A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Filters
Identification of Essential Protein based on Functional Modules and Weighted Protein-Protein Interaction Networks
2016
International Journal of u- and e- Service, Science and Technology
Preserved Fulltext
In this paper, we propose a naive essential protein discovery method, named PMN, based on the integration of weighted interactome network and functional modules. ...
In this work we propose a new method, named PMN, for predicting essential proteins based on functional modules and weighted PPI networks. ...
For a protein pair of a weighted PPI network, the higher the weight is, the more likely the two proteins interact with each other. ...
doi:10.14257/ijunesst.2016.9.8.29
fatcat:2y6m4bxowzcy5bo7njngihk7t4
Identification of Essential Proteins Based on Ranking Edge-Weights in Protein-Protein Interaction Networks
2014
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Existing methods for essential protein identification generally rely on knock-out experiments and/or the relative density of their interactions (edges) with other proteins in a Protein-Protein Interaction ...
Here, we present a computational method, called EW, to first rank protein-protein interactions in terms of their Edge Weights, and then identify sub-PPI-networks consisting of only the highly-ranked edges ...
In this paper, we present a novel strategy for essential protein identification based on edge weights (EW) for ranking proteinprotein interactions within a PPI network. ...
doi:10.1371/journal.pone.0108716
pmid:25268881
pmcid:PMC4182551
fatcat:ywyzml2apncedkcdg32pvyfnwm
Rule-Based Pruning and In Silico Identification of Essential Proteins in Yeast PPIN
2022
Cells
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
In the initial phase, careful assessment is performed by applying node and edge weights to identify and discard the non-essential proteins from the interaction network. ...
The rule-based refinement is done using protein complex and local interaction density information derived from the neighborhood properties of proteins in the network. ...
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/cells11172648
pmid:36078056
pmcid:PMC9454873
fatcat:ca6zfijzkbbizh27z6uj5563wm
An Iteration Method for Identifying Yeast Essential Proteins from Weighted PPI Network based on topological and functional features of proteins
2020
IEEE Access
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Wang et al. established a method for the identification of key proteins based on the prediction of key protein-protein interactions based on comprehensive edge weights [7]. ...
Li et al.: Iteration Method for Identifying Yeast Essential Proteins From Weighted PPI Network efficient prediction methods to identify potential essential proteins [1]-[3]. ...
proteins and 7669 interactions including 714 essential proteins from the GAVIN database. ...
doi:10.1109/access.2020.2993860
fatcat:rqrwkshpb5aq3ivxcia433gskq
An Iterative Method for Identifying Essential Proteins based on Non-negative Matrix Factorization
2020
IEEE Access
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
In PMNMF, a weighted PPI network is first constructed by extracting the topological information of proteins from the original PPI network, and then, by applying the NMF method on the weighted PPI network ...
Chen B et al [11] proposed an essential protein identification method based on multiple topological structures of PPI networks. ...
Author Name: Preparation of Papers for IEEE Access (February 2017) VOLUME XX, 2017 ...
doi:10.1109/access.2020.3046254
fatcat:qsmdpdl26vc7xgkpmef3kxks7i
An iteration method for identifying yeast essential proteins from heterogeneous network
2019
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Large-scale protein-protein interaction (PPI) data sets exist in Saccharomyces cerevisiae, which provides us with a valuable opportunity to predict identify essential proteins from PPI networks. ...
In RWHN, a weighted protein-protein interaction network and a domain-domain association network are constructed according to the original PPI network and the known proteindomain association network, firstly ...
Authors' contributions BHZ, ZHZ and LW obtained the protein-protein interaction data, domain data, information on orthologous proteins and the localization information of proteins. ...
doi:10.1186/s12859-019-2930-2
fatcat:g34sursdsfb25lne45c5jis7de
Essential Proteins Discovery Methods based on the Protein-Protein Interaction Networks
2017
American Journal of Biochemistry and Biotechnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
In this study, we firstly have introduced the basic characteristics and data set of essential proteins and essential proteins discovery method in the Protein-Protein Interaction Networks. ...
With the development of highthroughput sequencing techniques, plenty of computational methods based on the Protein-Protein Interaction Networks have been put forward to identify essential proteins. ...
Funding Information
Ethics The authors declare their responsibility for any ethical issues that may arise after the publication of this manuscript. ...
doi:10.3844/ajbbsp.2017.242.251
fatcat:byeqnujohnhgdavpw2csa6ykva
A new method for predicting essential proteins based on participation degree in protein complex and subgraph density
2018
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Identification of essential proteins from proteinprotein interaction (PPI) networks can be applied to pathway analysis and function prediction, furthermore, it can contribute to disease diagnosis and drug ...
