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    Knowles, David

    SchoolLawrence Berkeley National Lab
    DepartmentMolecular Biophys & Integ Bio
    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. Reinig MR, Novak SW, Tao X, Bentolila LA, Roberts DG, MacKenzie-Graham A, Godshalk SE, Raven MA, Knowles D, Kubby J. Enhancing image quality in cleared tissue with adaptive optics. J Biomed Opt. 2016 12 01; 21(12):121508. PMID: 27735018.
        View in: PubMed
      2. Barron JT, Arbeláez P, Keränen SV, Biggin MD, Knowles D, 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
      3. Knowles D, 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. PMID: 24123936; PMCID: PMC3819199.
      4. Knowles D. Three-dimensional morphology and gene expression mapping for the Drosophila blastoderm. Cold Spring Harb Protoc. 2012 Feb 01; 2012(2):150-61. PMID: 22301653; PMCID: PMC4428898.
      5. Fowlkes CC, Eckenrode KB, Bragdon MD, Meyer M, Wunderlich Z, Simirenko L, Luengo Hendriks CL, Keränen SV, Henriquez C, Knowles D, 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. PMID: 22046143; PMCID: PMC3203197.
      6. Aswani A, Keränen SV, Brown J, Fowlkes CC, Knowles D, Biggin MD, 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.
      7. 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 D, 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.
        View in: PubMed
      8. Rübel O, Weber GH, Huang MY, Bethel EW, Biggin MD, Fowlkes CC, Luengo Hendriks CL, Keränen SV, Eisen MB, Knowles D, 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
      9. MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keränen SV, Knowles D, 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. PMID: 19627575; PMCID: PMC2728534.
      10. Weber GH, Rübel O, Huang MY, DePace AH, Fowlkes CC, Keränen SV, Luengo Hendriks CL, Hagen H, Knowles D, 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. PMID: 19407353; PMCID: PMC3045837.
      11. 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 D, 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. PMID: 18423206.
        View in: PubMed
      12. 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 D, 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. PMID: 18271625; PMCID: PMC2235902.
      13. Luengo Hendriks CL, Keränen SV, Biggin MD, Knowles D. 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
      14. Long F, Peng H, Sudar D, Lelièvre SA, Knowles D. Phenotype clustering of breast epithelial cells in confocal images based on nuclear protein distribution analysis. BMC Cell Biol. 2007 Jul 10; 8 Suppl 1:S3. PMID: 17634093; PMCID: PMC1924508.
      15. Chandramouly G, Abad PC, Knowles D, Lelièvre SA. The control of tissue architecture over nuclear organization is crucial for epithelial cell fate. J Cell Sci. 2007 May 01; 120(Pt 9):1596-606. PMID: 17405811.
        View in: PubMed
      16. Abad PC, Lewis J, Mian IS, Knowles D, Sturgis J, Badve S, Xie J, Lelièvre SA. NuMA influences higher order chromatin organization in human mammary epithelium. Mol Biol Cell. 2007 Feb; 18(2):348-61. PMID: 17108325; PMCID: PMC1783787.
      17. Knowles D, Sudar D, Bator-Kelly C, Bissell MJ, Lelièvre SA. Automated local bright feature image analysis of nuclear protein distribution identifies changes in tissue phenotype. Proc Natl Acad Sci U S A. 2006 Mar 21; 103(12):4445-50. PMID: 16537359; PMCID: PMC1450191.
      18. 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 D. 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.
      19. Keränen SV, Fowlkes CC, Luengo Hendriks CL, Sudar D, Knowles D, 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. PMID: 17184547; PMCID: PMC1794437.
      20. Knowles D, Tilley L, Mohandas N, Chasis JA. Erythrocyte membrane vesiculation: model for the molecular mechanism of protein sorting. Proc Natl Acad Sci U S A. 1997 Nov 25; 94(24):12969-74. PMID: 9371784; PMCID: PMC24247.
      21. Mohandas N, Winardi R, Knowles D, Leung A, Parra M, George E, Conboy J, Chasis J. Molecular basis for membrane rigidity of hereditary ovalocytosis. A novel mechanism involving the cytoplasmic domain of band 3. J Clin Invest. 1992 Feb; 89(2):686-92. PMID: 1737855; PMCID: PMC442903.

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