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    Biggin, Mark

    TitleBiologist Staff Scientist/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentBiological Systems & Eng
    Address1 Cyclotron Road
    Berkeley CA 94720
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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. Li JJ, Chew GL, Biggin M. Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them. Nucleic Acids Res. 2017 Nov 16; 45(20):11821-11836. PMID: 29040683.
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      2. Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner SE, Butland G, Jin J, Witkowska HE, Chandonia JM, Biggin M. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. Mol Cell Proteomics. 2016 Jun; 15(6):2186-202. PMID: 27099342.
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      3. Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner SE, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin M, Chandonia JM, Butland G. Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. Mol Cell Proteomics. 2016 May; 15(5):1539-55. PMID: 26873250; PMCID: PMC4858938 [Available on 05/01/17].
      4. Li JJ, Biggin M. Gene expression. Statistics requantitates the central dogma. Science. 2015 Mar 06; 347(6226):1066-7. PMID: 25745146.
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      5. Li JJ, Bickel PJ, Biggin M. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ. 2014; 2:e270. PMID: 24688849; PMCID: PMC3940484.
      6. Barron JT, Arbeláez P, Keränen SV, Biggin M, Knowles DW, Malik J. Volumetric Semantic Segmentation using Pyramid Context Features. Proc IEEE Int Conf Comput Vis. 2013 Dec; 2013:3448-3455. PMID: 26029008.
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      7. Knowles DW, Biggin M. Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution. Wiley Interdiscip Rev Dev Biol. 2013 Nov-Dec; 2(6):767-79. PMID: 24123936; PMCID: PMC3819199.
      8. Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin M, Celniker SE. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci U S A. 2012 Dec 26; 109(52):21330-5. PMID: 23236164; PMCID: PMC3535648.
      9. Walian PJ, Allen S, Shatsky M, Zeng L, Szakal ED, Liu H, Hall SC, Fisher SJ, Lam BR, Singer ME, Geller JT, Brenner SE, Chandonia JM, Hazen TC, Witkowska HE, Biggin M, Jap BK. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. J Proteome Res. 2012 Dec 07; 11(12):5720-35. PMID: 23098413; PMCID: PMC3516867.
      10. Li XY, Biggin M. Genome-wide in vivo cross-linking of sequence-specific transcription factors. Methods Mol Biol. 2012; 809:3-26. PMID: 22113265.
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      11. Aswani A, Biggin M, Bickel P, Tomlin C. Nonparametric variable selection and modeling for spatial and temporal regulatory networks. Methods Cell Biol. 2012; 110:243-61. PMID: 22482952.
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      12. Dong M, Choi M, Biggin M, Jin J. A multichannel gel electrophoresis and continuous fraction collection apparatus for high-throughput protein separation and characterization. Methods Mol Biol. 2012; 869:373-84. PMID: 22585501.
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      13. Ogawa N, Biggin M. High-throughput SELEX determination of DNA sequences bound by transcription factors in vitro. Methods Mol Biol. 2012; 786:51-63. PMID: 21938619.
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      14. Kaplan T, Biggin M. Quantitative models of the mechanisms that control genome-wide patterns of animal transcription factor binding. Methods Cell Biol. 2012; 110:263-83. PMID: 22482953.
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      15. Fowlkes CC, Eckenrode KB, Bragdon MD, Meyer M, Wunderlich Z, Simirenko L, Luengo Hendriks CL, Keränen SV, Henriquez C, Knowles DW, Biggin M, Eisen MB, DePace AH. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. PLoS Genet. 2011 Oct; 7(10):e1002346. PMID: 22046143; PMCID: PMC3203197.
      16. Biggin M. Animal transcription networks as highly connected, quantitative continua. Dev Cell. 2011 Oct 18; 21(4):611-26. PMID: 22014521.
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      17. Chhabra SR, Butland G, Elias DA, Chandonia JM, Fok OY, Juba TR, Gorur A, Allen S, Leung CM, Keller KL, Reveco S, Zane GM, Semkiw E, Prathapam R, Gold B, Singer M, Ouellet M, Szakal ED, Jorgens D, Price MN, Witkowska HE, Beller HR, Arkin AP, Hazen TC, Biggin M, Auer M, Wall JD, Keasling JD. Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome. Appl Environ Microbiol. 2011 Nov; 77(21):7595-604. PMID: 21908633; PMCID: PMC3209177.
      18. Liu H, Yang L, Khainovski N, Dong M, Hall SC, Fisher SJ, Biggin M, Jin J, Witkowska HE. Automated iterative MS/MS acquisition: a tool for improving efficiency of protein identification using a LC-MALDI MS workflow. Anal Chem. 2011 Aug 15; 83(16):6286-93. PMID: 21761829.
