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Results: 1 to 20 of 23

1.

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.

PMID:
24123936
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Three-dimensional morphology and gene expression mapping for the Drosophila blastoderm.

Knowles DW.

Cold Spring Harb Protoc. 2012 Feb 1;2012(2):150-61. doi: 10.1101/pdb.top067843.

PMID:
22301653
[PubMed - indexed for MEDLINE]
3.

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.

PMID:
22046143
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
20684787
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
23762211
[PubMed]
Free PMC Article
6.

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.

PMID:
20150669
[PubMed - indexed for MEDLINE]
7.

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.

PMID:
19627575
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
19407353
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
18423206
[PubMed - indexed for MEDLINE]
Free Article
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.

PMID:
18271625
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
19547599
[PubMed]
12.

Phenotype clustering of breast epithelial cells in confocal images based on nuclear protein distribution analysis.

Long F, Peng H, Sudar D, Lelièvre SA, Knowles DW.

BMC Cell Biol. 2007 Jul 10;8 Suppl 1:S3.

PMID:
17634093
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The control of tissue architecture over nuclear organization is crucial for epithelial cell fate.

Chandramouly G, Abad PC, Knowles DW, Lelièvre SA.

J Cell Sci. 2007 May 1;120(Pt 9):1596-606. Epub 2007 Apr 3.

PMID:
17405811
[PubMed - indexed for MEDLINE]
Free Article
14.

Comments on the paper 'A novel 3D wavelet-based filter for visualizing features in noisy biological data', by Moss et al.

Hendriks CL, Knowles DW.

J Microsc. 2007 Jan;225(Pt 1):104-7; author reply 108.

PMID:
17286701
[PubMed - indexed for MEDLINE]
15.

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.

PMID:
17184547
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
17184546
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

NuMA influences higher order chromatin organization in human mammary epithelium.

Abad PC, Lewis J, Mian IS, Knowles DW, Sturgis J, Badve S, Xie J, Lelièvre SA.

Mol Biol Cell. 2007 Feb;18(2):348-61. Epub 2006 Nov 15.

PMID:
17108325
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Automated local bright feature image analysis of nuclear protein distribution identifies changes in tissue phenotype.

Knowles DW, Sudar D, Bator-Kelly C, Bissell MJ, Lelièvre SA.

Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4445-50. Epub 2006 Mar 10.

PMID:
16537359
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Analysis of integral membrane protein contributions to the deformability and stability of the human erythrocyte membrane.

Van Dort HM, Knowles DW, Chasis JA, Lee G, Mohandas N, Low PS.

J Biol Chem. 2001 Dec 14;276(50):46968-74. Epub 2001 Oct 10.

PMID:
11595743
[PubMed - indexed for MEDLINE]
Free Article
20.

Membrane dynamics of the water transport protein aquaporin-1 in intact human red cells.

Cho MR, Knowles DW, Smith BL, Moulds JJ, Agre P, Mohandas N, Golan DE.

Biophys J. 1999 Feb;76(2):1136-44.

PMID:
9916045
[PubMed - indexed for MEDLINE]
Free PMC Article

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