* equal contribution; # co-corresponding
2019
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 (in press) PDF Supp
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
TraceMontage: a Method for Merging Multiple Independent Neuronal Traces.
Dizaji SA, Walker L, Cai D bioRxiv 2019;doi.org/10.1101/703900
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;btz084 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.org/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(9):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(3):3353-72 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(6):540-7 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(14):17256-64 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(6):1013-25 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(10):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(6):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(3):e72 PDF
Tubulin modifications and their cellular functions.
Hammond JW, Cai D, Verhey KJ Current opinion in cell biology 2008;20(1):71-6 PDF
Tracking single Kinesin molecules in the cytoplasm of mammalian cells.
Cai D, Verhey KJ, Meyhöfer E Biophysical journal 2007;92(12):4137-44 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(1):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(1):11-7 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(21):2166-72 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(47):14230-1 PDF
Photoelectrochemistry as a novel strategy for DNA hybridization detection.
Li Q, Luo G, Feng J, Cai D, Ouyang Q The Analyst 2000;125(11):1908-10 PDF
Webinars
Confocal and Two-photon Microscopy Methods for Imaging the Brain.
Cai D, Winship I Leica / BioTechniques