@article{chen2005bidirectional,
  title={Bidirectional signals transduced by DAPK--ERK interaction promote the apoptotic effect of DAPK},
  author={Chen, Chun-Hau and Wang, Won-Jing and Kuo, Jean-Cheng and Tsai, Hsiao-Chien and Lin, Jia-Ren and Chang, Zee-Fen and Chen, Ruey-Hwa},
  journal={The EMBO journal},
  volume={24},
  number={2},
  pages={294--304},
  year={2005},
  publisher={Wiley Online Library}
}

@article{kuo2003uncoordinated,
  title={Uncoordinated regulation of stress fibers and focal adhesions by DAP kinase},
  author={Kuo, Jean-Cheng and Lin, Jia-Ren and Staddon, James M and Hosoya, Hiroshi and Chen, Ruey-Hwa},
  journal={Journal of cell science},
  volume={116},
  number={23},
  pages={4777--4790},
  year={2003},
  publisher={The Company of Biologists Ltd}
}

@article{lin2008eif3k,
  title={eIF3k regulates apoptosis in epithelial cells by releasing caspase 3 from keratin-containing inclusions},
  author={Lin, Yu-Min and Chen, Yi-Ru and Lin, Jia-Ren and Wang, Won-Jing and Inoko, Akihito and Inagaki, Masaki and Wu, Yi-Chun and Chen, Ruey-Hwa},
  journal={Journal of cell science},
  volume={121},
  number={14},
  pages={2382--2393},
  year={2008},
  publisher={The Company of Biologists Ltd}
}

@article{lin2011shprh,
  title={SHPRH and HLTF act in a damage-specific manner to coordinate different forms of postreplication repair and prevent mutagenesis},
  author={Lin, Jia-Ren and Zeman, Michelle K and Chen, Jia-Yun and Yee, Muh-Ching and Cimprich, Karlene A},
  journal={Molecular cell},
  volume={42},
  number={2},
  pages={237--249},
  year={2011},
  publisher={Elsevier}
}

@article{chen2012two,
  title={A two-dimensional ERK-AKT signaling code for an NGF-triggered cell-fate decision},
  author={Chen, Jia-Yun and Lin, Jia-Ren and Cimprich, Karlene A and Meyer, Tobias},
  journal={Molecular cell},
  volume={45},
  number={2},
  pages={196--209},
  year={2012},
  publisher={Elsevier}
}

@article{gajendran2007application,
  title={An application of bioinformatics and text mining to the discovery of novel genes related to bone biology},
  author={Gajendran, Varun K and Lin, Jia-Ren and Fyhrie, David P},
  journal={Bone},
  volume={40},
  number={5},
  pages={1378--1388},
  year={2007},
  publisher={Elsevier}
}

@article{cimprich2008mechanisms,
  title={Mechanisms for Maintaining Genome Stability at the Replication Fork},
  author={Cimprich, Karlene A and McDougall, Christina and Lin, Jia-Ren},
  journal={The FASEB Journal},
  volume={22},
  pages={246--3},
  year={2008},
  publisher={Federation of American Societies for Experimental Biology}
}

@article{choi2013nek8,
  title={NEK8 links the ATR-regulated replication stress response and S phase CDK activity to renal ciliopathies},
  author={Choi, Hyo Jei Claudia and Lin, Jia-Ren and Vannier, Jean-Baptiste and Slaats, Gisela G and Kile, Andrew C and Paulsen, Renee D and Manning, Danielle K and Beier, David R and Giles, Rachel H and Boulton, Simon J and others},
  journal={Molecular cell},
  volume={51},
  number={4},
  pages={423--439},
  year={2013},
  publisher={Elsevier}
}

@article{chen2013dosage,
  title={Dosage of Dyrk1a Shifts Cells within a p21-Cyclin D1 Signaling Map to Control the Decision to Enter the Cell Cycle},
  author={Chen, Jia-Yun and Lin, Jia-Ren and Tsai, Feng-Chiao and Meyer, Tobias},
  journal={Molecular cell},
  volume={52},
  number={1},
  pages={87--100},
  year={2013},
  publisher={Elsevier}
}

@article{zeman2014dna,
  title={DNA damage-specific deubiquitination regulates Rad18 functions to suppress mutagenesis},
  author={Zeman, Michelle K and Lin, Jia-Ren and Freire, Raimundo and Cimprich, Karlene A},
  journal={The Journal of cell biology},
  volume={206},
  number={2},
  pages={183--197},
  year={2014},
  publisher={Rockefeller Univ Press}
}

@article{lin2015highly,
  title={Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method},
  author={Lin, Jia-Ren and Fallahi-Sichani, Mohammad and Sorger, Peter K},
  journal={Nature communications},
  volume={6},
  number={1},
  pages={8390},
  year={2015},
  publisher={Nature Publishing Group UK London}
}

