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COMBINING TEXT MINING AND SEQUENCE ANALYSIS TO DISCOVER PROTEIN FUNCTIONAL REGIONS

E. ESKIN, E. AGICHTEIN
2003 Biocomputing 2004  
and annotations ÙÖ ½ Ö Ñ ÛÓÖ ÓÖ ÜØ Ò Ò Ò ÓÑ Ò Ò Ì ÜØÙ Ð ÒÒÓØ Ø ÓÒ× Û Ø Ë ÕÙ Ò Ø º Ì × × × Ñ Ð Ö ØÓ Ø ÛÓÖ Ý AE Ö Ò ÊÓ×ظ¾¼¼¾ Û Ö Ø Ý × ÓÛ Ø Ø × ÕÙ Ò ÓÑÓÐÓ Ý Ò Ù× ØÓ ÔÖ Ø ÐÓ Ð Þ Ø ÓÒº Ò ÐÐÝ Û Ø Ò Ù× Ø  ...  Ò AE Ö Ò ÊÓ×ظ¾¼¼¾ º Ì × « Ø Ú ÐÝ Ù Ñ ÒØ× Ø × × Ø Ó Ð Ð × ÕÙ Ò × Û Ø Ð Ö Ö × Ø Ó × ÕÙ Ò × Û Ø ÔÖ Ø ÐÓ Ð Þ Ø ÓÒ׺ Ï Ø Ò Ó ÒØÐÝ Ð ÖÒ × ÕÙ Ò Ò Ø ÜØ Ð ×× ¬ Ö ÓÚ Ö Ø ÜØ Ò Ø × Øº Predict class of unlabeled sequences  ... 
doi:10.1142/9789812704856_0028 fatcat:2ymfceblhnc4lpwhdzp6wqrszu

Pattern Recognition in Bioinformatics: An Introduction [chapter]

J. C. Rajapakse, L. Wong, R. Acharya
2006 Lecture Notes in Computer Science  
Research on detecting specific patterns of DNA sequences such as genes, protein coding regions, promoters, etc., leads to uncover functional aspects of cells.  ...  The knowledge in databases of biomedicine and phenotypes, combined with genotypes, is increasingly unmanageable by traditional text-based methods.  ...  of sequences: DNA, protein, structures, etc. • Phylogenic analysis of species, sequences, structures • Structural genomics and proteomics • Functional and molecular imaging • Data mining, data integration  ... 
doi:10.1007/11818564_1 fatcat:ybz5p7nghjcedlzzgleqxv53sq

Survey of Natural Language Processing Techniques in Bioinformatics

Zhiqiang Zeng, Hua Shi, Yun Wu, Zhiling Hong
2015 Computational and Mathematical Methods in Medicine  
Then, we analyze the applications of text mining and natural language processing techniques in bioinformatics, including predicting protein structure and function, detecting noncoding RNA.  ...  First, we aim to search for knowledge on biology, retrieve references using text mining methods, and reconstruct databases.  ...  The structural analysis of protein mainly focuses on certain protein sequences and classifies regions into the -helix, -lamella, and protein disordered regions.  ... 
doi:10.1155/2015/674296 pmid:26525745 pmcid:PMC4615216 fatcat:z4txhlt4jfhmtlaje4mbrdnxme

The next generation of literature analysis: Integration of genomic analysis into text mining

M. Scherf, A. Epple, T. Werner
2005 Briefings in Bioinformatics  
and text to discover relations or biological concepts is still a challenge.  ...  TEXT MINING IN MOLECULAR BIOLOGY AND BIOMEDICINE Text mining deals with the analysis of text and the extraction of information.  ... 
doi:10.1093/bib/6.3.287 pmid:16212776 fatcat:bccqazrfmfez5evzv4xbg34kou

wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases

Jose MG Izarzugaza, Miguel Vazquez, Angela del Pozo, Alfonso Valencia
2013 BMC Bioinformatics  
This research was supported by OpenPhacts European project (115191-2) and Spanish Ministry of Science and Innovation project BIO2007-6685  ...  Acknowledgements The authors thank the members of the Structural Biology and Biocomputing Programme (CNIO), especially A. Rausell, D. Juan, I. Ezkurdia and T.  ...  Briefly, iHOP is a powerful text mining system to automatically extract protein protein interactions from PubMed abstracts.  ... 
doi:10.1186/1471-2105-14-345 pmid:24289158 pmcid:PMC3879071 fatcat:wblb72yq5nelnlseujbysgukgy

