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Robin DeAnne Dowell-Deen

TitleProfessor
InstitutionUniversity of Colorado Boulder
DepartmentBiology-MCD Instruction
Phone303/492-8204

    Collapse Research 
    Collapse research activities and funding
    R03HD103995     (DOWELL-DEEN, ROBIN DEANNE)Sep 17, 2020 - Sep 16, 2022
    NIH
    Measuring global, loci-specific RNA degradation to interrogate RNA dysregulation in down syndrome during development
    Role: Principal Investigator
    R03AG061466     (DOWELL-DEEN, ROBIN DEANNE)Feb 1, 2019 - Dec 31, 2021
    NIH
    How does the naturally-occurring delta-Np53 isoform influence aging?
    Role: Principal Investigator
    R01GM125871     (DOWELL-DEEN, ROBIN DEANNE)Sep 5, 2018 - Jun 30, 2022
    NIH
    A Technique for Measuring Transcription Factor Activity
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Wilson ZN, Scott AL, Dowell RD, Odorizzi G. PI(3,5)P2 controls vacuole potassium transport to support cellular osmoregulation. Mol Biol Cell. 2018 07 15; 29(13):1718-1731. PMID: 29791245.
      View in: PubMed
    2. Russell PH, Vestal B, Shi W, Rudra PD, Dowell R, Radcliffe R, Saba L, Kechris K. miR-MaGiC improves quantification accuracy for small RNA-seq. BMC Res Notes. 2018 May 15; 11(1):296. PMID: 29764489.
      View in: PubMed
    3. Tripodi IJ, Allen MA, Dowell RD. Detecting Differential Transcription Factor Activity from ATAC-Seq Data. Molecules. 2018 May 10; 23(5). PMID: 29748466.
      View in: PubMed
    4. Sanchez GJ, Richmond PA, Bunker EN, Karman SS, Azofeifa J, Garnett AT, Xu Q, Wheeler GE, Toomey CM, Zhang Q, Dowell RD, Liu X. Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers. Nucleic Acids Res. 2018 02 28; 46(4):1756-1776. PMID: 29240919.
      View in: PubMed
    5. Azofeifa JG, Allen MA, Hendrix JR, Read T, Rubin JD, Dowell RD. Enhancer RNA profiling predicts transcription factor activity. Genome Res. 2018 Feb 15. PMID: 29449408.
      View in: PubMed
    6. Trexler CL, Odell AT, Jeong MY, Dowell RD, Leinwand LA. Transcriptome and Functional Profile of Cardiac Myocytes Is Influenced by Biological Sex. Circ Cardiovasc Genet. 2017 Oct; 10(5). PMID: 29030402.
      View in: PubMed
    7. Scott AL, Richmond PA, Dowell RD, Selmecki AM. The Influence of Polyploidy on the Evolution of Yeast Grown in a Sub-Optimal Carbon Source. Mol Biol Evol. 2017 10 01; 34(10):2690-2703. PMID: 28957510.
      View in: PubMed
    8. 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. Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications. Cell Rep. 2017 08 01; 20(5):1173-1186. PMID: 28768201.
      View in: PubMed
    9. Audetat KA, Galbraith MD, Odell AT, Lee T, Pandey A, Espinosa JM, Dowell RD, Taatjes DJ. A Kinase-Independent Role for Cyclin-Dependent Kinase 19 in p53 Response. Mol Cell Biol. 2017 07 01; 37(13). PMID: 28416637.
      View in: PubMed
    10. Bhandare S, Goldberg DS, Dowell R. Discriminating between HuR and TTP binding sites using the k-spectrum kernel method. PLoS One. 2017; 12(3):e0174052. PMID: 28333956.
      View in: PubMed
    11. Rudra P, Shi WJ, Vestal B, Russell PH, Odell A, Dowell RD, Radcliffe RA, Saba LM, Kechris K. Model based heritability scores for high-throughput sequencing data. BMC Bioinformatics. 2017 Mar 02; 18(1):143. PMID: 28253840.
