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    Hiten Madhani, MD, PhD

    SchoolUCSF School of Medicine
    DepartmentBiochemistry and Biophysics
    Address600 16th Street
    San Francisco CA 94158
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      Collapse Biography 
      Collapse Awards and Honors
      UCSF2014Fellow of the American Academy of Microbiology
      UCSF2005 - 2010Lymphoma and Leukemia Society Scholar Award
      UCSF2000 - 2005David and Lucille Packard Foundation Fellowship
      UCSF1999 - 2002Burroughs-Wellcome Career Award
      Whitehead Institute1995 - 1999Helen Hay Whitney Postdoctoral Research Fellowship
      UCSF1987Dean's Prize for Student Research
      Stanford University1986Fox Award for Outstanding Undergraduate in Biology
      Stanford University1986Firestone Medal

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      Collapse Publications
      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. Al-Sady B, Greenstein RA, El-Samad HJ, Braun S, Madhani HD. Sensitive and Quantitative Three-Color Protein Imaging in Fission Yeast Using Spectrally Diverse, Recoded Fluorescent Proteins with Experimentally-Characterized In Vivo Maturation Kinetics. PLoS One. 2016; 11(8):e0159292. PMID: 27479698.
        View in: PubMed
      2. Homer CM, Summers DK, Goranov AI, Clarke SC, Wiesner DL, Diedrich JK, Moresco JJ, Toffaletti D, Upadhya R, Caradonna I, Petnic S, Pessino V, Cuomo CA, Lodge JK, Perfect J, Yates JR, Nielsen K, Craik CS, Madhani HD. Intracellular Action of a Secreted Peptide Required for Fungal Virulence. Cell Host Microbe. 2016 Jun 8; 19(6):849-64. PMID: 27212659.
        View in: PubMed
      3. Dumesic PA, Rosenblad MA, Samuelsson T, Nguyen T, Moresco JJ, Yates JR, Madhani HD. Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans. Nucleic Acids Res. 2015 Oct 15; 43(18):9017-27. PMID: 26275773; PMCID: PMC4605306.
      4. Desjardins CA, Sanscrainte ND, Goldberg JM, Heiman D, Young S, Zeng Q, Madhani HD, Becnel JJ, Cuomo CA. Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes. Nat Commun. 2015; 6:7121. PMID: 25968466; PMCID: PMC4435813.
      5. Garcia JF, Al-Sady B, Madhani HD. Intrinsic Toxicity of Unchecked Heterochromatin Spread Is Suppressed by Redundant Chromatin Boundary Functions in Schizosacchromyces pombe. G3 (Bethesda). 2015 Jul; 5(7):1453-61. PMID: 25957277; PMCID: PMC4502379.
      6. Dumesic PA, Homer CM, Moresco JJ, Pack LR, Shanle EK, Coyle SM, Strahl BD, Fujimori DG, Yates JR, Madhani HD. Product binding enforces the genomic specificity of a yeast polycomb repressive complex. Cell. 2015 Jan 15; 160(1-2):204-18. PMID: 25533783; PMCID: PMC4303595 [Available on 01/15/16].
      7. Brown JC, Nelson J, VanderSluis B, Deshpande R, Butts A, Kagan S, Polacheck I, Krysan DJ, Myers CL, Madhani HD. Unraveling the biology of a fungal meningitis pathogen using chemical genetics. Cell. 2014 Nov 20; 159(5):1168-87. PMID: 25416953; PMCID: PMC4243055 [Available on 11/20/15].
      8. Goranov AI, Madhani HD. Functional profiling of human fungal pathogen genomes. Cold Spring Harb Perspect Med. 2015 Mar; 5(3):a019596. PMID: 25377143.
        View in: PubMed
      9. Butts A, Koselny K, Chabrier-Roselló Y, Semighini CP, Brown JC, Wang X, Annadurai S, DiDone L, Tabroff J, Childers WE, Abou-Gharbia M, Wellington M, Cardenas ME, Madhani HD, Heitman J, Krysan DJ. Estrogen receptor antagonists are anti-cryptococcal agents that directly bind EF hand proteins and synergize with fluconazole in vivo. MBio. 2014; 5(1):e00765-13. PMID: 24520056; PMCID: PMC3950514.
      10. Madhani HD. snRNA catalysts in the spliceosome's ancient core. Cell. 2013 Dec 5; 155(6):1213-5. PMID: 24315092; PMCID: PMC4162089.
