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Items: 1 to 20 of 172


Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator.

Nocedal I, Mancera E, Johnson AD.

Elife. 2017 Mar 22;6. pii: e23250. doi: 10.7554/eLife.23250.


CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design.

Zhang S, Chen Y.

PLoS One. 2016 Aug 3;11(8):e0160435. doi: 10.1371/journal.pone.0160435. eCollection 2016.


Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets.

Hogan GJ, Brown PO, Herschlag D.

PLoS Biol. 2015 Nov 20;13(11):e1002307. doi: 10.1371/journal.pbio.1002307. eCollection 2015.


Mechanisms of mutational robustness in transcriptional regulation.

Payne JL, Wagner A.

Front Genet. 2015 Oct 27;6:322. doi: 10.3389/fgene.2015.00322. eCollection 2015. Review.


The RNAPII-CTD Maintains Genome Integrity through Inhibition of Retrotransposon Gene Expression and Transposition.

Aristizabal MJ, Negri GL, Kobor MS.

PLoS Genet. 2015 Oct 23;11(10):e1005608. doi: 10.1371/journal.pgen.1005608. eCollection 2015 Oct.


Intersecting transcription networks constrain gene regulatory evolution.

Sorrells TR, Booth LN, Tuch BB, Johnson AD.

Nature. 2015 Jul 16;523(7560):361-5. doi: 10.1038/nature14613. Epub 2015 Jul 8.


Comparative Analysis of Transmembrane Regulators of the Filamentous Growth Mitogen-Activated Protein Kinase Pathway Uncovers Functional and Regulatory Differences.

Adhikari H, Caccamise LM, Pande T, Cullen PJ.

Eukaryot Cell. 2015 Sep;14(9):868-83. doi: 10.1128/EC.00085-15. Epub 2015 Jun 26.


Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana.

Lehti-Shiu MD, Uygun S, Moghe GD, Panchy N, Fang L, Hufnagel DE, Jasicki HL, Feig M, Shiu SH.

Plant Physiol. 2015 Aug;168(4):1717-34. doi: 10.1104/pp.15.00689. Epub 2015 Jun 23.


Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models.

Naval-Sánchez M, Potier D, Hulselmans G, Christiaens V, Aerts S.

Mol Biol Evol. 2015 Sep;32(9):2441-55. doi: 10.1093/molbev/msv107. Epub 2015 May 4.


Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.

Mathelier A, Lefebvre C, Zhang AW, Arenillas DJ, Ding J, Wasserman WW, Shah SP.

Genome Biol. 2015 Apr 23;16:84. doi: 10.1186/s13059-015-0648-7.


An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome.

Cheng C, Andrews E, Yan KK, Ung M, Wang D, Gerstein M.

Genome Biol. 2015 Mar 31;16:63. doi: 10.1186/s13059-015-0624-2.


Examining the role of components of Slc11a1 (Nramp1) in the susceptibility of New Zealand sea lions (Phocarctos hookeri) to disease.

Osborne AJ, Pearson J, Chilvers BL, Kennedy MA, Gemmell NJ.

PLoS One. 2015 Apr 14;10(4):e0122703. doi: 10.1371/journal.pone.0122703. eCollection 2015.


Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus.

Lind AL, Wisecaver JH, Smith TD, Feng X, Calvo AM, Rokas A.

PLoS Genet. 2015 Mar 18;11(3):e1005096. doi: 10.1371/journal.pgen.1005096. eCollection 2015 Mar.


Using the ENCODE Resource for Functional Annotation of Genetic Variants.

Pazin MJ.

Cold Spring Harb Protoc. 2015 Mar 11;2015(6):522-36. doi: 10.1101/pdb.top084988. Review.


An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.

Jin J, He K, Tang X, Li Z, Lv L, Zhao Y, Luo J, Gao G.

Mol Biol Evol. 2015 Jul;32(7):1767-73. doi: 10.1093/molbev/msv058. Epub 2015 Mar 6.


Pervasive variation of transcription factor orthologs contributes to regulatory network evolution.

Nadimpalli S, Persikov AV, Singh M.

PLoS Genet. 2015 Mar 6;11(3):e1005011. doi: 10.1371/journal.pgen.1005011. eCollection 2015 Mar.


Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture.

Vietri Rudan M, Barrington C, Henderson S, Ernst C, Odom DT, Tanay A, Hadjur S.

Cell Rep. 2015 Mar 3;10(8):1297-309. doi: 10.1016/j.celrep.2015.02.004. Epub 2015 Feb 26.


Fine-tuning of histone H3 Lys4 methylation during pseudohyphal differentiation by the CDK submodule of RNA polymerase II.

Law MJ, Ciccaglione K.

Genetics. 2015 Feb;199(2):435-53. doi: 10.1534/genetics.114.172841. Epub 2014 Dec 1.


Structure-based modeling of protein: DNA specificity.

Joyce AP, Zhang C, Bradley P, Havranek JJ.

Brief Funct Genomics. 2015 Jan;14(1):39-49. doi: 10.1093/bfgp/elu044. Epub 2014 Nov 19. Review.

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