, and compared with the most recent method LBCC, PCSD can correctly predict more essential proteins from certain numbers of top ranked proteins on the DIP dataset, which indicates that PCSD is very effective ...
the identification accuracies of essential proteins were affected. ...
doi:10.1371/journal.pone.0198998
pmid:29894517
pmcid:PMC5997351
fatcat:ohafbg7i2vgwtjiqrzknmjf3tu
Identification of Essential Proteins Based on Improved HITS Algorithm
2019
Genes
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
With the development of high-throughput technologies, many protein–protein interaction (PPI) data are available, which facilitates the studies of essential proteins at the network level. ...
In this paper, we propose a novel method by applying Hyperlink-Induced Topic Search (HITS) on weighted PPI networks to detect essential proteins, named HSEP. ...
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/genes10020177
pmid:30823614
pmcid:PMC6409685
fatcat:abjkeozzpjbvxdmzorbc7kbp3a
An Effective Statistical Integrative Algorithm (Aeiapp) for Protein Prediction
2019
VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
The proposed integrative approach helps to extract essential proteins in protein-protein interaction network (PPI) by analyzing neighborhood of the active target protein. ...
Experimental results reviewed based on protein-protein interaction network for homosapiens showed that AEIAPP based approach shows an improvement in the essential protein identification by assuming the ...
PROPOSED METHODOLOGY: In this methodology of finding essential proteins from protein-protein interaction network, the dataset is collected from STRINGDB database. ...
doi:10.35940/ijitee.k1253.0981119
fatcat:rphtyhhhrnfldd3y67wqoyfldy
Method for Essential Protein Prediction Based on a Novel Weighted Protein-Domain Interaction Network
2021
Frontiers in Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
In WPDINM, a weighted PPI network is constructed first by combining the gene expression data of proteins with topological information extracted from the original PPI network. ...
In recent years a number of calculative models based on protein-protein interaction (PPI) networks have been proposed successively. ...
Step 2: Based on known PPIs and known protein-domain interactions (PDIs) downloaded from given benchmark databases, a weighted DDI network is then constructed. ...
doi:10.3389/fgene.2021.645932
pmid:33815480
pmcid:PMC8010314
fatcat:aiftpjogg5g6laalmq6jdlrt4e
A Novel Computational Approach for Identifying Essential Proteins From Multiplex Biological Networks
2020
Frontiers in Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Ever-increasing amounts of high-throughput data provide us with opportunities to detect essential proteins from protein interaction networks (PINs). ...
The identification of essential proteins can help in understanding the minimum requirements for cell survival and development. ...
The x-axis represents the proteins in protein-protein interaction (PPI) network ranked by MON and 11 other methods, ranked from left to right as strongest to weakest identification of essentiality. ...
doi:10.3389/fgene.2020.00343
pmid:32373163
pmcid:PMC7186452
fatcat:hcsoz5pyybh77atoyuisrpmxgq
Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies
2008
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
We introduce a new method that combines information about protein-interaction network properties and Gene Ontology terms. ...
The investigation uses the proteininteraction network for all essential immunome human genes available in the Immunome Knowledge Base and an analysis of their enriched gene ontology annotations. ...
Different networks, ranging from social interactions (33, 34) via protein-protein interactions (35, 36) to the spreading of epidemics (37) as well as human made networks like the Internet (38, 39) ...
doi:10.1093/nar/gkn982
pmid:19073697
pmcid:PMC2632920
fatcat:riw2rrqwcfexljyrg5sy7fhbc4
Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks
2019
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Detecting protein complex in protein-protein interaction (PPI) networks plays a significant part in bioinformatics field. ...
networks (MRDPNs) and discover the potential cores of protein complexes in MRDPNs. ...
Availability of data and materials The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. ...
doi:10.1186/s12859-019-2649-0
fatcat:qqbwocwf2zayzi6v4yb5cc6hza
Symmetry in cancer networks identified: Proposal for multi-cancer biomarkers
[article]
2019
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
In this study, proteomics data from seven major cancers were used to construct two weighted protein-protein interaction (PPI) networks i.e., one for the normal and another for the cancer conditions. ...
One of the most challenging problems in biomedicine and genomics is the identification of disease biomarkers. ...
Conflicts of interest Nothing to disclose. ...
arXiv:1910.01801v1
fatcat:sixwvpg5araxbeb7acv5rv2vmi
« Previous
Showing results 1 — 15 out of 121,386 results