A Systems Biology Approach to Transcription Factor Binding Site Prediction

PLoS ONE ◽

10.1371/journal.pone.0009878 ◽

2010 ◽

Vol 5 (3) ◽

pp. e9878 ◽

Author(s):

Xiang Zhou ◽

Pavel Sumazin ◽

Presha Rajbhandari ◽

Andrea Califano

Keyword(s):

Transcription Factor ◽

Systems Biology ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Site Prediction ◽

Factor Binding ◽

Binding Site Prediction

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The Next Generation of Transcription Factor Binding Site Prediction

PLoS Computational Biology ◽

10.1371/journal.pcbi.1003214 ◽

2013 ◽

Vol 9 (9) ◽

pp. e1003214 ◽

Author(s):

Anthony Mathelier ◽

Wyeth W. Wasserman

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Next Generation ◽

Factor Binding Site ◽

Site Prediction ◽

Factor Binding ◽

Binding Site Prediction

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Evaluating tools for transcription factor binding site prediction

BMC Bioinformatics ◽

10.1186/s12859-016-1298-9 ◽

2016 ◽

Vol 17 (1) ◽

Author(s):

Narayan Jayaram ◽

Daniel Usvyat ◽

Andrew C. R. Martin

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Site Prediction ◽

Factor Binding ◽

Binding Site Prediction

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Enhancing the interpretability of transcription factor binding site prediction using attention mechanism

Scientific Reports ◽

10.1038/s41598-020-70218-4 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Sungjoon Park ◽

Yookyung Koh ◽

Hwisang Jeon ◽

Hyunjae Kim ◽

Yoonsun Yeo ◽

...

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Attention Mechanism ◽

Factor Binding Site ◽

Site Prediction ◽

Factor Binding ◽

Binding Site Prediction

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SiTaR: a novel tool for transcription factor binding site prediction

Bioinformatics ◽

10.1093/bioinformatics/btr492 ◽

2011 ◽

Vol 27 (20) ◽

pp. 2806-2811 ◽

Author(s):

Eugen Fazius ◽

Vladimir Shelest ◽

Ekaterina Shelest

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Site Prediction ◽

Factor Binding ◽

Binding Site Prediction

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Probabilistic Approaches to Transcription Factor Binding Site Prediction

Methods in Molecular Biology - Computational Biology of Transcription Factor Binding ◽

10.1007/978-1-60761-854-6_7 ◽

2010 ◽

pp. 97-119 ◽

Author(s):

Stefan Posch ◽

Jan Grau ◽

André Gohr ◽

Jens Keilwagen ◽

Ivo Grosse

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Site Prediction ◽

Factor Binding ◽

Binding Site Prediction

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The Motif Tool Assessment Platform (MTAP) for Sequence-Based Transcription Factor Binding Site Prediction Tools

Methods in Molecular Biology - Computational Biology of Transcription Factor Binding ◽

10.1007/978-1-60761-854-6_8 ◽

2010 ◽

pp. 121-141 ◽

Author(s):

Daniel Quest ◽

Hesham Ali

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Site Prediction ◽

Factor Binding ◽

Binding Site Prediction ◽

Prediction Tools

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A novel method for improved accuracy of transcription factor binding site prediction

Nucleic Acids Research ◽

10.1093/nar/gky237 ◽

2018 ◽

Vol 46 (12) ◽

pp. e72-e72 ◽

Author(s):

Abdullah M Khamis ◽

Olaa Motwalli ◽

Romina Oliva ◽

Boris R Jankovic ◽

Yulia A Medvedeva ◽

...

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Site Prediction ◽

Factor Binding ◽

Binding Site Prediction ◽

Novel Method ◽

Improved Accuracy

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Guide to Genome-Wide Bacterial Transcription Factor Binding Site Prediction Using OmpR as Model

Selected Works in Bioinformatics ◽

10.5772/24321 ◽

2011 ◽

Author(s):

Phu Vuong ◽

Rajeev Misr

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Site Prediction ◽

Factor Binding ◽

Binding Site Prediction ◽

Bacterial Transcription ◽

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Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors

PLoS Computational Biology ◽

10.1371/journal.pcbi.1005176 ◽

2017 ◽

Vol 13 (7) ◽

pp. e1005176 ◽

Author(s):

Saeed Omidi ◽

Mihaela Zavolan ◽

Mikhail Pachkov ◽

Jeremie Breda ◽

Severin Berger ◽

...

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Site Prediction ◽

Factor Binding ◽

Binding Site Prediction

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Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP

Nucleic Acids Research ◽

10.1093/nar/gkp381 ◽

2009 ◽

Vol 37 (12) ◽

pp. e85-e85 ◽

Author(s):

Adam Ameur ◽

Alvaro Rada-Iglesias ◽

Jan Komorowski ◽

Claes Wadelius

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Snp Genotyping ◽

Factor Binding Site ◽

Site Prediction ◽

Factor Binding ◽

Binding Site Prediction ◽

Regulatory Snps

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