Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional imagesMichael Chiang,
Sam Hallman, Amanda Cinquin, Nabora Mochel, Adrian Paz, Shimako Kawauchi, Anne Calof, Ken Cho,
Charless Fowlkes, Oliver Cinquin
BMC Bioinformatics, 2015, 16:397.
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Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotypingJennifer 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]
Quantitative Analysis of Axonal Transport by Using Compartmentalized and Surface Micropatterned Culture of NeuronsHyung Kim, Jeong Park, Jae Byun, Wayne Poon, Carl Cotman,
Charless Fowlkes, Noo Jeon
ACS Chemical Neuroscience, 2012, 3, 6, 433--438.
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A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of DrosophilaCharless 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]
Shirnk-Film Configurable Multiscale Wrinkles for Functional Alignment of Human Embryonic Stem Cells and their Cardiac DerivativesAaron 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]
Multi-scale Biomimetic Topography for the Alignment of Neonatal and Embryonic Stem Cell-derived Heart CellsJesus 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]
Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression DataOliver 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.
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Visual Exploration of Three-dimensional Gene Expression Using Physical Views and Linked Abstract ViewsGunther 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.
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A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosohpila BlastodermCharless 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]
3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution I: Data Acquisition PipelineCris 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.
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PointCloudXplore: Visual Analysis of 3D Gene Expression Data Using Physical Views and Parallel CoordinatesO. 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.
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