David W. Knowles, 21st Feb 2007: Invited Speaker UCSF BIOLOGICAL IMAGING DEVELOPMENT CENTER
Lawrence Berkeley National Laboratory, Dept. of Cell Biology & Imaging: Announcement 
"Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution"

David W. Knowles, 7th Feb 2007: Invited Speaker: UCSF Comprehensive Cancer Center: Breast Oncology Program
Novel Image-based Screen of Mammary Tumors

C. Luengo Hendriks, S.V.E. Keranen, C. C. Fowlkes, G. H. Weber, M-Y Huang, B. Hamann, D. Sudar, J. Malik, M. Biggin, D. Knowles 2006
Quantitative live imaging describes morphogenetic nuclear movements in early Drosophila embryo
ISAC 2006, Quebec City, (May 2006)

O. Rubel, G. Weber, S. Keranen, C. Fowlkes, C. Luengo Hendriks, N.Y. Shah, M.D. Biggin, H. Hagen, D.W. Knowles, J. Malik, D. Sudar and B. Hamann
PointCloudXplore: Visual Analysis of 3D Gene Expression Data Using Physical Views and Parallel Coordinates
EuroVIS, Lisbon, Portugal, (May 2006)

David W. Knowles 2006
3D Analysis of Gene and Morphology
Quantitative Modeling of Gene Expression and Morphology in the Drosophila Blastoderm
Workshop: March 24 - 26, 2006 LBNL, CA

D.W. Knowles, C.L. Luengo Hendriks, S.V.E. Keränen, C.C. Fowlkes, G.H. Weber, O. Rübel, M.-Y. Huang, H. Peng, A. DePace, L. Simirenko, B. Hamann, D. Sudar, J. Malik, M. Eisen and M.D. Biggin 2006
Berkeley Drosophila Transcription Network Project: 3D blastoderm gene expression atlas: Platform presentation
47th Annual Drosophila Research Conference, Houston, Texas, March 29-April 2, 2006

C. Fowlkes, C. Luengo Hendriks, S. Keranen, Angela DePace, Gunther Weber, Oliver Rubel, M-Y Huang, L. Simirenko, B. Hamann, M. Eisen, D. Sudar, D. W. Knowles, M. Biggin, J. Malik 2006
Complex Interactions Between D/V and A/P Patterning Systems Before Gastrulation Revealed by a 3-D Atlas of Gene Expression Patterns
47th Drosophila Research Conference, Houston, TX, (April 2006)

C.L. Luengo Hendriks, S.V.E. Keränen, C.C. Fowlkes, G.H. Weber, O. Rübel, M.-Y. Huang, H. Peng, A. DePace, L. Simirenko, B. Hamann, D. Sudar, J. Malik, M. Eisen, M.D. Biggin and D.W. Knowles 2006
Quantitative live imaging describes morphogenetic nuclear movements prior to gastrulation
47th Annual Drosophila Research Conference, Houston, Texas, March 29-April 2, 2006

S. Keranen, C. Luengo Hendriks, C. Fowlkes, G. Weber, O. Rubel, M-Y Huang, L. Simirenko, D. Sudar, B. Hamann, J. Malik, M. Eisen, M. Biggin, D. W. Knowles 2005
A morphogenetic framework for analyzing gene expression in Drosophila melanogaster blastoderms
Systems Biology: Global Regulation of Gene Expression, Cold Spring Harbor, New York (March 2006).

O. Rubel, G. Weber, M.-Y. Huang, C. Fowlkes, S. Keranen, C. Luengo Hendriks, M. Biggin, H. Hagen, D. Knowles, J. Malik, D. Sudar, B. Hamann.  2005
Interactive visualization of measured gene expression patterns in three dimensions at cellular resolution
Software demonstration at Supercomputing 2005, Seattle, Washington, (Nov. 2005).

G. Weber, O. Rubel, M.-Y. Huang, C. Fowlkes, S. Keranen, C. Luengo Hendriks, M. Biggin, H. Hagen, D. Knowles, J. Malik, D Sudar, B. Hamann. 2005
Interactive visualization of measured gene expression patterns in three dimensions at cellular resolution
Software demonstration at IEEE Visualization 2005, Minneapolis, Minnesota, (Oct. 2005).

D. W. Knowles, C. Luengo Hendriks, S. Keranen, C. Fowlkes, G. Weber, O. Rubel, H. Peng, A. DePace, B. Hamann, D. Sudar, M. Eisen, J. Malik M. Biggin,  2005
Berkeley Drosophila transcription network project: 3D blastoderm gene expression atlas
Genome Informatics, Cold Spring Harbor, New York, (Oct. 2005).

David W. Knowles 2005
Novel Visualization and Quantitative Analysis Methods in BioImaging
Invited Tutorial:  IEEE Computational Systems Bioinformatice Conference, Stanford, CA

Fuhui Long, Hanchuan Peng, Damir Sudar, Sophie Lelièvre, David W. Knowles 2005
Cell Phenotype Classification Based on 3D Cell Image Analysis
csbw, p. 374,  2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05),  2005

Charless C. Fowlkes, Jitendra Malik, Cris L. Luengo Hendriks, Soile V. E. Keranen, Mark D. Biggin, David W. Knowles, Damir Sudar,
Registering Drosophila Embryos at Cellular Resolution to Build a Quantitative 3D Atlas of Gene Expression Patterns and Morphology
csbw, pp. 354-357,  2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05),  2005. (PDF)

David W. Knowles, Fuhui Long, Damir Sudar, Carol Bator-Kelly, Mina J. Bissell, Sophie A. Lelièvre 2005
Novel Image Analysis to Link Sub-Nuclear Distribution of Proteins with Cell Phenotype in Breast Neoplasia
Era of Hope DOD Breast Cancer Research Program Proceedings
 
