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    22833 Publications
    3073 Total Profiles
    24 Edited Profiles

    Biggin, Mark

    TitleBiologist Staff Scientist/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentGenomics
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-7606

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Li JJ, Biggin MD. Gene expression. Statistics requantitates the central dogma. Science. 2015 Mar 6; 347(6226):1066-7.
        View in: PubMed
      2. Li JJ, Bickel PJ, Biggin MD. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ. 2014; 2:e270.
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      3. Knowles DW, Biggin MD. 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.
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      4. Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin MD, 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.
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      5. 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 MD, Jap BK. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. J Proteome Res. 2012 Dec 7; 11(12):5720-35.
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      6. Li XY, Biggin MD. Genome-wide in vivo cross-linking of sequence-specific transcription factors. Methods Mol Biol. 2012; 809:3-26.
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      7. Aswani A, Biggin MD, Bickel P, Tomlin C. Nonparametric variable selection and modeling for spatial and temporal regulatory networks. Methods Cell Biol. 2012; 110:243-61.
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      8. Dong M, Choi M, Biggin MD, 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.
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      9. Ogawa N, Biggin MD. High-throughput SELEX determination of DNA sequences bound by transcription factors in vitro. Methods Mol Biol. 2012; 786:51-63.
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      10. Kaplan T, Biggin MD. Quantitative models of the mechanisms that control genome-wide patterns of animal transcription factor binding. Methods Cell Biol. 2012; 110:263-83.
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      11. Fowlkes CC, Eckenrode KB, Bragdon MD, Meyer M, Wunderlich Z, Simirenko L, Luengo Hendriks CL, Keränen SV, Henriquez C, Knowles DW, Biggin MD, 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.
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      12. Biggin MD. Animal transcription networks as highly connected, quantitative continua. Dev Cell. 2011 Oct 18; 21(4):611-26.
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      13. 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 MD, 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.
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      14. Liu H, Yang L, Khainovski N, Dong M, Hall SC, Fisher SJ, Biggin MD, 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.
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      15. Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 2011; 12(5):R43.
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      16. Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol. 2011; 12(4):R34.
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      17. Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet. 2011; 7(2):e1001290.
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      18. Aswani A, Keränen SV, Brown J, Fowlkes CC, Knowles DW, Biggin MD, Bickel P, Tomlin CJ. Nonparametric identification of regulatory interactions from spatial and temporal gene expression data. BMC Bioinformatics. 2010; 11:413.
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      19. Biggin MD. MyoD, a lesson in widespread DNA binding. Dev Cell. 2010 Apr 20; 18(4):505-6.
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      20. Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol. 2010 Mar; 8(3):e1000343.
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      21. Choi M, Nordmeyer RA, Cornell E, Dong M, Biggin MD, 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.
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      22. Rübel O, Weber GH, Huang MY, Bethel EW, Biggin MD, 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.
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      23. 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 MD, 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.
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      24. 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 MD, 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.
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      25. Weber GH, Rübel O, Huang MY, DePace AH, Fowlkes CC, Keränen SV, Luengo Hendriks CL, Hagen H, Knowles DW, Malik J, Biggin MD, 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.
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      26. 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 MD, Eisen MB, Malik J. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 2008 Apr 18; 133(2):364-74.
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      27. Dong M, Yang LL, Williams K, Fisher SJ, Hall SC, Biggin MD, 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.
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      28. Lee C, Li X, Hechmer A, Eisen M, Biggin MD, 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.
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      29. 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 MD. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 2008 Feb; 6(2):e27.
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      30. Cornell E, Fisher WW, Nordmeyer R, Yegian D, Dong M, Biggin MD, Celniker SE, Jin J. Automating fruit fly Drosophila embryo injection for high throughput transgenic studies. Rev Sci Instrum. 2008 Jan; 79(1):013705.
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      31. Misulovin Z, Schwartz YB, Li XY, Kahn TG, Gause M, MacArthur S, Fay JC, Eisen MB, Pirrotta V, Biggin MD, Dorsett D. Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma. 2008 Feb; 117(1):89-102.
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      32. Luengo Hendriks CL, Keränen SV, Biggin MD, Knowles DW. Automatic channel unmixing for high-throughput quantitative analysis of fluorescence images. Opt Express. 2007 Sep 17; 15(19):12306-17.
