Publications

2018
AssafArbelle, Jose Reyes, Jia-Yun Chen, Galit Lahav, and Tammy Riklin Raviv. 7/2018. “A probabilistic approach to joint cell tracking and segmentation in high-throughput microscopy videos.” Medical Image Analysis, 47, Pp. 140-152. Publisher's VersionAbstract
We present a novel computational framework for the analysis of high-throughput microscopy videos of living cells. The proposed framework is generally useful and can be applied to different datasets acquired in a variety of laboratory settings. This is accomplished by tying together two fundamental aspects of cell lineage construction, namely cell segmentation and tracking, via a Bayesian inference of dynamic models. In contrast to most existing approaches, which aim to be general, no assumption of cell shape is made. Spatial, temporal, and cross-sectional variation of the analysed data are accommodated by two key contributions. First, time series analysis is exploited to estimate the temporal cell shape uncertainty in addition to cell trajectory. Second, a fast marching (FM) algorithm is used to integrate the inferred cell properties with the observed image measurements in order to obtain image likelihood for cell segmentation, and association. The proposed approach has been tested on eight different time-lapse microscopy data sets, some of which are high-throughput, demonstrating promising results for the detection, segmentation and association of planar cells. Our results surpass the state of the art for the Fluo-C2DL-MSC data set of the Cell Tracking Challenge (Maška et al., 2014).
2016
Jia‐Ren Lin, Mohammad Fallahi-Sichani, Jia-Yun Chen, and Peter K Sorger. 2016. “Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single‐cell Imaging.” Current Protocols in Chemical Biology, Pp. 251-264.
2013
Kai Zhang, Rotem Fishel Ben Kenan, Yasuko Osakada, Wei Xu, Rachel S Sinit, Liang Chen, Xiaobei Zhao, Jia-Yun Chen, Bianxiao Cui, and Chengbiao Wu. 2013. “Defective axonal transport of Rab7 GTPase results in dysregulated trophic signaling.” The Journal of Neuroscience, 33, 17, Pp. 7451-7462.
Jia-Yun Chen, Jia-Ren Lin, Feng-Chiao Tsai, and Tobias Meyer. 2013. “Dosage of Dyrk1a Shifts Cells within a p21-Cyclin D1 Signaling Map to Control the Decision to Enter the Cell Cycle.” Molecular cell, 52, 1, Pp. 87-100.
2012
Chun-Yi Huang, Jia-Yun Chen, Shu-Chun Wu, Chieh-Hsiang Tan, Ruei-Ying Tzeng, Pei-Ju Lu, Yu-Feng Wu, Ruey-Hwa Chen, and Yi-Chun Wu. 2012. “C. elegans EIF-3. K Promotes Programmed Cell Death through CED-3 Caspase.” PloS one, 7, 5, Pp. e36584.
Jia-Yun Chen, Jia-Ren Lin, Karlene A Cimprich, and Tobias Meyer. 2012. “A two-dimensional ERK-AKT signaling code for an NGF-triggered cell-fate decision.” Molecular cell, 45, 2, Pp. 196-209.
2011
Jia-Ren Lin, Michelle K Zeman, Jia-Yun Chen, Muh-Ching Yee, and Karlene A Cimprich. 2011. “SHPRH and HLTF act in a damage-specific manner to coordinate different forms of postreplication repair and prevent mutagenesis.” Molecular cell, 42, 2, Pp. 237-249.
2003
Xiaochen Wang, Yi-Chun Wu, Valerie A Fadok, Ming-Chia Lee, Keiko Gengyo-Ando, Li-Chun Cheng, Duncan Ledwich, Pei-Ken Hsu, Jia-Yun Chen, and Bin-Kuan Chou. 2003. “Cell corpse engulfment mediated by C. elegans phosphatidylserine receptor through CED-5 and CED-12.” Science, 302, 5650, Pp. 1563-1566.
2002
Chuan-Wei Jang, Chun-Hau Chen, Chun-Chieh Chen, Jia-Yun Chen, Yi-Hsien Su, and Ruey-Hwa Chen. 2002. “TGF-β induces apoptosis through Smad-mediated expression of DAP-kinase.” Nature cell biology, 4, 1, Pp. 51-58.