Biotechnology | Neuroscience
* equal contribution; # co-corresponding
2021
nGauge: Integrated and extensible neuron morphology analysis in Python.
Walker LA*, Williams JS*, Li Y, Roossien DH, Michki NS, Cai D bioRxiv doi:10.1101/2021.05.14.434407
ExoBow: A transgenic strategy to study CD63 exosomes in vivo.
Adem B, Bastos N, Ruivo CF, Vieira PF, Seidler B, Machado JC, Saur D, Cai D, Melo SA bioRxiv doi:10.1101/2021.03.10.434407
Bitbow: a digital format of Brainbow enables highly efficient neuronal lineage tracing and morphology reconstruction in single brains.
Li Y, Walker LA, Zhao Y, Edwards EM, Michki NS, Cheng HPJ, Ghazzi M, Chen TY, Chen M, Roossien DH, Cai D
Frontiers in Neural Circuits (2021) 2021.732183 PDF Supp
The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and a multi-informatic analysis paradigm.
Michki NS, Li Y, Sanjasaz K, Zhao Y, Shen FY, Walker LA, Lee CY, Cai D Cell Reports (2021) 35:109039 PDF Table1 Table2 U-M RNA center
Triple-Negative Breast Cancer Cells Recruit Neutrophils by Secreting TGF-β and CXCR2 Ligands.
SenGupta S, Hein LE, Xu Y, Zhang J, Konwerski JR, Li Y, Johnson C, Cai D, Smith JL, Parent CA Frontiers in Immunology (2021) 12:973 PDF
Unsupervised Neural Tracing in Densely Labeled Multispectral Brainbow Images.
Duan B, Walker LA, Shen FY, Roossien DH, Cai D#, Yan Y# IEEE 18th International Symposium on Biomedical Imaging (ISBI), 2021:1122-1126 PDF Supp
2020
Long-range remote focusing by image-plane aberration correction.
Jiang H, Wang C, Wei B, Gan W, Cai D, Cui M
Optics Express (2020) 28:34008-34014 PDF
High Density Carbon Fiber Arrays for Chronic Electrophysiology, Fast Scan Cyclic Voltammetry, and Correlative Anatomy.
Patel PR, Popov P, Caldwell CM, Welle E, Egert D, Pettibone JR, Roossien, DH, Becker, J, Berke, J, Chestek, CA#, Cai, D#
Journal of Neural Engineering (2020) 17:056029 PDF
Cellular-scale silicon probes for high-density, precisely-localized neurophysiology.
Egert D, Pettibone JR, Lemke S, Patel PR, Caldwell CM, Cai D, Ganguly K, Chestek CA, Berke J
Journal of Neurophysiology (2020) 124(6):1578-1587 PDF
Light microscopy based approach for mapping connectivity with molecular specificity.
Shen FY, Harrington MM, Walker LA, Cheng HPJ, Boyden ES, Cai D Nature Communications (2020) 11:4632 PDF Supp
2019
TraceMontage: a Method for Merging Multiple Independent Neuronal Traces.
Dizaji SA, Walker LA, Cai D Journal of Neuroscience Methods (2019) 332:108560 PDF Supp
Identification of neuronal lineages in the Drosophila peripheral nervous system with a “digital” multi-spectral lineage tracing system.
Veling MW*, Li Y*, Veling MT*, Litts C, Michki N, Liu H, Ye B#, Cai D# Cell Reports (2019) 29:3303-3312 PDF
A Weakly Supervised Multi-task Ranking Framework for Actor-Action Semantic Segmentation.
Yan Y#, Xu C, Cai D#, Corso JJ International Journal of Computer Vision (2019) doi:10.1007/s11263-019-01244-7 PDF
Single-cell RT-LAMP mRNA detection by integrated droplet sorting and merging.
Chung MT, Kurabayashi K#, Cai D# Lab on a Chip (2019) 19:2425-2434 PDF Supp
Multispectral tracing in densely labeled mouse brain with nTracer.
Roossien DH, Sadis BV*, Yan Y*, Webb JM*, Min LY, Dizaji AS, Bogart LJ, Mazuski C, Huth RS, Stecher JS, Akula S, Shen F, Xiao T, Vandenbrink M, Lichtman JW, Hensch TK, Herzog ED, Cai D Bioinformatics (2019) 35:3544-3546 PDF Supp
2018
Quantitative simulation of extracellular single unit recording from the surface of cortex.
Hill M, Rios E, Sudhakar SK, Roossien DH, Caldwell C, Cai D, Ahmed OJ, Lempka SF, Chestek CA Journal of Neural Engineering 2018;15:056007 PDF
Sort'N merge: A deterministic microfluidic platform for co-encapsulating distinct particles in microdroplets.
Chung MT, Nunez D, Cai D, Kurabayashi K IEEE Micro Electro Mechanical Systems (MEMS) (2018) 265-268 PDF
A Recurrent Neural Network Approach for Automated Neural Tracing in Multispectral 3D Images.
Yan Y, Roossien DH, Sadis BV, Corso JJ, Cai D bioRxiv (2018) doi:10.1101/230441
2017
Deterministic droplet-based co-encapsulation and pairing of microparticles via active sorting and downstream merging.
Chung MT, Nunez D, Cai D#, Kurabayashi K# Lab on a Chip (2017) 17:3664-3671 PDF
Imaging Neural Architecture in Brainbow Samples.