@article{zhao2015abstracts,
  title={Abstracts The Society of Biomolecular Imaging and Informatics Second Annual Conference September 15--17, 2015 Boston, MA, USA},
  author={Zhao, Wenpu and Fogg, Darin K and Kaplan, Mariana J and Fennell, Myles and Commisso, Cosimo and Ramirez, Craig and Garippa, Ralph and Bar-Sagi, Dafna and Hesley, Jayne and Sirenko, Oksana and others},
  journal={ASSAY and Drug Development Technologies},
  volume={13},
  number={9},
  pages={585--599},
  year={2015},
  publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}

@phdthesis{lin2012understanding,
  title={Understanding the Mechanism of Mammalian Damage Tolerance Proteins in Suppressing Damage-Specific Mutagenesis},
  author={Lin, Jia-Ren},
  year={2012},
  school={Stanford University}
}

@article{tirosh2016dissecting,
  title={Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq},
  author={Tirosh, Itay and Izar, Benjamin and Prakadan, Sanjay M and Wadsworth, Marc H and Treacy, Daniel and Trombetta, John J and Rotem, Asaf and Rodman, Christopher and Lian, Christine and Murphy, George and others},
  journal={Science},
  volume={352},
  number={6282},
  pages={189--196},
  year={2016},
  publisher={American Association for the Advancement of Science}
}

@article{lin2016cyclic,
  title={Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging},
  author={Lin, Jia-Ren and Fallahi-Sichani, Mohammad and Chen, Jia-Yun and Sorger, Peter K},
  journal={Current protocols in chemical biology},
  volume={8},
  number={4},
  pages={251--264},
  year={2016}
}

@article{lin2017multiplexed,
  title={Multiplexed Single-Cell Imaging: Past, Present, and Future},
  author={Lin, Jia-Ren},
  journal={ASSAY and Drug Development Technologies},
  volume={15},
  number={1},
  pages={8--10},
  year={2017},
  publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}

@article{fallahi2017adaptive,
  title={Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de-differentiated state},
  author={Fallahi-Sichani, Mohammad and Becker, Verena and Izar, Benjamin and Baker, Gregory J and Lin, Jia-Ren and Boswell, Sarah A and Shah, Parin and Rotem, Asaf and Garraway, Levi A and Sorger, Peter K},
  journal={Molecular systems biology},
  volume={13},
  number={1},
  pages={905},
  year={2017}
}

@article{lin2017abstract,
  title={Abstract B21: Probing tumor heterogeneity and immune infiltration with Cyclic Immunofluorescence (CycIF), a robust, multiplexed imaging method},
  author={Lin, Jia-Ren and Izar, Benjamin and Hawthorne, Sabrina and Nordberg, Josh and Kaldjian, Eric and Sorger, Peter},
  journal={Cancer Immunology Research},
  volume={5},
  number={3\_Supplement},
  pages={B21--B21},
  year={2017},
  publisher={The American Association for Cancer Research}
}

@article{lin2017slide,
  title={Slide-based multi-parametric immunophenotyping of human blood samples by cyclic immunofluorescence using the Accucyte-CyteFinder system},
  author={Lin, Jia-Ren and U'Ren, Lance and Baker, Gregory J and Nordberg, Joshua J and Maliga, Zoltan and Stilwell, Jackie L and Kaldjian, Eric P and Sorger, Peter K},
  journal={Cancer Research},
  volume={77},
  number={13\_Supplement},
  pages={1705--1705},
  year={2017},
  publisher={The American Association for Cancer Research}
}

@article{fallahi2017abstract,
  title={Abstract PR17: Single-cell analysis reveals an adaptive, slowly-dividing, de-differentiated, drug-resistant cell state selectively inhibitable by drug combinations},
  author={Fallahi-Sichani, Mohammad and Becker, Verena and Izar, Benjamin and Baker, Gregory J and Lin, Jia-Ren and Boswell, Sarah A and Garraway, Levi A and Sorger, Peter K},
  journal={Molecular Cancer Therapeutics},
  volume={16},
  number={10\_Supplement},
  pages={PR17--PR17},
  year={2017},
  publisher={The American Association for Cancer Research}
}

@article{keenan2018library,
  title={The library of integrated network-based cellular signatures NIH program: system-level cataloging of human cells response to perturbations},
  author={Keenan, Alexandra B and Jenkins, Sherry L and Jagodnik, Kathleen M and Koplev, Simon and He, Edward and Torre, Denis and Wang, Zichen and Dohlman, Anders B and Silverstein, Moshe C and Lachmann, Alexander and others},
  journal={Cell systems},
  volume={6},
  number={1},
  pages={13--24},
  year={2018},
  publisher={Cell Press}
}

@article{coy2018multiplexed,
  title={Multiplexed immunofluorescence reveals potential PD-1/PD-L1 pathway vulnerabilities in craniopharyngioma},
  author={Coy, Shannon and Rashid, Rumana and Lin, Jia-Ren and Du, Ziming and Donson, Andrew M and Hankinson, Todd C and Foreman, Nicholas K and Manley, Peter E and Kieran, Mark W and Reardon, David A and others},
  journal={Neuro-oncology},
  volume={20},
  number={8},
  pages={1101--1112},
  year={2018},
  publisher={Oxford University Press US}
}

