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Items: 1 to 20 of 36


Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation.

Cuartero S, Weiss FD, Dharmalingam G, Guo Y, Ing-Simmons E, Masella S, Robles-Rebollo I, Xiao X, Wang YF, Barozzi I, Djeghloul D, Amano MT, Niskanen H, Petretto E, Dowell RD, Tachibana K, Kaikkonen MU, Nasmyth KA, Lenhard B, Natoli G, Fisher AG, Merkenschlager M.

Nat Immunol. 2018 Sep;19(9):932-941. doi: 10.1038/s41590-018-0184-1. Epub 2018 Aug 20.


PI(3,5)P2 controls vacuole potassium transport to support cellular osmoregulation.

Wilson ZN, Scott AL, Dowell RD, Odorizzi G.

Mol Biol Cell. 2018 Jul 15;29(13):1718-1731. doi: 10.1091/mbc.E18-01-0015. Epub 2018 May 23.


Detecting Differential Transcription Factor Activity from ATAC-Seq Data.

Tripodi IJ, Allen MA, Dowell RD.

Molecules. 2018 May 10;23(5). pii: E1136. doi: 10.3390/molecules23051136.


Enhancer RNA profiling predicts transcription factor activity.

Azofeifa JG, Allen MA, Hendrix JR, Read T, Rubin JD, Dowell RD.

Genome Res. 2018 Feb 15. doi: 10.1101/gr.225755.117. [Epub ahead of print]


Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers.

Sanchez GJ, Richmond PA, Bunker EN, Karman SS, Azofeifa J, Garnett AT, Xu Q, Wheeler GE, Toomey CM, Zhang Q, Dowell RD, Liu X.

Nucleic Acids Res. 2018 Feb 28;46(4):1756-1776. doi: 10.1093/nar/gkx1225.


Transcriptome and Functional Profile of Cardiac Myocytes Is Influenced by Biological Sex.

Trexler CL, Odell AT, Jeong MY, Dowell RD, Leinwand LA.

Circ Cardiovasc Genet. 2017 Oct;10(5). pii: e001770. doi: 10.1161/CIRCGENETICS.117.001770.


The Influence of Polyploidy on the Evolution of Yeast Grown in a Sub-Optimal Carbon Source.

Scott AL, Richmond PA, Dowell RD, Selmecki AM.

Mol Biol Evol. 2017 Oct 1;34(10):2690-2703. doi: 10.1093/molbev/msx205.


Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications.

Ebmeier CC, Erickson B, Allen BL, Allen MA, Kim H, Fong N, Jacobsen JR, Liang K, Shilatifard A, Dowell RD, Old WM, Bentley DL, Taatjes DJ.

Cell Rep. 2017 Aug 1;20(5):1173-1186. doi: 10.1016/j.celrep.2017.07.021.


A Kinase-Independent Role for Cyclin-Dependent Kinase 19 in p53 Response.

Audetat KA, Galbraith MD, Odell AT, Lee T, Pandey A, Espinosa JM, Dowell RD, Taatjes DJ.

Mol Cell Biol. 2017 Jun 15;37(13). pii: e00626-16. doi: 10.1128/MCB.00626-16. Print 2017 Jul 1.


Model based heritability scores for high-throughput sequencing data.

Rudra P, Shi WJ, Vestal B, Russell PH, Odell A, Dowell RD, Radcliffe RA, Saba LM, Kechris K.

BMC Bioinformatics. 2017 Mar 2;18(1):143. doi: 10.1186/s12859-017-1539-6.


A generative model for the behavior of RNA polymerase.

Azofeifa JG, Dowell RD.

Bioinformatics. 2017 Jan 15;33(2):227-234. doi: 10.1093/bioinformatics/btw599. Epub 2016 Sep 23.


A Modeling Framework for Generation of Positional and Temporal Simulations of Transcriptional Regulation.

Knox DA, Dowell RD.

IEEE/ACM Trans Comput Biol Bioinform. 2016 May-Jun;13(3):459-471. doi: 10.1109/TCBB.2015.2459708.


RNA Pol II transcription model and interpretation of GRO-seq data.

Lladser ME, Azofeifa JG, Allen MA, Dowell RD.

J Math Biol. 2017 Jan;74(1-2):77-97. doi: 10.1007/s00285-016-1014-4. Epub 2016 May 3.


Survey of cryptic unstable transcripts in yeast.

Vera JM, Dowell RD.

BMC Genomics. 2016 Apr 26;17:305. doi: 10.1186/s12864-016-2622-5.


Identification of Mediator Kinase Substrates in Human Cells using Cortistatin A and Quantitative Phosphoproteomics.

Poss ZC, Ebmeier CC, Odell AT, Tangpeerachaikul A, Lee T, Pelish HE, Shair MD, Dowell RD, Old WM, Taatjes DJ.

Cell Rep. 2016 Apr 12;15(2):436-50. doi: 10.1016/j.celrep.2016.03.030. Epub 2016 Mar 31.


Foxc1 reinforces quiescence in self-renewing hair follicle stem cells.

Wang L, Siegenthaler JA, Dowell RD, Yi R.

Science. 2016 Feb 5;351(6273):613-7. doi: 10.1126/science.aad5440.


An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq.

Azofeifa JG, Allen MA, Lladser ME, Dowell RD.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep-Oct;14(5):1070-1081. doi: 10.1109/TCBB.2016.2520919. Epub 2016 Jan 26.


A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity.

Read T, Richmond PA, Dowell RD.

PLoS Genet. 2016 Jan 11;12(1):e1005746. doi: 10.1371/journal.pgen.1005746. eCollection 2016 Jan.


Prolonged Cre expression driven by the α-myosin heavy chain promoter can be cardiotoxic.

Pugach EK, Richmond PA, Azofeifa JG, Dowell RD, Leinwand LA.

J Mol Cell Cardiol. 2015 Sep;86:54-61. doi: 10.1016/j.yjmcc.2015.06.019. Epub 2015 Jul 2.


Engineered calcium-precipitable restriction enzyme.

Hendrix J, Read T, Lalonde JF, Jensen PK, Heymann W, Lovelace E, Zimmermann SA, Brasino M, Rokicki J, Dowell RD.

ACS Synth Biol. 2014 Dec 19;3(12):969-71. doi: 10.1021/sb500042m.


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