@article {696306,
	title = {Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays},
	journal = {PLOS Computational Biology},
	volume = {18},
	number = {9},
	year = {2022},
	pages = {e1010505},
	publisher = {Public Library of Science San Francisco, CA USA},
	isbn = {1553-734X},
	author = {Ternes, Luke and Lin, Jia-Ren and Chen, Yu-An and Gray, Joe W and Chang, Young Hwan}
}
@article {696305,
	title = {A human breast atlas integrating single-cell proteomics and transcriptomics},
	journal = {Developmental Cell},
	year = {2022},
	publisher = {Elsevier},
	isbn = {1534-5807},
	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}
}
@article {696302,
	title = {Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma},
	journal = {bioRxiv},
	year = {2022},
	publisher = {Cold Spring Harbor Laboratory},
	author = {Gaglia, Giorgio and Burger, Megan and Ritch, Cecily C and Rammos, Danae and Dai, Yang and Crossland, Grace E and Tavana, Sara Z and Simon Warchol and Jaeger, Alex M and Naranjo, Santiago}
}
@article {696293,
	title = {MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging},
	journal = {Nature methods},
	volume = {19},
	number = {3},
	year = {2022},
	pages = {311-315},
	publisher = {Nature Publishing Group},
	isbn = {1548-7105},
	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}
}
@article {696296,
	title = {MITI Minimum Information guidelines for highly multiplexed tissue images},
	journal = {Nature Methods},
	volume = {19},
	number = {3},
	year = {2022},
	pages = {262-267},
	publisher = {Nature Publishing Group},
	isbn = {1548-7105},
	author = {Schapiro, Denis and Yapp, Clarence and Sokolov, Artem and Reynolds, Sheila M and Chen, Yu-An and Sudar, Damir and Xie, Yubin and Muhlich, Jeremy and Arias-Camison, Raquel and Arena, Sarah}
}
@article {696303,
	title = {Multi-modal digital pathology for colorectal cancer diagnosis by high-plex immunofluorescence imaging and traditional histology of the same tissue section},
	journal = {bioRxiv},
	year = {2022},
	publisher = {Cold Spring Harbor Laboratory},
	author = {Lin, Jia-Ren and Chen, Yu-An and Campton, Daniel and Cooper, Jeremy and Coy, Shannon and Yapp, Clarence and Tefft, Juliann and McCarty, Erin and Ligon, Keith and Rodig, Scott J}
}
@article {696304,
	title = {Oncometabolite d-2HG alters T cell metabolism to impair CD8+ T cell function},
	journal = {Science},
	volume = {377},
	number = {6614},
	year = {2022},
	pages = {1519-1529},
	publisher = {American Association for the Advancement of Science},
	isbn = {0036-8075},
	author = {Giulia Notarangelo and Spinelli, Jessica B and Perez, Elizabeth M and Baker, Gregory J and Kurmi, Kiran and Elia, Ilaria and Stopka, Sylwia A and Gerard Baquer and Lin, Jia-Ren and Golby, Alexandra J}
}
@article {696299,
	title = {Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma},
	journal = {Nature communications},
	volume = {13},
	number = {1},
	year = {2022},
	pages = {1-24},
	publisher = {Nature Publishing Group},
	isbn = {2041-1723},
	author = {Coy, Shannon and Wang, Shu and Stopka, Sylwia A and Lin, Jia-Ren and Yapp, Clarence and Ritch, Cecily C and Lisa Salhi and Baker, Gregory J and Rashid, Rumana and Gerard Baquer}
}
@article {696294,
	title = {Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer},
	journal = {Nature communications},
	volume = {13},
	number = {1},
	year = {2022},
	pages = {1-14},
	publisher = {Nature Publishing Group},
	isbn = {2041-1723},
	author = {Launonen, I-M and Lyytik{\"a}inen, Nuppu and Casado, Julia and Anttila, Ella A and Szab{\'o}, Ang{\'e}la and Haltia, U-M and Jacobson, CA and Lin, Jia-Ren and Maliga, Zoltan and Howitt, BE}
}
@article {696300,
	title = {Temporal and spatial topography of cell proliferation in cancer},
	journal = {Nature Cell Biology},
	volume = {24},
	number = {3},
	year = {2022},
	pages = {316-326},
	publisher = {Nature Publishing Group},
	isbn = {1476-4679},
	author = {Gaglia, Giorgio and Kabraji, Sheheryar and Rammos, Danae and Dai, Yang and Verma, Ana and Wang, Shu and Mills, Caitlin E and Chung, Mirra and Bergholz, Johann S and Coy, Shannon}
}
@article {696301,
	title = {A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets},
	journal = {bioRxiv},
	year = {2022},
	publisher = {Cold Spring Harbor Laboratory},
	author = {Creason, Allison L and Watson, Cameron and Gu, Qiang and Persson, Daniel and Sargent, Luke L and Chen, Yu-An and Lin, Jia-Ren and Sivagnanam, Shamilene and W{\"u}nnemann, Florian and Nirmal, Ajit J}
}
@article {696298,
	title = {Evolution of delayed resistance to immunotherapy in a melanoma responder},
	journal = {Nature medicine},
	volume = {27},
	number = {6},
	year = {2021},
	pages = {985-992},
	publisher = {Nature Publishing Group},
	isbn = {1546-170X},
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}
@article {696291,
	title = {HAND1 and BARX1 Act as Transcriptional and Anatomic Determinants of Malignancy in Gastrointestinal Stromal TumorAnatomic and Transcriptional Determinants of GIST},
	journal = {Clinical Cancer Research},
	volume = {27},
	number = {6},
	year = {2021},
	pages = {1706-1719},
	publisher = {American Association for Cancer Research},
	isbn = {1078-0432},
	author = {Hemming, Matthew L and Coy, Shannon and Lin, Jia-Ren and Andersen, Jessica L and Przybyl, Joanna and Emanuele Mazzola and Abdelhamid Ahmed, Amr H and van de Rijn, Matt and Sorger, Peter K and Armstrong, Scott A}
