Wang S, Lin J-R, Sontag ED, Sorger PK. Inferring reaction network structure from single-cell, multiplex data, using toric systems theory. bioRxiv. 2019 :731018.

Bandopadhayay P, Piccioni F, O’Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nature communications. 2019;10 (1) :2400.

Elgart V, Lin J-R, Loscalzo J. Determinants of drug-target interactions at the single cell level. PLoS computational biology. 2018;14 (12) :e1006601.

Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su M-J, Melms JC, Leeson R, Kanodia A, Mei S, Lin J-R. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 2018;175 (4) :984-997. e24.

Jia-Ren Lin, Benjamin Izar SWCYSMPSSSPSMK. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. eLIFE. 2018;7 :e31657.

Coy S, Rashid R, Lin J-R, Du Z, Donson AM, Hankinson TC, Foreman NK, Manley PE, Kieran MW, Reardon DA. Multiplexed Immunofluorescence Reveals Potential PD-1/PD-L1 Pathway Vulnerabilities in Craniopharyngioma. Neuro-oncology. 2018 :noy035.

Herrera KGN, Zaganjor E, Ishikawa Y, Spinelli JB, Yoon H, Lin J-R, Satterstrom KF, Ringel A, Mulei S, Souza A. Small-Molecule Screen Identifies De Novo Nucleotide Synthesis as a Vulnerability of Cells Lacking SIRT3. Cell reports. 2018;22 (8) :1945-1955.

Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Systems. 2017.

Fallahi‐Sichani M, Becker V, Izar B, Baker GJ, Lin J‐R, Boswell SA, Shah P, Rotem A, Garraway LA, Sorger PK. Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de‐differentiated state. Molecular Systems Biology. 2017;13 (1) :905.

Lin J-R. Multiplexed Single-Cell Imaging: Past, Present, and Future. ASSAY and Drug Development Technologies [Internet]. 2016. Publisher's Version lin_adt_preprint.pdf

Lin J‐R, Fallahi‐Sichani M, Chen J‐Y, Sorger PK. Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single‐cell Imaging. Current Protocols in Chemical Biology. 2016 :251-264. current_protocol_cycif_preprint.pdf

Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016;352 (6282) :189-196.

Lin J-R, Fallahi-Sichani M, Sorger PK. Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method. Nature Communications. 2015;6.

Zeman MK, Lin J-R, Freire R, Cimprich KA. DNA damage-specific deubiquitination regulates Rad18 functions to suppress mutagenesis. The Journal of cell biology. 2014;206 (2) :183-197.

Chen J-Y, Lin J-R, Tsai F-C, Meyer T. Dosage of Dyrk1a Shifts Cells within a p21-Cyclin D1 Signaling Map to Control the Decision to Enter the Cell Cycle. Molecular cell. 2013;52 (1) :87-100.

Choi HJC, Lin J-R, Vannier J-B, Slaats GG, Kile AC, Paulsen RD, Manning DK, Beier DR, Giles RH, Boulton SJ. NEK8 links the ATR-regulated replication stress response and S phase CDK activity to renal ciliopathies. Molecular cell. 2013;51 (4) :423-439.

Chen J-Y, Lin J-R, Cimprich KA, Meyer T. A two-dimensional ERK-AKT signaling code for an NGF-triggered cell-fate decision. Molecular cell. 2012;45 (2) :196-209.

Lin J-R, Zeman MK, Chen J-Y, Yee M-C, Cimprich KA. SHPRH and HLTF act in a damage-specific manner to coordinate different forms of postreplication repair and prevent mutagenesis. Molecular cell. 2011;42 (2) :237-249.

Lin Y-M, Chen Y-R, Lin J-R, Wang W-J, Inoko A, Inagaki M, Wu Y-C, Chen R-H. eIF3k regulates apoptosis in epithelial cells by releasing caspase 3 from keratin-containing inclusions. Journal of cell science. 2008;121 (14) :2382-2393.

Gajendran VK, Lin J-R, Fyhrie DP. An application of bioinformatics and text mining to the discovery of novel genes related to bone biology. Bone. 2007;40 (5) :1378-1388.