BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

212 related articles for article (PubMed ID: 29165643)

  • 1. Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding.
    Li J; Sagendorf JM; Chiu TP; Pasi M; Perez A; Rohs R
    Nucleic Acids Res; 2017 Dec; 45(22):12877-12887. PubMed ID: 29165643
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Quantitative modeling of transcription factor binding specificities using DNA shape.
    Zhou T; Shen N; Yang L; Abe N; Horton J; Mann RS; Bussemaker HJ; Gordân R; Rohs R
    Proc Natl Acad Sci U S A; 2015 Apr; 112(15):4654-9. PubMed ID: 25775564
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.
    Andrabi M; Hutchins AP; Miranda-Saavedra D; Kono H; Nussinov R; Mizuguchi K; Ahmad S
    Sci Rep; 2017 Jun; 7(1):4071. PubMed ID: 28642456
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding.
    Chiu TP; Rao S; Mann RS; Honig B; Rohs R
    Nucleic Acids Res; 2017 Dec; 45(21):12565-12576. PubMed ID: 29040720
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model.
    Oliver P; Peralta-Gil M; Tabche ML; Merino E
    BMC Genomics; 2016 Aug; 17(1):686. PubMed ID: 27567672
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles.
    Kuznetsov VA
    Methods Mol Biol; 2017; 1613():193-276. PubMed ID: 28849563
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Base-resolution methylation patterns accurately predict transcription factor bindings in vivo.
    Xu T; Li B; Zhao M; Szulwach KE; Street RC; Lin L; Yao B; Zhang F; Jin P; Wu H; Qin ZS
    Nucleic Acids Res; 2015 Mar; 43(5):2757-66. PubMed ID: 25722376
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Prediction of TF target sites based on atomistic models of protein-DNA complexes.
    Angarica VE; Pérez AG; Vasconcelos AT; Collado-Vides J; Contreras-Moreira B
    BMC Bioinformatics; 2008 Oct; 9():436. PubMed ID: 18922190
    [TBL] [Abstract][Full Text] [Related]  

  • 9. A unified approach for quantifying and interpreting DNA shape readout by transcription factors.
    Rube HT; Rastogi C; Kribelbauer JF; Bussemaker HJ
    Mol Syst Biol; 2018 Feb; 14(2):e7902. PubMed ID: 29472273
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study.
    Korolev N; Lyubartsev AP; Nordenskiöld L; Laaksonen A
    J Mol Biol; 2001 May; 308(5):907-17. PubMed ID: 11352581
    [TBL] [Abstract][Full Text] [Related]  

  • 11. A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.
    Yang J; Ramsey SA
    Bioinformatics; 2015 Nov; 31(21):3445-50. PubMed ID: 26130577
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.
    Bauer AL; Hlavacek WS; Unkefer PJ; Mu F
    PLoS Comput Biol; 2010 Nov; 6(11):e1001007. PubMed ID: 21124945
    [TBL] [Abstract][Full Text] [Related]  

  • 13. DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo.
    Mathelier A; Xin B; Chiu TP; Yang L; Rohs R; Wasserman WW
    Cell Syst; 2016 Sep; 3(3):278-286.e4. PubMed ID: 27546793
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Using DNA duplex stability information for transcription factor binding site discovery.
    Gordân R; Hartemink AJ
    Pac Symp Biocomput; 2008; ():453-64. PubMed ID: 18229707
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Sequence features of DNA binding sites reveal structural class of associated transcription factor.
    Narlikar L; Hartemink AJ
    Bioinformatics; 2006 Jan; 22(2):157-63. PubMed ID: 16267080
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Covariation between homeodomain transcription factors and the shape of their DNA binding sites.
    Dror I; Zhou T; Mandel-Gutfreund Y; Rohs R
    Nucleic Acids Res; 2014 Jan; 42(1):430-41. PubMed ID: 24078250
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data.
    Tan C; Takada S
    J Chem Theory Comput; 2018 Jul; 14(7):3877-3889. PubMed ID: 29806939
    [TBL] [Abstract][Full Text] [Related]  

  • 18. An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization.
    Qian Z; Lu L; Liu X; Cai YD; Li Y
    Bioinformatics; 2007 Sep; 23(18):2449-54. PubMed ID: 17623704
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Structure-based ab initio prediction of transcription factor-binding sites.
    Liu LA; Bader JS
    Methods Mol Biol; 2009; 541():23-41. PubMed ID: 19381536
    [TBL] [Abstract][Full Text] [Related]  

  • 20. An in-the-groove view of DNA structures in complexes with proteins.
    Suzuki M; Yagi N
    J Mol Biol; 1996 Feb; 255(5):677-87. PubMed ID: 8636970
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.