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    Afzal, Veena

    TitleBiologist Scientist/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentEnviron Genomics & Systems Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-5476
    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 JA, 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. Gompers AL, Su-Feher L, Ellegood J, Copping NA, Riyadh MA, Stradleigh TW, Pride MC, Schaffler MD, Wade AA, Catta-Preta R, Zdilar I, Louis S, Kaushik G, Mannion BJ, Plajzer-Frick I, Afzal V, Visel A, Pennacchio LA, Dickel DE, Lerch JP, Crawley JN, Zarbalis KS, Silverman JL, Nord AS. Germline Chd8 haploinsufficiency alters brain development in mouse. Nat Neurosci. 2017 Aug; 20(8):1062-1073. PMID: 28671691.
        View in: PubMed
      3. 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 JA, 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
      4. 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 JA, 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
      5. 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. PMID: 25188404; PMCID: PMC4154669.
      6. 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. PMID: 24752179; PMCID: PMC4032856.
      7. 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. PMID: 24658141; PMCID: PMC4008384.
      8. 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. PMID: 24360275; PMCID: PMC3989111.
      9. 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. PMID: 24159046; PMCID: PMC3991470.
      10. 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. PMID: 23375746; PMCID: PMC3660042.
      11. 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. 2011 Dec 04; 44(1):89-93. PMID: 22138689; PMCID: PMC3246570.
      12. 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. PMID: 20729851; PMCID: PMC3138496.
      13. Visel A, Zhu Y, May D, Afzal V, Gong E, Attanasio C, Blow MJ, Cohen JC, Rubin EM, Pennacchio LA. Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature. 2010 Mar 18; 464(7287):409-12. PMID: 20173736; PMCID: PMC2938076.
      14. 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. PMID: 19268701; PMCID: PMC2683195.
      15. 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. PMID: 19212405; PMCID: PMC2745234.
      16. 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 05; 321(5894):1346-50. PMID: 18772437; PMCID: PMC2658639.
      17. 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. PMID: 18176564; PMCID: PMC2647775.
      18. Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, Pennacchio LA, Rubin EM. Deletion of ultraconserved elements yields viable mice. PLoS Biol. 2007 Sep; 5(9):e234. PMID: 17803355; PMCID: PMC1964772.
      19. 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.
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      20. Huby T, Doucet C, Dachet C, Ouzilleau B, Ueda Y, Afzal V, Rubin E, Chapman MJ, Lesnik P. Knockdown expression and hepatic deficiency reveal an atheroprotective role for SR-BI in liver and peripheral tissues. J Clin Invest. 2006 Oct; 116(10):2767-76. PMID: 16964311; PMCID: PMC1560348.
      21. Prabhakar S, Poulin F, Shoukry M, Afzal V, Rubin EM, Couronne O, Pennacchio LA. Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res. 2006 Jul; 16(7):855-63. PMID: 16769978; PMCID: PMC1484452.
      22. Poulin F, Nobrega MA, Plajzer-Frick I, Holt A, Afzal V, Rubin EM, Pennacchio LA. In vivo characterization of a vertebrate ultraconserved enhancer. Genomics. 2005 Jun; 85(6):774-81. PMID: 15885503.
        View in: PubMed
      23. Baroukh N, Ahituv N, Chang J, Shoukry M, Afzal V, Rubin EM, Pennacchio LA. Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene. Mamm Genome. 2005 Feb; 16(2):91-5. PMID: 15859353.
        View in: PubMed
      24. Nóbrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM. Megabase deletions of gene deserts result in viable mice. Nature. 2004 Oct 21; 431(7011):988-93. PMID: 15496924.
        View in: PubMed
      25. 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.
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      26. Nobrega MA, Ovcharenko I, Afzal V, Rubin EM. Scanning human gene deserts for long-range enhancers. Science. 2003 Oct 17; 302(5644):413. PMID: 14563999.
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      27. Huby T, Afzal V, Doucet C, Lawn RM, Gong EL, Chapman MJ, Thillet J, Rubin EM. Regulation of the expression of the apolipoprotein(a) gene: evidence for a regulatory role of the 5' distal apolipoprotein(a) transcription control region enhancer in yeast artificial chromosome transgenic mice. Arterioscler Thromb Vasc Biol. 2003 Sep 01; 23(9):1633-9. PMID: 12842837.
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      28. Mao JR, Taylor G, Dean WB, Wagner DR, Afzal V, Lotz JC, Rubin EM, Bristow J. Tenascin-X deficiency mimics Ehlers-Danlos syndrome in mice through alteration of collagen deposition. Nat Genet. 2002 Apr; 30(4):421-5. PMID: 11925569.
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      29. Mohrs M, Blankespoor CM, Wang ZE, Loots GG, Afzal V, Hadeiba H, Shinkai K, Rubin EM, Locksley RM. Deletion of a coordinate regulator of type 2 cytokine expression in mice. Nat Immunol. 2001 Sep; 2(9):842-7. PMID: 11526400.
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      30. Cavelier LB, Qiu Y, Bielicki JK, Afzal V, Cheng JF, Rubin EM. Regulation and activity of the human ABCA1 gene in transgenic mice. J Biol Chem. 2001 May 25; 276(21):18046-51. PMID: 11279093.
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      31. Shi ZT, Afzal V, Coller B, Patel D, Chasis JA, Parra M, Lee G, Paszty C, Stevens M, Walensky L, Peters LL, Mohandas N, Rubin E, Conboy JG. Protein 4.1R-deficient mice are viable but have erythroid membrane skeleton abnormalities. J Clin Invest. 1999 Feb; 103(3):331-40. PMID: 9927493; PMCID: PMC407893.
      32. Wolff S, Afzal V. Segregation of DNA polynucleotide strands into sister chromatids and the use of endoreduplicated cells to track sister chromatid exchanges induced by crosslinks, alkylations, or x-ray damage. Proc Natl Acad Sci U S A. 1996 Jun 11; 93(12):5765-9. PMID: 8650167; PMCID: PMC39135.
      33. Cleaver JE, Mitchell DL, Feeney L, Afzal V. Chromatid exchanges may be induced by damage in sites of transcriptional activity. Mutagenesis. 1996 Mar; 11(2):183-7. PMID: 8671736.
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      34. Afzal V, Feeney L, Thomas GH, Volpe JP, Cleaver JE. Sister chromatid exchanges in cells defective in mismatch, post-replication and excision repair. Mutagenesis. 1995 Sep; 10(5):457-62. PMID: 8544762.
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