Literature DB >> 25848058

Shapely DNA attracts the right partner.

Teresa M Przytycka1, David Levens2.   

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Year:  2015        PMID： 25848058      PMCID： PMC4403220          DOI： 10.1073/pnas.1503951112

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


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  17 in total

1.  A biophysical approach to transcription factor binding site discovery.

Authors:  Marko Djordjevic; Anirvan M Sengupta; Boris I Shraiman
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

2.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.

Authors:  C Tuerk; L Gold
Journal:  Science       Date:  1990-08-03       Impact factor: 47.728

3.  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

4.  Quantitative modeling of transcription factor binding specificities using DNA shape.

Authors:  Tianyin Zhou; Ning Shen; Lin Yang; Namiko Abe; John Horton; Richard S Mann; Harmen J Bussemaker; Raluca Gordân; Remo Rohs
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-09       Impact factor: 11.205

5.  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

6.  High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.

Authors:  Phaedra Agius; Aaron Arvey; William Chang; William Stafford Noble; Christina Leslie
Journal:  PLoS Comput Biol       Date:  2010-09-09       Impact factor: 4.475

7.  Evaluation of methods for modeling transcription factor sequence specificity.

Authors:  Matthew T Weirauch; Atina Cote; Raquel Norel; Matti Annala; Yue Zhao; Todd R Riley; Julio Saez-Rodriguez; Thomas Cokelaer; Anastasia Vedenko; Shaheynoor Talukder; Harmen J Bussemaker; Quaid D Morris; Martha L Bulyk; Gustavo Stolovitzky; Timothy R Hughes
Journal:  Nat Biotechnol       Date:  2013-01-27       Impact factor: 54.908

8.  Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions.

Authors:  Jiajian Liu; Gary D Stormo
Journal:  Nucleic Acids Res       Date:  2005-09-25       Impact factor: 16.971

9.  The role of DNA shape in protein-DNA recognition.

Authors:  Remo Rohs; Sean M West; Alona Sosinsky; Peng Liu; Richard S Mann; Barry Honig
Journal:  Nature       Date:  2009-10-29       Impact factor: 49.962

10.  DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.

Authors:  Tianyin Zhou; Lin Yang; Yan Lu; Iris Dror; Ana Carolina Dantas Machado; Tahereh Ghane; Rosa Di Felice; Remo Rohs
Journal:  Nucleic Acids Res       Date:  2013-05-22       Impact factor: 16.971
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  2 in total

1.  Integrated microfluidic approach for quantitative high-throughput measurements of transcription factor binding affinities.

Authors:  Yair Glick; Yaron Orenstein; Dana Chen; Dorit Avrahami; Tsaffrir Zor; Ron Shamir; Doron Gerber
Journal:  Nucleic Acids Res       Date:  2015-12-03       Impact factor: 16.971

2.  ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning.

Authors:  Maja Malkowska; Julian Zubek; Dariusz Plewczynski; Lucjan S Wyrwicz
Journal:  PeerJ       Date:  2018-11-29       Impact factor: 2.984
  2 in total

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