Publications

Featured Publications

MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging.

MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging.

Schapiro, D., Sokolov, A., Yapp, C., Muhlich, J.L., Hess, J., Lin, J-R., Chen, Y-A., Nariya, M.K., ... Sorger, P.K. (2021)
Nature Methods, 19, 311–315 https://doi.org/10.1038/s41592-021-01308-y
The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution.

The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution.

Nirmal, A.J., Maliga, Z., Vallius, T., Quattrochi, B., Chen, A.C., Jacobson, C.A., Pelletier, R.J., ... Lian, C.G., Murphy, G.F., Santagata, S., Sorger, P.K.
Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer.

Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer.

Lin, J.-R., Wang, S., Coy, S., Tyler, M., Yapp, C., Chen, Y.-A., Heiser, C.N., Lau, K.S., Santagata, S., Sorger, P.K. (2021).
Manuscript Submitted
Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer.

Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer.

Mehta, A.K., Cheney, E.M., Hartl, C.A., Pantelidou, C., Oliwa, M., Castrillon, J.A., Lin, Lin, J.-R., ... Guerriero, J.(2021).
Nature Cancer, 2(1), 66–82. https://doi.org/10.1038/s43018-020-00148-7
Temporal and spatial topography of cell proliferation in cancer.

Temporal and spatial topography of cell proliferation in cancer.

Gaglia, G., Kabraji, S., Angyropoulu, D., Dai, Y., Wang, S., Bergholz, J., Coy, S., Lin, J.-R., ... Santagata, P. (2022).
Nature Cell Biology, 24(3), 316-326 https://doi.org/10.1038/s41556-022-00860-9

Methods and software

Scope2Screen: Focus+context techniques for pathology tumor assessment in multivariate image data.

Scope2Screen: Focus+context techniques for pathology tumor assessment in multivariate image data.

Jessup, J., Krueger, R., Warchol, S., Hoffer. J., Muhlich, J.L., Ritch, C.C., Gaglia, G., Coy, S., Chen Y.-A., Lin J-.R., Santagata, S., Sorger, P.K., & Pfister, H. (2021).
IEEE Transactions on Visualization and Computer Graphics (IEEE VIS), 2021 https://vcg.seas.harvard.edu/publications/scope2screen
MITI minimum information guidelines for highly multiplexed tissue images.

MITI minimum information guidelines for highly multiplexed tissue images.

Schapiro, D., Yapp, C., Sokolov, A., Reynolds, S.M., Chen, Y.-A., Sudar, D., Xie, Y., Muhlich, J., ... Sorger, P.K. (2022).
Nature Methods, 19, 262–267 https://doi.org/10.1038/s41592-022-01415-4
Stitching and registering highly multiplexed whole slide images of tissues and tumors using ASHLAR software.

Stitching and registering highly multiplexed whole slide images of tissues and tumors using ASHLAR software.

Muhlich, J., Chen, Y.-A., Russell, R., & Sorger, P.K. (2021).
Manuscript Submitted
Micro-region transcriptomics of fixed human tissue using pick-seq.

Micro-region transcriptomics of fixed human tissue using pick-seq.

Maliga, Z., Nirmal, A. J., Ericson, N. G., Boswell, S. A., U’Ren, L., Podyminogin, R., Chow, J., Chen, Y.-A., … Sorger, P. K. (2021).
Manuscript Submitted
UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues

UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues

Yapp, C., Novikov, E., Jang, W.-D., Chen, Y.-A., Cicconet, M., Maliga, Z., Jacobson, C. A., Wei, D., Santagata, S., Pfister, H., & Sorger, P. K. (2021).
Nature Cancer, 2(1), 66–82.
Channel embedding for informative protein identification from highly multiplexed images.

Channel embedding for informative protein identification from highly multiplexed images.

Magid, S.M., Jang, W.-D., Schapiro, D., Wei, D., Tompkin, J., Sorger, P.K., & Pfister, H. (2020).
Medical Image Computing and Computer-Assisted Intervention (MICCAI), 12265, 3–13. https://doi.org/10.1007/978-3-030-59722-1_1
Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung.

Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung.

Kalocsay, M., Maliga, Z., Nirmal, A.J., Eisert, R.J., Bradshaw, G.A., Solomon, I. H., Chen, Y-A., Pelletier, R.J., ... Sorger, P.K. (2020).
Manuscript Submitted
Minerva: A light-weight, narrative image browser for multiplexed tissue images.

Minerva: A light-weight, narrative image browser for multiplexed tissue images.

