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Black, Douglas Lyne

Title(s)Professor, Mimg
Phone47644
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    Collapse Research 
    Collapse Research Activities and Funding
    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

    Collapse Bibliographic 
    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. 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. Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers. Proc Natl Acad Sci U S A. 2020 Feb 21. PMID: 32086391.
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    2. Zhang Z, Pan Z, Ying Y, Xie Z, Adhikari S, Phillips J, Carstens RP, Black DL, Wu Y, Xing Y. Deep-learning augmented RNA-seq analysis of transcript splicing. Nat Methods. 2019 04; 16(4):307-310. PMID: 30923373.
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    3. Cao Q, Shin WS, Chan H, Vuong CK, Dubois B, Li B, Murray KA, Sawaya MR, Feigon J, Black DL, Eisenberg DS, Jiang L. 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. PMID: 30420778.
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    4. Yeom KH, Mitchell S, Linares AJ, Zheng S, Lin CH, Wang XJ, Hoffmann A, Black DL. 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. PMID: 30401736.
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    5. Cao Q, Shin WS, Chan H, Vuong CK, Dubois B, Li B, Murray KA, Sawaya MR, Feigon J, Black DL, Eisenberg DS, Jiang L. 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. PMID: 30297750.
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    6. 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. Rbfox1 Regulates Synaptic Transmission through the Inhibitory Neuron-Specific vSNARE Vamp1. Neuron. 2018 04 04; 98(1):127-141.e7. PMID: 29621484.
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    7. Ying Y, Wang XJ, Vuong CK, Lin CH, Damianov A, Black DL. Splicing Activation by Rbfox Requires Self-Aggregation through Its Tyrosine-Rich Domain. Cell. 2017 Jul 13; 170(2):312-323.e10. PMID: 28708999.
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    8. Ke S, Pandya-Jones A, Saito Y, Fak JJ, Vågbø CB, Geula S, Hanna JH, Black DL, Darnell JE, Darnell RB. 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. PMID: 28637692.
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    9. Wongpalee SP, Vashisht A, Sharma S, Chui D, Wohlschlegel JA, Black DL. Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing. Elife. 2016 11 24; 5. PMID: 27882870.
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    10. 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. Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex. Cell. 2016 Aug 25; 166(5):1147-1162.e15. PMID: 27565344.
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    11. Keppetipola NM, Yeom KH, Hernandez AL, Bui T, Sharma S, Black DL. Multiple determinants of splicing repression activity in the polypyrimidine tract binding proteins, PTBP1 and PTBP2. RNA. 2016 08; 22(8):1172-80. PMID: 27288314.
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    12. Vuong CK, Black DL, Zheng S. The neurogenetics of alternative splicing. Nat Rev Neurosci. 2016 May; 17(5):265-81. PMID: 27094079.
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    13. Damianov A, Ying Y, Lin CH, Lee JA, Tran D, Vashisht AA, Bahrami-Samani E, Xing Y, Martin KC, Wohlschlegel JA, Black DL. Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR. Cell. 2016 Apr 21; 165(3):606-19. PMID: 27104978.
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    14. Linares AJ, Lin CH, Damianov A, Adams KL, Novitch BG, Black DL. The splicing regulator PTBP1 controls the activity of the transcription factor Pbx1 during neuronal differentiation. Elife. 2015 Dec 24; 4:e09268. PMID: 26705333.
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    15. Lee JA, Damianov A, Lin CH, Fontes M, Parikshak NN, Anderson ES, Geschwind DH, Black DL, Martin KC. Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes. Neuron. 2016 Jan 06; 89(1):113-28. PMID: 26687839.
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    16. Black D. Reflections on the RNA journal at 20 and its role in the question of splice site choice. RNA. 2015 Apr; 21(4):497-9. PMID: 25780111.
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    17. Sharma S, Wongpalee SP, Vashisht A, Wohlschlegel JA, Black DL. 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. PMID: 25403181.
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    18. Han A, Stoilov P, Linares AJ, Zhou Y, Fu XD, Black DL. 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. PMID: 24499931.
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    19. Li Q, Zheng S, Han A, Lin CH, Stoilov P, Fu XD, Black DL. The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation. Elife. 2014; 3:e01201. PMID: 24448406.
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    20. 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. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol. 2013 Dec; 20(12):1434-42. PMID: 24213538.
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    21. Zheng S, Black DL. Alternative pre-mRNA splicing in neurons: growing up and extending its reach. Trends Genet. 2013 Aug; 29(8):442-8. PMID: 23648015.
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    22. Zheng S, Damoiseaux R, Chen L, Black DL. A broadly applicable high-throughput screening strategy identifies new regulators of Dlg4 (Psd-95) alternative splicing. Genome Res. 2013 Jun; 23(6):998-1007. PMID: 23636947.
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    23. Pandya-Jones A, Bhatt DM, Lin CH, Tong AJ, Smale ST, Black DL. 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. PMID: 23616639.
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    24. Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, Lissner MM, Natoli G, Black DL, Smale ST. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell. 2012 Jul 20; 150(2):279-90. PMID: 22817891.
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    25. Keppetipola N, Sharma S, Li Q, Black DL. 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. PMID: 22655688.
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    26. Anderson ES, Lin CH, Xiao X, Stoilov P, Burge CB, Black DL. The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. RNA. 2012 May; 18(5):1041-9. PMID: 22456266.