@inproceedings{coy2018multiplexed,
  title={Multiplexed Immunofluorescence Reveals Potential Immune Checkpoint Vulnerabilities in Craniopharyngioma},
  author={Coy, Shannon and Rashid, Rumana and Lin, Jia-Ren and Du, Ziming and Manley, Peter E and Kieran, Mark W and Reardon, David A and Sorger, Peter and Santagata, Sandro},
  booktitle={LABORATORY INVESTIGATION},
  volume={98},
  pages={656--657},
  year={2018},
  organization={NATURE PUBLISHING GROUP 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA}
}

@article{coy2018cran,
  title={CRAN-11. MULTIPLEXED IMMUNOFLUORESCENCE REVEALS POTENTIAL PD-1/PD-L1 PATHWAY VULNERABILITIES IN CRANIOPHARYNGIOMA},
  author={Coy, Shannon and Rashid, Rumana and Lin, Jia-Ren and Du, Ziming and Donson, Andrew M and Hankinson, Todd C and Foreman, Nicholas K and Manley, Peter E and Kieran, Mark W and Reardon, David A and others},
  journal={Neuro-Oncology},
  volume={20},
  number={suppl\_2},
  pages={i39--i39},
  year={2018},
  publisher={Oxford University Press US}
}

@article{farkkila2018dna,
  title={DNA damage and immunoprofiling with highly multiplexed tissue immunofluorescence (t-CycIF) in high-grade serous ovarian cancer},
  author={Farkkila, Anniina and Chopra, Sameer S and Lin, Jia-Ren and Maliga, Zoltan and Koruchupakkal, Bose and Strickland, Kyle C and Howitt, Brooke E and Santagata, Sandro and Matulonis, Ursula A and Elias, Kevin and others},
  journal={Cancer Research},
  volume={78},
  number={13\_Supplement},
  pages={139--139},
  year={2018},
  publisher={The American Association for Cancer Research}
}

@article{jia2018highly,
  title={Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes},
  author={Jia-Ren Lin, Benjamin Izar, Shu Wang, Clarence Yapp, Shaolin Mei, Parin M Shah, Sandro Santagata, Peter K Sorger},
  journal={eLIFE},
  volume={7},
  pages={e31657},
  year={2018},
  publisher={eLife Sciences Publications, Ltd}
}

@article{herrera2018small,
  title={Small-Molecule Screen Identifies De Novo Nucleotide Synthesis as a Vulnerability of Cells Lacking SIRT3},
  author={Herrera, Karina N Gonzalez and Zaganjor, Elma and Ishikawa, Yoshinori and Spinelli, Jessica B and Yoon, Haejin and Lin, Jia-Ren and Satterstrom, F Kyle and Ringel, Alison and Mulei, Stacy and Souza, Amanda and others},
  journal={Cell reports},
  volume={22},
  number={8},
  pages={1945--1955},
  year={2018},
  publisher={Elsevier}
}

@article{jerby2018cancer,
  title={A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade},
  author={Jerby-Arnon, Livnat and Shah, Parin and Cuoco, Michael S and Rodman, Christopher and Su, Mei-Ju and Melms, Johannes C and Leeson, Rachel and Kanodia, Abhay and Mei, Shaolin and Lin, Jia-Ren and others},
  journal={Cell},
  volume={175},
  number={4},
  pages={984--997},
  year={2018},
  publisher={Elsevier}
}

@article{dunn2018mismatch,
  title={Mismatch repair deficiency in high-grade meningioma: a rare but recurrent event associated with dramatic immune activation and clinical response to PD-1 blockade},
  author={Dunn, Ian F and Du, Ziming and Touat, Mehdi and Sisti, Michael B and Wen, Patrick Y and Umeton, Renato and Dubuc, Adrian M and Ducar, Matthew and Canoll, Peter D and Severson, Eric and others},
  journal={JCO precision oncology},
  volume={2},
  pages={1--12},
  year={2018},
  publisher={American Society of Clinical Oncology}
}

@inproceedings{lin2017probing,
  title={Probing tumor heterogeneity and immune infiltration with Cyclic Immunofluorescence (CycIF), a robust, multiplexed imaging method},
  author={Lin, Jia-Ren and Izar, Benjamin and Hawthorne, Sabrina and Nordberg, Josh and Kaldjian, Eric and Sorger, Peter},
  booktitle={CANCER IMMUNOLOGY RESEARCH},
  volume={5},
  number={3},
  year={2017},
  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}
}

