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Douglas Lyne Black

Title(s)Professor, MIMG
SchoolMedicine
Address609 Charles E. Young Drive, Ea 1602A
Los Angeles CA 90024
Phone47644
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    Mechanisms of Post-transcriptional Gene Regulation by PTB and Rbfox Proteins
    NIH/NIGMS R35GM136426Apr 1, 2020 - Mar 31, 2025
    Role: Principal Investigator
    Multi-omic analysis of Myc-driven splicing for prostate cancer therapeutic development
    NIH/NCI R01CA220238Apr 1, 2018 - Mar 31, 2023
    Role: Co-Principal Investigator
    Mechanisms of Alternative Splicing Regulation by Rbfox Proteins
    NIH/NIGMS R01GM114463Sep 16, 2016 - Jul 31, 2020
    Role: Principal Investigator
    Elucidating an Xist-dependent program of sexually dimorphic alternative splicing in the mammalian brain
    NIH/NIMH R01MH109166Jul 1, 2016 - Apr 30, 2021
    Role: Principal Investigator
    Ribonomics of Gene Regulation to predict Innate Immune Responses
    NIH/NHGRI U01HG007912Jan 5, 2015 - Nov 30, 2017
    Role: Co-Principal Investigator
    Genomic Measurement of Alternative Splicing by DNA Array
    NIH/NIGMS R24GM070857Apr 1, 2004 - Mar 31, 2009
    Role: Principal Investigator
    The Regulation of Neuronal Exon Splicing
    NIH/NIGMS R01GM049662Aug 1, 1993 - Sep 14, 2011
    Role: Principal Investigator
    NEURON-SPECIFIC REGULATION OF C-SRC ALTERNATIVE SPLICING
    NIH/NIGMS R29GM049662Aug 1, 1993 - Jul 31, 1998
    Role: Principal Investigator

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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. to make corrections and additions.
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    1. Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers. Proc Natl Acad Sci U S A. 2020 03 10; 117(10):5269-5279. Phillips JW, Pan Y, Tsai BL, Xie Z, Demirdjian L, Xiao W, Yang HT, Zhang Y, Lin CH, Cheng D, Hu Q, Liu S, Black DL, Witte ON, Xing Y. PMID: 32086391.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    2. Deep-learning augmented RNA-seq analysis of transcript splicing. Nat Methods. 2019 04; 16(4):307-310. Zhang Z, Pan Z, Ying Y, Xie Z, Adhikari S, Phillips J, Carstens RP, Black DL, Wu Y, Xing Y. PMID: 30923373.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    3. Author Correction: Inhibiting amyloid-ß cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design. Nat Chem. 2018 12; 10(12):1267. Cao Q, Shin WS, Chan H, Vuong CK, Dubois B, Li B, Murray KA, Sawaya MR, Feigon J, Black DL, Eisenberg DS, Jiang L. PMID: 30420778.
      View in: PubMed   Mentions: 1     Fields:    
    4. Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. Proc Natl Acad Sci U S A. 2018 11 20; 115(47):E11061-E11070. Yeom KH, Mitchell S, Linares AJ, Zheng S, Lin CH, Wang XJ, Hoffmann A, Black DL. PMID: 30401736.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    5. Inhibiting amyloid-ß cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design. Nat Chem. 2018 12; 10(12):1213-1221. Cao Q, Shin WS, Chan H, Vuong CK, Dubois B, Li B, Murray KA, Sawaya MR, Feigon J, Black DL, Eisenberg DS, Jiang L. PMID: 30297750.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    6. Rbfox1 Regulates Synaptic Transmission through the Inhibitory Neuron-Specific vSNARE Vamp1. Neuron. 2018 04 04; 98(1):127-141.e7. Vuong CK, Wei W, Lee JA, Lin CH, Damianov A, de la Torre-Ubieta L, Halabi R, Otis KO, Martin KC, O'Dell TJ, Black DL. PMID: 29621484.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    7. Splicing Activation by Rbfox Requires Self-Aggregation through Its Tyrosine-Rich Domain. Cell. 2017 Jul 13; 170(2):312-323.e10. Ying Y, Wang XJ, Vuong CK, Lin CH, Damianov A, Black DL. PMID: 28708999.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    8. m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. Genes Dev. 2017 05 15; 31(10):990-1006. Ke S, Pandya-Jones A, Saito Y, Fak JJ, Vågbø CB, Geula S, Hanna JH, Black DL, Darnell JE, Darnell RB. PMID: 28637692.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansAnimalsCells
    9. Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing. Elife. 2016 11 24; 5. Wongpalee SP, Vashisht A, Sharma S, Chui D, Wohlschlegel JA, Black DL. PMID: 27882870.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    10. Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex. Cell. 2016 Aug 25; 166(5):1147-1162.e15. Zhang X, Chen MH, Wu X, Kodani A, Fan J, Doan R, Ozawa M, Ma J, Yoshida N, Reiter JF, Black DL, Kharchenko PV, Sharp PA, Walsh CA. PMID: 27565344.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansAnimalsCells
    11. Multiple determinants of splicing repression activity in the polypyrimidine tract binding proteins, PTBP1 and PTBP2. RNA. 2016 08; 22(8):1172-80. Keppetipola NM, Yeom KH, Hernandez AL, Bui T, Sharma S, Black DL. PMID: 27288314.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    12. The neurogenetics of alternative splicing. Nat Rev Neurosci. 2016 May; 17(5):265-81. Vuong CK, Black DL, Zheng S. PMID: 27094079.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansAnimalsCells
    13. Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR. Cell. 2016 Apr 21; 165(3):606-19. Damianov A, Ying Y, Lin CH, Lee JA, Tran D, Vashisht AA, Bahrami-Samani E, Xing Y, Martin KC, Wohlschlegel JA, Black DL. PMID: 27104978.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    14. The splicing regulator PTBP1 controls the activity of the transcription factor Pbx1 during neuronal differentiation. Elife. 2015 Dec 24; 4:e09268. Linares AJ, Lin CH, Damianov A, Adams KL, Novitch BG, Black DL. PMID: 26705333.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    15. Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes. Neuron. 2016 Jan 06; 89(1):113-28. Lee JA, Damianov A, Lin CH, Fontes M, Parikshak NN, Anderson ES, Geschwind DH, Black DL, Martin KC. PMID: 26687839.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansAnimalsCells
    16. Reflections on the RNA journal at 20 and its role in the question of splice site choice. RNA. 2015 Apr; 21(4):497-9. Black D. PMID: 25780111.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    17. Stem-loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly. Genes Dev. 2014 Nov 15; 28(22):2518-31. Sharma S, Wongpalee SP, Vashisht A, Wohlschlegel JA, Black DL. PMID: 25403181.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    18. De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function. PLoS Comput Biol. 2014 Jan; 10(1):e1003442. Han A, Stoilov P, Linares AJ, Zhou Y, Fu XD, Black DL. PMID: 24499931.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    19. The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation. Elife. 2014; 3:e01201. Li Q, Zheng S, Han A, Lin CH, Stoilov P, Fu XD, Black DL. PMID: 24448406.
      View in: PubMed   Mentions: 57     Fields:    Translation:AnimalsCells
    20. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol. 2013 Dec; 20(12):1434-42. Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark TJ, Gehman LT, Hoon S, Massirer KB, Pratt GA, Black DL, Gray JW, Conboy JG, Yeo GW. PMID: 24213538.
      View in: PubMed   Mentions: 91     Fields:    Translation:HumansAnimalsCells
    21. Alternative pre-mRNA splicing in neurons: growing up and extending its reach. Trends Genet. 2013 Aug; 29(8):442-8. Zheng S, Black DL. PMID: 23648015.
      View in: PubMed   Mentions: 42     Fields:    Translation:AnimalsCells
    22. A broadly applicable high-throughput screening strategy identifies new regulators of Dlg4 (Psd-95) alternative splicing. Genome Res. 2013 Jun; 23(6):998-1007. Zheng S, Damoiseaux R, Chen L, Black DL. PMID: 23636947.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    23. Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression. RNA. 2013 Jun; 19(6):811-27. Pandya-Jones A, Bhatt DM, Lin CH, Tong AJ, Smale ST, Black DL. PMID: 23616639.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    24. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell. 2012 Jul 20; 150(2):279-90. Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, Lissner MM, Natoli G, Black DL, Smale ST. PMID: 22817891.
