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Computational Approaches for Transcription Factor Binding Prediction

Smitha CS, Saritha R
<span title="2014-05-16">2014</span> <i title="Foundation of Computer Science"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b637noqf3vhmhjevdfk3h5pdsu" style="color: black;">International Journal of Computer Applications</a> </i> &nbsp;
The prediction results may be useful for identification of putative binding sites.  ...  So computational approaches are used for the prediction of DNA protein interaction and the prediction results can be experimentally verified.  ...  Binding sites are usually based on DNA or RNA motif identification [13] . Features Used for Binding Site Prediction Binding affinity can be used as a strategy for prediction.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5120/16384-5969">doi:10.5120/16384-5969</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/36euotnhqrfeppamf52mqeglrm">fatcat:36euotnhqrfeppamf52mqeglrm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170706143500/http://research.ijcaonline.org/volume94/number11/pxc3895969.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/04/c0/04c0c99d5239fe1388434a2f29a1e377d7ebfdb6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5120/16384-5969"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group

Tzong-Yi Lee, Wen-Chi Chang, Justin Hsu, Tzu-Hao Chang, Dray-Ming Shien
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Although numerous computational methods have been developed for predicting transcriptional start sites (TSSs) or transcription factor (TF) binding sites (TFBSs), they lack annotations for do not consider  ...  Additionally, an input sequence can also be analyzed for homogeneity of experimental mammalian promoter sequences, and conserved regulatory features between homologous promoters can be observed through  ...  Acknowledgements We appreciate Professor Hsien-Da Huang for his expertise.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-s1-s3">doi:10.1186/1471-2164-13-s1-s3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22369687">pmid:22369687</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3587379/">pmcid:PMC3587379</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xi4guhr4hbbypn2sjpb2pjrkf4">fatcat:xi4guhr4hbbypn2sjpb2pjrkf4</a> </span>
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DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

Tianyin Zhou, Lin Yang, Yan Lu, Iris Dror, Ana Carolina Dantas Machado, Tahereh Ghane, Rosa Di Felice, Remo Rohs
<span title="2013-05-22">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
We present a method and web server for predicting DNA structural features in a high-throughput (HT) manner for massive sequence data.  ...  It requires only nucleotide sequence as input and instantly predicts multiple structural features of DNA (minor groove width, roll, propeller twist and helix twist).  ...  VALIDATION We compared DNA shape predictions for seven DNA binding sites that exhibit Fis-binding affinities differing by three orders of magnitude (6) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt437">doi:10.1093/nar/gkt437</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23703209">pmid:23703209</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3692085/">pmcid:PMC3692085</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/77vkh3hbvbdj3do3syju6e3qzq">fatcat:77vkh3hbvbdj3do3syju6e3qzq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20151028032830/http://rohslab.cmb.usc.edu:80/Papers/2013_NAR_DNAshape.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8b/f2/8bf23d99b3fccdef32b32cd7bfa5bd2407ac895c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt437"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692085" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Acquisition of Rule-based Knowledge for Analyzing DNA-binding Sites in Proteins

Shinn-Jang Ho, Chia-Yun Chang, Liang-Tsung Huang, Shiow Fen Hwang, Shinn-Ying Ho
<span title="">2007</span> <i title="ICST"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ulydn26jlrc3hndxine2tszkoa" style="color: black;">Proceedings of the 2nd International ICST Conference on Scalable Information Systems</a> </i> &nbsp;
in prediction of binding sites.  ...  For mining accurate and interpretable knowledge, a large-scale dataset consisting of 982 DNA-binding proteins is constructed.  ...  The extracted rules can reveal what the significant features are for prediction of binding sites and realize the relationship between DNA and protein structures.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4108/infoscale.2007.972">doi:10.4108/infoscale.2007.972</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/infoscale/HoCHHH07.html">dblp:conf/infoscale/HoCHHH07</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s5gg2r5oj5f25n6eb5wgexot6q">fatcat:s5gg2r5oj5f25n6eb5wgexot6q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429021129/https://eudl.eu/pdf/10.4108/infoscale.2007.972" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/92/54/92546dad844231af08685403694a7baef76e1f24.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4108/infoscale.2007.972"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein–DNA binding