@article{bandopadhayay2019neuronal,
  title={Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma},
  author={Bandopadhayay, Pratiti and Piccioni, Federica and O’Rourke, Ryan and Ho, Patricia and Gonzalez, Elizabeth M and Buchan, Graham and Qian, Kenin and Gionet, Gabrielle and Girard, Emily and Coxon, Margo and others},
  journal={Nature communications},
  volume={10},
  number={1},
  pages={2400},
  year={2019},
  publisher={Nature Publishing Group UK London}
}

@misc{nathenson2019molecular,
  title={Molecular characterization and management of secondary resistance to serial TRK inhibitors.},
  author={Nathenson, Michael and Hemming, Matthew Louis and Malik, Karan and Lin, Jia-Ren and Santagata, Sandro and Du, Ziming and Marino-Enriquez, Adrian and Hagan, Timothy J and Chipashvili, Otari and Thornton, Katherine Anne and others},
  year={2019},
  publisher={American Society of Clinical Oncology}
}

@article{izar2019abstract,
  title={Abstract SY45-04: Development of therapeutic strategies by resolving the tumor ecosystem},
  author={Izar, Benjamin and Jerby-Arnon, Livnat and Tirosh, Itay and Shah, Parin and Cuoco, Michael C and Rodman, Christopher and Su, Mei-Ju and Melms, Johannes C and Leeson, Rachel and Kanodia, Abhay and others},
  journal={Cancer Research},
  volume={79},
  number={13\_Supplement},
  pages={SY45--04},
  year={2019},
  publisher={The American Association for Cancer Research}
}

@article{rashid2019highly,
  title={Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer},
  author={Rashid, Rumana and Gaglia, Giorgio and Chen, Yu-An and Lin, Jia-Ren and Du, Ziming and Maliga, Zoltan and Schapiro, Denis and Yapp, Clarence and Muhlich, Jeremy and Sokolov, Artem and others},
  journal={Scientific data},
  volume={6},
  number={1},
  pages={323},
  year={2019},
  publisher={Nature Publishing Group UK London}
}

@article{wang2019inferring,
  title={Inferring reaction network structure from single-cell, multiplex data, using toric systems theory},
  author={Wang, Shu and Lin, Jia-Ren and Sontag, Eduardo D and Sorger, Peter K},
  journal={PLoS computational biology},
  volume={15},
  number={12},
  pages={e1007311},
  year={2019},
  publisher={Public Library of Science}
}

@article{elgart2018determinants,
  title={Determinants of drug-target interactions at the single cell level},
  author={Elgart, Vlad and Lin, Jia-Ren and Loscalzo, Joseph},
  journal={PLoS computational biology},
  volume={14},
  number={12},
  pages={e1006601},
  year={2018},
  publisher={Public Library of Science}
}

@article{du2019qualifying,
  title={Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging.},
  author={Du, Ziming and Lin, Jia-Ren and Rashid, Rumana and Maliga, Zoltan and Wang, Shu and Aster, Jon C and Izar, B and Sorger, Peter K and Santagata, Sandro},
  journal={Nature protocols},
  volume={14},
  number={10},
  pages={2900--2930},
  year={2019}
}

@article{farkkila2019abstract,
  title={Abstract AP22: DNA DAMAGE RESPONSES AND IMMUNE PROFILING THROUGH HIGHLY MULTIPLEXED TISSUE IMMUNOFLUORESCENCE (T-CYCIF) IN HIGH-GRADE SEROUS OVARIAN CANCER},
  author={F{\"a}rkkil{\"a}, Anniina and Lin, Jia-Ren and Maliga, Zoltan and Chopra, Sameer S and Koruchupakkal, Bose and Howitt, Brooke E and Strickland, Kyle C and Santagata, Sandro and Swisher, Elizabeth M and Matulonis, Ursula A and others},
  journal={Clinical Cancer Research},
  volume={25},
  number={22\_Supplement},
  pages={AP22--AP22},
  year={2019},
  publisher={The American Association for Cancer Research}
}

@inproceedings{ericson2019pick,
  title={Pick-Seq (R): a spatial analysis tool for immuno-oncology biomarker discovery utilizing multi-parameter imaging and RNA sequencing of tissue micro-regions},
  author={Ericson, Nolan and Podyminogin, Rebecca and Chow, Jennifer and Chen, Yu-An and Lin, Jia-Ren and Maliga, Zoltan and Sorger, Peter and Teplitz, Kyla and Duplessis, Melinda and Kaldjian, Eric and others},
  booktitle={JOURNAL FOR IMMUNOTHERAPY OF CANCER},
  volume={7},
  year={2019},
  organization={BMC CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND}
}

@inproceedings{farkkila2019dna,
  title={DNA DAMAGE RESPONSES AND IMMUNE PROFILING THROUGH HIGHLY MULTIPLEXED TISSUE IMMUNOFLUORESCENCE (T-CYCIF) IN HIGH-GRADE SEROUS OVARIAN CANCER},
  author={Farkkila, Anniina and Lin, Jia-Ren and Maliga, Zoltan and Chopra, Sameer S and Koruchupakkal, Bose and Howitt, Brooke E and Strickland, Kyle C and Santagata, Sandro and Swisher, Elizabeth M and Matulonis, Ursula A and others},
  booktitle={CLINICAL CANCER RESEARCH},
  volume={25},
  number={22},
  pages={144--144},
  year={2019},
  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}
}

