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Mary Ann Allen

TitleAssoc Professor-Research
InstitutionUniversity of Colorado Boulder
DepartmentBiofrontiers Institute
Phone303/735-7395

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    R01HL156475     (ALLEN, MARY A)Feb 1, 2021 - Mar 31, 2025
    NIH
    Function of RUNX1 in diverse Down syndrome tissues
    Role: Principal Investigator

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    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. Cozzolino K, Sanford L, Hunter S, Molison K, Erickson B, Jones T, Courvan MCS, Ajit D, Galbraith MD, Espinosa JM, Bentley DL, Allen MA, Dowell RD, Taatjes DJ. Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome. bioRxiv. 2024 May 28. PMID: 37461585.
      View in: PubMed
    2. Sigauke RF, Sanford L, Maas ZL, Jones T, Stanley JT, Townsend HA, Allen MA, Dowell RD. Atlas of nascent RNA transcripts reveals enhancer to gene linkages. bioRxiv. 2023 Dec 08. PMID: 38105978.
      View in: PubMed
    3. Damon LJ, Ocampo D, Sanford L, Jones T, Allen MA, Dowell RD, Palmer AE. Cellular zinc status alters chromatin accessibility and binding of transcription factor p53 to genomic sites. bioRxiv. 2023 Nov 21. PMID: 38045276.
      View in: PubMed
    4. Hunter S, Hendrix J, Freeman J, Dowell RD, Allen MA. Transcription dosage compensation does not occur in Down syndrome. BMC Biol. 2023 11 10; 21(1):228. PMID: 37946204.
      View in: PubMed
    5. Rozen EJ, Ozeroff CD, Allen MA. RUN(X) out of blood: emerging RUNX1 functions beyond hematopoiesis and links to Down syndrome. Hum Genomics. 2023 09 05; 17(1):83. PMID: 37670378.
      View in: PubMed
    6. Lammer NC, Allen MA, Batey RT, Wuttke DS. Quantification of transcriptome changes to investigate the role of glucocorticoid receptor-RNA binding during dexamethasone treatment. BMC Res Notes. 2023 Aug 22; 16(1):181. PMID: 37608297.
      View in: PubMed
    7. Kurland JV, Cutler AA, Stanley JT, Betta ND, Van Deusen A, Pawlikowski B, Hall M, Antwine T, Russell A, Allen MA, Dowell R, Olwin B. Aging disrupts gene expression timing during muscle regeneration. Stem Cell Reports. 2023 06 13; 18(6):1325-1339. PMID: 37315524.
      View in: PubMed
    8. Hunter S, Dowell RD, Hendrix J, Freeman J, Allen MA. Transcription dosage compensation does not occur in Down syndrome. bioRxiv. 2023 Jun 09. PMID: 37333218.
      View in: PubMed
    9. Lammer NC, Ashraf HM, Ugay DA, Spencer SL, Allen MA, Batey RT, Wuttke DS. RNA binding by the glucocorticoid receptor attenuates dexamethasone-induced gene activation. Sci Rep. 2023 06 09; 13(1):9385. PMID: 37296231.
      View in: PubMed
    10. Cardiello JF, Westfall J, Dowell R, Allen MA. Characterizing Primary transcriptional responses to short term heat shock in paired fraternal lymphoblastoid lines with and without Down syndrome. bioRxiv. 2023 Feb 02. PMID: 36712041.
      View in: PubMed
    11. Walker CJ, Batan D, Bishop CT, Ramirez D, Aguado BA, Schroeder ME, Crocini C, Schwisow J, Moulton K, Macdougall L, Weiss RM, Allen MA, Dowell R, Leinwand LA, Anseth KS. Extracellular matrix stiffness controls cardiac valve myofibroblast activation through epigenetic remodeling. Bioeng Transl Med. 2022 Sep; 7(3):e10394. PMID: 36176599.
      View in: PubMed
    12. Hunter S, Sigauke RF, Stanley JT, Allen MA, Dowell RD. Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries. BMC Genomics. 2022 Mar 07; 23(1):187. PMID: 35255806.
      View in: PubMed
