* equal contribution; # co-corresponding​


nGauge: Integrated and extensible neuron morphology analysis in Python.

Walker LA*, Williams JS*, Li Y, Roossien DH, Michki NS, Cai D    Neuroinformatics doi.org/10.1007/s12021-022-09573-8   PDF


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


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


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


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


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)14:593–599   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) 34:987-992   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) 23:3353-3372   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


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


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

Cai D, Winship I    Leica / BioTechniques