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      19. Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin M, Stamatoyannopoulos JA. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 2011; 12(5):R43. PMID: 21569360; PMCID: PMC3219966.
      20. Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin M. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol. 2011; 12(4):R34. PMID: 21473766; PMCID: PMC3218860.
      21. Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin M, Eisen MB. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet. 2011 Feb 03; 7(2):e1001290. PMID: 21304941; PMCID: PMC3033374.
      22. Aswani A, Keränen SV, Brown J, Fowlkes CC, Knowles DW, Biggin M, Bickel P, Tomlin CJ. Nonparametric identification of regulatory interactions from spatial and temporal gene expression data. BMC Bioinformatics. 2010 Aug 04; 11:413. PMID: 20684787; PMCID: PMC2933715.
      23. Rübel O, Ahern S, Bethel EW, Biggin M, Childs H, Cormier-Michel E, Depace A, Eisen MB, Fowlkes CC, Geddes CG, Hagen H, Hamann B, Huang MY, Keränen SV, Knowles DW, Hendriks CL, Malik J, Meredith J, Messmer P, Ushizima D, Weber GH, Wu K. Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data. Procedia Comput Sci. 2010 May; 1(1):1757-1764. PMID: 23762211.
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      24. Biggin M. MyoD, a lesson in widespread DNA binding. Dev Cell. 2010 Apr 20; 18(4):505-6. PMID: 20412764.
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      25. Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin M, Eisen MB. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol. 2010 Mar 23; 8(3):e1000343. PMID: 20351773; PMCID: PMC2843597.
      26. Choi M, Nordmeyer RA, Cornell E, Dong M, Biggin M, Jin J. A multichannel gel electrophoresis and continuous fraction collection apparatus for high-throughput protein separation and characterization. Electrophoresis. 2010 Jan; 31(3):440-7. PMID: 20119951.
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      27. Rübel O, Weber GH, Huang MY, Bethel EW, Biggin M, Fowlkes CC, Luengo Hendriks CL, Keränen SV, Eisen MB, Knowles DW, Malik J, Hagen H, Hamann B. Integrating data clustering and visualization for the analysis of 3D gene expression data. IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar; 7(1):64-79. PMID: 20150669.
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      28. Han BG, Dong M, Liu H, Camp L, Geller J, Singer M, Hazen TC, Choi M, Witkowska HE, Ball DA, Typke D, Downing KH, Shatsky M, Brenner SE, Chandonia JM, Biggin M, Glaeser RM. Survey of large protein complexes in D. vulgaris reveals great structural diversity. Proc Natl Acad Sci U S A. 2009 Sep 29; 106(39):16580-5. PMID: 19805340; PMCID: PMC2742403.
      29. MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keränen SV, Knowles DW, Stapleton M, Bickel P, Biggin M, Eisen MB. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol. 2009; 10(7):R80. PMID: 19627575; PMCID: PMC2728534.
      30. Weber GH, Rübel O, Huang MY, DePace AH, Fowlkes CC, Keränen SV, Luengo Hendriks CL, Hagen H, Knowles DW, Malik J, Biggin M, Hamann B. Visual exploration of three-dimensional gene expression using physical views and linked abstract views. IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun; 6(2):296-309. PMID: 19407353; PMCID: PMC3045837.
      31. Fowlkes CC, Hendriks CL, Keränen SV, Weber GH, Rübel O, Huang MY, Chatoor S, DePace AH, Simirenko L, Henriquez C, Beaton A, Weiszmann R, Celniker S, Hamann B, Knowles DW, Biggin M, Eisen MB, Malik J. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 2008 Apr 18; 133(2):364-74. PMID: 18423206.
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      32. Dong M, Yang LL, Williams K, Fisher SJ, Hall SC, Biggin M, Jin J, Witkowska HE. A "tagless" strategy for identification of stable protein complexes genome-wide by multidimensional orthogonal chromatographic separation and iTRAQ reagent tracking. J Proteome Res. 2008 May; 7(5):1836-49. PMID: 18336004.
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      33. Lee C, Li X, Hechmer A, Eisen M, Biggin M, Venters BJ, Jiang C, Li J, Pugh BF, Gilmour DS. NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Mol Cell Biol. 2008 May; 28(10):3290-300. PMID: 18332113; PMCID: PMC2423147.
      34. Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin M. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 2008 Feb; 6(2):e27. PMID: 18271625; PMCID: PMC2235902.