    13. Walker CJ, Crocini C, Ramirez D, Killaars AR, Grim JC, Aguado BA, Clark K, Allen MA, Dowell RD, Leinwand LA, Anseth KS. Author Correction: Nuclear mechanosensing drives chromatin remodelling in persistently activated fibroblasts. Nat Biomed Eng. 2021 Dec; 5(12):1517-1518. PMID: 34050334.
      View in: PubMed
    14. Janiszewski LN, Minson M, Allen MA, Dowell RD, Palmer AE. Characterization of Global Gene Expression, Regulation of Metal Ions, and Infection Outcomes in Immune-Competent 129S6 Mouse Macrophages. Infect Immun. 2021 10 15; 89(11):e0027321. PMID: 34370511.
      View in: PubMed
    15. Walker CJ, Crocini C, Ramirez D, Killaars AR, Grim JC, Aguado BA, Clark K, Allen MA, Dowell RD, Leinwand LA, Anseth KS. Nuclear mechanosensing drives chromatin remodelling in persistently activated fibroblasts. Nat Biomed Eng. 2021 12; 5(12):1485-1499. PMID: 33875841.
      View in: PubMed
    16. Stanley JT, Gilchrist AR, Stabell AC, Allen MA, Sawyer SL, Dowell RD. Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue Protease. Pac Symp Biocomput. 2020; 25:487-498. PMID: 31797621.
      View in: PubMed
    17. Cardiello JF, Sanchez GJ, Allen MA, Dowell RD. Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs. Transcription. 2020 02; 11(1):3-18. PMID: 31856658.
      View in: PubMed
    18. Sasse SK, Gruca M, Allen MA, Kadiyala V, Song T, Gally F, Gupta A, Pufall MA, Dowell RD, Gerber AN. Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression. Genome Res. 2019 11; 29(11):1753-1765. PMID: 31519741.
      View in: PubMed
    19. 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. Identification and characterization of a novel anti-inflammatory lipid isolated from Mycobacterium vaccae, a soil-derived bacterium with immunoregulatory and stress resilience properties. Psychopharmacology (Berl). 2019 May; 236(5):1653-1670. PMID: 31119329.
      View in: PubMed
    20. Melnick M, Gonzales P, Cabral J, Allen MA, Dowell RD, Link CD. Heat shock in C. elegans induces downstream of gene transcription and accumulation of double-stranded RNA. PLoS One. 2019; 14(4):e0206715. PMID: 30958820.
      View in: PubMed
    21. 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
    22. Azofeifa JG, Allen MA, Hendrix JR, Read T, Rubin JD, Dowell RD. Enhancer RNA profiling predicts transcription factor activity. Genome Res. 2018 03 01; 28(3):334-344. PMID: 29449408.
      View in: PubMed
    23. 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
    24. 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
    25. 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
    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. 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
    28. Allen MA, Hillier LW, Waterston RH, Blumenthal T. A global analysis of C. elegans trans-splicing. Genome Res. 2011 Feb; 21(2):255-64. PMID: 21177958.
      View in: PubMed
    29. Lasda EL, Allen MA, Blumenthal T. Polycistronic pre-mRNA processing in vitro: snRNP and pre-mRNA role reversal in trans-splicing. Genes Dev. 2010 Aug 01; 24(15):1645-58. PMID: 20624853.
      View in: PubMed
    30. Cui M, Allen MA, Larsen A, Macmorris M, Han M, Blumenthal T. Genes involved in pre-mRNA 3'-end formation and transcription termination revealed by a lin-15 operon Muv suppressor screen. Proc Natl Acad Sci U S A. 2008 Oct 28; 105(43):16665-70. PMID: 18946043.
      View in: PubMed
    31. Vicens Q, Allen MA, Gilbert SD, Reznik B, Gooding AR, Batey RT. The Cech Symposium: a celebration of 25 years of ribozymes, 10 years of TERT, and 60 years of Tom. RNA. 2008 Mar; 14(3):397-403. PMID: 18203922.
      View in: PubMed
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