Big Data and Network Biology 2015

Shigehiko Kanaya, Md. Altaf-Ul-Amin, Samuel K. Kiboi, Farit Mochamad Afendi
2015 BioMed Research International  
Acknowledgments Our heartfelt thanks are due to authors for their excellent and fundamental contributions and their patience in communicating with us.  ...  Finally we acknowledge the dedicated works of all reviewers of these papers for their critical and helpful comments.  ...  The paper "Discovering Distinct Functional Modules of Specific Cancer Types Using Protein-Protein Interaction Networks" proposes a new graph theory based method to identify distinct functional modules  ... 
doi:10.1155/2015/604623 pmid:26609530 pmcid:PMC4644560 fatcat:vykzxrxdejcbzeot3nuprgcz4u

ProFAT: a web-based tool for the functional annotation of protein sequences

Charles Richard Bradshaw, Vineeth Surendranath, Bianca Habermann
2006 BMC Bioinformatics  
ProFAT combines sensitive sequence database search methods and a fold recognition algorithm with a simple text-mining approach.  ...  The functional annotation of proteins relies on published information concerning their close and remote homologues in sequence databases.  ...  We thank Andreas Henschel for MOSIX-related advice and furthermore thank Sabine Bernauer and Michael Volkmer for critical reading of the manuscript. This work was supported by the Max Planck Society.  ... 
doi:10.1186/1471-2105-7-466 pmid:17059594 pmcid:PMC1636073 fatcat:tsdru2b465cvzgrvnxtmf6ycve

Combining literature text mining with microarray data: advances for system biology modeling

A. Faro, D. Giordano, C. Spampinato
2011 Briefings in Bioinformatics  
Finally, an easy to use and freely accessible tool, GeneWizard, that exploits text mining and microarray data fusion for supporting researchers in discovering gene^disease relationships is described.  ...  Under this scenario, this article reviews the knowledge discovery systems that fuse information from the literature, gathered by text mining, with microarray data for enriching the lists of down and upregulated  ...  The detected molecular functions are used to identify a sequence of DNA by querying the RefSeq protein database.  ... 
doi:10.1093/bib/bbr018 pmid:21677032 fatcat:lvtg7ea74ngb5h6i2ywss6cjru

A Novel Approach for Predicting Disordered Regions in A Protein Sequence

Meijing Li, Seong Beom Cho, Keun Ho Ryu
2014 Osong Public Health and Research Perspectives  
Second, the disordered and ordered regions in a protein sequence were predicted by searching the generated emerging protein subsequence with a sliding window, which tends to overlap.  ...  We first adapted the approach to generate emerging protein subsequences on public protein sequence data.  ...  Therefore, finding the protein disordered regions helps to study functions of proteins [2] .  ... 
doi:10.1016/j.phrp.2014.06.006 pmid:25379372 pmcid:PMC4215001 fatcat:mj2sdcfsifaotp2u5ldlsor2wi

Investigation of data mining technique and artificial intelligence algorithm in microflora bioinformatics

Huixing Li, Yan Xue, Xiancai Zeng, M.S. Tahir, L. Xing
2021 E3S Web of Conferences  
, genetic data analysis, and protein structure and function prediction.  ...  Furthermore, typical applications in bioinformatics are discussed in terms of gene expression data analysis, genome sequence information analysis, biological sequence difference and similarity analysis  ...  Data analysis and mining objects include structured data, text, Web data, multimedia data, social network data, etc. The mining methods are mainly classified and clustered through machine learning.  ... 
doi:10.1051/e3sconf/202126701040 fatcat:rktiwri365e2lo3xwf3kdmy454

A combined approach to data mining of textual and structured data to identify cancer-related targets

