Original Journal Papers

Ji Yu
Point-supervised Single-cell Segmentation via Collaborative Knowledge Sharing
IEEE Transactions on Medical Imaging, in press, DOI: 10.1109/TMI.2023.3312988

Shrestha, Prem; Kuang, Nicholas; Yu, Ji
Efficient end-to-end learning for cell segmentation with machine generated weak annotations.
Communications biology 6:232, (2023)

Din, Nizam Ud; Yu, Ji
Training a deep learning model for single-cell segmentation without manual annotation.
Scientific reports 11:23995 (2021)

Yu J, Elmokadem A.
Single-molecule localization microscopy as nonlinear inverse problem.
PNAS pii: 201912634 (2019)

Zhang, Ke; Lyu, Wanqing; Yu, Ji; Koleske, Anthony J
Abl2 is recruited to ventral actin waves through cytoskeletal interactions to promote lamellipodium extension.
Molecular biology of the cell 29:2863-2873 (2018)

Alapin, Jessica M; Dines, Monica; Vassiliev, Maria; Tamir, Tal; Ram, Alon; Locke, Clifford; Yu, Ji; Lamprecht, Raphael
Activation of EphB2 Forward Signaling Enhances Memory Consolidation.
Cell reports 23(7):2014-2025 (2018)

Locke, Clifford; Machida, Kazuya; Wu, Yi; Yu, Ji
Optogenetic activation of EphB2 receptor in dendrites induced actin polymerization by activating Arg kinase.
Biology open 6:1820-1830 (2017)

Marchenko, Olena O; Das, Sulagna; Yu, Ji; Novak, Igor L; Rodionov, Vladimir I; Efimova, Nadia; Svitkina, Tatyana; Wolgemuth, Charles W; Loew, Leslie M
A minimal actomyosin-based model predicts the dynamics of filopodia on neuronal dendrites.
Molecular biology of the cell 28(8):1021-1033 (2017)

Jadwin, JA*; Oh, D*; Curran, TG; Ogiue-Ikeda, M; Jia, L; White, FM; Machida, K; Yu, J; Mayer, B
Time-resolved multimodal analysis of Src Homology 2 (SH2) domain binding in signaling by receptor tyrosine kinases.
eLife 5:e11835 (2016)

Rezaul, K; Gupta, D; Semenova, I; Ikeda, K; Kraikivski, P; Yu, J; Cowan, A; Zaliapin, I; Rodionov, V
Engineered tug-of-war between kinesin and dynein controls direction of microtubule transport in vivo.
Traffic 17(5):475-86 (2016)

Elmokadem A, Yu J
Optimal Drift Correction for Super-resolution Localization Microscopy with Bayesian Inference.
Biophys J. 109(9), 1772 (2015)

Das S, Yin T, Yang, Q,Zhang J, Wu YI, Yu J
Single-molecule tracking of small GTPase Rac1 uncovers spatial regulation of membrane translocation and mechanism for polarized signaling.
PNAS 112(3), E267 (2015)

Troiano AJ Jr, Zhang J, Cowan AE, Yu J, Setlow P
Analysis of the dynamics of a Bacillus subtilis spore germination protein complex during spore germination and outgrowth.
J Bacteriol. (2014)

Zhang JQ, Griffiths KK, Cowan A, Setlow P and Yu J.
Expression Level of Bacillus subtilis Germinant Receptor Determines the Average Rate but not the Heterogeneity of Spore Germination.
J Bacteriol. 195(8):1735-40 (2013)

Oh D, Ogiue-Ikeda M, Jadwin JA, Machida K, Mayer BJ and Yu J.
Fast rebinding increases dwell-time of Src Homology 2 (SH2) containing proteins near plasma membrane.
PNAS 109(35):14024-9 (2012)

Tatavarty V, Das S, Yu J.
Polarization of actin cytoskeleton is reduced in dendritic protrusions during early spine development in hippocampal neuron.
Mol Biol Cell. 23(16):3167-77(2012)

Tatavarty V, Ifrim MF, Levin M, Korza G, Barbarese E, Yu J, Carson JH.
Single-molecule imaging of translational output from individual RNA granules in neurons.
Mol Biol Cell. 23(5):918-29 (2012)

Zhang J, Garner W, Setlow P, Yu J.
Quantitative Analysis of Spatial-Temporal Correlations during Germination of Spores of Bacillus Species.
J Bacteriol. 193(15):3765-72 (2011)

Griffiths KK, Zhang J, Cowan AE, Yu J, Setlow P.
Germination proteins in the inner membrane of dormant Bacillus subtilis spores colocalize in a discrete cluster.
Mol Microbiol. 81(4) 1061 (2011)

Pengfei Zhang, Will Garner, Xuan Yi, Ji Yu, Yong-qing Li and Peter Setlow
Factors Affecting Variability in Time between Addition of Nutrient Germinants and Rapid Dipicolinic Acid Release during Germination of Spores of Bacillus Species.
J Bacteriol. 192(14), p3608-3619 (2010)

Vedakumar Tatavarty, Eun-Ji Kim, Vladimir Rodionov, Ji Yu
Investigating sub-spine actin dynamics in rat hippocampal neurons with super-resolution optical imaging.
Plos One 4(11):e7724 (2009)

Lili Niu and Ji Yu
Investigating Intracellular Dynamics of FtsZ Cytoskeleton with Photo-activation Single-molecule Tracking.
Biophy. J 95(4), 2009-16 (2008)

Reviews, Comments, and Book Chapters

Mayer BJ, Yu J.
Protein Clusters in Phosphotyrosine Signal Transduction.
J Mol Biol. (2018)

Yu J.
Single-Molecule Studies in Live Cells.
Annual review of physical chemistry (2016)

Yu J.
To unscramble an egg.
Nature Methods 20(3):208-9 (2013)

Vats P, Yu J, Rothfield L.
The dynamic nature of the bacterial cytoskeleton.
Cell Mol Life Sci. 66(20):3353-62(2009)