Tsu-Pei Chiu, Satyanarayan Rao, Richard S. Mann, Barry Honig, Remo Rohs
<span title="2017-10-11">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
the direct role of EP in protein-DNA binding using massive sequencing data.  ...  Protein-DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome.  ...  The authors thank Lin Yang for providing preprocessed HT-SELEX data and Federico Comoglio for contributions to DNAshapeR.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx915">doi:10.1093/nar/gkx915</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29040720">pmid:29040720</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5716191/">pmcid:PMC5716191</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rua2cuxscvaunldufyu3ymmvou">fatcat:rua2cuxscvaunldufyu3ymmvou</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222225353/http://pdfs.semanticscholar.org/3ba2/af5f354a87dafa766f5b18bc24d1a7a21eab.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3b/a2/3ba2af5f354a87dafa766f5b18bc24d1a7a21eab.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx915"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716191" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational tools for protein-DNA interactions

Christopher Kauffman, George Karypis
<span title="2011-11-02">2011</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/agmngghlr5hyrpto64zks3fhry" style="color: black;">Wiley Interdisciplinary Reviews Data Mining and Knowledge Discovery</a> </i> &nbsp;
A wide range of topics is covered including physics-based models for direct and indirect recognition, identification of transcription factor binding sites, and methods to predict DNA-binding proteins.  ...  Our goal is to introduce this important problem domain to data mining researchers by identifying the key issues and challenges inherent to the area as well as provide directions for fruitful future research  ...  Features of both the genome binding site (DNA sequence) and the protein are used to train classifier for each TF family.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/widm.48">doi:10.1002/widm.48</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/teuqk5c56zaufkralr3xk6ivgm">fatcat:teuqk5c56zaufkralr3xk6ivgm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120124182550/http://glaros.dtc.umn.edu/gkhome/fetch/papers/DNASurveyWIRE2011.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/07/53/0753c371b6cd1f5fc59a2397eb708c3afe5ec84f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/widm.48"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

An Overview of the Prediction of Protein DNA-Binding Sites

Jingna Si, Rui Zhao, Rongling Wu
<span title="2015-03-06">2015</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading.  ...  In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods  ...  Author Contributions Jingna Si designed the study, performed the literature mining, and drafted the manuscript. Rui Zhao and Rongling Wu read and revised the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms16035194">doi:10.3390/ijms16035194</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25756377">pmid:25756377</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4394471/">pmcid:PMC4394471</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/syzihxgpqvfj7o5hwx4nbgcj7q">fatcat:syzihxgpqvfj7o5hwx4nbgcj7q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150927065012/http://www.mdpi.com/1422-0067/16/3/5194/pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/92/28/92288beb279aa50b4acc24fadd71f514c8534e26.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms16035194"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394471" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bridging protein local structures and protein functions

Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen
<span title="2008-04-18">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/spfkqu35dnd7rjl5ooxt2ihb4q" style="color: black;">Amino Acids</a> </i> &nbsp;
We also discuss remaining problems and possible directions for this exciting and challenging area.  ...  One of the major goals of molecular and evolutionary biology is to understand the functions of proteins by extracting functional information from protein sequences, structures and interactions.  ...  The authors are grateful to the anonymous referees as well as editors for comments and for helping to improve the earlier version.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00726-008-0088-8">doi:10.1007/s00726-008-0088-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18421562">pmid:18421562</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/micrifjcrfetnafnm4fx45ouom">fatcat:micrifjcrfetnafnm4fx45ouom</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200321152145/http://zhangroup.aporc.org/images/files/aminoacidweb.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c9/53/c9532d4fdff5aea4044eba3830c6854ee1c4acfa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00726-008-0088-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Locating transcription factor binding sites by fully convolutional neural network

