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Items: 1 to 20 of 155


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 22;14(2):e7902. doi: 10.15252/msb.20177902.


Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.

Omidi S, Zavolan M, Pachkov M, Breda J, Berger S, van Nimwegen E.

PLoS Comput Biol. 2017 Jul 28;13(7):e1005176. doi: 10.1371/journal.pcbi.1005176. eCollection 2017 Jul.


Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations.

Zhou S, Treloar AE, Lupien M.

Cancer Discov. 2016 Nov;6(11):1215-1229. Epub 2016 Oct 19. Review.


CIBZ Regulates Mesodermal and Cardiac Differentiation of by Suppressing T and Mesp1 Expression in Mouse Embryonic Stem Cells.

Kotoku T, Kosaka K, Nishio M, Ishida Y, Kawaichi M, Matsuda E.

Sci Rep. 2016 Sep 23;6:34188. doi: 10.1038/srep34188.


Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm.

Zhang J, Gao B, Chai H, Ma Z, Yang G.

BMC Bioinformatics. 2016 Aug 26;17(1):323. doi: 10.1186/s12859-016-1201-8.


Dry and wet approaches for genome-wide functional annotation of conventional and unconventional transcriptional activators.

Levati E, Sartini S, Ottonello S, Montanini B.

Comput Struct Biotechnol J. 2016 Jun 29;14:262-70. doi: 10.1016/j.csbj.2016.06.004. eCollection 2016. Review.


Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.

Megraw M, Cumbie JS, Ivanchenko MG, Filichkin SA.

Plant Cell. 2016 Feb;28(2):286-303. doi: 10.1105/tpc.15.00852. Epub 2016 Feb 11. Review.


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

Glick Y, Orenstein Y, Chen D, Avrahami D, Zor T, Shamir R, Gerber D.

Nucleic Acids Res. 2016 Apr 7;44(6):e51. doi: 10.1093/nar/gkv1327. Epub 2015 Dec 3.


Different Bla-g T cell antigens dominate responses in asthma versus rhinitis subjects.

Dillon MB, Schulten V, Oseroff C, Paul S, Dullanty LM, Frazier A, Belles X, Piulachs MD, Visness C, Bacharier L, Bloomberg GR, Busse P, Sidney J, Peters B, Sette A.

Clin Exp Allergy. 2015 Dec;45(12):1856-67. doi: 10.1111/cea.12643.


Reliable scaling of position weight matrices for binding strength comparisons between transcription factors.

Ma X, Ezer D, Navarro C, Adryan B.

BMC Bioinformatics. 2015 Aug 20;16:265. doi: 10.1186/s12859-015-0666-1.


Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.

Afek A, Cohen H, Barber-Zucker S, Gordân R, Lukatsky DB.

PLoS Comput Biol. 2015 Aug 18;11(8):e1004429. doi: 10.1371/journal.pcbi.1004429. eCollection 2015 Aug.


GABPα Binding to Overlapping ETS and CRE DNA Motifs Is Enhanced by CREB1: Custom DNA Microarrays.

He X, Syed KS, Tillo D, Mann I, Weirauch MT, Vinson C.

G3 (Bethesda). 2015 Jul 16;5(9):1909-18. doi: 10.1534/g3.115.020248.


The jigsaw puzzle of sequence phenotype inference: Piecing together Shannon entropy, importance sampling, and Empirical Bayes.

Shreif Z, Striegel DA, Periwal V.

J Theor Biol. 2015 Sep 7;380:399-413. doi: 10.1016/j.jtbi.2015.06.010. Epub 2015 Jun 17.


Context influences on TALE-DNA binding revealed by quantitative profiling.

Rogers JM, Barrera LA, Reyon D, Sander JD, Kellis M, Joung JK, Bulyk ML.

Nat Commun. 2015 Jun 11;6:7440. doi: 10.1038/ncomms8440.


A structure-based Multiple-Instance Learning approach to predicting in vitro transcription factor-DNA interaction.

Gao Z, Ruan J.

BMC Genomics. 2015;16 Suppl 4:S3. doi: 10.1186/1471-2164-16-S4-S3. Epub 2015 Apr 21.


The wrapping loop and Rap1 C-terminal (RCT) domain of yeast Rap1 modulate access to different DNA binding modes.

Feldmann EA, De Bona P, Galletto R.

J Biol Chem. 2015 May 1;290(18):11455-66. doi: 10.1074/jbc.M115.637678. Epub 2015 Mar 24.


Chromatin mediation of a transcriptional memory effect in yeast.

Paul E, Tirosh I, Lai W, Buck MJ, Palumbo MJ, Morse RH.

G3 (Bethesda). 2015 Mar 5;5(5):829-38. doi: 10.1534/g3.115.017418.


Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes.

Andrilenas KK, Penvose A, Siggers T.

Brief Funct Genomics. 2015 Jan;14(1):17-29. doi: 10.1093/bfgp/elu046. Epub 2014 Nov 26. Review.


Protein-DNA binding in the absence of specific base-pair recognition.

Afek A, Schipper JL, Horton J, Gordân R, Lukatsky DB.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17140-5. doi: 10.1073/pnas.1410569111. Epub 2014 Oct 13.


A force-based, parallel assay for the quantification of protein-DNA interactions.

Limmer K, Pippig DA, Aschenbrenner D, Gaub HE.

PLoS One. 2014 Feb 27;9(2):e89626. doi: 10.1371/journal.pone.0089626. eCollection 2014.

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