      11. Dumesic PA, Madhani HD. Recognizing the enemy within: licensing RNA-guided genome defense. Trends Biochem Sci. 2014 Jan; 39(1):25-34. PMID: 24280023; PMCID: PMC3902128.
      12. Madhani HD. The frustrated gene: origins of eukaryotic gene expression. Cell. 2013 Nov 7; 155(4):744-9. PMID: 24209615; PMCID: PMC4163148.
      13. Dumesic PA, Madhani HD. The spliceosome as a transposon sensor. RNA Biol. 2013 Nov; 10(11):1653-60. PMID: 24418889; PMCID: PMC3907475.
      14. Marina DB, Shankar S, Natarajan P, Finn KJ, Madhani HD. A conserved ncRNA-binding protein recruits silencing factors to heterochromatin through an RNAi-independent mechanism. Genes Dev. 2013 Sep 1; 27(17):1851-6. PMID: 24013500; PMCID: PMC3778239.
      15. Al-Sady B, Madhani HD, Narlikar GJ. Division of labor between the chromodomains of HP1 and Suv39 methylase enables coordination of heterochromatin spread. Mol Cell. 2013 Jul 11; 51(1):80-91. PMID: 23849629; PMCID: PMC3752401.
      16. Canzio D, Liao M, Naber N, Pate E, Larson A, Wu S, Marina DB, Garcia JF, Madhani HD, Cooke R, Schuck P, Cheng Y, Narlikar GJ. A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly. Nature. 2013 Apr 18; 496(7445):377-81. PMID: 23485968; PMCID: PMC3907283.
      17. Dumesic PA, Natarajan P, Chen C, Drinnenberg IA, Schiller BJ, Thompson J, Moresco JJ, Yates JR, Bartel DP, Madhani HD. Stalled spliceosomes are a signal for RNAi-mediated genome defense. Cell. 2013 Feb 28; 152(5):957-68. PMID: 23415457; PMCID: PMC3645481.
      18. Brown JC, Madhani HD. Approaching the functional annotation of fungal virulence factors using cross-species genetic interaction profiling. PLoS Genet. 2012; 8(12):e1003168. PMID: 23300468; PMCID: PMC3531484.
      19. Xu M, Soloveychik M, Ranger M, Schertzberg M, Shah Z, Raisner R, Venkatasubrahmanyan S, Tsui K, Gebbia M, Hughes T, van Bakel H, Nislow C, Madhani HD, Meneghini MD. Timing of transcriptional quiescence during gametogenesis is controlled by global histone H3K4 demethylation. Dev Cell. 2012 Nov 13; 23(5):1059-71. PMID: 23123093; PMCID: PMC3806484.
      20. Braun S, Madhani HD. Shaping the landscape: mechanistic consequences of ubiquitin modification of chromatin. EMBO Rep. 2012 Jul; 13(7):619-30. PMID: 22688965; PMCID: PMC3388787.
      21. Rougemaille M, Braun S, Coyle S, Dumesic PA, Garcia JF, Isaac RS, Libri D, Narlikar GJ, Madhani HD. Ers1 links HP1 to RNAi. Proc Natl Acad Sci U S A. 2012 Jul 10; 109(28):11258-63. PMID: 22733737; PMCID: PMC3396509.
      22. Madhani HD. Quorum sensing in fungi: Q&A. PLoS Pathog. 2011 Oct; 7(10):e1002301. PMID: 22046125; PMCID: PMC3203159.
      23. Kiely CM, Marguerat S, Garcia JF, Madhani HD, Bähler J, Winston F. Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe. Mol Cell Biol. 2011 Oct; 31(20):4193-204. PMID: 21844224; PMCID: PMC3187285.
      24. El-Samad H, Madhani HD. Can a systems perspective help us appreciate the biological meaning of small effects? Dev Cell. 2011 Jul 19; 21(1):11-3. PMID: 21763599; PMCID: PMC3615985.
      25. Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ. Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress. Proc Natl Acad Sci U S A. 2011 Jun 28; 108(26):10620-5. PMID: 21673141; PMCID: PMC3127919.
      26. Chun CD, Brown JC, Madhani HD. A major role for capsule-independent phagocytosis-inhibitory mechanisms in mammalian infection by Cryptococcus neoformans. Cell Host Microbe. 2011 Mar 17; 9(3):243-51. PMID: 21402362; PMCID: PMC3077425.
