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Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes.

Li JJ, Chew GL, Biggin MD.

Genome Biol. 2019 Aug 9;20(1):162. doi: 10.1186/s13059-019-1761-9.


Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy.

Arbel H, Basu S, Fisher WW, Hammonds AS, Wan KH, Park S, Weiszmann R, Booth BW, Keranen SV, Henriquez C, Shams Solari O, Bickel PJ, Biggin MD, Celniker SE, Brown JB.

Proc Natl Acad Sci U S A. 2019 Jan 15;116(3):900-908. doi: 10.1073/pnas.1808833115. Epub 2018 Dec 31.


A Multichannel Gel Electrophoresis and Continuous Fraction Collection Apparatus for High-Throughput Protein Separation and Characterization.

Dong M, Choi M, Biggin MD, Jin J.

Methods Mol Biol. 2019;1855:437-448. doi: 10.1007/978-1-4939-8793-1_36.


Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them.

Li JJ, Chew GL, Biggin MD.

Nucleic Acids Res. 2017 Nov 16;45(20):11821-11836. doi: 10.1093/nar/gkx898.


Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions.

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 MD.

Mol Cell Proteomics. 2016 Jun;15(6):2186-202. doi: 10.1074/mcp.M115.057117. Epub 2016 Apr 20.


Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported.

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 MD, Chandonia JM, Butland G.

Mol Cell Proteomics. 2016 May;15(5):1539-55. doi: 10.1074/mcp.M115.054692. Epub 2016 Feb 12.


Gene expression. Statistics requantitates the central dogma.

Li JJ, Biggin MD.

Science. 2015 Mar 6;347(6226):1066-7. doi: 10.1126/science.aaa8332. No abstract available.


System wide analyses have underestimated protein abundances and the importance of transcription in mammals.

Li JJ, Bickel PJ, Biggin MD.

PeerJ. 2014 Feb 27;2:e270. doi: 10.7717/peerj.270. eCollection 2014.


Volumetric Semantic Segmentation using Pyramid Context Features.

Barron JT, Arbeláez P, Keränen SV, Biggin MD, Knowles DW, Malik J.

Proc IEEE Int Conf Comput Vis. 2013 Dec;2013:3448-3455.


Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution.

Knowles DW, Biggin MD.

Wiley Interdiscip Rev Dev Biol. 2013 Nov-Dec;2(6):767-79. doi: 10.1002/wdev.107. Epub 2013 Feb 4. Review.


DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila.

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.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21330-5. doi: 10.1073/pnas.1209589110. Epub 2012 Dec 10.


High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris.

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.

J Proteome Res. 2012 Dec 7;11(12):5720-35. doi: 10.1021/pr300548d. Epub 2012 Oct 25.


A multichannel gel electrophoresis and continuous fraction collection apparatus for high-throughput protein separation and characterization.

Dong M, Choi M, Biggin MD, Jin J.

Methods Mol Biol. 2012;869:373-84. doi: 10.1007/978-1-61779-821-4_30.


Quantitative models of the mechanisms that control genome-wide patterns of animal transcription factor binding.

Kaplan T, Biggin MD.

Methods Cell Biol. 2012;110:263-83. doi: 10.1016/B978-0-12-388403-9.00011-4.


Nonparametric variable selection and modeling for spatial and temporal regulatory networks.

Aswani A, Biggin MD, Bickel P, Tomlin C.

Methods Cell Biol. 2012;110:243-61. doi: 10.1016/B978-0-12-388403-9.00010-2.


Genome-wide in vivo cross-linking of sequence-specific transcription factors.

Li XY, Biggin MD.

Methods Mol Biol. 2012;809:3-26. doi: 10.1007/978-1-61779-376-9_1.


A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

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.

PLoS Genet. 2011 Oct;7(10):e1002346. doi: 10.1371/journal.pgen.1002346. Epub 2011 Oct 27.


Animal transcription networks as highly connected, quantitative continua.

Biggin MD.

Dev Cell. 2011 Oct 18;21(4):611-26. doi: 10.1016/j.devcel.2011.09.008. Review.


High-throughput SELEX determination of DNA sequences bound by transcription factors in vitro.

Ogawa N, Biggin MD.

Methods Mol Biol. 2012;786:51-63. doi: 10.1007/978-1-61779-292-2_3.


Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome.

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.

Appl Environ Microbiol. 2011 Nov;77(21):7595-604. doi: 10.1128/AEM.05495-11. Epub 2011 Sep 9.


Automated iterative MS/MS acquisition: a tool for improving efficiency of protein identification using a LC-MALDI MS workflow.

Liu H, Yang L, Khainovski N, Dong M, Hall SC, Fisher SJ, Biggin MD, Jin J, Witkowska HE.

Anal Chem. 2011 Aug 15;83(16):6286-93. doi: 10.1021/ac200911v. Epub 2011 Jul 15. Erratum in: Anal Chem. 2011 Aug 15;83(16):6293.


Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.

Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA.

Genome Biol. 2011;12(5):R43. doi: 10.1186/gb-2011-12-5-r43. Epub 2011 May 11.


The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding.

Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD.

Genome Biol. 2011;12(4):R34. doi: 10.1186/gb-2011-12-4-r34. Epub 2011 Apr 7.


Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development.

Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB.

PLoS Genet. 2011 Feb 3;7(2):e1001290. doi: 10.1371/journal.pgen.1001290.


Nonparametric identification of regulatory interactions from spatial and temporal gene expression data.

Aswani A, Keränen SV, Brown J, Fowlkes CC, Knowles DW, Biggin MD, Bickel P, Tomlin CJ.

BMC Bioinformatics. 2010 Aug 4;11:413. doi: 10.1186/1471-2105-11-413.


Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data.

Rübel O, Ahern S, Bethel EW, Biggin MD, 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, Prabhat, Ushizima D, Weber GH, Wu K.

Procedia Comput Sci. 2010 May;1(1):1757-1764.


MyoD, a lesson in widespread DNA binding.

Biggin MD.

Dev Cell. 2010 Apr 20;18(4):505-6. doi: 10.1016/j.devcel.2010.04.004.


Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.

Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB.

PLoS Biol. 2010 Mar 23;8(3):e1000343. doi: 10.1371/journal.pbio.1000343.


Integrating data clustering and visualization for the analysis of 3D gene expression data.

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.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar;7(1):64-79. doi: 10.1109/TCBB.2008.49.


A multichannel gel electrophoresis and continuous fraction collection apparatus for high-throughput protein separation and characterization.

Choi M, Nordmeyer RA, Cornell E, Dong M, Biggin MD, Jin J.

Electrophoresis. 2010 Jan;31(3):440-7. doi: 10.1002/elps.200900435.


Survey of large protein complexes in D. vulgaris reveals great structural diversity.

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.

Proc Natl Acad Sci U S A. 2009 Sep 29;106(39):16580-5. doi: 10.1073/pnas.0813068106. Epub 2009 Sep 11.


Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions.

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.

Genome Biol. 2009;10(7):R80. doi: 10.1186/gb-2009-10-7-r80. Epub 2009 Jul 23.


Visual exploration of three-dimensional gene expression using physical views and linked abstract views.

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.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):296-309. doi: 10.1109/TCBB.2007.70249.


A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm.

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.

Cell. 2008 Apr 18;133(2):364-74. doi: 10.1016/j.cell.2008.01.053.


A "tagless" strategy for identification of stable protein complexes genome-wide by multidimensional orthogonal chromatographic separation and iTRAQ reagent tracking.

Dong M, Yang LL, Williams K, Fisher SJ, Hall SC, Biggin MD, Jin J, Witkowska HE.

J Proteome Res. 2008 May;7(5):1836-49. doi: 10.1021/pr700624e. Epub 2008 Mar 13.


NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila.

Lee C, Li X, Hechmer A, Eisen M, Biggin MD, Venters BJ, Jiang C, Li J, Pugh BF, Gilmour DS.

Mol Cell Biol. 2008 May;28(10):3290-300. doi: 10.1128/MCB.02224-07. Epub 2008 Mar 10.


Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.

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.

PLoS Biol. 2008 Feb;6(2):e27. doi: 10.1371/journal.pbio.0060027.


Automating fruit fly Drosophila embryo injection for high throughput transgenic studies.

Cornell E, Fisher WW, Nordmeyer R, Yegian D, Dong M, Biggin MD, Celniker SE, Jin J.

Rev Sci Instrum. 2008 Jan;79(1):013705. doi: 10.1063/1.2827516.


Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome.

Misulovin Z, Schwartz YB, Li XY, Kahn TG, Gause M, MacArthur S, Fay JC, Eisen MB, Pirrotta V, Biggin MD, Dorsett D.

Chromosoma. 2008 Feb;117(1):89-102. Epub 2007 Oct 27.


Automatic channel unmixing for high-throughput quantitative analysis of fluorescence images.

Luengo Hendriks CL, Keränen SV, Biggin MD, Knowles DW.

Opt Express. 2007 Sep 17;15(19):12306-17.


Octomeric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris.

Garczarek F, Dong M, Typke D, Witkowska HE, Hazen TC, Nogales E, Biggin MD, Glaeser RM.

J Struct Biol. 2007 Jul;159(1):9-18. Epub 2007 Feb 17.


Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics.

Keränen SV, Fowlkes CC, Luengo Hendriks CL, Sudar D, Knowles DW, Malik J, Biggin MD.

Genome Biol. 2006;7(12):R124.


Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline.

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.

Genome Biol. 2006;7(12):R123.


Large-scale turnover of functional transcription factor binding sites in Drosophila.

Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB.

PLoS Comput Biol. 2006 Oct;2(10):e130. Epub 2006 Aug 21.


Zeste maintains repression of Ubx transgenes: support for a new model of Polycomb repression.

Hur MW, Laney JD, Jeon SH, Ali J, Biggin MD.

Development. 2002 Mar;129(6):1339-43.


Transcriptional regulation in Drosophila: the post-genome challenge.

Biggin MD, Tjian R.

Funct Integr Genomics. 2001 Mar;1(4):223-34. Review.


To bind or not to bind.

Biggin MD.

Nat Genet. 2001 Aug;28(4):303-4.


An in vivo UV crosslinking assay that detects DNA binding by sequence-specific transcription factors.

Carr A, Biggin MD.

Methods Mol Biol. 1999;119:497-508. Review. No abstract available.


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