219 related articles for article (PubMed ID: 35978548)
21. Pbx-1 Hox heterodimers bind DNA on inseparable half-sites that permit intrinsic DNA binding specificity of the Hox partner at nucleotides 3' to a TAAT motif.
Knoepfler PS; Lu Q; Kamps MP
Nucleic Acids Res; 1996 Jun; 24(12):2288-94. PubMed ID: 8710498
[TBL] [Abstract][Full Text] [Related]
22. How motif environment influences transcription factor search dynamics: Finding a needle in a haystack.
Dror I; Rohs R; Mandel-Gutfreund Y
Bioessays; 2016 Jul; 38(7):605-12. PubMed ID: 27192961
[TBL] [Abstract][Full Text] [Related]
23. 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]
24. Mechanism of cognate sequence discrimination by the ETS-family transcription factor ETS-1.
Huang K; Xhani S; Albrecht AV; Ha VLT; Esaki S; Poon GMK
J Biol Chem; 2019 Jun; 294(25):9666-9678. PubMed ID: 31048376
[TBL] [Abstract][Full Text] [Related]
25. Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site.
Al-Zyoud WA; Hynson RM; Ganuelas LA; Coster AC; Duff AP; Baker MA; Stewart AG; Giannoulatou E; Ho JW; Gaus K; Liu D; Lee LK; Böcking T
Nucleic Acids Res; 2016 Feb; 44(3):1411-20. PubMed ID: 26681693
[TBL] [Abstract][Full Text] [Related]
26. Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins.
Kribelbauer JF; Loker RE; Feng S; Rastogi C; Abe N; Rube HT; Bussemaker HJ; Mann RS
Mol Cell; 2020 Apr; 78(1):152-167.e11. PubMed ID: 32053778
[TBL] [Abstract][Full Text] [Related]
27. Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding.
Le DD; Shimko TC; Aditham AK; Keys AM; Longwell SA; Orenstein Y; Fordyce PM
Proc Natl Acad Sci U S A; 2018 Apr; 115(16):E3702-E3711. PubMed ID: 29588420
[TBL] [Abstract][Full Text] [Related]
28. Flanking sequence context-dependent transcription factor binding in early Drosophila development.
Stringham JL; Brown AS; Drewell RA; Dresch JM
BMC Bioinformatics; 2013 Oct; 14():298. PubMed ID: 24093548
[TBL] [Abstract][Full Text] [Related]
29. DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis.
Hancock SP; Stella S; Cascio D; Johnson RC
PLoS One; 2016; 11(3):e0150189. PubMed ID: 26959646
[TBL] [Abstract][Full Text] [Related]
30. TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
Yang L; Zhou T; Dror I; Mathelier A; Wasserman WW; Gordân R; Rohs R
Nucleic Acids Res; 2014 Jan; 42(Database issue):D148-55. PubMed ID: 24214955
[TBL] [Abstract][Full Text] [Related]
31. DNA-dependent formation of transcription factor pairs alters their binding specificity.
Jolma A; Yin Y; Nitta KR; Dave K; Popov A; Taipale M; Enge M; Kivioja T; Morgunova E; Taipale J
Nature; 2015 Nov; 527(7578):384-8. PubMed ID: 26550823
[TBL] [Abstract][Full Text] [Related]
32. 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]
33. The influence of transcription factor competition on the relationship between occupancy and affinity.
Zabet NR; Foy R; Adryan B
PLoS One; 2013; 8(9):e73714. PubMed ID: 24086290
[TBL] [Abstract][Full Text] [Related]
34. 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]
35. Discovering epistatic feature interactions from neural network models of regulatory DNA sequences.
Greenside P; Shimko T; Fordyce P; Kundaje A
Bioinformatics; 2018 Sep; 34(17):i629-i637. PubMed ID: 30423062
[TBL] [Abstract][Full Text] [Related]
36. 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]
37. Synthetic and genomic regulatory elements reveal aspects of
King DM; Hong CKY; Shepherdson JL; Granas DM; Maricque BB; Cohen BA
Elife; 2020 Feb; 9():. PubMed ID: 32043966
[TBL] [Abstract][Full Text] [Related]
38. High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants.
Aditham AK; Markin CJ; Mokhtari DA; DelRosso N; Fordyce PM
Cell Syst; 2021 Feb; 12(2):112-127.e11. PubMed ID: 33340452
[TBL] [Abstract][Full Text] [Related]
39. An equilibrium partitioning model connecting gene expression and cis-motif content.
Mellor J; DeLisi C
Bioinformatics; 2006 Jul; 22(14):e368-74. PubMed ID: 16873495
[TBL] [Abstract][Full Text] [Related]
40. Discerning the Role of DNA Sequence, Shape, and Flexibility in Recognition by
Murthy S; Dey U; Olymon K; Abbas E; Yella VR; Kumar A
ACS Chem Biol; 2024 Jun; ():. PubMed ID: 38902964
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]