      27. Canzio D, Chang EY, Shankar S, Kuchenbecker KM, Simon MD, Madhani HD, Narlikar GJ, Al-Sady B. Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly. Mol Cell. 2011 Jan 7; 41(1):67-81. PMID: 21211724; PMCID: PMC3752404.
      28. Braun S, Garcia JF, Rowley M, Rougemaille M, Shankar S, Madhani HD. The Cul4-Ddb1(Cdt)² ubiquitin ligase inhibits invasion of a boundary-associated antisilencing factor into heterochromatin. Cell. 2011 Jan 7; 144(1):41-54. PMID: 21215368; PMCID: PMC3645473.
      29. McCullagh E, Seshan A, El-Samad H, Madhani HD. Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway. Nat Cell Biol. 2010 Oct; 12(10):954-62. PMID: 20852627; PMCID: PMC2948760.
      30. Chun CD, Madhani HD. Ctr2 links copper homeostasis to polysaccharide capsule formation and phagocytosis inhibition in the human fungal pathogen Cryptococcus neoformans. PLoS One. 2010; 5(9). PMID: 20824073; PMCID: PMC2932688.
      31. Garcia JF, Dumesic PA, Hartley PD, El-Samad H, Madhani HD. Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions. Genes Dev. 2010 Aug 15; 24(16):1758-71. PMID: 20675407; PMCID: PMC2922504.
      32. Chun CD, Madhani HD. Applying genetics and molecular biology to the study of the human pathogen Cryptococcus neoformans. Methods Enzymol. 2010; 470:797-831. PMID: 20946836; PMCID: PMC3611884.
      33. Bao MZ, Shock TR, Madhani HD. Multisite phosphorylation of the Saccharomyces cerevisiae filamentous growth regulator Tec1 is required for its recognition by the E3 ubiquitin ligase adaptor Cdc4 and its subsequent destruction in vivo. Eukaryot Cell. 2010 Jan; 9(1):31-6. PMID: 19897738; PMCID: PMC2805291.
      34. Hwang WW, Madhani HD. Nonredundant requirement for multiple histone modifications for the early anaphase release of the mitotic exit regulator Cdc14 from nucleolar chromatin. PLoS Genet. 2009 Aug; 5(8):e1000588. PMID: 19662160; PMCID: PMC2716543.
      35. Hartley PD, Madhani HD. Mechanisms that specify promoter nucleosome location and identity. Cell. 2009 May 1; 137(3):445-58. PMID: 19410542; PMCID: PMC2677553.
      36. Shock TR, Thompson J, Yates JR, Madhani HD. Hog1 mitogen-activated protein kinase (MAPK) interrupts signal transduction between the Kss1 MAPK and the Tec1 transcription factor to maintain pathway specificity. Eukaryot Cell. 2009 Apr; 8(4):606-16. PMID: 19218425; PMCID: PMC2669196.
      37. Madhani HD, Francis NJ, Kingston RE, Kornberg RD, Moazed D, Narlikar GJ, Panning B, Struhl K. Epigenomics: a roadmap, but to where? Science. 2008 Oct 3; 322(5898):43-4. PMID: 18832628; PMCID: PMC4479142.
      38. Liu OW, Chun CD, Chow ED, Chen C, Madhani HD, Noble SM. Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans. Cell. 2008 Oct 3; 135(1):174-88. PMID: 18854164; PMCID: PMC2628477.
      39. Raisner RM, Madhani HD. Genomewide screen for negative regulators of sirtuin activity in Saccharomyces cerevisiae reveals 40 loci and links to metabolism. Genetics. 2008 Aug; 179(4):1933-44. PMID: 18689887; PMCID: PMC2516070.
      40. Rougemaille M, Shankar S, Braun S, Rowley M, Madhani HD. Ers1, a rapidly diverging protein essential for RNA interference-dependent heterochromatic silencing in Schizosaccharomyces pombe. J Biol Chem. 2008 Sep 19; 283(38):25770-3. PMID: 18658154; PMCID: PMC2533792.
      41. Breslow DK, Cameron DM, Collins SR, Schuldiner M, Stewart-Ornstein J, Newman HW, Braun S, Madhani HD, Krogan NJ, Weissman JS. A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods. 2008 Aug; 5(8):711-8. PMID: 18622397; PMCID: PMC2756093.
      42. Venkatasubrahmanyam S, Hwang WW, Meneghini MD, Tong AH, Madhani HD. Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z. Proc Natl Acad Sci U S A. 2007 Oct 16; 104(42):16609-14. PMID: 17925448; PMCID: PMC2034229.