      35. Cornell E, Fisher WW, Nordmeyer R, Yegian D, Dong M, Biggin M, Celniker SE, Jin J. Automating fruit fly Drosophila embryo injection for high throughput transgenic studies. Rev Sci Instrum. 2008 Jan; 79(1):013705. PMID: 18248037.
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      36. Misulovin Z, Schwartz YB, Li XY, Kahn TG, Gause M, MacArthur S, Fay JC, Eisen MB, Pirrotta V, Biggin M, Dorsett D. Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma. 2008 Feb; 117(1):89-102. PMID: 17965872; PMCID: PMC2258211.
      37. Luengo Hendriks CL, Keränen SV, Biggin M, Knowles DW. Automatic channel unmixing for high-throughput quantitative analysis of fluorescence images. Opt Express. 2007 Sep 17; 15(19):12306-17. PMID: 19547599.
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      38. Garczarek F, Dong M, Typke D, Witkowska HE, Hazen TC, Nogales E, Biggin M, Glaeser RM. Octomeric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris. J Struct Biol. 2007 Jul; 159(1):9-18. PMID: 17400475.
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      39. Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin M, Eisen MB. Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol. 2006 Oct; 2(10):e130. PMID: 17040121; PMCID: PMC1599766.
      40. Schwartz YB, Kahn TG, Nix DA, Li XY, Bourgon R, Biggin M, Pirrotta V. Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat Genet. 2006 Jun; 38(6):700-5. PMID: 16732288.
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      41. Keränen SV, Fowlkes CC, Luengo Hendriks CL, Sudar D, Knowles DW, Malik J, Biggin M. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics. Genome Biol. 2006; 7(12):R124. PMID: 17184547; PMCID: PMC1794437.
      42. Luengo Hendriks CL, Keränen SV, Fowlkes CC, Simirenko L, Weber GH, DePace AH, Henriquez C, Kaszuba DW, Hamann B, Eisen MB, Malik J, Sudar D, Biggin M, Knowles DW. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol. 2006; 7(12):R123. PMID: 17184546; PMCID: PMC1794436.
      43. Hur MW, Laney JD, Jeon SH, Ali J, Biggin M. Zeste maintains repression of Ubx transgenes: support for a new model of Polycomb repression. Development. 2002 Mar; 129(6):1339-43. PMID: 11880343.
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      44. Biggin M. To bind or not to bind. Nat Genet. 2001 Aug; 28(4):303-4. PMID: 11479583.
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      45. Biggin M, Tjian R. Transcriptional regulation in Drosophila: the post-genome challenge. Funct Integr Genomics. 2001 Mar; 1(4):223-34. PMID: 11793241.
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      46. Carr A, Biggin M. Accessibility of transcriptionally inactive genes is specifically reduced at homeoprotein-DNA binding sites in Drosophila. Nucleic Acids Res. 2000 Jul 15; 28(14):2839-46. PMID: 10908343; PMCID: PMC102649.
      47. Toth J, Biggin M. The specificity of protein-DNA crosslinking by formaldehyde: in vitro and in drosophila embryos. Nucleic Acids Res. 2000 Jan 15; 28(2):e4. PMID: 10606672; PMCID: PMC102536.
      48. Carr A, Biggin M. A comparison of in vivo and in vitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos. EMBO J. 1999 Mar 15; 18(6):1598-608. PMID: 10075930; PMCID: PMC1171247.
      49. Carr A, Biggin M. An in vivo UV crosslinking assay that detects DNA binding by sequence-specific transcription factors. Methods Mol Biol. 1999; 119:497-508. PMID: 10804535.
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      50. Biggin M. Ultraviolet cross-linking assay to measure sequence-specific DNA binding in vivo. Methods Enzymol. 1999; 304:496-515. PMID: 10372378.
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      51. Liang Z, Biggin M. Eve and ftz regulate a wide array of genes in blastoderm embryos: the selector homeoproteins directly or indirectly regulate most genes in Drosophila. Development. 1998 Nov; 125(22):4471-82. PMID: 9778506.
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      52. Biggin M, McGinnis W. Regulation of segmentation and segmental identity by Drosophila homeoproteins: the role of DNA binding in functional activity and specificity. Development. 1997 Nov; 124(22):4425-33. PMID: 9409661.
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      53. Laney JD, Biggin M. Zeste-mediated activation by an enhancer is independent of cooperative DNA binding in vivo. Proc Natl Acad Sci U S A. 1997 Apr 15; 94(8):3602-4. PMID: 9108023; PMCID: PMC20486.