C.L. Luengo Hendriks, D.W. Knowles, S.V.E. Keränen, G.H. Weber, M.D. Biggin, and D. Sudar 2005
Automated delineation of cells and nuclei and quantification of gene expression in 3D images of whole Drosophila blastoderm embryos
46th Annual Drosophila Research Conference, San Diego, CA  Proceedings
 
Charless C. Fowlkes, C.L. Luengo Hendriks, S.V.E. Keränen, M.D. Biggin, D.W. Knowles, D. Sudar, and J. Malik 2005
Building Composite Maps of Gene Expression Patterns and Morphology: Registering 3D Representations of Drosophila Embryos
46th Annual Drosophila Research Conference, San Diego, CA Proceedings
 
Soile V. E. Keränen, Cris L. Luengo Hendriks, Damir Sudar, Mark D. Biggin, David W. Knowles 2005
Counting Gene Expressing Nuclei in Whole Drosophila Blastoderm Embryos
46th Annual Drosophila Research Conference, San Diego, CA Proceedings
 
Hanchuan Peng, Soile V.E. Keränen, David W. Knowles, Cris L. Luengo Hendriks, Damir Sudar, Mark Biggin, Michael B. Eisen, and Eugene W. Myers 2005
Reconstructing a Developmental Time Series of 3D Gene Expression Patterns in Drosophila Embryos
46th Annual Drosophila Research Conference, San Diego, CA Proceedings
 
Knowles D.W., Keranen S., Biggin M., Sudar S. 2002
Mapping organism expression levels at cellular resolution in developing Drosophila 
Proceedings of SPIE -- Volume 4621
Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing IX, Jose-Angel Conchello, Carol J. Cogswell, Tony Wilson, Editors, May 2002, pp. 57-64 [SPIE] [ Reprint]

Sudar, Damir; Parvin, Bahram; Callahan, Daniel E.; Schwarz, Richard I.; Knowles, David W.; Ortiz de Solorzano, Carlos; Barcellos-Hoff, Mary H. 2002
Microscopy environment for quantitative spatial and temporal analysis of multicellular interactions
Proc. SPIE Vol. 4621, p. 47-51, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing IX, Jose-Angel Conchello; Carol J. Cogswell; Tony Wilson; Eds.

Knowles D., Keranen S., Dasgupta S., Biggin M., Sudar D. 2002
Quantitative 3D imaging to analyze developmental variability in pregastrula Drosophila embryos
Biophy. J.  82:492a  Abstract,  Poster (pdf)
 
David W. Knowles, Mark D. Biggin, Stephen Richards, Damir Sudar 2001
MAPPING ORGANISM EXPRESSION LEVELS AT CELLULAR RESOLUTION IN DEVELOPING DROSOPHILA
Microsc. Microanal. 7:10-11 Proceedings
 
David W. Knowles, Sophie A. Lelièvre, Carlos Ortiz de Solórzano, Stephen J. Lockett, Mina J. Bissell, Damir Sudar 2001
QUANTITATIVE MODEL-BASED IMAGE ANALYSIS OF NuMA DISTRIBUTION  LINKS NUCLEAR ORGANIZATION WITH CELL PHENOTYPE
Microsc. Microanal. 7:578-579 Proceedings
 
S. J. Lockett, K. Chin, C. Ortiz de Solorzano, W. Chou, A. Jones, D. Knowles, J. Gray 2000
3D BREAST CANCER TISSUE ANALYSIS REVEALS HIGH CELL-TO-CELL HETEROGENEITY IN THE COPY NUMBERS OF SPECIFIC DNA SEQUENCES
AACR submitted [Full Text]
 
David W. Knowles, Sophie A. Lelievre, William S. Chou, Aaron Lee, Wanling Wen, Carlos Ortiz de Solorzano, Mina J. Bissell, Stephen J. Lockett 2000
QUANTITATIVE MODEL-BASED IMAGE ANALYSIS OF SUB-VISUAL CHANGES IN NuMA DISTRIBUTION LINKS NUCLEAR ORGANIZATION WITH CELL PHENOTYPE
Biophys. J. 78:250A 2000 [Full Text] [PDF Version]
 
David W. Knowles, Carlos Ortiz de Solorzano, Stephen J. Lockett 2000
ANALYSIS OF THE 3D SPATIAL ORGANIZATION OF CELLS AND SUB CELLULAR STRUCTURES IN TISSUE
In Optical Diagnostics of Living Cells III, Daniel L. Farkas, Robert C. Leif Editors
Proceedings of SPIE. Vol 3921:66-73  [Full Text]
 
D.W. Knowles, N. Mohandas,  E.A. Evans, J.A. Chasis 1998
NETWORK TOPOLOGY VERSUS INTRINSIC MOLECULAR ELASTICITY IN EXPLAINING ALTERED RIGIDITY OF BIOLOGICAL MEMBRANES
Biophys. J. 74:A197 [Full Text]
 
Knowles D.W., Gimm J.A., Butler J., Mohandas N. 1999
Opposing lateral forces are recruited by the cell to segregate highly mobile membrane bound proteins
Biophys. J. 76:A390 [Full Text]
 
Knowles D.W., Mohandas N., Evans E.A., Chasis J.A. 1998
Network topology versus intrinsic molecular elasticity in explaining altered rigidity of biological membranes
Biophys. J. 74:A393 [Full Text]
 
Knowles D.W., Gimm J.A., Oddone G., Mohandas N. 1997
Complex behaviour of the spectrin based network during membrane deformation
Biophys. J. 72:A197 [Full Text]