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    22833 Publications
    3073 Total Profiles
    24 Edited Profiles

    Akiyama, Jennifer

    TitleResearch Assoc Staff
    SchoolLawrence Berkeley National Lab
    DepartmentGenomics
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-5090

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. He A, Gu F, Hu Y, Ma Q, Yi Ye L, Akiyama JA, Visel A, Pennacchio LA, Pu WT. Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease. Nat Commun. 2014; 5:4907.
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      2. Wu H, Nord AS, Akiyama JA, 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.
        View in: PubMed
      3. Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, 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.
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      4. Dickel DE, Zhu Y, Nord AS, Wylie JN, Akiyama JA, 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.
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      5. Nord AS, Blow MJ, Attanasio C, Akiyama JA, 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.
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      6. Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R, Phouanenavong S, Akiyama JA, 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.
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      7. Parker SC, Stitzel ML, Taylor DL, Orozco JM, Erdos MR, Akiyama JA, van Bueren KL, Chines PS, Narisu N. 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.
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      8. 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 JA, 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.
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      9. May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama JA, 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. 2012 Jan; 44(1):89-93.
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      10. Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, 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.
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      11. Visel A, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA. Functional autonomy of distant-acting human enhancers. Genomics. 2009 Jun; 93(6):509-13.
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      12. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, 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.
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      13. Prabhakar S, Visel A, Akiyama JA, 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 5; 321(5894):1346-50.
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      14. Visel A, Prabhakar S, Akiyama JA, 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.
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      15. 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.
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      16. 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.
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      17. 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.
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      18. 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.
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      19. 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.
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      20. 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.
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      21. 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.
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      22. 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.
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      23. 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.
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      24. 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.
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      25. 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.
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      26. 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.
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      27. 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.
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