Roossien DH, Cai D Methods in Molecular Biology (2017) 1642:211-228 PDF
Weakly Supervised Actor-Action Segmentation via Robust Multi-Task Ranking.
Yan Y, Xu C, Cai D, Corso JJ IEEE Conference on Computer Vision and Pattern Recognition (CVPR) (2017) PDF
Iterative expansion microscopy.
Chang JB, Chen F, Yoon YG, Jung EE, Babcock H, Kang JS, Asano S, Suk HJ, Pak N, Tillberg PW, Wassie AT, Cai D, Boyden ES
2016
Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies.
Tillberg PW, Chen F, Piatkevich KD, Zhao Y, Yu CJ, English BP, Gao L, Martorell A, Suk HJ, Yoshida F, DeGennaro EM, Roossien DH, Gong G, Seneviratne U, Tannenbaum SR, Desimone R, Cai D, Boyden ES Nature Biotechnology (2016) 34:987-992 PDF
Automated scalable segmentation of neurons from multispectral images.
Sümbül U, Roossien DH, Chen F, Barry N, Boyden ES, Cai D, Cunningham JP, Paninski L
Advances in Neural Information Processing Systems (NIPS) (2016) 28 PDF
KIF5C S176 Phosphorylation Regulates Microtubule Binding and Transport Efficiency in Mammalian Neurons.
Padzik A, Deshpande P, Hollos P, Franker M, Rannikko EH, Cai D, Prus P, Mågård M, Westerlund N, Verhey KJ, James P, Hoogenraad CC, Coffey ET
2012-2015
Pulse-shaping based two-photon FRET stoichiometry.
Flynn DC, Bhagwat AR, Brenner MH, Núñez MF, Mork BE, Cai D, Swanson JA, Ogilvie JP Optical express (2015) 23:3353-3372 PDF OSA
Two-photon fluorescence resonance energy transfer stoichiometry in living cells.
Bhagwat AR, Flynn DC, Brenner MH, Núñez MF, Ogilvie JP, Cai D, Swanson JA IEEE Conference on Lasers and Electro-Optics (CLEO) (2014) PDF
Improved tools for the Brainbow toolbox.
Cai D, Cohen KB, Luo T, Lichtman JW, Sanes JR Nature methods (2013) 10:540-547 PDF BPoD CPS
Two-photon imaging of multiple fluorescent proteins by phase-shaping and linear unmixing with a single broadband laser.
Brenner MH*, Cai D*, Swanson JA, Ogilvie JP Optical express (2013) 21:17256-17264 PDF
Pulse-shaping multiphoton FRET microscopy.
Brenner MH, Cai D, Nichols SR, Straight SW, Hoppe AD, Swanson JA, Ogilvie JP Proceedings of SPIE (2012) 8226 PDF
2006-2010
Recording single motor proteins in the cytoplasm of mammalian cells.
Cai D, Kaul N, Lionberger TA, Wiener DM, Verhey KJ, Meyhöfer E Methods in enzymology (2010) 475:81-107 PDF
Autoinhibition of the kinesin-2 motor KIF17 via dual intramolecular mechanisms.
Hammond JW, Blasius TL, Soppina V, Cai D, Verhey KJ The Journal of cell biology (2010) 189:1013-1025 PDF
Single molecule imaging reveals differences in microtubule track selection between Kinesin motors.
Cai D, McEwen DP, Martens JR, Meyhöfer E, Verhey KJ PLoS biology (2009) 7:e1000216 PDF
A lipid receptor sorts polyomavirus from the endolysosome to the endoplasmic reticulum to cause infection.
Qian M*, Cai D*, Verhey KJ, Tsai B PLoS pathogens (2009) 5:e1000465 PDF
Mammalian Kinesin-3 motors are dimeric in vivo and move by processive motility upon release of autoinhibition.
Hammond JW, Cai D, Blasius TL, Li Z, Jiang Y, Jih GT, Meyhöfer E, Verhey KJ PLoS biology (2009) 7:e72 PDF
Tubulin modifications and their cellular functions.
Hammond JW, Cai D, Verhey KJ Current opinion in cell biology (2008) 20:71-76 PDF
Tracking single Kinesin molecules in the cytoplasm of mammalian cells.
Cai D, Verhey KJ, Meyhöfer E Biophysical journal (2007) 92:4137-4144 PDF
Kinesin-1 structural organization and conformational changes revealed by FRET stoichiometry in live cells.
Cai D, Hoppe AD, Swanson JA, Verhey KJ The Journal of cell biology (2007) 176:51-63 PDF
Two binding partners cooperate to activate the molecular motor Kinesin-1.
Blasius TL, Cai D, Jih GT, Toret CP, Verhey KJ The Journal of cell biology (2007) 176:11-17 PDF
Microtubule acetylation promotes kinesin-1 binding and transport.
Reed NA, Cai D, Blasius TL, Jih GT, Meyhöfer E, Gaertig J, Verhey KJ Current biology (2006) 16:2166-2172 PDF
Before 2006
RNA degradation in cell extracts: real-time monitoring by fluorescence resonance energy transfer.
Uhler SA, Cai D, Man Y, Figge C, Walter NG Journal of the American Chemical Society (2003) 125:14230-14231 PDF
Photoelectrochemistry as a novel strategy for DNA hybridization detection.
Li Q, Luo G, Feng J, Cai D, Ouyang Q The Analyst (2000) 125:1908-10 PDF
Webinars
Confocal and Two-photon Microscopy Methods for Imaging the Brain.
Cai D, Winship I Leica / BioTechniques