}
@article {696295,
	title = {Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer},
	journal = {bioRxiv},
	year = {2021},
	publisher = {Cold Spring Harbor Laboratory},
	author = {Lin, Jia-Ren and Wang, Shu and Coy, Shannon and Tyler, Madison A and Yapp, Clarence and Chen, Yu-An and Heiser, Cody Nicholas and Lau, Ken and Santagata, Sandro and Sorger, Peter Karl}
}
@article {696297,
	title = {Scope2Screen: Focus+ Context Techniques for Pathology Tumor Assessment in Multivariate Image Data},
	journal = {IEEE Transactions on Visualization and Computer Graphics},
	volume = {28},
	number = {1},
	year = {2021},
	pages = {259-269},
	publisher = {IEEE},
	isbn = {1077-2626},
	author = {Jared Jessup and Krueger, Robert and Simon Warchol and John Hoffer and Muhlich, Jeremy and Ritch, Cecily C and Gaglia, Giorgio and Coy, Shannon and Chen, Yu-An and Lin, Jia-Ren}
}
@article {696292,
	title = {Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer},
	journal = {Nature Cancer},
	volume = {2},
	number = {1},
	year = {2021},
	pages = {66-82},
	publisher = {Nature Publishing Group},
	isbn = {2662-1347},
	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}
}
@article {696290,
	title = {Fibroblast{\textendash}tumor cell signaling limits HER2 kinase therapy response via activation of MTOR and antiapoptotic pathways},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {117},
	number = {28},
	year = {2020},
	pages = {16500-16508},
	publisher = {National Academy of Sciences},
	isbn = {0027-8424},
	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}
}
@article {696288,
	title = {The Human Tumor Atlas Network: charting tumor transitions across space and time at single-cell resolution},
	journal = {Cell},
	volume = {181},
	number = {2},
	year = {2020},
	pages = {236-249},
	publisher = {Elsevier},
	isbn = {0092-8674},
	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 Emek Demir}
}
@article {696287,
	title = {Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1},
	journal = {JCO precision oncology},
	volume = {4},
	year = {2020},
	publisher = {American Society of Clinical Oncology},
	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}
}
@article {696289,
	title = {A single-cell landscape of high-grade serous ovarian cancer},
	journal = {Nature Medicine},
	volume = {26},
	number = {8},
	year = {2020},
	pages = {1271-1279},
	publisher = {Nature Publishing Group},
	isbn = {1546-170X},
	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 Parin Shah}
}
@article {696284,
	title = {Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer},
	journal = {Scientific Data},
	volume = {6},
	number = {1},
	year = {2019},
	pages = {1-10},
	publisher = {Nature Publishing Group},
	isbn = {2052-4463},
	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}
}
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	title = {Inferring reaction network structure from single-cell, multiplex data, using toric systems theory},
	journal = {PLoS computational biology},
	volume = {15},
	number = {12},
	year = {2019},
	pages = {e1007311},
	publisher = {Public Library of Science},
	isbn = {1553-7358},
	author = {Wang, Shu and Lin, Jia-Ren and Sontag, Eduardo D and Sorger, Peter K}
}
@article {696286,
	title = {Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging.},
	journal = {Nature protocols},
	volume = {14},
	number = {10},
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	pages = {2900-2930},
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}
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	title = {Inferring reaction network structure from single-cell, multiplex data, using toric systems theory},
	journal = {bioRxiv},
	year = {2019},
	pages = {731018},
	publisher = {Cold Spring Harbor Laboratory},
	author = {Wang, Shu and Lin, Jia-Ren and Sontag, Eduardo D and Sorger, Peter K}
}
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	title = {Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma},
	journal = {Nature communications},
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	year = {2019},
	pages = {2400},
	publisher = {Nature Publishing Group},
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}
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	title = {Determinants of drug-target interactions at the single cell level},
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	volume = {14},
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	pages = {e1006601},
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}
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	title = {A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade},
	journal = {Cell},
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	title = {Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes},
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}
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	title = {Multiplexed Immunofluorescence Reveals Potential PD-1/PD-L1 Pathway Vulnerabilities in Craniopharyngioma},
	journal = {Neuro-oncology},
	year = {2018},
	pages = {noy035},
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	title = {Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging},
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}
