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Items: 44

1.

Remodeling of Zn2+ homeostasis upon differentiation of mammary epithelial cells.

Han Y, Sanford L, Simpson DM, Dowell RD, Palmer AE.

Metallomics. 2020 Mar 25;12(3):346-362. doi: 10.1039/c9mt00301k.

PMID:
31950952
2.

Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs.

Cardiello JF, Sanchez GJ, Allen MA, Dowell RD.

Transcription. 2020 Feb;11(1):3-18. doi: 10.1080/21541264.2019.1704128. Epub 2019 Dec 19.

PMID:
31856658
3.

Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue Protease.

Stanley JT, Gilchrist AR, Stabell AC, Allen MA, Sawyer SL, Dowell RD.

Pac Symp Biocomput. 2020;25:487-498.

4.

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression.

Sasse SK, Gruca M, Allen MA, Kadiyala V, Song T, Gally F, Gupta A, Pufall MA, Dowell RD, Gerber AN.

Genome Res. 2019 Nov;29(11):1753-1765. doi: 10.1101/gr.248187.119. Epub 2019 Sep 13.

PMID:
31519741
5.

Transcriptional Responses to IFN-γ Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19 Functions.

Steinparzer I, Sedlyarov V, Rubin JD, Eislmayr K, Galbraith MD, Levandowski CB, Vcelkova T, Sneezum L, Wascher F, Amman F, Kleinova R, Bender H, Andrysik Z, Espinosa JM, Superti-Furga G, Dowell RD, Taatjes DJ, Kovarik P.

Mol Cell. 2019 Nov 7;76(3):485-499.e8. doi: 10.1016/j.molcel.2019.07.034. Epub 2019 Sep 5.

PMID:
31495563
6.

Identification and characterization of a novel anti-inflammatory lipid isolated from Mycobacterium vaccae, a soil-derived bacterium with immunoregulatory and stress resilience properties.

Smith DG, Martinelli R, Besra GS, Illarionov PA, Szatmari I, Brazda P, Allen MA, Xu W, Wang X, Nagy L, Dowell RD, Rook GAW, Rosa Brunet L, Lowry CA.

Psychopharmacology (Berl). 2019 May;236(5):1653-1670. doi: 10.1007/s00213-019-05253-9. Epub 2019 May 22.

7.

Heat shock in C. elegans induces downstream of gene transcription and accumulation of double-stranded RNA.

Melnick M, Gonzales P, Cabral J, Allen MA, Dowell RD, Link CD.

PLoS One. 2019 Apr 8;14(4):e0206715. doi: 10.1371/journal.pone.0206715. eCollection 2019.

8.

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.

9.

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.

10.

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.

11.

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]

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

PMID:
27295631
20.

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.

PMID:
27142882
21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

PMID:
25524101
28.

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms.

Allen MA, Andrysik Z, Dengler VL, Mellert HS, Guarnieri A, Freeman JA, Sullivan KD, Galbraith MD, Luo X, Kraus WL, Dowell RD, Espinosa JM.

Elife. 2014 May 27;3:e02200. doi: 10.7554/eLife.02200.

29.

CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes.

Rokicki J, Knox D, Dowell RD, Copley SD.

BMC Genomics. 2014 Jan 24;15:65. doi: 10.1186/1471-2164-15-65.

30.

HIF1A employs CDK8-mediator to stimulate RNAPII elongation in response to hypoxia.

Galbraith MD, Allen MA, Bensard CL, Wang X, Schwinn MK, Qin B, Long HW, Daniels DL, Hahn WC, Dowell RD, Espinosa JM.

Cell. 2013 Jun 6;153(6):1327-39. doi: 10.1016/j.cell.2013.04.048.

31.

Genome-wide maps of polyadenylation reveal dynamic mRNA 3'-end formation in mammalian cell lineages.

Wang L, Dowell RD, Yi R.

RNA. 2013 Mar;19(3):413-25. doi: 10.1261/rna.035360.112. Epub 2013 Jan 16.

32.

sizzled function and secreted factor network dynamics.

Shi J, Zhang H, Dowell RD, Klymkowsky MW.

Biol Open. 2012 Mar 15;1(3):286-94. doi: 10.1242/bio.2012019. Epub 2012 Feb 3.

33.

The similarity of gene expression between human and mouse tissues.

Dowell RD.

Genome Biol. 2011;12(1):101. doi: 10.1186/gb-2011-12-1-101. Epub 2011 Jan 17.

34.

Transcription factor binding variation in the evolution of gene regulation.

Dowell RD.

Trends Genet. 2010 Nov;26(11):468-75. doi: 10.1016/j.tig.2010.08.005. Epub 2010 Sep 23. Review.

PMID:
20864205
35.

Genotype to phenotype: a complex problem.

Dowell RD, Ryan O, Jansen A, Cheung D, Agarwala S, Danford T, Bernstein DA, Rolfe PA, Heisler LE, Chin B, Nislow C, Giaever G, Phillips PC, Fink GR, Gifford DK, Boone C.

Science. 2010 Apr 23;328(5977):469. doi: 10.1126/science.1189015.

36.

Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast.

Wolf JJ, Dowell RD, Mahony S, Rabani M, Gifford DK, Fink GR.

Genetics. 2010 Jun;185(2):513-22. doi: 10.1534/genetics.110.113944. Epub 2010 Apr 9.

37.

Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast.

Bumgarner SL, Dowell RD, Grisafi P, Gifford DK, Fink GR.

Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18321-6. doi: 10.1073/pnas.0909641106. Epub 2009 Sep 30.

38.

Automated discovery of functional generality of human gene expression programs.

Gerber GK, Dowell RD, Jaakkola TS, Gifford DK.

PLoS Comput Biol. 2007 Aug;3(8):e148. Epub 2007 Jun 13.

39.

Tissue-specific transcriptional regulation has diverged significantly between human and mouse.

Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, Fraenkel E.

Nat Genet. 2007 Jun;39(6):730-2. Epub 2007 May 21.

40.
41.

High-resolution computational models of genome binding events.

Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

Nat Biotechnol. 2006 Aug;24(8):963-70. Erratum in: Nat Biotechnol. 2006 Oct;24(10):1293.

PMID:
16900145
42.

Core transcriptional regulatory circuitry in human hepatocytes.

Odom DT, Dowell RD, Jacobsen ES, Nekludova L, Rolfe PA, Danford TW, Gifford DK, Fraenkel E, Bell GI, Young RA.

Mol Syst Biol. 2006;2:2006.0017. Epub 2006 May 2.

43.
44.

The distributed annotation system.

Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L.

BMC Bioinformatics. 2001;2:7. Epub 2001 Oct 10.

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