@article{pastorello2020abstract,
  title={Abstract P5-02-03: Highly multiplexed tissue-based cyclic immunofluorescence in breast cancer for precision oncology},
  author={Pastorello, Ricardo G and Lin, Jia-Ren and Du, Ziming and Mei, Shaolin and Taneja, Krishan and Dillon, Deborah A and Schnitt, Stuart J and Sorger, Peter K and Mittendorf, Elizabeth A and Santagata, Sandro and others},
  journal={Cancer Research},
  volume={80},
  number={4\_Supplement},
  pages={P5--02},
  year={2020},
  publisher={The American Association for Cancer Research}
}

@inproceedings{podyminogin2019pick,
  title={Pick-Seq (R): a novel technology to retrieve tissue micro-regions for RNA sequencing},
  author={Podyminogin, Rebecca and Ericson, Nolan and Chow, Jennifer and Lin, Jia-Ren and Chen, Yu-An and Maliga, Zoltan and Teplitz, Kyla and Tsai, Tessa Pei-Ching and Quintanilla, Adrian and Sorger, Peter and others},
  booktitle={BRITISH JOURNAL OF CANCER},
  volume={121},
  pages={1--2},
  year={2019},
  organization={NATURE PUBLISHING GROUP MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND}
}

@article{hemming2020response,
  title={Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1},
  author={Hemming, Matthew L and Nathenson, Michael J and Lin, Jia-Ren and Mei, Shaolin and Du, Ziming and Malik, Karan and Marino-Enriquez, Adrian and Jagannathan, Jyothi P and Sorger, Peter K and Bertagnolli, Monica and others},
  journal={JCO precision oncology},
  volume={4},
  pages={79--90},
  year={2020},
  publisher={American Society of Clinical Oncology}
}

@article{rashid2020interpretative,
  title={Interpretative guides for interacting with tissue atlas and digital pathology data using the Minerva browser},
  author={Rashid, Rumana and Chen, Yu-An and Hoffer, John and Muhlich, Jeremy L and Lin, Jia-Ren and Krueger, Robert and Pfister, Hanspeter and Mitchell, Richard and Santagata, Sandro and Sorger, Peter},
  journal={bioRxiv},
  year={2020},
  publisher={Cold Spring Harbor Laboratory}
}

@article{rozenblatt2020human,
  title={The Human Tumor Atlas Network: charting tumor transitions across space and time at single-cell resolution},
  author={Rozenblatt-Rosen, Orit and Regev, Aviv and Oberdoerffer, Philipp and Nawy, Tal and Hupalowska, Anna and Rood, Jennifer E and Ashenberg, Orr and Cerami, Ethan and Coffey, Robert J and Demir, Emek and others},
  journal={Cell},
  volume={181},
  number={2},
  pages={236--249},
  year={2020},
  publisher={Elsevier}
}

@article{izar2020single,
  title={A single-cell landscape of high-grade serous ovarian cancer},
  author={Izar, Benjamin and Tirosh, Itay and Stover, Elizabeth H and Wakiro, Isaac and Cuoco, Michael S and Alter, Idan and Rodman, Christopher and Leeson, Rachel and Su, Mei-Ju and Shah, Parin and others},
  journal={Nature Medicine},
  volume={26},
  number={8},
  pages={1271--1279},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{coy2020tami,
  title={TAMI-45. PHENOGENOMIC CHARACTERIZATION OF IMMUNOMODULATORY PURINERGIC SIGNALING IN GLIOBLASTOMA},
  author={Coy, Shannon and Rashid, Rumana and Stopka, Sylwia and Lin, Jia-Ren and Euskirchen, Philipp and Hwang, Jaeho and Khadka, Prasidda and Bandopadhayay, Pratiti and Wen, Patrick and Sorger, Peter and others},
  journal={Neuro-Oncology},
  volume={22},
  number={Supplement\_2},
  pages={ii222--ii223},
  year={2020},
  publisher={Oxford University Press US}
}

@article{zervantonakis2020fibroblast,
  title={Fibroblast--tumor cell signaling limits HER2 kinase therapy response via activation of MTOR and antiapoptotic pathways},
  author={Zervantonakis, Ioannis K and Poskus, Matthew D and Scott, Alexis L and Selfors, Laura M and Lin, Jia-Ren and Dillon, Deborah A and Pathania, Shailja and Sorger, Peter K and Mills, Gordon B and Brugge, Joan S},
  journal={Proceedings of the National Academy of Sciences},
  volume={117},
  number={28},
  pages={16500--16508},
  year={2020},
  publisher={National Academy of Sciences}
}

