Publications

2022
Ternes L, Lin J-R, Chen Y-A, Gray JW, Chang YH. Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays. PLOS Computational Biology. 2022;18 (9) :e1010505.
Gray KG, Li CM-C, Rosenbluth JM, Selfors LM, Girnius N, Lin J-R, Schackmann RCJ, Goh WL, Moore K, Shapiro HK. A human breast atlas integrating single-cell proteomics and transcriptomics. Developmental Cell. 2022.
Gaglia G, Burger M, Ritch CC, Rammos D, Dai Y, Crossland GE, Tavana SZ, Warchol S, Jaeger AM, Naranjo S. Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma. bioRxiv. 2022.
Schapiro D, Sokolov A, Yapp C, Chen Y-A, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK. MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging. Nature methods. 2022;19 (3) :311-315.
Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen Y-A, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S. MITI Minimum Information guidelines for highly multiplexed tissue images. Nature Methods. 2022;19 (3) :262-267.
Lin J-R, Chen Y-A, Campton D, Cooper J, Coy S, Yapp C, Tefft J, McCarty E, Ligon K, Rodig SJ. Multi-modal digital pathology for colorectal cancer diagnosis by high-plex immunofluorescence imaging and traditional histology of the same tissue section. bioRxiv. 2022.
Notarangelo G, Spinelli JB, Perez EM, Baker GJ, Kurmi K, Elia I, Stopka SA, Baquer G, Lin J-R, Golby AJ. Oncometabolite d-2HG alters T cell metabolism to impair CD8+ T cell function. Science. 2022;377 (6614) :1519-1529.
Coy S, Wang S, Stopka SA, Lin J-R, Yapp C, Ritch CC, Salhi L, Baker GJ, Rashid R, Baquer G. Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma. Nature communications. 2022;13 (1) :1-24.
Launonen I-M, Lyytikäinen N, Casado J, Anttila EA, Szabó A, Haltia U-M, Jacobson CA, Lin J-R, Maliga Z, Howitt BE. Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer. Nature communications. 2022;13 (1) :1-14.
Gaglia G, Kabraji S, Rammos D, Dai Y, Verma A, Wang S, Mills CE, Chung M, Bergholz JS, Coy S. Temporal and spatial topography of cell proliferation in cancer. Nature Cell Biology. 2022;24 (3) :316-326.
Creason AL, Watson C, Gu Q, Persson D, Sargent LL, Chen Y-A, Lin J-R, Sivagnanam S, Wünnemann F, Nirmal AJ. A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets. bioRxiv. 2022.
2021
Liu D, Lin J-R, Robitschek EJ, Kasumova GG, Heyde A, Shi A, Kraya A, Zhang G, Moll T, Frederick DT. Evolution of delayed resistance to immunotherapy in a melanoma responder. Nature medicine. 2021;27 (6) :985-992.
Hemming ML, Coy S, Lin J-R, Andersen JL, Przybyl J, Mazzola E, Abdelhamid Ahmed AH, van de Rijn M, Sorger PK, Armstrong SA. HAND1 and BARX1 Act as Transcriptional and Anatomic Determinants of Malignancy in Gastrointestinal Stromal TumorAnatomic and Transcriptional Determinants of GIST. Clinical Cancer Research. 2021;27 (6) :1706-1719.
Lin J-R, Wang S, Coy S, Tyler MA, Yapp C, Chen Y-A, Heiser CN, Lau K, Santagata S, Sorger PK. Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer. bioRxiv. 2021.
Jessup J, Krueger R, Warchol S, Hoffer J, Muhlich J, Ritch CC, Gaglia G, Coy S, Chen Y-A, Lin J-R. Scope2Screen: Focus+ Context Techniques for Pathology Tumor Assessment in Multivariate Image Data. IEEE Transactions on Visualization and Computer Graphics. 2021;28 (1) :259-269.
Mehta AK, Cheney EM, Hartl CA, Pantelidou C, Oliwa M, Castrillon JA, Lin J-R, Hurst KE, de Oliveira Taveira M, Johnson NT. Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer. Nature Cancer. 2021;2 (1) :66-82.
2020
Zervantonakis IK, Poskus MD, Scott AL, Selfors LM, Lin J-R, Dillon DA, Pathania S, Sorger PK, Mills GB, Brugge JS. Fibroblast–tumor cell signaling limits HER2 kinase therapy response via activation of MTOR and antiapoptotic pathways. Proceedings of the National Academy of Sciences. 2020;117 (28) :16500-16508.
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E. The Human Tumor Atlas Network: charting tumor transitions across space and time at single-cell resolution. Cell. 2020;181 (2) :236-249.
Hemming ML, Nathenson MJ, Lin J-R, Mei S, Du Z, Malik K, Marino-Enriquez A, Jagannathan JP, Sorger PK, Bertagnolli M. Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1. JCO precision oncology. 2020;4.
Izar B, Tirosh I, Stover EH, Wakiro I, Cuoco MS, Alter I, Rodman C, Leeson R, Su M-J, Shah P. A single-cell landscape of high-grade serous ovarian cancer. Nature Medicine. 2020;26 (8) :1271-1279.

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