Literature DB >> 16601727

What are DNA sequence motifs?

Patrik D'haeseleer1.   

Abstract

Sequence motifs are becoming increasingly important in the analysis of gene regulation. How do we define sequence motifs, and why should we use sequence logos instead of consensus sequences to represent them? Do they have any relation with binding affinity? How do we search for new instances of a motif in this sea of DNA?

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Year:  2006        PMID： 16601727     DOI： 10.1038/nbt0406-423

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


  66 in total

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Journal:  J Biol Chem       Date:  2012-04-23       Impact factor: 5.157

Review 2.  DNA motifs that sculpt the bacterial chromosome.

Authors:  Fabrice Touzain; Marie-Agnès Petit; Sophie Schbath; Meriem El Karoui
Journal:  Nat Rev Microbiol       Date:  2011-01       Impact factor: 60.633

3.  The evolution of complex gene regulation by low-specificity binding sites.

Authors:  Alexander J Stewart; Joshua B Plotkin
Journal:  Proc Biol Sci       Date:  2013-08-14       Impact factor: 5.349

4.  DECOD: fast and accurate discriminative DNA motif finding.

Authors:  Peter Huggins; Shan Zhong; Idit Shiff; Rachel Beckerman; Oleg Laptenko; Carol Prives; Marcel H Schulz; Itamar Simon; Ziv Bar-Joseph
Journal:  Bioinformatics       Date:  2011-07-12       Impact factor: 6.937

5.  Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.

Authors:  Marinka Zitnik; Francis Nguyen; Bo Wang; Jure Leskovec; Anna Goldenberg; Michael M Hoffman
Journal:  Inf Fusion       Date:  2018-09-21       Impact factor: 12.975

6.  Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework.

Authors:  Jinyu Yang; Anjun Ma; Adam D Hoppe; Cankun Wang; Yang Li; Chi Zhang; Yan Wang; Bingqiang Liu; Qin Ma
Journal:  Nucleic Acids Res       Date:  2019-09-05       Impact factor: 16.971

7.  FISim: a new similarity measure between transcription factor binding sites based on the fuzzy integral.

Authors:  Fernando Garcia; Francisco J Lopez; Carlos Cano; Armando Blanco
Journal:  BMC Bioinformatics       Date:  2009-07-20       Impact factor: 3.169

8.  RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways.

Authors:  Deepak Sharma; Debasisa Mohanty; Avadhesha Surolia
Journal:  Nucleic Acids Res       Date:  2009-05-21       Impact factor: 16.971

9.  Many sequence-specific chromatin modifying protein-binding motifs show strong positional preferences for potential regulatory regions in the Saccharomyces cerevisiae genome.

Authors:  Loren Hansen; Leonardo Mariño-Ramírez; David Landsman
Journal:  Nucleic Acids Res       Date:  2010-01-04       Impact factor: 16.971

10.  Fur controls iron homeostasis and oxidative stress defense in the oligotrophic alpha-proteobacterium Caulobacter crescentus.

Authors:  José F da Silva Neto; Vânia S Braz; Valéria C S Italiani; Marilis V Marques
Journal:  Nucleic Acids Res       Date:  2009-06-11       Impact factor: 16.971
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