      43. Chow ED, Liu OW, O'Brien S, Madhani HD. Exploration of whole-genome responses of the human AIDS-associated yeast pathogen Cryptococcus neoformans var grubii: nitric oxide stress and body temperature. Curr Genet. 2007 Sep; 52(3-4):137-48. PMID: 17661046.
        View in: PubMed
      44. Cantin GT, Shock TR, Park SK, Madhani HD, Yates JR. Optimizing TiO2-based phosphopeptide enrichment for automated multidimensional liquid chromatography coupled to tandem mass spectrometry. Anal Chem. 2007 Jun 15; 79(12):4666-73. PMID: 17523591; PMCID: PMC2535607.
      45. Liu OW, Kelly MJ, Chow ED, Madhani HD. Parallel beta-helix proteins required for accurate capsule polysaccharide synthesis and virulence in the yeast Cryptococcus neoformans. Eukaryot Cell. 2007 Apr; 6(4):630-40. PMID: 17337638; PMCID: PMC1865648.
      46. Chun CD, Liu OW, Madhani HD. A link between virulence and homeostatic responses to hypoxia during infection by the human fungal pathogen Cryptococcus neoformans. PLoS Pathog. 2007 Feb; 3(2):e22. PMID: 17319742; PMCID: PMC1803011.
      47. Tompa R, Madhani HD. Histone H3 lysine 36 methylation antagonizes silencing in Saccharomyces cerevisiae independently of the Rpd3S histone deacetylase complex. Genetics. 2007 Feb; 175(2):585-93. PMID: 17179083; PMCID: PMC1800606.
      48. Madhani HD. Functional analysis of protein kinase networks in living cells: beyond "knock-outs" and "knock-downs". Methods. 2006 Nov; 40(3):251-4. PMID: 16884918.
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      49. Kung C, Kenski DM, Krukenberg K, Madhani HD, Shokat KM. Selective kinase inhibition by exploiting differential pathway sensitivity. Chem Biol. 2006 Apr; 13(4):399-407. PMID: 16632252; PMCID: PMC2932700.
      50. Raisner RM, Madhani HD. Patterning chromatin: form and function for H2A.Z variant nucleosomes. Curr Opin Genet Dev. 2006 Apr; 16(2):119-24. PMID: 16503125.
        View in: PubMed
      51. Schwartz MA, Madhani HD. Control of MAPK signaling specificity by a conserved residue in the MEK-binding domain of the yeast scaffold protein Ste5. Curr Genet. 2006 Jun; 49(6):351-63. PMID: 16463042.
        View in: PubMed
      52. Raisner RM, Hartley PD, Meneghini MD, Bao MZ, Liu CL, Schreiber SL, Rando OJ, Madhani HD. Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin. Cell. 2005 Oct 21; 123(2):233-48. PMID: 16239142; PMCID: PMC2039754.
      53. Kung C, Kenski DM, Dickerson SH, Howson RW, Kuyper LF, Madhani HD, Shokat KM. Chemical genomic profiling to identify intracellular targets of a multiplex kinase inhibitor. Proc Natl Acad Sci U S A. 2005 Mar 8; 102(10):3587-92. PMID: 15738404; PMCID: PMC552777.
      54. Bao MZ, Schwartz MA, Cantin GT, Yates JR, Madhani HD. Pheromone-dependent destruction of the Tec1 transcription factor is required for MAP kinase signaling specificity in yeast. Cell. 2004 Dec 29; 119(7):991-1000. PMID: 15620357.
        View in: PubMed
      55. Kobor MS, Venkatasubrahmanyam S, Meneghini MD, Gin JW, Jennings JL, Link AJ, Madhani HD, Rine J. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2004 May; 2(5):E131. PMID: 15045029; PMCID: PMC374244.
      56. Schwartz MA, Madhani HD. Principles of MAP kinase signaling specificity in Saccharomyces cerevisiae. Annu Rev Genet. 2004; 38:725-48. PMID: 15568991.
        View in: PubMed
      57. Meneghini MD, Wu M, Madhani HD. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell. 2003 Mar 7; 112(5):725-36. PMID: 12628191.
        View in: PubMed
      58. Hwang WW, Venkatasubrahmanyam S, Ianculescu AG, Tong A, Boone C, Madhani HD. A conserved RING finger protein required for histone H2B monoubiquitination and cell size control. Mol Cell. 2003 Jan; 11(1):261-6. PMID: 12535538.