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      33. Garczarek F, Dong M, Typke D, Witkowska HE, Hazen TC, Nogales E, Biggin MD, Glaeser RM. Octomeric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris. J Struct Biol. 2007 Jul; 159(1):9-18.
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      34. Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB. Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol. 2006 Oct; 2(10):e130.
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      35. 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.
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      36. Keränen SV, Fowlkes CC, Luengo Hendriks CL, Sudar D, Knowles DW, Malik J, Biggin MD. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics. Genome Biol. 2006; 7(12):R124.
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      37. 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 MD, 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.
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      38. Hur MW, Laney JD, Jeon SH, Ali J, Biggin MD. Zeste maintains repression of Ubx transgenes: support for a new model of Polycomb repression. Development. 2002 Mar; 129(6):1339-43.
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      39. Biggin MD. To bind or not to bind. Nat Genet. 2001 Aug; 28(4):303-4.
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      40. Biggin MD, Tjian R. Transcriptional regulation in Drosophila: the post-genome challenge. Funct Integr Genomics. 2001 Mar; 1(4):223-34.
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      41. Carr A, Biggin MD. 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.
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      42. Toth J, Biggin MD. The specificity of protein-DNA crosslinking by formaldehyde: in vitro and in drosophila embryos. Nucleic Acids Res. 2000 Jan 15; 28(2):e4.
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      43. Carr A, Biggin MD. 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.
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      44. Carr A, Biggin MD. An in vivo UV crosslinking assay that detects DNA binding by sequence-specific transcription factors. Methods Mol Biol. 1999; 119:497-508.
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      45. Biggin MD. Ultraviolet cross-linking assay to measure sequence-specific DNA binding in vivo. Methods Enzymol. 1999; 304:496-515.
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      46. Liang Z, Biggin MD. 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.
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      47. Biggin MD, 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.
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      48. Laney JD, Biggin MD. 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.
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      49. Walter J, Biggin MD. Measurement of in vivo DNA binding by sequence-specific transcription factors using UV cross-linking. Methods. 1997 Feb; 11(2):215-24.
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      50. Laney JD, Biggin MD. Redundant control of Ultrabithorax by zeste involves functional levels of zeste protein binding at the Ultrabithorax promoter. Development. 1996 Jul; 122(7):2303-11.
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      51. Austin RJ, Biggin MD. Purification of the Drosophila RNA polymerase II general transcription factors. Proc Natl Acad Sci U S A. 1996 Jun 11; 93(12):5788-92.
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      52. Walter J, Biggin MD. DNA binding specificity of two homeodomain proteins in vitro and in Drosophila embryos. Proc Natl Acad Sci U S A. 1996 Apr 2; 93(7):2680-5.
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      53. TenHarmsel A, Biggin MD. Bending DNA can repress a eukaryotic basal promoter and inhibit TFIID binding. Mol Cell Biol. 1995 Oct; 15(10):5492-8.
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      54. Austin RJ, Biggin MD. 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.
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      55. Walter J, Dever CA, Biggin MD. 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.
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      56. TenHarmsel A, Austin RJ, Savenelli N, Biggin MD. 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.
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      57. Laney JD, Biggin MD. zeste, a nonessential gene, potently activates Ultrabithorax transcription in the Drosophila embryo. Genes Dev. 1992 Aug; 6(8):1531-41.
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      58. 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.
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      59. Biggin MD, Tjian R. Transcription factors and the control of Drosophila development. Trends Genet. 1989 Nov; 5(11):377-83.
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      60. Biggin MD, Tjian R. A purified Drosophila homeodomain protein represses transcription in vitro. Cell. 1989 Aug 11; 58(3):433-40.
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      61. Biggin MD, 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 3; 53(5):713-22.
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      62. Biggin MD, Tjian R. Transcription factors that activate the Ultrabithorax promoter in developmentally staged extracts. Cell. 1988 Jun 3; 53(5):699-711.
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      63. 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.
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      64. Pellett PE, Biggin MD, 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.
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      65. Baer R, Bankier AT, Biggin MD, Deininger PL, Farrell PJ, Gibson TJ, Hatfull G, Hudson GS, Satchwell SC, Séguin C, et al. DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature. 1984 Jul 19-25; 310(5974):207-11.
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      66. 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.
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      67. Biggin MD, 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.
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