Hoffer, J., Rashid, R., Muhlich, J.L., Chen, Y.-A., Russell, D.P.W., Ruokonen, J., Krueger, R., Pfister, H., Santagata, S., & Sorger, P.K. (2020).
Journal of Open Source Software, 5(54), 2579 https://doi.org/10.21105/joss.02579
Online narrative guides for illuminating tissue atlas data and digital pathology images.

Online narrative guides for illuminating tissue atlas data and digital pathology images.

Rumana, R., Chen, Y.-A., Hoffer, J., Muhlich, J.L., Lin, J.-R., Krueger, R., Pfister, H., Mitchell, R., Santagata, S., & Sorger, P. K. (2020).
Manuscript Submitted
Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data.

Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data.

Krueger, R., Beyer, J., Jang, W.-D., Kim, N. W., Sokolov, A., Sorger, P. K., & Pfister, H. (2020).
IEEE Transactions on Visualization and Computer Graphics, 26(1), 227–237. https://doi.org/10.1109/TVCG.2019.2934547
Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging.

Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging.

Du, Z., Lin, J.-R., Rashid, R., Maliga, Z., Wang, S., Aster, J. C., Izar, B., Sorger, P. K., & Santagata, S. (2019).
Nature Protocols, 14(10), 2900–2930. https://doi.org/10.1038/s41596-019-0206-y
Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer.

Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer.

Rashid, R., Gaglia, G., Chen, Y.-A., Lin, J.-R., Du, Z., Maliga, Z., Schapiro, D., Yapp, C., Muhlich, J., Sokolov, A., Sorger, P., & Santagata, S. (2019).
Scientific Data, 6(1), 323. https://doi.org/10.1038/s41597-019-0332-y
Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-cycif and conventional optical microscopes.

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-cycif and conventional optical microscopes.

Lin, J.-R., Izar, B., Wang, S., Yapp, C., Mei S., Shah, P.M., Santagata, S., & Sorger, P.K. (2018).

Profiling and Atlasing

A human breast atlas integrating single-cell proteomics and transcriptomics.

A human breast atlas integrating single-cell proteomics and transcriptomics.

Gray, G.K., Li, C.M.-C., Rosenbluth, J.M., Selfors, L.M., Girnius, N., Lin, J.-R., Schackmann, R.C.J., Goh, W.L., Moore, K., Shapiro, H.K., Mei, S., D’Andrea, K., Nathanson, K.L., Sorger, P.K., Santagata, S., Regev, A., Garber, J.E., Dillon, D.A., Brugge, J.S. (2022).
Developmental Cell, 57(22), 1400-1420. https://doi.org/10.1016/j.devcel.2022.05.003
Evolution of delayed resistance to immunotherapy in a melanoma responder.

Evolution of delayed resistance to immunotherapy in a melanoma responder.

Liu, D., Lin, J.-R., Robitschek, E.J., Kasumova, G.G., Heyde, A., Shi, A., Kraya, A., ... Boland, G.M. (2021).
Nature Medicine, 27, 985–992. https://doi.org/10.1038/s41591-021-01331-8
Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma.

Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma.

Jerby-Arnon, L., Neftel, C., Shore, M. E., Weisman, H. R., Mathewson, N. D., McBride, M. J., Haas, B., Izar, B., … Regev, A. (2021).
Nature Medicine, 27(2), 289–300. https://doi.org/10.1038/s41591-020-01212-6
Clinical efficacy and molecular response correlates of the WEE1 inhibitor adavosertib combined with cisplatin in patients with metastatic triple-negative breast cancer.

Clinical efficacy and molecular response correlates of the WEE1 inhibitor adavosertib combined with cisplatin in patients with metastatic triple-negative breast cancer.

Keenan, T.E., Li, T., Vallius, T., Guerriero, J.L., Tayob, N., Kochupurakkal, B., Davis, J., Pastorello, R., ... Tolaney, S.M. (2021).
Clinical Cancer Research, 2(1), 66-82. https://doi.org/10.1158/1078-0432.CCR-20-3089
HAND1 and BARX1 act as transcriptional and anatomic determinants of malignancy in gastrointestinal stromal tumor.

HAND1 and BARX1 act as transcriptional and anatomic determinants of malignancy in gastrointestinal stromal tumor.