      View in: PubMed   Mentions: 177     Fields:    Translation:AnimalsCells
    25. Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2. Crit Rev Biochem Mol Biol. 2012 Jul-Aug; 47(4):360-78. Keppetipola N, Sharma S, Li Q, Black DL. PMID: 22655688.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansAnimalsCells
    26. The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. RNA. 2012 May; 18(5):1041-9. Anderson ES, Lin CH, Xiao X, Stoilov P, Burge CB, Black DL. PMID: 22456266.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    27. The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function. Genes Dev. 2012 Mar 01; 26(5):445-60. Gehman LT, Meera P, Stoilov P, Shiue L, O'Brien JE, Meisler MH, Ares M, Otis TS, Black DL. PMID: 22357600.
      View in: PubMed   Mentions: 73     Fields:    Translation:AnimalsCells
    28. PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2. Nat Neurosci. 2012 Jan 15; 15(3):381-8, S1. Zheng S, Gray EE, Chawla G, Porse BT, O'Dell TJ, Black DL. PMID: 22246437.
      View in: PubMed   Mentions: 77     Fields:    Translation:AnimalsCells
    29. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet. 2011 May 29; 43(7):706-11. Gehman LT, Stoilov P, Maguire J, Damianov A, Lin CH, Shiue L, Ares M, Mody I, Black DL. PMID: 21623373.
      View in: PubMed   Mentions: 126     Fields:    Translation:AnimalsCells
    30. U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression. Mol Cell. 2011 Mar 04; 41(5):579-88. Sharma S, Maris C, Allain FH, Black DL. PMID: 21362553.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    31. Regulation of the mutually exclusive exons 8a and 8 in the CaV1.2 calcium channel transcript by polypyrimidine tract-binding protein. J Biol Chem. 2011 Mar 25; 286(12):10007-16. Tang ZZ, Sharma S, Zheng S, Chawla G, Nikolic J, Black DL. PMID: 21282112.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    32. Tapas and RNA in Renaissance Spain. RNA Biol. 2010 Mar-Apr; 7(2):130-2. Black DL, Gorospe M. PMID: 20534974.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    33. Autoregulation of Fox protein expression to produce dominant negative splicing factors. RNA. 2010 Feb; 16(2):405-16. Damianov A, Black DL. PMID: 20042473.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansAnimalsCells
    34. An inducible change in Fox-1/A2BP1 splicing modulates the alternative splicing of downstream neuronal target exons. Genes Dev. 2009 Oct 01; 23(19):2284-93. Lee JA, Tang ZZ, Black DL. PMID: 19762510.
      View in: PubMed   Mentions: 77     Fields:    Translation:AnimalsCells
    35. Co-transcriptional splicing of constitutive and alternative exons. RNA. 2009 Oct; 15(10):1896-908. Pandya-Jones A, Black DL. PMID: 19656867.
      View in: PubMed   Mentions: 111     Fields:    Translation:HumansCells
    36. Developmental control of CaV1.2 L-type calcium channel splicing by Fox proteins. Mol Cell Biol. 2009 Sep; 29(17):4757-65. Tang ZZ, Zheng S, Nikolic J, Black DL. PMID: 19564422.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimalsCells
    37. Sam68 regulates a set of alternatively spliced exons during neurogenesis. Mol Cell Biol. 2009 Jan; 29(1):201-13. Chawla G, Lin CH, Han A, Shiue L, Ares M, Black DL. PMID: 18936165.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansAnimalsCells
    38. A high-throughput screening strategy identifies cardiotonic steroids as alternative splicing modulators. Proc Natl Acad Sci U S A. 2008 Aug 12; 105(32):11218-23. Stoilov P, Lin CH, Damoiseaux R, Nikolic J, Black DL. PMID: 18678901.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    39. MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA. 2008 Aug; 14(8):1470-9. Xing Y, Stoilov P, Kapur K, Han A, Jiang H, Shen S, Black DL, Wong WH. PMID: 18566192.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansAnimalsCells
    40. To cross or not to cross: alternatively spliced forms of the Robo3 receptor regulate discrete steps in axonal midline crossing. Neuron. 2008 May 08; 58(3):297-8. Black DL, Zipursky SL. PMID: 18466738.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    41. Polypyrimidine tract binding protein controls the transition from exon definition to an intron defined spliceosome. Nat Struct Mol Biol. 2008 Feb; 15(2):183-91. Sharma S, Kohlstaedt LA, Damianov A, Rio DC, Black DL. PMID: 18193060.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansCells
    42. Neuronal regulation of alternative pre-mRNA splicing. Nat Rev Neurosci. 2007 Nov; 8(11):819-31. Li Q, Lee JA, Black DL. PMID: 17895907.
