Loading...

Biggin, Mark

TitleBiologist Staff Scientist/Engr
InstitutionLawrence Berkeley National Lab
DepartmentBiological Systems & Eng
Address1 Cyclotron Road
Berkeley CA 94720
Phone510/486-7606
vCardDownload vCard

    Collapse Research 
    Collapse Research Activities and Funding
    Quantitative Modeling of Transcriptional Information in the Drosophila Genome
    NIH/NIGMS P01GM099655Sep 13, 2012 - Jun 30, 2017
    Role: Principal Investigator
    Transcription Network Controlling Drosophila Development
    NIH/NIGMS R01GM070444Aug 1, 2003 - Jul 31, 2009
    Role: Principal Investigator
    MAINTAINANCE OF HOMEOTIC GENE TRANSCRIPTION
    NIH/NIGMS R01GM056803Jan 1, 1999 - Dec 31, 2002
    Role: Principal Investigator
    TRANSCRIPTION OF GENES CONTROLLING DEVELOPMENT
    NIH/NIGMS R01GM042387Jul 1, 1989 - Dec 31, 2004
    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.
    List All   |   Timeline
    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.
      View in: PubMed
    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 06; 15(6):2186-202. PMID: 27099342.
      View in: PubMed
    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 05; 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.
      View in: PubMed
    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.
      View in: PubMed
    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. 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.
      View in: PubMed
    11. 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.
      View in: PubMed
    12. 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.
      View in: PubMed
    13. Li XY, Biggin M. Genome-wide in vivo cross-linking of sequence-specific transcription factors. Methods Mol Biol. 2012; 809:3-26. PMID: 22113265.
      View in: PubMed
    14. 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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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. Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data. Procedia Comput Sci. 2010 May; 1(1):1757-1764. PMID: 23762211.
      View in: PubMed
    24. Biggin M. MyoD, a lesson in widespread DNA binding. Dev Cell. 2010 Apr 20; 18(4):505-6. PMID: 20412764.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    44. Biggin M. To bind or not to bind. Nat Genet. 2001 Aug; 28(4):303-4. PMID: 11479583.
      View in: PubMed
    45. Biggin M, Tjian R. Transcriptional regulation in Drosophila: the post-genome challenge. Funct Integr Genomics. 2001 Mar; 1(4):223-34. PMID: 11793241.
      View in: PubMed
    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. Biggin M. Ultraviolet cross-linking assay to measure sequence-specific DNA binding in vivo. Methods Enzymol. 1999; 304:496-515. PMID: 10372378.
      View in: PubMed
    50. 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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    63. Biggin M, Tjian R. Transcription factors and the control of Drosophila development. Trends Genet. 1989 Nov; 5(11):377-83. PMID: 2692246.
      View in: PubMed
    64. Biggin M, Tjian R. A purified Drosophila homeodomain protein represses transcription in vitro. Cell. 1989 Aug 11; 58(3):433-40. PMID: 2569362.
      View in: PubMed
    65. 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.
      View in: PubMed
    66. 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.
      View in: PubMed

    This site is running Profiles RNS version v2.10.1-576-g789c7b32 on PROFILES-PWEB02.