Overview:

Newly developed microscopy techniques are providing an unprecedented look at the biochemical processes that underpin life. These range from cryo electron microscopy, which reveals structures at the scale of individual macromolecules, to confocal fluorescence microscopy, which can measure concentrations of a particular protein at a neural synapse or across an entire developing animal. Just as microarrays allowed the move from individual genes to studying the entire genome in parallel, quantitative imaging opens a whole new spatial dimension of gene expression. Successfully harvesting biological insights from the increasing flood of imaging data will require a whole new computational and statistical toolbox for dealing with the spatial aspects of morphology and gene expression.

Publications:
icon
Hierarchical Planar Correlation Clustering for Cell Segmentation
Julian Yarkony, Chong Zhang, Charless Fowlkes
Energy Minimization Methods in Computer Vision and Pattern Recognition, 2015, 492--504.
[pdf]
icon
A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate
Max Staller, Charless Fowlkes, Meghan Bragdon, Zeba Wunderlich, Javier Estrada, Angela DePace
Development, 2015, 142, 3, 587--596.
[pdf]
icon
Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images
Michael Chiang, Sam Hallman, Amanda Cinquin, Nabora Mochel, Adrian Paz, Shimako Kawauchi, Anne Calof, Ken Cho, Charless Fowlkes, Oliver Cinquin
BMC Bioinformatics, 2015, 16:397.
[pdf]
icon
Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping
Jennifer Treweek, Ken Chan, Nicholas Flytzanis, Bin Yang, Benjamin Deverman, Alon Greenbaum, Antti Lignell, Cheng Xiao, Long Cai, Mark Ladinsky, Pamela Bjorkman, Charless Fowlkes, Viviana Gradinaru
Nature Protocols, 2015, 10, 11, 1860--1896.
[pdf]
icon
A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila
Charless Fowlkes, Kelly Eckenrode, Meghan Bragdon, Miriah Meyer, Zeba Wunderlich, Lisa Simirenko, Cris Luengo, Soile Keränen, Clara, Henriquez, David Knowles, Mark Biggin, Michael Eisen, Angela DePace
PLoS Genetics, 2011, 7, e1002346.
[pdf]
icon
Shirnk-Film Configurable Multiscale Wrinkles for Functional Alignment of Human Embryonic Stem Cells and their Cardiac Derivatives
Aaron Chen, Deborah Lieu, Lauren Freshauf, Valerie Lew, Himanshu Sharma, Jianxian Wang, Diep Nguyen, Ioannis Karakikes, Roger Hajjar, Ajay Gopinathan, Elliot Botvinick, Charless Fowlkes, Ronald Li, Michelle Khine
Advanced Materials, 2011, 23, 5785-5791.
[pdf]
icon
Analysis of Gap Gene Reguation in a 3D Organism-Scale Model of the Drosophila melanogaster Embryo
James Hengenius, Michael Gribskov, Ann Rundell, Charless Fowlkes, David Umulis
PLoS ONE, 2011, 6, e26797.
[pdf]
icon
Multi-scale Biomimetic Topography for the Alignment of Neonatal and Embryonic Stem Cell-derived Heart Cells
Jesus Luna, Jesus Ciriza, Marcos Ojeda-Garcia, Marco Kong, Anthony Herren, Deborah Lieu, Ronald Li, Charless Fowlkes, Michelle Khine, Kara McCloskey
Tissue Engineering: Part C, 2011, 17(5).
[pdf]
icon
Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data
Oliver Rübel, Gunther Weber, Min-Yu Huang, E. Bethel, Mark Biggin, Charless Fowlkes, Cris Hendriks, Soile Keränen, Michael Eisen, David Knowles, Jitendra Malik, Hans Hagen, Bernd Hamann
IEEE Transactions on Computational Biology and Bioinformatics, 2010, 7(1), 64-79.
[pdf]
icon
Nonparametric identification of regulatory interactions from spatial and temporal gene expression data
Anil Aswani, Soile Keräen, James Brown, Charless Fowlkes, David Knowles, Mark Biggin, Peter Bickel, Claire Tomlin
BMC Bioinformatics, 2010, 11:413.
[pdf]
icon
Visual Exploration of Three-dimensional Gene Expression Using Physical Views and Linked Abstract Views
Gunther Weber, Oliber Rubel, Min-Yu Huang, Angela DePace, Charless Fowlkes, Soile Keranen, Cris Hendriks, Hans Hagen, David Knowles, Jitendra Malik, Mark Biggin, Bernd Hamann
IEEE Transactions on Computational Biology and Bioinformatics, 2009, 6(2), 296-309.
[pdf]
icon
A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosohpila Blastoderm
Charless Fowlkes, Cris Luengo, Soile Keränen, Gunther Weber, Oliver Rübel, Min-Yu, Huang, Sohail Chatoor, Lisa Simirenko, Angela DePace, Clara, Henriquez, Amy Beaton, Richard Weiszmann, Susan Celniker, Bernd Hamann, David Knowles, Mark Biggin, Michael Eisen, Jitendra Malik
Cell, 2008, 133, 364-374.
[pdf]
icon
3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution II: Dynamics
Soile Keränen, Charless Fowlkes, Cris Hendriks, Damir Sudar, David Knowles, Jitendra Malik, Mark Biggin
Genome Biology, 2006, 7:R124.
[pdf]
icon
Inferring nuclear movements from fixed material
Charless Fowlkes, Jitendra Malik
UC Berkeley, 2006, UCB//EECS-06-142.
[pdf]
icon
3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution I: Data Acquisition Pipeline
Cris Hendriks, Soile Keränen, Charless Fowlkes, Lisa Simirenko, Gunther Weber, Clara Henriquez, David Kaszuba, Bernd Hamann, Michael Eisen, Jitendra Malik, Damir Sudar, Mark Biggin, David Knowles
Genome Biology, 2006, 7:R123.
[pdf]
icon
PointCloudXplore: Visual Analysis of 3D Gene Expression Data Using Physical Views and Parallel Coordinates
O. Rubel, G.H. Weber, S.V.E. Keranen, Charless Fowlkes, C.L. Hendriks, L. Simirenko, N.Y. Shah, M.B. Eisen, M.D. Biggin, H. Hagen, D. Sudar, J. Malik, D.W. Knowles, B. Hamann
Eurographics/IEEE VGTC Symposium on Visualization, 2006, 203--210.
[pdf]
icon
Registering Drosophila Embryos at Cellular Resolution to Build a Quantitative 3D Atlas of Gene Expression Patterns and Morphology
Charless Fowlkes, Cris Hendriks, Soile Keränen, Mark Biggin, David Knowles, Damir Sudar, Jitendra Malik
CSB 2005 Workshop on BioImage Data Minning and Informatics, 2005.
[pdf]
icon
Extracting Global Structure from Gene Expression Profiles
Charless Fowlkes, Qun Shan, Serge Belongie, Jitendra Malik
Methods of Microarray Data Analysis II, 2002.
[pdf]