Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

Yue Zhao; Shuxiang Ruan; Manishi Pandey; Gary D. Stormo

doi:10.1534/genetics.112.138685

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

Genetics ◽

10.1534/genetics.112.138685 ◽

2012 ◽

Vol 191 (3) ◽

pp. 781-790 ◽

Cited By ~ 95

Author(s):

Yue Zhao ◽

Shuxiang Ruan ◽

Manishi Pandey ◽

Gary D. Stormo

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Factor Binding ◽

Binding Site Identification ◽

Site Identification

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Transcription Factor Binding Site Identification by Phylogenetic Footprinting

Frontiers in Computational and Systems Biology - Computational Biology ◽

10.1007/978-1-84996-196-7_6 ◽

2010 ◽

pp. 113-131

Author(s):

Haiyan Hu ◽

Xiaoman Li

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Phylogenetic Footprinting ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Factor Binding ◽

Binding Site Identification ◽

Site Identification

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Transcription factor binding site identification using the self-organizing map

Bioinformatics ◽

10.1093/bioinformatics/bti256 ◽

2005 ◽

Vol 21 (9) ◽

pp. 1807-1814 ◽

Cited By ~ 44

Author(s):

S. Mahony ◽

D. Hendrix ◽

A. Golden ◽

T. J. Smith ◽

D. S. Rokhsar

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

The Self ◽

Self Organizing Map ◽

Factor Binding Site ◽

Factor Binding ◽

Binding Site Identification ◽

Site Identification

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Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms

Functional & Integrative Genomics ◽

10.1007/s10142-007-0054-7 ◽

2007 ◽

Vol 7 (4) ◽

pp. 335-345 ◽

Cited By ~ 14

Author(s):

Anthony R. Borneman ◽

Zhengdong D. Zhang ◽

Joel Rozowsky ◽

Michael R. Seringhaus ◽

Mark Gerstein ◽

...

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

High Density ◽

Factor Binding Site ◽

Factor Binding ◽

Binding Site Identification ◽

Site Identification

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Transcription Factor–Binding Site Identification and Enrichment Analysis

Methods in Molecular Biology - Detection of Cell Death Mechanisms ◽

10.1007/978-1-0716-1162-3_20 ◽

2020 ◽

pp. 241-261

Author(s):

Joe L. Guy ◽

Gil G. Mor

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Enrichment Analysis ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Factor Binding ◽

Binding Site Identification ◽

Site Identification

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Sequential Integration of Fuzzy Clustering and Expectation Maximization for Transcription Factor Binding Site Identification

Journal of Computational Biology ◽

10.1089/cmb.2017.0230 ◽

2018 ◽

Vol 25 (11) ◽

pp. 1247-1256

Author(s):

Ali Yousefian-Jazi ◽

Jinwook Choi

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Fuzzy Clustering ◽

Expectation Maximization ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Factor Binding ◽

Binding Site Identification ◽

Site Identification

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Transcription factor-binding site identification and gene classification via fusion of the supervised-weighted discrete kernel clustering and support vector machine

Journal of Applied Statistics ◽

10.1080/02664763.2013.845143 ◽

2013 ◽

Vol 41 (3) ◽

pp. 573-581 ◽

Cited By ~ 1

Author(s):

Insuk Sohn ◽

Jooyong Shim ◽

Changha Hwang ◽

Sujong Kim ◽

Jae Won Lee

Keyword(s):

Support Vector Machine ◽

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Support Vector ◽

Factor Binding Site ◽

Factor Binding ◽

Kernel Clustering ◽

Binding Site Identification ◽

Site Identification

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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 ◽

Cited By ~ 2

Author(s):

Pieter Meysman ◽

Kathleen Marchal ◽

Kristof Engelen

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Factor Binding

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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 ◽

Factor Binding

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Disentangling transcription factor binding site complexity

Nucleic Acids Research ◽

10.1093/nar/gky683 ◽

2018 ◽

Cited By ~ 1

Author(s):

Ralf Eggeling

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Transcription Factor Binding ◽

Factor Binding Site ◽

Factor Binding

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