PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments

Bioinformatics ◽

10.1093/bioinformatics/btw448 ◽

2016 ◽

Vol 32 (17) ◽

pp. i629-i638 ◽

Author(s):

Tuomo Hartonen ◽

Biswajyoti Sahu ◽

Kashyap Dave ◽

Teemu Kivioja ◽

Jussi Taipale

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

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Identifying Common Structural DNA Properties in Transcription Factor Binding Site Sets of the LacI-GalR Family

Current Bioinformatics ◽

10.2174/1574893611308040010 ◽

2013 ◽

Vol 8 (4) ◽

pp. 483-488 ◽

Author(s):

Pieter Meysman ◽

Kathleen Marchal ◽

Kristof Engelen

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

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Characterization of a myeloid-specific enhancer of the chicken lysozyme gene. Major role for an Ets transcription factor-binding site.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)32378-5 ◽

1994 ◽

Vol 269 (27) ◽

pp. 17794-17801

Author(s):

B. Ahne ◽

W.H. Strätling

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Factor Binding ◽

Lysozyme Gene ◽

Ets Transcription Factor ◽

Chicken Lysozyme

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Transcription factor binding site detection using convolutional neural networks with a functional group-based data representation

Journal of Physics Conference Series ◽

10.1088/1742-6596/1824/1/012001 ◽

2021 ◽

Vol 1824 (1) ◽

pp. 012001

Author(s):

Gergely Pap ◽

Györgypál Zoltán ◽

Krisztián Ádám ◽

László Tóth ◽

Zoltán Hegedűs

Keyword(s):

Neural Networks ◽

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Convolutional Neural Networks ◽

Functional Group ◽

Transcription Factor Binding ◽

Data Representation ◽

Factor Binding Site ◽

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Disentangling transcription factor binding site complexity

Nucleic Acids Research ◽

10.1093/nar/gky683 ◽

2018 ◽

Author(s):

Ralf Eggeling

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

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CAE-CNN: Predicting transcription factor binding site with convolutional autoencoder and convolutional neural network

Expert Systems with Applications ◽

10.1016/j.eswa.2021.115404 ◽

2021 ◽

pp. 115404

Author(s):

Yongqing Zhang ◽

Shaojie Qiao ◽

Yuanqi Zeng ◽

Dongrui Gao ◽

Nan Han ◽

...

Keyword(s):

Neural Network ◽

Transcription Factor ◽

Convolutional Neural Network ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Factor Binding ◽

Convolutional Autoencoder

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LASAGNA-Search: an integrated web tool for transcription factor binding site search and visualization

BioTechniques ◽

10.2144/000113999 ◽

2013 ◽

Vol 54 (3) ◽

Author(s):

Chih Lee ◽

Chun-Hsi Huang

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Web Tool ◽

Factor Binding Site ◽

Factor Binding ◽

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A Novel Alignment-Free Method for Comparing Transcription Factor Binding Site Motifs

PLoS ONE ◽

10.1371/journal.pone.0008797 ◽

2010 ◽

Vol 5 (1) ◽

pp. e8797 ◽

Author(s):

Minli Xu ◽

Zhengchang Su

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Factor Binding ◽

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Effects of phosphate neutralization on the shape of the AP-1 transcription factor binding site in duplex DNA

Nucleic Acids Research ◽

10.1093/nar/26.10.2298 ◽

1998 ◽

Vol 26 (10) ◽

pp. 2298-2305 ◽

Author(s):

L. A. Tomky ◽

J. K. Strauss-Soukup ◽

L. J. Maher

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

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Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse

BMC Genomics ◽

10.1186/1471-2164-10-144 ◽

2009 ◽

Vol 10 (1) ◽

pp. 144 ◽

Author(s):

Christine Steinhoff ◽

Martina Paulsen ◽

Szymon Kielbasa ◽

Jorn Walter ◽

Martin Vingron

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Expression Profile ◽

Transcription Factor Binding ◽

Imprinted Genes ◽

Factor Binding Site ◽

Factor Binding ◽

Human And Mouse

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Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences

Current Protocols in Bioinformatics ◽

10.1002/0471250953.bi0211s47 ◽

2014 ◽

Vol 47 (1) ◽

Author(s):

Federico Zambelli ◽

Graziano Pesole ◽

Giulio Pavesi

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Nucleotide Sequences ◽

Factor Binding Site ◽

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