      View in: PubMed
    12. Azofeifa JG, Dowell RD. A generative model for the behavior of RNA polymerase. Bioinformatics. 2017 01 15; 33(2):227-234. PMID: 27663494.
      View in: PubMed
    13. Dowell R, Odell A, Richmond P, Malmer D, Halper-Stromberg E, Bennett B, Larson C, Leach S, Radcliffe RA. Genome characterization of the selected long- and short-sleep mouse lines. Mamm Genome. 2016 12; 27(11-12):574-586. PMID: 27651241.
      View in: PubMed
    14. Lladser ME, Azofeifa JG, Allen MA, Dowell RD. RNA Pol II transcription model and interpretation of GRO-seq data. J Math Biol. 2017 01; 74(1-2):77-97. PMID: 27142882.
      View in: PubMed
    15. Knox DA, Dowell RD. A Modeling Framework for Generation of Positional and Temporal Simulations of Transcriptional Regulation. IEEE/ACM Trans Comput Biol Bioinform. 2016 May-Jun; 13(3):459-471. PMID: 27295631.
      View in: PubMed
    16. Vera JM, Dowell RD. Survey of cryptic unstable transcripts in yeast. BMC Genomics. 2016 Apr 26; 17:305. PMID: 27113450.
      View in: PubMed
    17. Kamens HM, Corley RP, Richmond PA, Darlington TM, Dowell R, Hopfer CJ, Stallings MC, Hewitt JK, Brown SA, Ehringer MA. Evidence for Association Between Low Frequency Variants in CHRNA6/CHRNB3 and Antisocial Drug Dependence. Behav Genet. 2016 09; 46(5):693-704. PMID: 27085880.
      View in: PubMed
    18. Poss ZC, Ebmeier CC, Odell AT, Tangpeerachaikul A, Lee T, Pelish HE, Shair MD, Dowell RD, Old WM, Taatjes DJ. Identification of Mediator Kinase Substrates in Human Cells using Cortistatin A and Quantitative Phosphoproteomics. Cell Rep. 2016 Apr 12; 15(2):436-50. PMID: 27050516.
      View in: PubMed
    19. Wang L, Siegenthaler JA, Dowell RD, Yi R. Foxc1 reinforces quiescence in self-renewing hair follicle stem cells. Science. 2016 Feb 05; 351(6273):613-7. PMID: 26912704.
      View in: PubMed
    20. Azofeifa JG, Allen MA, Lladser ME, Dowell RD. An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq. IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep-Oct; 14(5):1070-1081. PMID: 26829802.
      View in: PubMed
    21. Read T, Richmond PA, Dowell RD. A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity. PLoS Genet. 2016 Jan; 12(1):e1005746. PMID: 26751950.
      View in: PubMed
    22. Pugach EK, Richmond PA, Azofeifa JG, Dowell RD, Leinwand LA. Prolonged Cre expression driven by the a-myosin heavy chain promoter can be cardiotoxic. J Mol Cell Cardiol. 2015 Sep; 86:54-61. PMID: 26141530.
      View in: PubMed
    23. Bennett B, Larson C, Richmond PA, Odell AT, Saba LM, Tabakoff B, Dowell R, Radcliffe RA. Quantitative trait locus mapping of acute functional tolerance in the LXS recombinant inbred strains. Alcohol Clin Exp Res. 2015 Apr; 39(4):611-20. PMID: 25833023.
      View in: PubMed
    24. Selmecki AM, Maruvka YE, Richmond PA, Guillet M, Shoresh N, Sorenson AL, De S, Kishony R, Michor F, Dowell R, Pellman D. Polyploidy can drive rapid adaptation in yeast. Nature. 2015 Mar 19; 519(7543):349-52. PMID: 25731168.
      View in: PubMed
    25. Hendrix J, Read T, Lalonde JF, Jensen PK, Heymann W, Lovelace E, Zimmermann SA, Brasino M, Rokicki J, Dowell RD. Engineered calcium-precipitable restriction enzyme. ACS Synth Biol. 2014 Dec 19; 3(12):969-71. PMID: 25524101.