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    27. Gehman LT, Meera P, Stoilov P, Shiue L, O'Brien JE, Meisler MH, Ares M, Otis TS, Black DL. The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function. Genes Dev. 2012 Mar 01; 26(5):445-60. PMID: 22357600.
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    28. Zheng S, Gray EE, Chawla G, Porse BT, O'Dell TJ, Black DL. PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2. Nat Neurosci. 2012 Jan 15; 15(3):381-8, S1. PMID: 22246437.
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    29. Gehman LT, Stoilov P, Maguire J, Damianov A, Lin CH, Shiue L, Ares M, Mody I, Black DL. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet. 2011 May 29; 43(7):706-11. PMID: 21623373.
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    30. Sharma S, Maris C, Allain FH, Black DL. U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression. Mol Cell. 2011 Mar 04; 41(5):579-88. PMID: 21362553.
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    31. Tang ZZ, Sharma S, Zheng S, Chawla G, Nikolic J, Black DL. 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. PMID: 21282112.
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    32. Black DL, Gorospe M. Tapas and RNA in Renaissance Spain. RNA Biol. 2010 Mar-Apr; 7(2):130-2. PMID: 20534974.
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    33. Damianov A, Black DL. Autoregulation of Fox protein expression to produce dominant negative splicing factors. RNA. 2010 Feb; 16(2):405-16. PMID: 20042473.
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    34. Lee JA, Tang ZZ, Black DL. 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. PMID: 19762510.
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    35. Pandya-Jones A, Black DL. Co-transcriptional splicing of constitutive and alternative exons. RNA. 2009 Oct; 15(10):1896-908. PMID: 19656867.
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    36. Tang ZZ, Zheng S, Nikolic J, Black DL. Developmental control of CaV1.2 L-type calcium channel splicing by Fox proteins. Mol Cell Biol. 2009 Sep; 29(17):4757-65. PMID: 19564422.
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    37. Chawla G, Lin CH, Han A, Shiue L, Ares M, Black DL. Sam68 regulates a set of alternatively spliced exons during neurogenesis. Mol Cell Biol. 2009 Jan; 29(1):201-13. PMID: 18936165.
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    38. Stoilov P, Lin CH, Damoiseaux R, Nikolic J, Black DL. 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. PMID: 18678901.
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    39. Xing Y, Stoilov P, Kapur K, Han A, Jiang H, Shen S, Black DL, Wong WH. MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA. 2008 Aug; 14(8):1470-9. PMID: 18566192.
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    40. Black DL, Zipursky SL. 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. PMID: 18466738.
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    41. Sharma S, Kohlstaedt LA, Damianov A, Rio DC, Black DL. 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. PMID: 18193060.
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    42. Li Q, Lee JA, Black DL. Neuronal regulation of alternative pre-mRNA splicing. Nat Rev Neurosci. 2007 Nov; 8(11):819-31. PMID: 17895907.
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    43. Boutz PL, Stoilov P, Li Q, Lin CH, Chawla G, Ostrow K, Shiue L, Ares M, Black DL. 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. PMID: 17606642.
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    44. Lee JA, Xing Y, Nguyen D, Xie J, Lee CJ, Black DL. Depolarization and CaM kinase IV modulate NMDA receptor splicing through two essential RNA elements. PLoS Biol. 2007 Feb; 5(2):e40. PMID: 17298178.
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    45. Boutz PL, Chawla G, Stoilov P, Black DL. MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development. Genes Dev. 2007 Jan 01; 21(1):71-84. PMID: 17210790.
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    46. Sharma S, Black DL. Maps, codes, and sequence elements: can we predict the protein output from an alternatively spliced locus? Neuron. 2006 Nov 22; 52(4):574-6. PMID: 17114042.
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    47. Black DL, Graveley BR. Splicing bioinformatics to biology. Genome Biol. 2006; 7(5):317. PMID: 16732900.
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    48. Auweter SD, Fasan R, Reymond L, Underwood JG, Black DL, Pitsch S, Allain FH. Molecular basis of RNA recognition by the human alternative splicing factor Fox-1. EMBO J. 2006 Jan 11; 25(1):163-73. PMID: 16362037.
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    49. Xie J, Jan C, Stoilov P, Park J, Black DL. A consensus CaMK IV-responsive RNA sequence mediates regulation of alternative exons in neurons. RNA. 2005 Dec; 11(12):1825-34. PMID: 16314456.
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    50. Underwood JG, Boutz PL, Dougherty JD, Stoilov P, Black DL. Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals. Mol Cell Biol. 2005 Nov; 25(22):10005-16. PMID: 16260614.
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    51. Sharma S, Falick AM, Black DL. 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. PMID: 16109373.
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    52. Amir-Ahmady B, Boutz PL, Markovtsov V, Phillips ML, Black DL. Exon repression by polypyrimidine tract binding protein. RNA. 2005 May; 11(5):699-716. PMID: 15840818.
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    53. Black DL. A simple answer for a splicing conundrum. Proc Natl Acad Sci U S A. 2005 Apr 05; 102(14):4927-8. PMID: 15795368.
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    54. Hall MP, Huang S, Black DL. 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. PMID: 14657238.
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    55. Xie J, Lee JA, Kress TL, Mowry KL, Black DL. 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. PMID: 12851456.
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    56. Rooke N, Markovtsov V, Cagavi E, Black DL. Roles for SR proteins and hnRNP A1 in the regulation of c-src exon N1. Mol Cell Biol. 2003 Mar; 23(6):1874-84. PMID: 12612063.
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    57. Black DL. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem. 2003; 72:291-336. PMID: 12626338.
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