Qinhu Zhang, Siguo Wang, Zhanheng Chen, Ying He, Qi Liu, De-Shuang Huang
<span title="2021-01-26">2021</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
In recent years, an increasing number of deep learning (DL) based methods have been proposed for predicting TF binding sites (TFBSs) and achieved impressive prediction performance.  ...  However, these methods mainly focus on predicting the sequence specificity of TF-DNA binding, which is equivalent to a sequence-level binary classification task, and fail to identify motifs and TFBSs accurately  ...  Key Points • In the task of predicting transcription factor binding sites (TFBSs), most of methods based on deep learning mainly focus on predicting the sequence specificity of TF-DNA binding and fail  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbaa435">doi:10.1093/bib/bbaa435</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33498086">pmid:33498086</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8425303/">pmcid:PMC8425303</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n6khq5iz2jestocmm44ho2dvwm">fatcat:n6khq5iz2jestocmm44ho2dvwm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210130073502/https://watermark.silverchair.com/bbaa435.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAArMwggKvBgkqhkiG9w0BBwagggKgMIICnAIBADCCApUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMFwpwwZz6t7rLVboxAgEQgIICZnja5E0607gV4e3PC5CYOoOzt_wnKVsQYeVZoZMybsokf4KwXXQU6xjxq8y2jz05WBRTiL9qhxqNEpWJ9u3ic9yKSad4JyLJ3-sn1u1aIQjuxgflClQVoszeg4tvTK39MfHy8gZ_LT8NC0zDWnt4eFwaTE2FCrvFJ8xFsP16xTz-kcprmAQgowHWCAVo_6CwwxdqwfEO-Oqq6yHfMge1MBkB91Z2lPKFYB24isYOU5AGuBhBX3DnYNpwYh3avi1GVfv5iW3z85lrY_1HmMxxqXvYQC6KgH9tDBgEu9WmrzizYAWwtpVjvOzIwaj0CaJHDiO4pZAaNZElcF8AuaK4h2SOhX8BfUUQHdNYHye-YW8pRfB_74JjXdMhOaQsy3PY0aa8nPrgLWmzFMaRIeRpyWcBZKynX07elSl9wQ-rr-ys5gYhULz3FgGXKeIiI6Xhk2tn5gb-4__SZpm-sK4Znjl__QxS0LDP3wtpkBun01q5TQKNOWG2fmZ2_UohI_xl__m0kQ7-6qeIarkNsJC-FfJjgU3VF8LA7ebswxw0cEFQMsZ7EXQqihlQYQVThZIlOIpDI32lGvvFnhIf--0GhrGX0oF15ImUZ1YsSXosY-do2zx_7M3Df7lNspgQ0F039KTa5BjeowRFzVlL7W4ISg320gvL3Pk_iUxozXmxJMqAe4VWd496t8QN8Pr400QMdfURa-Lvm1MOTmMVB5k3DzFcSAVrSYTD23FYfXNdtDyW8aSNALBlLYya_P3YUJL8L7HHOk8y29Kp3MgYL5iAg8SCms4T2CytHEyvlI9rwfy582o1-c06" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/86/c5/86c56bcb2109f872f0bdb4a5f2d1d91d59ededde.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbaa435"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8425303" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

GBshape: a genome browser database for DNA shape annotations

Tsu-Pei Chiu, Lin Yang, Tianyin Zhou, Bradley J. Main, Stephen C.J. Parker, Sergey V. Nuzhdin, Thomas D. Tullius, Remo Rohs
<span title="2014-10-17">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
predictions for the entire genomes of 94 organisms.  ...  Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif.  ...  ACKNOWLEDGEMENTS The authors thank Iris Dror for her initial work on the TSS analysis and valuable comments on the manuscript, and Luigi Manna for the setup and maintenance of the Rohs lab servers and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku977">doi:10.1093/nar/gku977</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25326329">pmid:25326329</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4384032/">pmcid:PMC4384032</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e4rub2w52ncbzgdqnvobhtjh6i">fatcat:e4rub2w52ncbzgdqnvobhtjh6i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305091445/http://pdfs.semanticscholar.org/c750/4742def3da09ba322fd2a02d1699152c347d.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c7/50/c7504742def3da09ba322fd2a02d1699152c347d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku977"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384032" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites

<span title="2020-01-08">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The structural profiles for each TFBS entry now include 13 shape features and minor groove electrostatic potential for standard DNA and four shape features for methylated DNA.  ...  TFBSshape (https://tfbsshape.usc.edu) is a motif database for analyzing structural profiles of transcription factor binding sites (TFBSs).  ...  The feature values were predicted using our R/Bioconductor package DNAshapeR (45), where DNA shape features are derived from data mining of trajectories from all-atom Monte Carlo (MC) simulations for DNA  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz970">doi:10.1093/nar/gkz970</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31665425">pmid:31665425</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7145579/">pmcid:PMC7145579</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sh4xvrr4nrg4xjlzk4x2odou6y">fatcat:sh4xvrr4nrg4xjlzk4x2odou6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200512165007/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7145579&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8b/ba/8bba522865bd4a76b14ee88c0465a7356e6f8c2b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz970"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145579" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Mining the Association Rules of Transcription Factor Binding Sites in Human Tandem Repeats Using Aprior Algorithm

Zhong yu Liu
<span title="">2009</span> <i title="OMICS Publishing Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cfj7yw2qavhc5f35je6wes764m" style="color: black;">Journal of computer science and systems biology</a> </i> &nbsp;
Herein, the combinations of transcription factor binding sites in the tandem repeats are obtained and, then, data mining techniques are applied to mine the association rules from the combinations of binding  ...  This study attempts to mine rules on how combinations of individual binding sites are distributed tandem repeats in human genome (http://www.trbase2.cn).  ...  Data Mining Association rule mining for TF binding sites in tandem repeats Association rule mining and Agrawal and Srikanth, (1993) algorithm Association rule mining is important for extracting knowledge  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/jcsb.1000030">doi:10.4172/jcsb.1000030</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xylssnv445eyjpmeldfeskvphe">fatcat:xylssnv445eyjpmeldfeskvphe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170705125207/https://www.omicsonline.com/ArchiveJCSB/2009/June/01/JCSB2.180.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/94/2f/942f3e25379853f2305424f2c915829970ec62e9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/jcsb.1000030"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