      View in: PubMed
    26. Allen MA, Andrysik Z, Dengler VL, Mellert HS, Guarnieri A, Freeman JA, Sullivan KD, Galbraith MD, Luo X, Kraus WL, Dowell RD, Espinosa JM. Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms. Elife. 2014 May 27; 3:e02200. PMID: 24867637.
      View in: PubMed
    27. Rokicki J, Knox D, Dowell RD, Copley SD. CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes. BMC Genomics. 2014 Jan 24; 15:65. PMID: 24460813.
      View in: PubMed
    28. Galbraith MD, Allen MA, Bensard CL, Wang X, Schwinn MK, Qin B, Long HW, Daniels DL, Hahn WC, Dowell RD, Espinosa JM. HIF1A employs CDK8-mediator to stimulate RNAPII elongation in response to hypoxia. Cell. 2013 Jun 06; 153(6):1327-39. PMID: 23746844.
      View in: PubMed
    29. Wang L, Dowell RD, Yi R. Genome-wide maps of polyadenylation reveal dynamic mRNA 3'-end formation in mammalian cell lineages. RNA. 2013 Mar; 19(3):413-25. PMID: 23325109.
      View in: PubMed
    30. Allen M, Dowell R. Retrospective reflections of a whistleblower: opinions on misconduct responses. Account Res. 2013; 20(5-6):339-48. PMID: 24028481.
      View in: PubMed
    31. Shi J, Zhang H, Dowell RD, Klymkowsky MW. sizzled function and secreted factor network dynamics. Biol Open. 2012 Mar 15; 1(3):286-94. PMID: 23213419.
      View in: PubMed
    32. Danford T, Dowell R, Agarwala S, Grisafi P, Fink G, Gifford D. Discovering regulatory overlapping RNA transcripts. J Comput Biol. 2011 Mar; 18(3):295-303. PMID: 21385035.
      View in: PubMed
    33. Dowell RD. The similarity of gene expression between human and mouse tissues. Genome Biol. 2011; 12(1):101. PMID: 21241524.
      View in: PubMed
    34. Dowell RD. Transcription factor binding variation in the evolution of gene regulation. Trends Genet. 2010 Nov; 26(11):468-75. PMID: 20864205.
      View in: PubMed
    35. 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. Genotype to phenotype: a complex problem. Science. 2010 Apr 23; 328(5977):469. PMID: 20413493.
      View in: PubMed
    36. Wolf JJ, Dowell RD, Mahony S, Rabani M, Gifford DK, Fink GR. Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast. Genetics. 2010 Jun; 185(2):513-22. PMID: 20382833.
      View in: PubMed
    37. Bumgarner SL, Dowell RD, Grisafi P, Gifford DK, Fink GR. Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A. 2009 Oct 27; 106(43):18321-6. PMID: 19805129.
      View in: PubMed
    38. Gerber GK, Dowell RD, Jaakkola TS, Gifford DK. Automated discovery of functional generality of human gene expression programs. PLoS Comput Biol. 2007 Aug; 3(8):e148. PMID: 17696603.
      View in: PubMed
    39. Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, Fraenkel E. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet. 2007 Jun; 39(6):730-2. PMID: 17529977.
      View in: PubMed
    40. Dowell RD, Eddy SR. Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics. 2006 Sep 04; 7:400. PMID: 16952317.
      View in: PubMed
    41. Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. High-resolution computational models of genome binding events. Nat Biotechnol. 2006 Aug; 24(8):963-70. PMID: 16900145.
      View in: PubMed
    42. Odom DT, Dowell RD, Jacobsen ES, Nekludova L, Rolfe PA, Danford TW, Gifford DK, Fraenkel E, Bell GI, Young RA. Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol. 2006; 2:2006.0017. PMID: 16738562.
      View in: PubMed
    43. Dowell RD, Eddy SR. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics. 2004 Jun 04; 5:71. PMID: 15180907.
      View in: PubMed
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