      View in: PubMed   Mentions: 187     Fields:    Translation:HumansAnimalsCells
    43. A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev. 2007 Jul 01; 21(13):1636-52. Boutz PL, Stoilov P, Li Q, Lin CH, Chawla G, Ostrow K, Shiue L, Ares M, Black DL. PMID: 17606642.
      View in: PubMed   Mentions: 231     Fields:    Translation:HumansAnimalsCells
    44. Depolarization and CaM kinase IV modulate NMDA receptor splicing through two essential RNA elements. PLoS Biol. 2007 Feb; 5(2):e40. Lee JA, Xing Y, Nguyen D, Xie J, Lee CJ, Black DL. PMID: 17298178.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansAnimalsCells
    45. MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development. Genes Dev. 2007 Jan 01; 21(1):71-84. Boutz PL, Chawla G, Stoilov P, Black DL. PMID: 17210790.
      View in: PubMed   Mentions: 116     Fields:    Translation:HumansAnimalsCells
    46. Maps, codes, and sequence elements: can we predict the protein output from an alternatively spliced locus? Neuron. 2006 Nov 22; 52(4):574-6. Sharma S, Black DL. PMID: 17114042.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    47. Splicing bioinformatics to biology. Genome Biol. 2006; 7(5):317. Black DL, Graveley BR. PMID: 16732900.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    48. Molecular basis of RNA recognition by the human alternative splicing factor Fox-1. EMBO J. 2006 Jan 11; 25(1):163-73. Auweter SD, Fasan R, Reymond L, Underwood JG, Black DL, Pitsch S, Allain FH. PMID: 16362037.
      View in: PubMed   Mentions: 108     Fields:    Translation:HumansCells
    49. A consensus CaMK IV-responsive RNA sequence mediates regulation of alternative exons in neurons. RNA. 2005 Dec; 11(12):1825-34. Xie J, Jan C, Stoilov P, Park J, Black DL. PMID: 16314456.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    50. Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals. Mol Cell Biol. 2005 Nov; 25(22):10005-16. Underwood JG, Boutz PL, Dougherty JD, Stoilov P, Black DL. PMID: 16260614.
      View in: PubMed   Mentions: 146     Fields:    Translation:HumansAnimalsCells
    51. Polypyrimidine tract binding protein blocks the 5' splice site-dependent assembly of U2AF and the prespliceosomal E complex. Mol Cell. 2005 Aug 19; 19(4):485-96. Sharma S, Falick AM, Black DL. PMID: 16109373.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansCells
    52. Exon repression by polypyrimidine tract binding protein. RNA. 2005 May; 11(5):699-716. Amir-Ahmady B, Boutz PL, Markovtsov V, Phillips ML, Black DL. PMID: 15840818.
      View in: PubMed   Mentions: 55     Fields:    Translation:Cells
    53. A simple answer for a splicing conundrum. Proc Natl Acad Sci U S A. 2005 Apr 05; 102(14):4927-8. Black DL. PMID: 15795368.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    54. Differentiation-induced colocalization of the KH-type splicing regulatory protein with polypyrimidine tract binding protein and the c-src pre-mRNA. Mol Biol Cell. 2004 Feb; 15(2):774-86. Hall MP, Huang S, Black DL. PMID: 14657238.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimalsCells
    55. Protein kinase A phosphorylation modulates transport of the polypyrimidine tract-binding protein. Proc Natl Acad Sci U S A. 2003 Jul 22; 100(15):8776-81. Xie J, Lee JA, Kress TL, Mowry KL, Black DL. PMID: 12851456.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansAnimalsCells
    56. Roles for SR proteins and hnRNP A1 in the regulation of c-src exon N1. Mol Cell Biol. 2003 Mar; 23(6):1874-84. Rooke N, Markovtsov V, Cagavi E, Black DL. PMID: 12612063.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    57. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem. 2003; 72:291-336. Black DL. PMID: 12626338.
      View in: PubMed   Mentions: 961     Fields:    Translation:AnimalsCells
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