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An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs

Fernando Garcia-Alcalde, Armando Blanco, Adrian J Shepherd
2010 BMC Bioinformatics  
Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs).  ...  Here we present a new method for matching sequences to TFBS motifs based on intuitionistic fuzzy sets (IFS) theory, an approach that has been shown to be particularly appropriate for tackling problems  ...  Acknowledgements We would like to thank the anonymous reviewers for their helpful comments which significantly improved the quality of the paper.  ... 
doi:10.1186/1471-2105-11-551 pmid:21059262 pmcid:PMC3098096 fatcat:znu63tm5d5bcvgc7ukr4tw4via

Structural insights into the inhibition of bacterial RecA by naphthalene polysulfonated compounds

Ziyuan Zhou, Qing Pan, Xinchen Lv, Jing Yuan, Yang Zhang, Ming-Xia Zhang, Ming Ke, Xiao-Mei Mo, Yong-Li Xie, Yingxia Liu, Ting Chen, Mingchan Liang (+7 others)
2020 iScience  
For validation, we generated recombinant RecA proteins (wild-type versus Y103 mutant) to determine the binding affinities for RecA protein interactions with suramin and underexamined NPS in isothermal  ...  The corresponding dissociation constants (K d) ranged from 11.5 to 18.8 μM, and Y103 was experimentally shown to be critical to RecA-NPS interactions.  ...  In contrast, those compounds determined to lack inhibitory activities against RecA (cpd05-cpd08) have the lowest binding scores.  ... 
doi:10.1016/j.isci.2020.101952 pmid:33458611 pmcid:PMC7797525 fatcat:gculd63pincspo6rxbweloqrb4

De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese Endemic Acer miaotaiense (Aceraceae)

Xiang Li, Meng Li, Lu Hou, Zhiyong Zhang, Xiaoming Pang, Yingyue Li
2018 Genes  
Because of the lack of genomic information and the limited number of available molecular markers, there are insufficient tools to determine the genetic diversity of this species.  ...  Furthermore, 12,819 expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were generated, 300 were randomly selected and synthesized, 19 primer pairs were identified as highly polymorphic  ...  In addition, the PIC values for all of the loci ranged from 0.147 (BFAM-254) to 0.820 (BFAM-219), with an average of 0.604, and 14 of 19 loci had highly informative scores (PIC > 0.50) ( Table 2) .  ... 
doi:10.3390/genes9080378 pmid:30060522 fatcat:s3j6jzkdhveqxfjgzz3bsswtq4

EMBnet.journal 18 Suppl. B

EMBnet Journal
2012 EMBnet journal  
that alter the binding affinity of transcription factor binding sites (TFBS), which have been shown to play an important role in the regulatory machinery of the cell.  ...  (Bryne et al, 2008 ) PFAM TFBS (Transcription Factor Binding Sites) matrix for any resequenced region in the database.  ...  It is now well known that tumors may arise as a result of a series of DNA sequence abnormalities and mutations.  ... 
doi:10.14806/ej.18.b.592 fatcat:wlwsmbdlfzbjtk7vyhiabdov6q

Affilin® binding proteins selected against a class B GPCR ectodomain [article]

Bo Song, Universitäts- Und Landesbibliothek Sachsen-Anhalt, Martin-Luther Universität, Lilie, Hauke, Dr., Kolmar, Harald, Prof. Dr., Fändrich, Marcus, Dr.
An avidin with reversible binding characteristics has been created by nitration or iodination of the binding site tyrosine.  ...  binding sites on scaffolds.  ...  According to the cooperation agreements, parts of this thesis will be allowed to publish after the application of concerned patent, which is now in progress. Poster: Song, B., Hoffmann, A., Kunert  ... 
doi:10.25673/655 fatcat:tmg4vetdkzcyphomrmdczjyhpy

Lisbon, Portugal BIOTECHNO 2013 Editors BIOTECHNO 2013 Committee BIOTECHNO Advisory Chairs BIOTECHNO 2013 Technical Program Committee

Hesham Ali, Stephen Anthony, Stephen Anthony, Basim Alhadidi, Albalqa, Stephen Anthony, Siegfried Benkner, Tom Bersano, Christian Blum, Cesar German, Castellanos Dominguez, Rolf Drechsler (+31 others)
Bioinformatics deals with the system-level study of complex interactions in biosystems providing a quantitative systemic approach to understand them and appropriate tool support and concepts to model them  ...  The focus is driven by fundamentals in approaching and applying biotechnologies in terms of engineering methods, special electronics, and special materials and systems.  ...  [11] where they combined the promoter sequence motifs with gene expression profiles to infer transcriptional modules.  ... 

Informational Space of Meaning for Scientific Texts [article]

Neslihan Suzen, Evgeny M. Mirkes, Alexander N. Gorban
2020 arXiv   pre-print
This new approach is applied to construct the Meaning Space based on Leicester Scientific Corpus (LSC) and Leicester Scientific Dictionary-Core (LScDC).  ...  In Natural Language Processing, automatic extracting the meaning of texts constitutes an important problem.  ...  This paper aims to propose an approach to computational analysis of meaning for a large family of texts.  ... 
arXiv:2004.13717v1 fatcat:jhhwyxgb2zcmpelaovrprgbkqi