@article{hemming2021hand1,
  title={HAND1 and BARX1 act as transcriptional and anatomic determinants of malignancy in gastrointestinal stromal tumor},
  author={Hemming, Matthew L and Coy, Shannon and Lin, Jia-Ren and Andersen, Jessica L and Przybyl, Joanna and Mazzola, Emanuele and Abdelhamid Ahmed, Amr H and van de Rijn, Matt and Sorger, Peter K and Armstrong, Scott A and others},
  journal={Clinical Cancer Research},
  volume={27},
  number={6},
  pages={1706--1719},
  year={2021},
  publisher={American Association for Cancer Research}
}

@article{mehta2021targeting,
  title={Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer},
  author={Mehta, Anita K and Cheney, Emily M and Hartl, Christina A and Pantelidou, Constantia and Oliwa, Madisson and Castrillon, Jessica A and Lin, Jia-Ren and Hurst, Katie E and de Oliveira Taveira, Mateus and Johnson, Nathan T and others},
  journal={Nature Cancer},
  volume={2},
  number={1},
  pages={66--82},
  year={2021},
  publisher={Nature Publishing Group}
}

@article{guerriero2021abstract,
  title={Abstract PS18-02: Highly multiplexed tissue-based cyclic immunofluorescence (t-CyCIF) for precision oncology identifies novel patterns of HER2 heterogeneity in breast cancer},
  author={Guerriero, Jennifer L and Lin, Jia-Ren and Pastorello, Ricardo G and Du, Ziming and Mei, Shaolin and Taneja, Krishan and Schnitt, Stuart J and Dillon, Deborah A and Sorger, Peter K and Santagata, Sandro and others},
  journal={Cancer Research},
  volume={81},
  number={4\_Supplement},
  pages={PS18--02},
  year={2021},
  publisher={The American Association for Cancer Research}
}

@article{schapiro2022mcmicro,
  title={MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging},
  author={Schapiro, Denis and Sokolov, Artem and Yapp, Clarence and Chen, Yu-An and Muhlich, Jeremy L and Hess, Joshua and Creason, Allison L and Nirmal, Ajit J and Baker, Gregory J and Nariya, Maulik K and others},
  journal={Nature methods},
  volume={19},
  number={3},
  pages={311--315},
  year={2022},
  publisher={Nature Publishing Group}
}

@article{launonen2022single,
  title={Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer},
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@article{lin2023multiplexed,
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  journal={Cell},
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  year={2021},
  publisher={Wolters Kluwer Health}
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@article{lin2021rapid,
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  author={Lin, Jia-Ren and Campton, Daniel E and Cooper, Jeremy and Chen, Yu-An and McCarty, Erin F and Ligon, Keith L and Kaldjian, Eric P and Teplitz, Kyla and Reese, Steve and Santagata, Sandro and others},
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@article{schapiro2022miti,
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@article{jessup2021scope2screen,
  title={Scope2Screen: Focus+ Context Techniques for Pathology Tumor Assessment in Multivariate Image Data},
  author={Jessup, Jared and Krueger, Robert and Warchol, Simon and Hoffer, John and Muhlich, Jeremy and Ritch, Cecily C and Gaglia, Giorgio and Coy, Shannon and Chen, Yu-An and Lin, Jia-Ren and others},
  journal={IEEE Transactions on Visualization and Computer Graphics},
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@article{liu2021evolution,
  title={Evolution of delayed resistance to immunotherapy in a melanoma responder},
  author={Liu, David and Lin, Jia-Ren and Robitschek, Emily J and Kasumova, Gyulnara G and Heyde, Alex and Shi, Alvin and Kraya, Adam and Zhang, Gao and Moll, Tabea and Frederick, Dennie T and others},
  journal={Nature medicine},
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@article{coy2022single,
  title={Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma},
  author={Coy, Shannon and Wang, Shu and Stopka, Sylwia A and Lin, Jia-Ren and Yapp, Clarence and Ritch, Cecily C and Salhi, Lisa and Baker, Gregory J and Rashid, Rumana and Baquer, Gerard and others},
  journal={Nature communications},
  volume={13},
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@article{gaglia2022temporal,
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@article{wangtemporal,
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}

