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    Akiyama, Jennifer

    TitleResearch Associate Supervsr II
    SchoolLawrence Berkeley National Lab
    DepartmentEnviron Genomics & Systems Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-5090
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Monti R, Barozzi I, Osterwalder M, Lee E, Kato M, Garvin TH, Plajzer-Frick I, Pickle CS, Akiyama J, Afzal V, Beerenwinkel N, Dickel DE, Visel A, Pennacchio LA. Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. PLoS Comput Biol. 2017 Aug; 13(8):e1005720. PMID: 28827824.
        View in: PubMed
      2. Kvon EZ, Kamneva OK, Melo US, Barozzi I, Osterwalder M, Mannion BJ, Tissières V, Pickle CS, Plajzer-Frick I, Lee EA, Kato M, Garvin TH, Akiyama J, Afzal V, Lopez-Rios J, Rubin EM, Dickel DE, Pennacchio LA, Visel A. Progressive Loss of Function in a Limb Enhancer during Snake Evolution. Cell. 2016 Oct 20; 167(3):633-642.e11. PMID: 27768887.
        View in: PubMed
      3. Dickel DE, Barozzi I, Zhu Y, Fukuda-Yuzawa Y, Osterwalder M, Mannion BJ, May D, Spurrell CH, Plajzer-Frick I, Pickle CS, Lee E, Garvin TH, Kato M, Akiyama J, Afzal V, Lee AY, Gorkin DU, Ren B, Rubin EM, Visel A, Pennacchio LA. Genome-wide compendium and functional assessment of in vivo heart enhancers. Nat Commun. 2016 Oct 05; 7:12923. PMID: 27703156.
        View in: PubMed
      4. Chatterjee S, Kapoor A, Akiyama J, Auer DR, Lee D, Gabriel S, Berrios C, Pennacchio LA, Chakravarti A. Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease. Cell. 2016 Oct 06; 167(2):355-368.e10. PMID: 27693352.
        View in: PubMed
      5. Rosin JM, Li W, Cox LL, Rolfe SM, Latorre V, Akiyama J, Visel A, Kuramoto T, Bobola N, Turner EE, Cox TC. A distal 594 bp ECR specifies Hmx1 expression in pinna and lateral facial morphogenesis and is regulated by the Hox-Pbx-Meis complex. Development. 2016 Jul 15; 143(14):2582-92. PMID: 27287804; PMCID: PMC4958336 [Available on 07/15/17].
      6. Aldiri I, Ajioka I, Xu B, Zhang J, Chen X, Benavente C, Finkelstein D, Johnson D, Akiyama J, Pennacchio LA, Dyer MA. Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma. Development. 2015 Dec 01; 142(23):4092-106. PMID: 26628093; PMCID: PMC4712833.
      7. He A, Gu F, Hu Y, Ma Q, Ye LY, Akiyama J, Visel A, Pennacchio LA, Pu WT. Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease. Nat Commun. 2014 Sep 24; 5:4907. PMID: 25249388; PMCID: PMC4236193.
      8. Wu H, Nord AS, Akiyama J, Shoukry M, Afzal V, Rubin EM, Pennacchio LA, Visel A. Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genet. 2014 Sep; 10(9):e1004610. PMID: 25188404; PMCID: PMC4154669.
      9. Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama J, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, Bernstein BE, Rubin EM, Visel A, Pennacchio LA. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Res. 2014 Jun; 24(6):920-9. PMID: 24752179; PMCID: PMC4032856.
      10. Dickel DE, Zhu Y, Nord AS, Wylie JN, Akiyama J, Afzal V, Plajzer-Frick I, Kirkpatrick A, Göttgens B, Bruneau BG, Visel A, Pennacchio LA. Function-based identification of mammalian enhancers using site-specific integration. Nat Methods. 2014 May; 11(5):566-71. PMID: 24658141; PMCID: PMC4008384.
      11. Nord AS, Blow MJ, Attanasio C, Akiyama J, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Rubenstein JL, Rubin EM, Pennacchio LA, Visel A. Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell. 2013 Dec 19; 155(7):1521-31. PMID: 24360275; PMCID: PMC3989111.
      12. Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R, Phouanenavong S, Akiyama J, Shoukry M, Afzal V, Rubin EM, FitzPatrick DR, Ren B, Hallgrímsson B, Pennacchio LA, Visel A. Fine tuning of craniofacial morphology by distant-acting enhancers. Science. 2013 Oct 25; 342(6157):1241006. PMID: 24159046; PMCID: PMC3991470.
      13. Parker SC, Stitzel ML, Taylor DL, Orozco JM, Erdos MR, Akiyama J, van Bueren KL, Chines PS, Narisu N, Black BL, Visel A, Pennacchio LA, Collins FS. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc Natl Acad Sci U S A. 2013 Oct 29; 110(44):17921-6. PMID: 24127591; PMCID: PMC3816444.
      14. Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K, Silberberg SN, Blow MJ, Hansen DV, Nord AS, Akiyama J, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Kaplan T, Kriegstein AR, Rubin EM, Ovcharenko I, Pennacchio LA, Rubenstein JL. A high-resolution enhancer atlas of the developing telencephalon. Cell. 2013 Feb 14; 152(4):895-908. PMID: 23375746; PMCID: PMC3660042.
      15. May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama J, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Afzal V, Simpson PC, Rubin EM, Black BL, Bristow J, Pennacchio LA, Visel A. Large-scale discovery of enhancers from human heart tissue. Nat Genet. 2011 Dec 04; 44(1):89-93. PMID: 22138689; PMCID: PMC3246570.
