Image-based
Screening of Mammary Tumors
The
BioImaging Group is developing methods for turning high
resolution fluorescence images
of human mammary epithelial tissue into tissue-maps which report the
probable nonneoplastic,
premalignant and malignant phenotypes at cellular resolution.
Morphology
and
Gene Expression in Embryonic Drosophila
The BioImaging Group has
created
the first computational, quantitative, cellular resolution
atlas
of morphology and gene
expression for one of the most studied model animals:
Drosophila
melanogaster.
Automated
Scientific Analysis Processing (ASAP):
- Fluorescence Image Detection,
Segmentation and Quantitation
- Real Time Bright Field
Morphology Analysis
- Remote Software Developement
- Machine Independent Implementation
Publications:
DW Knowles, MD Biggin 2013
Building quantitative, three‐dimensional atlases of gene
expression and morphology at cellular resolution
Wiley Interdisciplinary Reviews: Developmental Biology 2013
DOI:
10.1002/wdev.107 Reprint
J Barron, M Biggin, P Arbelaez, D Knowles, S Keranen, J Malik 2013
Volumetric semantic segmentation using pyramid context
features
Proceedings of the IEEE International Conference on Computer Vision,
3448-3455 Reprint
Supplement
DW Knowles 2012
3D Image-Based Whole Embryo Morphology and Gene Expression
Mapping for the Drosophila blastoderm
Cold Spring Harbor Protocols 2012 (2), 150 Reprint
|
Protocols cover art |
Charless C Fowlkes, Kelly B Eckenrode, Meghan D Bragdon, Miriah Meyer,
Zeba Wunderlich, Lisa Simirenko, Cris L Luengo Hendriks, Soile VE
Keränen, Clara Henriquez, David W Knowles, Mark D Biggin, Michael
B Eisen, Angela H DePace 2011
A conserved developmental patterning network produces
quantitatively different output in multiple species of Drosophila
PLoS Genet 7 (10), e1002346 Reprint
Anil
Aswani, Soile V.E. Keranen, James Brown, Charless C. Fowlkes, David W.
Knowles, Mark D. Biggin, Peter Bickel and Claire J. Tomlin 2010. Nonparametric identification of regulatory
interactions from spatial and temporal gene expression data
BMC
Bioinformatics 2010, 11:413
doi:10.1186/1471-2105-11-413
Oliver
Rubel, Gunther H. Weber, Member, Min-Yu Huang, E. Wes
Bethel, Mark
D. Biggin, Charless C. Fowlkes, Cris L. Luengo Hendriks, Soile V. E.
Keranen, Michael B. Eisen, David W. Knowles, Jitendra Malik, Hans
Hagen, and Bernd Hamann 2010
Integrating Data
Clustering and Visualization for the Analysis of 3D Gene Expression Data
IEEE Transactions on Computational Biology and Bioinformatics. 2010,
Vol 7, No. 1, p64-79
[Reprint]
Stewart
MacArthur, Xiao-Yong Li, Jingyi Li, James B. Brown, Hou Cheng Chu, Lucy
Zeng, Brandi P. Grondona, Aaron Hechmer, Lisa Simirenko, Soile V.E.
Keränen, David W. Knowles, Mark Stapleton, Peter Bickel, Mark
D.
Biggin and Michael B. Eisen 2009. Developmental
roles of 21 Drosophila transcription factors are determined by
quantitative differences in binding to an overlapping set of thousands
of genomic regions
Genome Biology 2009, 10:R80
Gunther H. Weber, Oliver Rubel, Min-Yu Huang, Angela H. DePace,
Charless C. Fowlkes, Soile V. E. Keranen, Cris L. Luengo Hendriks, Hans
Hagen, David W. Knowles, Jitendra Malik, Mark D. Biggin,and Bernd
Hamann 2009
Visual Exploration of Three-dimensional Gene Expression Using Physical
Views and Linked Abstract Views
Computational
Biology and Bioinformatics, IEEE/ACM, Transactions on. 6:296-309, 2009
[Reprint]
Charless
C. Fowlkes, Cris L. Luengo Hendriks, Soile V.E. Keranen, Gunther H.
Weber,1,5 Oliver Rubel,Min-Yu Huang, Sohail Chatoor, Angela H. DePace,
Lisa Simirenko, Clara Henriquez, Amy Beaton, Richard Weiszmann, Susan
Celniker, Bernd Hamann, David W. Knowles, Mark D. Biggin, Michael B.
Eisen, and Jitendra Malik 2008
A quantitative spatiotemporal atlas of gene expression in
the Drosophila
blastoderm
Cell 133:364-374
April 18, 2008 [Reprint]
|
A
registration technique is described that takes image-based data from
hundreds of Drosophila
blastoderm embryos and builds a model
spatiotemporal embryo atlas from which we recover known gene-regulatory
interactions and predict hundreds of new ones. |
Xiaoyong Li, Stewart MacArthur, Richard
Bourgon, David Nix, Daniel A.
Pollard, Venky N. Iyer, Aaron Hechmer, Lisa Simirenko, Mark Stapleton,
Cris L. Luengo Hendriks, Hou Cheng Chu, Nobuo Ogawa, William Inwood,
Victor Sementchenko, Amy Beaton, Richard Weiszmann, Susan E. Celniker,
David W. Knowles, Tom Gingeras, Terence P. Speed, Michael B. Eisen and
Mark D. Biggin 2008
Transcription Factors Bind Thousands of Active and Inactive Regions in
the Drosophila Blastoderm
PLoS Biol. 6, e27 (2008)
Cris L. Luengo Hendriks, Soile V. E. Keränen, Mark D. Biggin
and David W. Knowles 2007
Automatic channel unmixing for high-throughput quantitative analysis of
fluorescence images
Optics Express 15(19):12306-12317
Fuhui Long, Hanchuan Peng, Damir Sudar, Sophie A.