      54. Walter J, Biggin M. Measurement of in vivo DNA binding by sequence-specific transcription factors using UV cross-linking. Methods. 1997 Feb; 11(2):215-24. PMID: 8993034.
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      55. Laney JD, Biggin M. Redundant control of Ultrabithorax by zeste involves functional levels of zeste protein binding at the Ultrabithorax promoter. Development. 1996 Jul; 122(7):2303-11. PMID: 8681810.
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      56. Austin RJ, Biggin M. Purification of the Drosophila RNA polymerase II general transcription factors. Proc Natl Acad Sci U S A. 1996 Jun 11; 93(12):5788-92. PMID: 8650170; PMCID: PMC39139.
      57. Walter J, Biggin M. DNA binding specificity of two homeodomain proteins in vitro and in Drosophila embryos. Proc Natl Acad Sci U S A. 1996 Apr 02; 93(7):2680-5. PMID: 8610101; PMCID: PMC39690.
      58. TenHarmsel A, Biggin M. Bending DNA can repress a eukaryotic basal promoter and inhibit TFIID binding. Mol Cell Biol. 1995 Oct; 15(10):5492-8. PMID: 7565700; PMCID: PMC230799.
      59. Austin RJ, Biggin M. A domain of the even-skipped protein represses transcription by preventing TFIID binding to a promoter: repression by cooperative blocking. Mol Cell Biol. 1995 Sep; 15(9):4683-93. PMID: 7651385; PMCID: PMC230711.
      60. Walter J, Dever CA, Biggin M. Two homeo domain proteins bind with similar specificity to a wide range of DNA sites in Drosophila embryos. Genes Dev. 1994 Jul 15; 8(14):1678-92. PMID: 7958848.
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      61. TenHarmsel A, Austin RJ, Savenelli N, Biggin M. Cooperative binding at a distance by even-skipped protein correlates with repression and suggests a mechanism of silencing. Mol Cell Biol. 1993 May; 13(5):2742-52. PMID: 8097276; PMCID: PMC359652.
      62. Laney JD, Biggin M. zeste, a nonessential gene, potently activates Ultrabithorax transcription in the Drosophila embryo. Genes Dev. 1992 Aug; 6(8):1531-41. PMID: 1644294.
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      63. Müller J, Thüringer F, Biggin M, Züst B, Bienz M. Coordinate action of a proximal homeoprotein binding site and a distal sequence confers the Ultrabithorax expression pattern in the visceral mesoderm. EMBO J. 1989 Dec 20; 8(13):4143-51. PMID: 2574106; PMCID: PMC401602.
      64. Biggin M, Tjian R. Transcription factors and the control of Drosophila development. Trends Genet. 1989 Nov; 5(11):377-83. PMID: 2692246.
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      65. Biggin M, Tjian R. A purified Drosophila homeodomain protein represses transcription in vitro. Cell. 1989 Aug 11; 58(3):433-40. PMID: 2569362.
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      66. Biggin M, Bickel S, Benson M, Pirrotta V, Tjian R. Zeste encodes a sequence-specific transcription factor that activates the Ultrabithorax promoter in vitro. Cell. 1988 Jun 03; 53(5):713-22. PMID: 3131017.
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      67. Biggin M, Tjian R. Transcription factors that activate the Ultrabithorax promoter in developmentally staged extracts. Cell. 1988 Jun 03; 53(5):699-711. PMID: 2897243.
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      68. Biggin M, Bodescot M, Perricaudet M, Farrell P. Epstein-Barr virus gene expression in P3HR1-superinfected Raji cells. J Virol. 1987 Oct; 61(10):3120-32. PMID: 3041034; PMCID: PMC255889.
      69. Pellett PE, Biggin M, Barrell B, Roizman B. Epstein-Barr virus genome may encode a protein showing significant amino acid and predicted secondary structure homology with glycoprotein B of herpes simplex virus 1. J Virol. 1985 Dec; 56(3):807-13. PMID: 2999435; PMCID: PMC252651.
      70. Baer R, Bankier AT, Biggin M, Deininger PL, Farrell PJ, Gibson TJ, Hatfull G, Hudson GS, Satchwell SC, Séguin C. DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature. 1984 Jul 19-25; 310(5974):207-11. PMID: 6087149.
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      71. Biggin M, Farrell PJ, Barrell BG. Transcription and DNA sequence of the BamHI L fragment of B95-8 Epstein-Barr virus. EMBO J. 1984 May; 3(5):1083-90. PMID: 6203743; PMCID: PMC557477.
      72. Biggin M, Gibson TJ, Hong GF. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul; 80(13):3963-5. PMID: 6575390; PMCID: PMC394179.

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