* equal contribution; # co-corresponding​


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


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


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

Nature Methods 2017;14(6):593–599   PDF


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 

Frontiers in cellular neuroscience 2016;10:00057   PDF


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


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


Confocal and Two-photon Microscopy Methods for Imaging the Brain.

Cai D, Winship I    Leica / BioTechniques