Hemming, M.L., Coy, S., Lin, J.-R., Andersen, J.L., Przybyl, J., Mazzola, E., Abdelhamid Ahmed, A.H., ... Santagata, S. (2021).
Clinical Cancer Research, 27(6), 1706-19. https://doi.org/10.1158/1078-0432.CCR-20-3538
Concurrent dexamethasone limits the clinical benefit of immune checkpoint blockade in glioblastoma.

Concurrent dexamethasone limits the clinical benefit of immune checkpoint blockade in glioblastoma.

Iorgulescu, J.B., Gokhale, P.C., Speranza, M.C., Eschle, B.K., Poitras, M.J., Wilkens, M.K., Soroko, K.M., ... Reardon, D.A. (2021).
Clinical Cancer Research, 27(1), 276–87. https://doi.org/10.1158/1078-0432.CCR-20-2291
Obesity shapes metabolism in the tumor microenvironment to suppress anti-tumor immunity.

Obesity shapes metabolism in the tumor microenvironment to suppress anti-tumor immunity.

Ringel, A.E., Drijvers, J.M., Baker, G.J., Catozzi, A., García-Cañaveras, J.C., Gassaway, B.M., Miller, B.C., ... Haigis, M.C. (2020).
Cell, 183(7), 1848-1866.e26. https://doi.org/10.1016/j.cell.2020.11.009
SARS-CoV-2 infection protects against rechallenge in rhesus macaques.

SARS-CoV-2 infection protects against rechallenge in rhesus macaques.

Chandrashekar, A., Liu, J., Martinot, A.J., McMahan, K., Mercado, N.B., Peter, L., Tostanoski, L.H., ... Barach, D.H. (2020).
Science 369(6505): 812–17. https://doi.org/10.1126/science.abc4776
Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1.

Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1.

Hemming, M. L., Nathenson, M. J., Lin, J.-R., Mei, S., Du, Z., Malik, K., Marino-Enriquez, A., Jagannathan, J. P., Sorger, P. K., Bertagnolli, M., Sicinska, E., Demetri, G. D., & Santagata, S. (2020).
JCO Precision Oncology, 4, 79–90. https://doi.org/10.1200/po.19.00287
Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer.

Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer.

Färkkilä, A., Gulhan, D. C., Casado, J., Jacobson, C. A., Nguyen, H., Kochupurakkal, B., Maliga, Z., Yapp, C., … Konstantinopoulos, P. A. (2020).
Nature Communications, 11(1), 1459. https://doi.org/10.1038/s41467-020-15315-8
HSF1 phase transition mediates stress adaptation and cell fate decisions.

HSF1 phase transition mediates stress adaptation and cell fate decisions.

Gaglia, G., Rashid, R., Yapp, C., Joshi, G. N., Li, C. G., Lindquist, S. L., Sarosiek, K. A., Whitesell, L., Sorger, P. K., & Santagata, S. (2020).
Nature Cell Biology, 22(2), 151–158. https://doi.org/10.1038/s41556-019-0458-3
Mismatch repair deficiency in high-grade meningioma: A rare but recurrent event associated with dramatic immune activation and clinical response to PD-1 blockade.

Mismatch repair deficiency in high-grade meningioma: A rare but recurrent event associated with dramatic immune activation and clinical response to PD-1 blockade.

Dunn, I. F., Du, Z., Touat, M., Sisti, M. B., Wen, P. Y., Umeton, R., Dubuc, A. M., Ducar, M., ... & Reardon, D.A. (2018).
JCO Precision Oncology, 2018. https://doi.org/10.1200/PO.18.00190
Multiplexed immunofluorescence reveals potential PD-1/PD-L1 pathway vulnerabilities in craniopharyngioma.

Multiplexed immunofluorescence reveals potential PD-1/PD-L1 pathway vulnerabilities in craniopharyngioma.

Coy, S., Rashid, R., Lin, J.R., Du, Z., Donson, A.M., Hankinson, T.C., Foreman, N.K., ... Santagata, S. (2018).
Neuro-Oncology, 20(8), 1101-12. https://doi.org/10.1093/neuonc/noy035
A cancer cell program promotes t cell exclusion and resistance to checkpoint blockade.

A cancer cell program promotes t cell exclusion and resistance to checkpoint blockade.

Jerby-Arnon, L., Shah, P., Cuoco, M. S., Rodman, C., Su, M.-J., Melms, J. C., Leeson, R., Kanodia, A., … Regev, A. (2018).
Cell, 175(4), 984-997.e24. https://doi.org/10.1016/j.cell.2018.09.006
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.

Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., … Garraway, L. A. (2016).
Science, 352(6282), 189–196. https://doi.org/10.1126/science.aad0501