Lelièvre, and David W. Knowles 2007
Phenotype Clustering of Breast Epithelial Cells in Confocal Images
based on Nuclear Protein Distribution Analysis
BMC Cell Biology 2007,
8(Suppl 1):S3
Gurushankar Chandramouly, Patricia C. Abad, David W. Knowles, and
Sophie A. Lelièvre 2007
Nuclear organization and tissue polarity cooperate to control cell fate
in mammary acini
J. Cell Sci. 120, 1596-1606 (2007)
[Reprint]
Luengo Hendriks C.L. & Knowles D.W. 2007
Comments on the paper
‘A novel
3D wavelet-based filter for visualizing features in noisy biological
data’, by Moss et al.
J. Microscopy, 225 (1): 104–107 [Reprint]
-->
[See Reply by
Moss et al]
Patricia C. Abad, Jason Lewis, I. Saira Mian, David
W. Knowles, Jennifer Sturgis, Sunil Badve, Jun Xie, Sophie A.
Lelièvre 2007
NuMA Influences Higher
Order Chromatin Organization in Human Mammary Epithelium
Mol. Biol. Cell, 18:348-361
[Reprint]
Soile
VE Keranen , Charless C Fowlkes , Cris L Luengo Hendriks , Damir Sudar
, David W Knowles , Jitendra Malik and Mark D Biggin 2006
3D morphology and gene expression in the Drosophila blastoderm at
cellular resolution II: dynamics
Genome
Biology 2006, 7:R124 Reprint
|
A new spatio-temporal
coordinate framework for studying
three-dimensional patterns of gene expression in the Drosophila
blastoderm is presented that takes account of previously undetected
morphological movements. |
Cris
L Luengo Hendriks , Soile VE Keranen , Charless C Fowlkes , Lisa
Simirenko , Gunther H Weber , Angela H DePace , Clara Henriquez , David
W Kaszuba , Bernd Hamann , Michael B Eisen , Jitendra Malik , Damir
Sudar , Mark D Biggin and David W Knowles 2006
3D
morphology and gene expression in the Drosophila blastoderm at cellular
resolution I: data acquisition pipeline
Genome
Biology 2006, 7:R123 Reprint
|
A
suite of methods that
provide the first quantitative three-dimensional description of gene
expression and morphology with cellular resolution in whole Drosophila
embryos is described. |
David W. Knowles,
Damir Sudar, Carol Bator-Kelly, Mina J. Bissell, and Sophie A.
Lelièvre 2006
Automated
local bright feature image analysis of nuclear protein distribution
identifies changes in tissue phenotype
Proc.
Natl. Acad. Sci. USA 103,
4445-4450
[Reprint]
|
Automated
image analysis was used to delineate individual nuclei and
compute the radial distribution of fluorescently-labeled
protein.
Nuclear distributions of NuMA were shown to change during epithelial
differentiation and nonneoplastic / malignant transformation. |
Koei
Chin, Carlos Ortiz de
Solorzano, David Knowles, Arthur Jones, William
Chou, Enrique Garcia
Rodriguez, Wen-Lin Kuo, Britt-Marie Ljung, Karen Chew, Kenneth Myambo,
Monica
Miranda, Sheryl Krig, James Garbe, Martha Stampfer, Paul Yaswen, Joe W.
Gray,
and Stephen J. Lockett 2004
In
situ
analysis of genome
instability in breast cancer
Nat
Genet. 2004 36:984-8 [Reprint]
Heidi
M. Van Dort, David
W.
Knowles,
Joel
A. Chasis, Gloria Lee, Narla Mohandas, and
Philip S. Low 2001
Analysis of integral membrane protein contributions to the
deformability and
stability of the human erythrocyte membrane
J Biol Chem 2001 276:46968-74 [Reprint]
Michael
Cho*, David
W. Knowles*,
Barbara L. Smith, John J. Moulds, Peter Agre, Narla Mohandas, David E.
Golan 1999
Membrane dynamics of the water transport protein AQP1 in intact human
red cells
Biophys. J. 76:1136-1144 (1999) [Reprint]
*Drs. Cho and Knowles
contributed equally to this work
|
Fluorescence
images and
corresponding density profiles
of AQP1, the water channel protein, on Red Blood Cell
Membranes under deformation shows the migration of
AQP1 molecules towards the membrane portion that
had been maximally dilated, the aspiration cap.
|
Knowles
D.W., Tilley L,
Mohandas N, Chasis JA 1997
Erythrocyte membrane vesiculation: model for the molecular mechanism of
protein
sorting
Proc Natl Acad Sci USA 94:12969-12974 (1987)
[Reprint]
|
Fluorescence images and
corresponding density profiles
of cytoskeletal actin demonstrates that the cytoskeleton
completely retracted to the cell body on the release of a
vesicle. This set the stage for studying the role of the
cytoskeleton in sorting membrane proteins.
|
Knowles
D.W., Chasis JA,
Evans EA, Mohandas N 1994
Cooperative action between band 3 and glycophorin A in human
erythrocytes: immobilization of band 3 induced by antibodies to
glycophorin A
Biophys J 1994 May;66(5):1726-1732 (1994) [Reprint]
--> This
work written up as [New
and Notable] [Reprint]
Mohandas
N, Winardi R, Knowles
D., Leung A, Parra M, George E, Conboy J, Chasis
J 1992
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):686-692 (1992)
[Reprint]
Selected
Abstracts Human
Erythrocyte