@article{creason2022web,
  title={A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets},
  author={Creason, Allison L and Watson, Cameron and Gu, Qiang and Persson, Daniel and Sargent, Luke and Chen, Yu-An and Lin, Jia-Ren and Sivagnanam, Shamilene and W{\"u}nnemann, Florian and Nirmal, Ajit J and others},
  journal={bioRxiv},
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@article{gaglia2023lymphocyte,
  title={Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma},
  author={Gaglia, Giorgio and Burger, Megan L and Ritch, Cecily C and Rammos, Danae and Dai, Yang and Crossland, Grace E and Tavana, Sara Z and Warchol, Simon and Jaeger, Alex M and Naranjo, Santiago and others},
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@article{notarangelo2022oncometabolite,
  title={Oncometabolite d-2HG alters T cell metabolism to impair CD8+ T cell function},
  author={Notarangelo, Giulia and Spinelli, Jessica B and Perez, Elizabeth M and Baker, Gregory J and Kurmi, Kiran and Elia, Ilaria and Stopka, Sylwia A and Baquer, Gerard and Lin, Jia-Ren and Golby, Alexandra J and others},
  journal={Science},
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  year={2022},
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@article{gray2022human,
  title={A human breast atlas integrating single-cell proteomics and transcriptomics},
  author={Gray, G Kenneth and Li, Carman Man-Chung and Rosenbluth, Jennifer M and Selfors, Laura M and Girnius, Nomeda and Lin, Jia-Ren and Schackmann, Ron CJ and Goh, Walter L and Moore, Kaitlin and Shapiro, Hana K and others},
  journal={Developmental cell},
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@article{ternes2022computational,
  title={Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays},
  author={Ternes, Luke and Lin, Jia-Ren and Chen, Yu-An and Gray, Joe W and Chang, Young Hwan},
  journal={PLOS Computational Biology},
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@article{lecky2022features,
  title={Features of poorly primed apoptotic subpopulations identified using functional measurements of apoptotic priming and multiplexed immunofluorescence on single cells},
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  journal={European Journal of Cancer},
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@inproceedings{robitschek2022acquired,
  title={ACQUIRED RESISTANCE TO IMMUNE CHECKPOINT BLOCKADE BY PHENOTYPIC PLASTICITY OF MELANOMA},
  author={Robitschek, Emily and Mehta, Arnav and Lin, Jia-Ren and Frederick, Dennie and Shi, Alvin and Larque, Ana and Miao, Benchun and Raghavan, Rumya and Sharova, Tatyana and Shin, John and others},
  booktitle={JOURNAL FOR IMMUNOTHERAPY OF CANCER},
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@article{burlingame20223d,
  title={3D multiplexed tissue imaging reconstruction and optimized region-of-interest (ROI) selection through deep learning model of channels embedding},
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  journal={bioRxiv},
  pages={2022--12},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
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@article{lin2018tcycif,
  title={tCyCIF protcol (Leica BOND) version 0.1},
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@article{maliga2023immune,
  title={Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence},
  author={Maliga, Zoltan and Kim, Daniel Y and Bui, Ai-Tram N and Lin, Jia-Ren and Dewan, Anna K and Murphy, George F and Nirmal, Ajit J and Lian, Christine G and Sorger, Peter K and LeBoeuf, Nicole R},
  journal={bioRxiv},
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@inproceedings{lin2022multi,
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  author={Lin, Jia-Ren and Chen, Yu-An and Campton, Daniel and Cooper, Jeremy and Coy, Shannon and Yapp, Clarence and McCarty, Erin and Ligon, Keith L and Reese, Steven and George, Tad and others},
  booktitle={CANCER RESEARCH},
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  number={23},
  year={2022},
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@article{lecky2023sequential,
  title={Sequential apoptotic and multiplexed proteomic evaluation of single cancer cells},
  author={Lecky, Emmalyn and Mukherji, Atreyi and German, Rebecca and Antonellis, Gabriella and Lin, Jia-Ren and Yorsz, Michael and McQueeney, Kelley E and Ryan, Jeremy and Ng, Kimmie and Sicinska, Ewa and others},
  journal={Science Advances},
  volume={9},
  number={25},
  pages={eadg4128},
  year={2023},
  publisher={American Association for the Advancement of Science}
}

@article{lin2023high,
  title={High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers},
  author={Lin, Jia-Ren and Chen, Yu-An and Campton, Daniel and Cooper, Jeremy and Coy, Shannon and Yapp, Clarence and Tefft, Juliann B and McCarty, Erin and Ligon, Keith L and Rodig, Scott J and others},
  journal={Nature cancer},
  volume={4},
  number={7},
  pages={1036--1052},
  year={2023},
  publisher={Nature Publishing Group US New York}
}

@article{lin2022tissue,
  title={Tissue Cyclic Immunofluorescence (t-CyCIF) version 3},
  author={Lin, Jia Ren and Izar, Benjamin and Maliga, Zoltan and Chen, Yu-An and Gaglia, Giorgio and Du, Ziming and Yapp, Clarence and Mei, Shaolin and Santagata, Sandro and Sorger, Peter},
  year={2022}
}

@article{lin2020ffpe,
  title={FFPE Tissue Pre-treatment Before t-CyCIF on Leica Bond RX},
  author={Lin, Jia Ren and Izar, Benjamin and Maliga, Zoltan and Chen, Yu-An and Gaglia, Giorgio and Du, Ziming and Yapp, Clarence and Mei, Shaolin and Santagata, Sandro and Sorger, Peter},
  year={2020}
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@article{creason2023longitudinal,
  title={Longitudinal and multimodal auditing of tumor adaptation to CDK4/6 inhibitors in HR+ metastatic breast cancers},
  author={Creason, Allison L and Egger, Jay and Watson, Cameron and Sivagnanam, Shamilene and Chin, Koei and MacPherson, Kevin and Lin, Jia-Ren and Chen, Yu-An and Johnson, Brett E and Feiler, Heidi S and others},
  journal={bioRxiv},
  pages={2023--09},
  year={2023},
  publisher={Cold Spring Harbor Laboratory}
}

