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Literature DB >> 21654663

Jury remains out on simple models of transcription factor specificity.

Quaid Morris, Martha L Bulyk, Timothy R Hughes.

Abstract

Entities: Chemical Disease Species

Mesh：

Substances：
Transcription Factors

Year: 2011 PMID： 21654663 PMCID： PMC4409134 DOI： 10.1038/nbt.1892

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

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5 in total

1. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.

Authors: Michael F Berger; Anthony A Philippakis; Aaron M Qureshi; Fangxue S He; Preston W Estep; Martha L Bulyk
Journal: Nat Biotechnol Date: 2006-09-24 Impact factor: 54.908

2. RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.

Authors: Xiaoyu Chen; Timothy R Hughes; Quaid Morris
Journal: Bioinformatics Date: 2007-07-01 Impact factor: 6.937

3. Diversity and complexity in DNA recognition by transcription factors.

Authors: Gwenael Badis; Michael F Berger; Anthony A Philippakis; Shaheynoor Talukder; Andrew R Gehrke; Savina A Jaeger; Esther T Chan; Genita Metzler; Anastasia Vedenko; Xiaoyu Chen; Hanna Kuznetsov; Chi-Fong Wang; David Coburn; Daniel E Newburger; Quaid Morris; Timothy R Hughes; Martha L Bulyk
Journal: Science Date: 2009-05-14 Impact factor: 47.728

4. Inferring binding energies from selected binding sites.

Authors: Yue Zhao; David Granas; Gary D Stormo
Journal: PLoS Comput Biol Date: 2009-12-04 Impact factor: 4.475

5. Genome-wide mapping of in vivo protein-DNA interactions.

Authors: David S Johnson; Ali Mortazavi; Richard M Myers; Barbara Wold
Journal: Science Date: 2007-05-31 Impact factor: 47.728

5 in total

15 in total

1. Specificity landscapes unmask submaximal binding site preferences of transcription factors.

Authors: Devesh Bhimsaria; José A Rodríguez-Martínez; Junkun Pan; Daniel Roston; Elif Nihal Korkmaz; Qiang Cui; Parameswaran Ramanathan; Aseem Z Ansari
Journal: Proc Natl Acad Sci U S A Date: 2018-10-19 Impact factor: 11.205

2. Varying levels of complexity in transcription factor binding motifs.

Authors: Jens Keilwagen; Jan Grau
Journal: Nucleic Acids Res Date: 2015-06-26 Impact factor: 16.971

3. Disentangling transcription factor binding site complexity.

Authors: Ralf Eggeling
Journal: Nucleic Acids Res Date: 2018-11-16 Impact factor: 16.971

Review 4. Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks.

Authors: Julia M Rogers; Martha L Bulyk
Journal: Wiley Interdiscip Rev Syst Biol Med Date: 2018-04-25

5. Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data.

Authors: Yaron Orenstein; Chaim Linhart; Ron Shamir
Journal: PLoS One Date: 2012-09-28 Impact factor: 3.240

6. Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation.

Authors: Junbai Wang; Agnieszka Malecka; Gunhild Trøen; Jan Delabie
Journal: BMC Genomics Date: 2015-06-11 Impact factor: 3.969