        View in: PubMed
      59. Brugnera E, Haney L, Grimsley C, Lu M, Walk SF, Tosello-Trampont AC, Macara IG, Madhani H, Fink GR, Ravichandran KS. Unconventional Rac-GEF activity is mediated through the Dock180-ELMO complex. Nat Cell Biol. 2002 Aug; 4(8):574-82. PMID: 12134158.
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      60. Madhani HD. Accounting for specificity in receptor tyrosine kinase signaling. Cell. 2001 Jul 13; 106(1):9-11. PMID: 11461696.
        View in: PubMed
      61. Madhani HD. Interplay of intrinsic and extrinsic signals in yeast differentiation. Proc Natl Acad Sci U S A. 2000 Dec 5; 97(25):13461-3. PMID: 11095703; PMCID: PMC34079.
      62. Madhani HD, Galitski T, Lander ES, Fink GR. Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutants. Proc Natl Acad Sci U S A. 1999 Oct 26; 96(22):12530-5. PMID: 10535956; PMCID: PMC22972.
      63. Rupp S, Summers E, Lo HJ, Madhani H, Fink G. MAP kinase and cAMP filamentation signaling pathways converge on the unusually large promoter of the yeast FLO11 gene. EMBO J. 1999 Mar 1; 18(5):1257-69. PMID: 10064592; PMCID: PMC1171216.
      64. Madhani HD, Fink GR. The control of filamentous differentiation and virulence in fungi. Trends Cell Biol. 1998 Sep; 8(9):348-53. PMID: 9728395.
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      65. Madhani HD, Fink GR. The riddle of MAP kinase signaling specificity. Trends Genet. 1998 Apr; 14(4):151-5. PMID: 9594663.
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      66. Madhani HD, Styles CA, Fink GR. MAP kinases with distinct inhibitory functions impart signaling specificity during yeast differentiation. Cell. 1997 Nov 28; 91(5):673-84. PMID: 9393860.
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      67. Madhani HD. Genetic abnormalities in Friedreich's ataxia. N Engl J Med. 1997 Apr 3; 336(14):1022; author reply 1022-3. PMID: 9091787.
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      68. Madhani HD, Fink GR. Combinatorial control required for the specificity of yeast MAPK signaling. Science. 1997 Feb 28; 275(5304):1314-7. PMID: 9036858.
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      69. Madhani HD, Guthrie C. Genetic interactions between the yeast RNA helicase homolog Prp16 and spliceosomal snRNAs identify candidate ligands for the Prp16 RNA-dependent ATPase. Genetics. 1994 Jul; 137(3):677-87. PMID: 8088513; PMCID: PMC1206027.
      70. Madhani HD, Guthrie C. Randomization-selection analysis of snRNAs in vivo: evidence for a tertiary interaction in the spliceosome. Genes Dev. 1994 May 1; 8(9):1071-86. PMID: 7926788.
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      71. Madhani HD, Guthrie C. Dynamic RNA-RNA interactions in the spliceosome. Annu Rev Genet. 1994; 28:1-26. PMID: 7534458.
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      72. Madhani HD, Guthrie C. A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Cell. 1992 Nov 27; 71(5):803-17. PMID: 1423631.
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      73. Madhani HD, Bordonné R, Guthrie C. Multiple roles for U6 snRNA in the splicing pathway. Genes Dev. 1990 Dec; 4(12B):2264-77. PMID: 2149118.
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      74. Guthrie C, Madhani HD. Greetings from the RNA world. RNA Processing sponsored by the Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA, May 16-20, 1990. New Biol. 1990 Aug; 2(8):684-7. PMID: 1704252.
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      75. Jacks T, Madhani HD, Masiarz FR, Varmus HE. Signals for ribosomal frameshifting in the Rous sarcoma virus gag-pol region. Cell. 1988 Nov 4; 55(3):447-58. PMID: 2846182.
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      76. Madhani HD, Bohr VA, Hanawalt PC. Differential DNA repair in transcriptionally active and inactive proto-oncogenes: c-abl and c-mos. Cell. 1986 May 9; 45(3):417-23. PMID: 3698104.
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      77. Madhani HD, Leadon SA, Smith CA, Hanawalt PC. alpha DNA in African green monkey cells is organized into extremely long tandem arrays. J Biol Chem. 1986 Feb 15; 261(5):2314-8. PMID: 3003109.
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