      16. Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama J, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Bristow J, Ren B, Black BL, Rubin EM, Visel A, Pennacchio LA. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet. 2010 Sep; 42(9):806-10. PMID: 20729851; PMCID: PMC3138496.
      17. Visel A, Akiyama J, Shoukry M, Afzal V, Rubin EM, Pennacchio LA. Functional autonomy of distant-acting human enhancers. Genomics. 2009 Jun; 93(6):509-13. PMID: 19268701; PMCID: PMC2683195.
      18. Visel A, Blow MJ, Li Z, Zhang T, Akiyama J, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009 Feb 12; 457(7231):854-8. PMID: 19212405; PMCID: PMC2745234.
      19. Prabhakar S, Visel A, Akiyama J, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, Fitzpatrick DR, Afzal V, Pennacchio LA, Rubin EM, Noonan JP. Human-specific gain of function in a developmental enhancer. Science. 2008 Sep 05; 321(5894):1346-50. PMID: 18772437; PMCID: PMC2658639.
      20. Visel A, Prabhakar S, Akiyama J, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio LA. Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet. 2008 Feb; 40(2):158-60. PMID: 18176564; PMCID: PMC2647775.
      21. Ahituv N, Akiyama J, Chapman-Helleboid A, Fruchart J, Pennacchio LA. In vivo characterization of human APOA5 haplotypes. Genomics. 2007 Dec; 90(6):674-9. PMID: 17936576.
        View in: PubMed
      22. Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM. In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006 Nov 23; 444(7118):499-502. PMID: 17086198.
        View in: PubMed
      23. Baroukh N, Bauge E, Akiyama J, Chang J, Afzal V, Fruchart JC, Rubin EM, Fruchart-Najib J, Pennacchio LA. Analysis of apolipoprotein A5, c3, and plasma triglyceride concentrations in genetically engineered mice. Arterioscler Thromb Vasc Biol. 2004 Jul; 24(7):1297-302. PMID: 15117734.
        View in: PubMed
      24. Hawgood S, Ochs M, Jung A, Akiyama J, Allen L, Brown C, Edmondson J, Levitt S, Carlson E, Gillespie AM, Villar A, Epstein CJ, Poulain FR. Sequential targeted deficiency of SP-A and -D leads to progressive alveolar lipoproteinosis and emphysema. Am J Physiol Lung Cell Mol Physiol. 2002 Nov; 283(5):L1002-10. PMID: 12376353.
        View in: PubMed
      25. Akiyama J, Hoffman A, Brown C, Allen L, Edmondson J, Poulain F, Hawgood S. Tissue distribution of surfactant proteins A and D in the mouse. J Histochem Cytochem. 2002 Jul; 50(7):993-6. PMID: 12070278.
        View in: PubMed
      26. Li G, Siddiqui J, Hendry M, Akiyama J, Edmondson J, Brown C, Allen L, Levitt S, Poulain F, Hawgood S. Surfactant protein-A--deficient mice display an exaggerated early inflammatory response to a beta-resistant strain of influenza A virus. Am J Respir Cell Mol Biol. 2002 Mar; 26(3):277-82. PMID: 11867335.
        View in: PubMed
      27. Hawgood S, Akiyama J, Brown C, Allen L, Li G, Poulain FR. GM-CSF mediates alveolar macrophage proliferation and type II cell hypertrophy in SP-D gene-targeted mice. Am J Physiol Lung Cell Mol Physiol. 2001 Jun; 280(6):L1148-56. PMID: 11350793.
        View in: PubMed
      28. Shibata K, Itoh M, Aizawa K, Nagaoka S, Sasaki N, Carninci P, Konno H, Akiyama J, Nishi K, Kitsunai T, Tashiro H, Itoh M, Sumi N, Ishii Y, Nakamura S, Hazama M, Nishine T, Harada A, Yamamoto R, Matsumoto H, Sakaguchi S, Ikegami T, Kashiwagi K, Fujiwake S, Inoue K, Togawa Y. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer. Genome Res. 2000 Nov; 10(11):1757-71. PMID: 11076861; PMCID: PMC310992.
      29. Akiyama J, Volik SV, Plajzer-Frick I, Prince A, Sago H, Weier HU, Vanderbilt JN, Hawgood S, Poulain FR. Characterization of the mouse collectin gene locus. Am J Respir Cell Mol Biol. 1999 Aug; 21(2):193-9. PMID: 10423401.
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      30. Poulain FR, Akiyama J, Allen L, Brown C, Chang R, Goerke J, Dobbs L, Hawgood S. Ultrastructure of phospholipid mixtures reconstituted with surfactant proteins B and D. Am J Respir Cell Mol Biol. 1999 May; 20(5):1049-58. PMID: 10226076.
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      31. Itoh M, Kitsunai T, Akiyama J, Shibata K, Izawa M, Kawai J, Tomaru Y, Carninci P, Shibata Y, Ozawa Y, Muramatsu M, Okazaki Y, Hayashizaki Y. Automated filtration-based high-throughput plasmid preparation system. Genome Res. 1999 May; 9(5):463-70. PMID: 10330126; PMCID: PMC310785.
      32. Botas C, Poulain F, Akiyama J, Brown C, Allen L, Goerke J, Clements J, Carlson E, Gillespie AM, Epstein C, Hawgood S. Altered surfactant homeostasis and alveolar type II cell morphology in mice lacking surfactant protein D. Proc Natl Acad Sci U S A. 1998 Sep 29; 95(20):11869-74. PMID: 9751757; PMCID: PMC21732.
      33. Wong CJ, Akiyama J, Allen L, Hawgood S. Localization and developmental expression of surfactant proteins D and A in the respiratory tract of the mouse. Pediatr Res. 1996 Jun; 39(6):930-7. PMID: 8725251.
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