Satyanarayan Rao, Tsu-Pei Chiu, Judith F. Kribelbauer, Richard S. Mann, Harmen J. Bussemaker, Remo Rohs
<span title="2018-02-06">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t46dy4kadfdgbm52javmafxiyy" style="color: black;">Epigenetics &amp; Chromatin</a> </i> &nbsp;
Roll and propeller twist were the DNA shape features most strongly affected by CpG methylation with an effect size depending on the local sequence context.  ...  Four DNA shape features-helix twist, minor groove width, propeller twist, and roll-were considered in this analysis. Distinct distributions of effect size were observed for different features.  ...  Acknowledgements The authors thank all members of the Mann, Bussenmaker, and Rohs laboratories for valuable input.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13072-018-0174-4">doi:10.1186/s13072-018-0174-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29409522">pmid:29409522</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5800008/">pmcid:PMC5800008</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ubgb6mzw4zh3xiyvunpskooyem">fatcat:ubgb6mzw4zh3xiyvunpskooyem</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180620202157/https://mannlab.zuckermaninstitute.columbia.edu/sites/default/files/content/s13072-018-0174-4.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f9/cb/f9cbf840ae7ede736e896b3cba49d89c5f5d24b2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13072-018-0174-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5800008" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

STIFDB2: An Updated Version of Plant Stress-Responsive TranscrIption Factor DataBase with Additional Stress Signals, Stress-Responsive Transcription Factor Binding Sites and Stress-Responsive Genes in Arabidopsis and Rice

Mahantesha Naika, Khader Shameer, Oommen K. Mathew, Ramanjini Gowda, Ramanathan Sowdhamini
<span title="2013-01-10">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qyzgzqbtjbd3xewtgies5bhl2e" style="color: black;">Plant and Cell Physiology</a> </i> &nbsp;
We have employed an integrated biocuration and genomic data mining approach to characterize the data set of transcription factors and consensus binding sites from literature mining and stress-responsive  ...  STIFDB2 currently has 38,798 associations of stress signals, stress-responsive genes and transcription factor binding sites predicted using the Stress-responsive Transcription Factor (STIF) algorithm,  ...  The authors thank University of Agricultural Sciences (Bangalore) and National Centre for Biological Sciences, Tata  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/pcp/pcs185">doi:10.1093/pcp/pcs185</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23314754">pmid:23314754</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3583027/">pmcid:PMC3583027</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bwqhyjponngx5mougabjfxyysa">fatcat:bwqhyjponngx5mougabjfxyysa</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3583027/PMC3583027-pcs185.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/73/e6/73e600560529bd3bc8862982df833eb24c5009ed.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/pcp/pcs185"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583027" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

28 GBshape: a genome browser database for DNA shape annotations

Tsu-Pei Chiu, Lin Yang, Tianyin Zhou, Bradley J. Main, Stephen C.J. Parker, Sergey V. Nuzhdin, Thomas D. Tullius, Remo Rohs
<span title="2015-05-18">2015</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kfwansfrvzehjdbhmp2vk4gr3e" style="color: black;">Journal of Biomolecular Structure and Dynamics</a> </i> &nbsp;
ACKNOWLEDGEMENTS The authors thank Iris Dror for her initial work on the TSS analysis and valuable comments on the manuscript, and Luigi Manna for the setup and maintenance of the Rohs lab servers and  ...  Prediction of DNA shape features from nucleotide sequence is based on high-throughput methods for deriving DNA shape features, by using pentamers to mine results from all-atom Monte Carlo simulations of  ...  a database of DNA shape features of transcription factor binding site motifs (22) , and ORChID, a database and prediction tool for hydroxyl radical cleavage patterns (17, 18) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/07391102.2015.1032568">doi:10.1080/07391102.2015.1032568</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xg5grhat6ngxvmlkuugfvii3bq">fatcat:xg5grhat6ngxvmlkuugfvii3bq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428144355/https://open.bu.edu/bitstream/handle/2144/30783/gku977.pdf;jsessionid=8BC45C71CB57FF593A709D6752608EFC?sequence=2" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ad/b2/adb2674b646cfbc4cb604c3498d79af3ff0fd9b7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/07391102.2015.1032568"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> tandfonline.com </button> </a>
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