doi:10.11234/gi1990.19.131
fatcat:3umodjwkjbgdjibie3tlct2q5q
Implications for domain fusion protein-protein interactions based on structural information
2004
BMC Bioinformatics
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We make use of this observation to improve domain fusion based protein interaction predictions, and demonstrate this by implementing it on a set of Saccharomyces cerevisiae proteins. ...
One of these methods is Domain Fusion, which has proven to be effective in predicting functional links between proteins. ...
We would also like to thank Dr Radha Krishna Murthy and Dr Li Yi for their valuable input. ...
doi:10.1186/1471-2105-5-161
pmid:15504241
pmcid:PMC529437
fatcat:oxrhlhcsgnd2rbmaae4ekkfic4
Classifying leukemia types with chromatin conformation data
2014
Genome Biology
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We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL ...
Conclusions: Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes. ...
Acknowledgements We thank Denis Paquette for excellent technical assistance and members of our laboratories for insightful discussions. ...
doi:10.1186/gb-2014-15-4-r60
pmid:24995990
pmcid:PMC4038739
fatcat:zejkqv7j2rgwzbshvqo6ommhwq
Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae
2010
BMC Systems Biology
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If such a hypothesis is correct for other species as well, similar methods can be applied to predict the roles of proteins in those species. ...
pairs with two and one gaps of Saccharomyces Cerevisiae's proteins, and their roles in the protein interaction network as non-hubs, intermediately connected, party hubs and date hubs. ...
Acknowledgements Authors would like to thank Professor Arne Elofsson for providing them with Repeated Domains data. This work was supported in part by a grant from NIGEB (No. 391) and IPM (No. ...
doi:10.1186/1752-0509-4-172
pmid:21167069
pmcid:PMC3018396
fatcat:pzjjsia5ubdn7goaisuy4ynxhu
Learning protein multi-view features in complex space
2013
Amino Acids
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Abstract Protein attribute prediction from primary sequences is an important task and how to extract discriminative features is one of the most crucial aspects. ...
Because single-view feature cannot reflect all the information of a protein, fusing multi-view features is considered as a promising route to improve prediction accuracy. ...
Acknowledgments The authors wish to thank the three anonymous reviewers whose constructive comments are very helpful for strengthening the presentation of this paper. ...
doi:10.1007/s00726-013-1472-6
pmid:23456487
fatcat:mozm24gjvvctdd2zxkb2yyfu6y
An ensemble of K-local hyperplanes for predicting protein-protein interactions
2006
Bioinformatics
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Prediction of protein-protein interaction is a difficult and important problem in biology. ...
A fusion of HKNN classifiers combined with the 'Sum rule' enables us to obtain an improvement over other state-of-the-art methods. ...
Martin at Sandia National Laboratories for sharing the datasets. The authors would like to thank O. Okun (University of Oulu, Finland) for sharing the HKNN code. ...
doi:10.1093/bioinformatics/btl055
pmid:16481334
fatcat:73ywsfluljartc7wwokqit7v4q
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