@article{baker2024quality,
  title={Quality control for single cell analysis of high-plex tissue profiles using CyLinter},
  author={Baker, Gregory J and Novikov, Edward and Zhao, Ziyuan and Vallius, Tuulia and Davis, Janae A and Lin, Jia-Ren and Muhlich, Jeremy L and Mittendorf, Elizabeth A and Santagata, Sandro and Guerriero, Jennifer L and others},
  journal={bioRxiv},
  year={2024},
  publisher={Cold Spring Harbor Laboratory Preprints}
}

@article{guerriero2024qualification,
  title={Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer},
  author={Guerriero, Jennifer L and Lin, Jia-Ren and Pastorello, Ricardo G and Du, Ziming and Chen, Yu-An and Townsend, Madeline G and Shimada, Kenichi and Hughes, Melissa E and Ren, Siyang and Tayob, Nabihah and others},
  journal={NPJ Breast Cancer},
  volume={10},
  number={1},
  pages={2},
  year={2024},
  publisher={Nature Publishing Group UK London}
}

@article{shi2022917,
  title={917 Reversing the immune-excluded (“cold”) tumor immune microenvironment in oral squamous cell carcinoma},
  author={Shi, Yewen and Rodriguez-Rosario, Alanis and Xie, Tongxin and Gleber-Netto, Frederico and Pickering, Curtis and Osman, Abdullah and Sikora, Andrew and Myers, Jeffrey and Rangel, Roberto and others},
  journal={J Immunother},
  volume={10},
  number={2},
  pages={A1--A1595},
  year={2022}
}

@article{haddox2024phase,
  title={Phase II study of eribulin plus pembrolizumab in metastatic soft-tissue sarcomas: clinical outcomes and biological correlates},
  author={Haddox, Candace L and Nathenson, Michael J and Mazzola, Emanuele and Lin, Jia-Ren and Baginska, Joanna and Nau, Allison and Weirather, Jason L and Choy, Edwin and Marino-Enriquez, Adrian and Morgan, Jeffrey A and others},
  journal={Clinical Cancer Research},
  volume={30},
  number={7},
  pages={1281--1292},
  year={2024},
  publisher={American Association for Cancer Research}
}

@article{maliga2024immune,
  title={Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence: A Pilot Study},
  author={Maliga, Zoltan and Kim, Daniel Y and Bui, Ai-Tram N and Lin, Jia-Ren and Dewan, Anna K and Jadeja, Saagar and Murphy, George F and Nirmal, Ajit J and Lian, Christine G and Sorger, Peter K and others},
  journal={The Journal of investigative dermatology},
  pages={S0022--202X},
  year={2024}
}

@article{kader2024abstract,
  title={Abstract LB311: Multimodal spatial profiling reveals the emergence of an immune suppressive microenvironment at the initial stages of high-grade serous ovarian cancer development},
  author={Kader, Tanjina and Lin, Jia-Ren and Coy, Shannon and Hug, Clemens and Chen, Yu-An and Pelletier, Roxanne J and Leon, Mariana and Lee, John and Xu, Yi-Lin and Yapp, Clarence and others},
  journal={Cancer Research},
  volume={84},
  number={7\_Supplement},
  pages={LB311--LB311},
  year={2024},
  publisher={AACR}
}

@article{ricciuti2024genomic,
  title={Genomic and immunophenotypic landscape of acquired resistance to PD-(L) 1 blockade in non--small-cell lung cancer},
  author={Ricciuti, Biagio and Lamberti, Giuseppe and Puchala, Sreekar R and Mahadevan, Navin R and Lin, Jia-Ren and Alessi, Joao V and Chowdhury, Alexander and Li, Yvonne Y and Wang, Xinan and Spurr, Liam and others},
  journal={Journal of Clinical Oncology},
  volume={42},
  number={11},
  pages={1311--1321},
  year={2024},
  publisher={Wolters Kluwer Health}
}

@article{hermida2023endocrine,
  title={Endocrine Therapy Synergizes with SMAC Mimetics to Potentiate Antigen Presentation and Tumor Regression in Hormone Receptor--Positive Breast Cancer},
  author={Hermida-Prado, Francisco and Xie, Yingtian and Sherman, Shira and Nagy, Zsuzsanna and Russo, Douglas and Akhshi, Tara and Chu, Zhengtao and Feit, Avery and Campisi, Marco and Chen, Minyue and others},
  journal={Cancer Research},
  volume={83},
  number={19},
  pages={3284--3304},
  year={2023},
  publisher={AACR}
}