Motif discovery and transcription factor binding sites before and after the next-generation sequencing era

Federico Zambelli; Graziano Pesole; Giulio Pavesi

doi:10.1093/bib/bbs016

Motif discovery and transcription factor binding sites before and after the next-generation sequencing era

Briefings in Bioinformatics ◽

10.1093/bib/bbs016 ◽

2012 ◽

Vol 14 (2) ◽

pp. 225-237 ◽

Cited By ~ 80

Author(s):

Federico Zambelli ◽

Graziano Pesole ◽

Giulio Pavesi

Keyword(s):

Transcription Factor ◽

Next Generation Sequencing ◽

Binding Sites ◽

Motif Discovery ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Next Generation ◽

Factor Binding ◽

Before And After ◽

Generation Sequencing

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Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites

IEEE/ACM Transactions on Computational Biology and Bioinformatics ◽

10.1109/tcbb.2015.2424421 ◽

2015 ◽

Vol 12 (6) ◽

pp. 1416-1428 ◽

Cited By ~ 3

Author(s):

Ka-Chun Wong ◽

Chengbin Peng ◽

Yue Li

Keyword(s):

Transcription Factor ◽

Next Generation Sequencing ◽

Binding Sites ◽

Probabilistic Inference ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Next Generation ◽

Factor Binding ◽

Generation Sequencing

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MD-SVM: a novel SVM-based algorithm for the motif discovery of transcription factor binding sites

BMC Bioinformatics ◽

10.1186/s12859-019-2735-3 ◽

2019 ◽

Vol 20 (S7) ◽

Cited By ~ 3

Author(s):

Jialu Hu ◽

Jingru Wang ◽

Jianan Lin ◽

Tianwei Liu ◽

Yuanke Zhong ◽

...

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Motif Discovery ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Factor Binding

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Comparative Analysis of Regulatory Motif Discovery Tools for Transcription Factor Binding Sites

Genomics Proteomics & Bioinformatics ◽

10.1016/s1672-0229(07)60023-0 ◽

2007 ◽

Vol 5 (2) ◽

pp. 131-142 ◽

Cited By ~ 19

Author(s):

Wei Wei ◽

Xiao-Dan Yu

Keyword(s):

Transcription Factor ◽

Comparative Analysis ◽

Binding Sites ◽

Motif Discovery ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Regulatory Motif ◽

Factor Binding

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Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites

Nucleic Acids Research ◽

10.1093/nar/gkr745 ◽

2011 ◽

Vol 39 (21) ◽

pp. e146-e146 ◽

Cited By ~ 7

Author(s):

Guido H. Jajamovich ◽

Xiaodong Wang ◽

Adam P. Arkin ◽

Michael S. Samoilov

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Motif Discovery ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Factor Binding

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Motif discovery for transcription factor binding sites using a priori information on potential similarity regions at different resolution scales

New Biotechnology ◽

10.1016/j.nbt.2010.01.059 ◽

2010 ◽

Vol 27 ◽

pp. S41

Author(s):

I.V. Kulakovskiy ◽

V.A. Boeva ◽

A.V. Favorov ◽

V.J. Makeev

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Motif Discovery ◽

A Priori ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

A Priori Information ◽

Factor Binding ◽

Priori Information

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Faculty Opinions recommendation of Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1017662.206496 ◽

2004 ◽

Author(s):

Carlos F Barbas

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Noncoding Rnas ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Human Chromosomes ◽

Factor Binding

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Faculty Opinions recommendation of Position specific variation in the rate of evolution in transcription factor binding sites.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1022543.258615 ◽

2004 ◽

Author(s):

Emmanouil Dermitzakis

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Factor Binding ◽

Rate Of Evolution ◽

Specific Variation

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Faculty Opinions recommendation of Divergence of transcription factor binding sites across related yeast species.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1089279.548953 ◽

2007 ◽

Author(s):

Emmanouil Dermitzakis

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Yeast Species ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Factor Binding

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Faculty Opinions recommendation of Genome-wide inference of natural selection on human transcription factor binding sites.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718018456.793479473 ◽

2013 ◽

Author(s):

Peter Keightley

Keyword(s):

Transcription Factor ◽

Natural Selection ◽

Binding Sites ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Factor Binding ◽

Genome Wide ◽

Human Transcription Factor

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Gene Variants and Haplotypes Modifying Transcription Factor Binding Sites in the Human Cyclooxygenase 1 and 2 (PTGS1 and PTGS2) Genes

Current Drug Metabolism ◽

10.2174/138920021502140327180336 ◽

2014 ◽

Vol 15 (2) ◽

pp. 182-195 ◽

Cited By ~ 13

Author(s):

Jose Agundez ◽

David Gonzalez-Alvarez ◽

Miguel Vega-Rodriguez ◽

Emilia Botello ◽

Elena Garcia-Martin

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Gene Variants ◽

Factor Binding ◽

Cyclooxygenase 1

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