Pavel Pospisil, Lakshmanan K Iyer, S James Adelstein, Amin I Kassis
2006 BMC Bioinformatics  
The proposed data mining strategy is of a general nature and can be applied to other biological databases for understanding biological functions and diseases.  ...  Our combined strategy applied to each cancer type identified a minimum of 375 proteins expressed within the extracellular space and/or attached to the plasma membrane.  ...  Prostate Cancer, and W81XWH-06-1-0204, Radiodiagnosis and Radiotherapy of Ovarian Cancer.  ... 
doi:10.1186/1471-2105-7-354 pmid:16857057 pmcid:PMC1555615 fatcat:4ug3qfv7gfcv7cxhjol4chc64u

Probing the Peculiarity of EhRabX10, a pseudoRab GTPase, from the Enteric Parasite Entamoeba histolytica through In Silico Modeling and Docking Studies

Mrinalini Roy, Sanket Kaushik, Anupam Jyoti, Vijay Kumar Srivastava, Prasanth Manohar
2021 BioMed Research International  
Here, we provide insights into a pseudoRab GTPase, EhRabX10, by performing physicochemical analysis, predictive 3D structure modeling, protein-protein interaction studies, and in silico molecular docking  ...  These cysts are the infective agent and help to spread the disease.  ...  0.708 Coexpression, text mining Yes EHI_014310 Calcium-gated potassium channel protein, putative 0.675 Coexpression, text mining No EHI_187770 SH3 domain protein 0.670 Coexpression, text mining  ... 
doi:10.1155/2021/9913625 pmid:34660804 pmcid:PMC8514894 fatcat:usxmlckybzbdvoc3iq7r6z53ju

Integrative data mining: the new direction in bioinformatics

P. Bertone, M. Gerstein
2001 IEEE Engineering in Medicine and Biology Magazine  
Functional Genomics and Microarray Technology With the introduction of complete genome sequences, much comprehensive functional analysis has been done on the proteins encoded by an organism's genome.  ...  Integrative database analysis and data mining are essential aspects of modern biology, enabling the synthesis of large-scale portraits of genome function.  ...  , gene expression analysis, and Bayesian systems for data mining.  ... 
doi:10.1109/51.940042 pmid:11494767 fatcat:kh4u7xxslve4ddmnkwurjmayp4

Candidate Gene Predictions: Bioinformatics Significance in Linkage Analysis

2015 International Journal of Science and Research (IJSR)  
In this context, the common criterion for in-silico candidate-gene identification relies on gene ontology, protein-protein interaction, sequence based features, functional annotation, data mining, and  ...  In addition to improve the disease-causing genes identification, development of disease-predicting software by incorporating existing data (wet-lab) will be a straightforward and effective step.  ...  Genes involved in pathway and gene ontology are identified by a combined analysis of integrated approach [26] , text-and data-mining integrated method [27] , and genetic maps and QTL combined analysis  ... 
doi:10.21275/v4i11.sub15940 fatcat:bafcil632vhgvg75rftlvijqhi

Contribution of a Novel B3GLCT Variant to Peters Plus Syndrome Discovered by a Combination of Next-Generation Sequencing and Automated Text Mining

Justyna Totoń-Żurańska, Przemysław Kapusta, Magda Rybak-Krzyszkowska, Katarzyna Lorenc, Julita Machlowska, Anna Skalniak, Erita Filipek, Dorota Pawlik, Paweł P. Wołkow
2019 International Journal of Molecular Sciences  
We suggest that the implementation of automatic text mining tools in combination with careful variant filtering could help translate sequencing results into diagnosis, thus, considerably accelerating the  ...  Here, we used AMELIE, an automatic text mining tool that enriches data with the most up-to-date information from literature, and wANNOVAR, which is based on well-documented databases and incorporates variant  ...  , using data from DNA sequencing of coding regions of 4813 genes in both parents and the affected child.  ... 
doi:10.3390/ijms20236006 pmid:31795264 pmcid:PMC6928627 fatcat:qswwecx4ojdhlffx3dkfspncwa
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