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19 results on '"Afiuni-Zadeh, Somaieh"'

1. Author Correction: In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancer

Author

Dervovic, Dzana, Malik, Ahmad A., Chen, Edward L. Y., Narimatsu, Masahiro, Adler, Nina, Afiuni-Zadeh, Somaieh, Krenbek, Dagmar, Martinez, Sebastien, Tsai, Ricky, Boucher, Jonathan, Berman, Jacob M., Teng, Katie, Ayyaz, Arshad, Lü, YiQing, Mbamalu, Geraldine, Loganathan, Sampath K., Lee, Jongbok, Zhang, Li, Guidos, Cynthia, Wrana, Jeffrey, Valipour, Arschang, Roux, Philippe P., Reimand, Jüri, Jackson, Hartland W., and Schramek, Daniel

Published
2023
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2. In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancer

Author

Dervovic, Dzana, Malik, Ahmad A., Chen, Edward L. Y., Narimatsu, Masahiro, Adler, Nina, Afiuni-Zadeh, Somaieh, Krenbek, Dagmar, Martinez, Sebastien, Tsai, Ricky, Boucher, Jonathan, Berman, Jacob M., Teng, Katie, Ayyaz, Arshad, Lü, YiQing, Mbamalu, Geraldine, Loganathan, Sampath K., Lee, Jongbok, Zhang, Li, Guidos, Cynthia, Wrana, Jeffrey, Valipour, Arschang, Roux, Philippe P., Reimand, Jüri, Jackson, Hartland W., and Schramek, Daniel

Published
2023
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4. Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data.

Author

Lee, Yuju, Chen, Edward L. Y., Chan, Darren C. H., Dinesh, Anuroopa, Afiuni-Zadeh, Somaieh, Klamann, Conor, Selega, Alina, Mrkonjic, Miralem, Jackson, Hartland W., and Campbell, Kieran R.

Subjects
PROTEIN fractionation, CYTOLOGY, LIFE sciences, PROTEIN expression, ARTIFICIAL intelligence
Abstract

Spatial protein expression technologies can map cellular content and organization by simultaneously quantifying the expression of >40 proteins at subcellular resolution within intact tissue sections and cell lines. However, necessary image segmentation to single cells is challenging and error prone, easily confounding the interpretation of cellular phenotypes and cell clusters. To address these limitations, we present STARLING, a probabilistic machine learning model designed to quantify cell populations from spatial protein expression data while accounting for segmentation errors. To evaluate performance, we develop a comprehensive benchmarking workflow by generating highly multiplexed imaging data of cell line pellet standards with controlled cell content and marker expression and additionally established a score to quantify the biological plausibility of discovered cellular phenotypes on patient-derived tissue sections. Moreover, we generate spatial expression data of the human tonsil—a densely packed tissue prone to segmentation errors—and demonstrate cellular states captured by STARLING identify known cell types not visible with other methods and enable quantification of intra- and inter- individual heterogeneity. Spatial expression assays are affected by segmentation errors leading to difficulty interpreting cell types. Here, the authors introduce a machine learning model to infer cell types accounting for such errors, and evaluation metrics and gold-standard datasets to enable further advances in this area. [ABSTRACT FROM AUTHOR]

Published
2025
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7. Supplementary Data from Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer

Author

Langille, Ellen, primary, Al-Zahrani, Khalid N., primary, Ma, Zhibo, primary, Liang, Minggao, primary, Uuskula-Reimand, Liis, primary, Espin, Roderic, primary, Teng, Katie, primary, Malik, Ahmad, primary, Bergholtz, Helga, primary, Ghamrasni, Samah El, primary, Afiuni-Zadeh, Somaieh, primary, Tsai, Ricky, primary, Alvi, Sana, primary, Elia, Andrew, primary, Lü, YiQing, primary, Oh, Robin H., primary, Kozma, Katelyn J., primary, Trcka, Daniel, primary, Narimatsu, Masahiro, primary, Liu, Jeff C., primary, Nguyen, Thomas, primary, Barutcu, Seda, primary, Loganathan, Sampath K., primary, Bremner, Rod, primary, Bader, Gary D., primary, Egan, Sean E., primary, Cescon, David W., primary, Sørlie, Therese, primary, Wrana, Jeffrey L., primary, Jackson, Hartland W., primary, Wilson, Michael D., primary, Witkiewicz, Agnieszka K., primary, Knudsen, Erik S., primary, Pujana, Miguel Angel, primary, Wahl, Geoffrey M., primary, and Schramek, Daniel, primary

Published
2023
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8. Data from Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer

Author

Langille, Ellen, primary, Al-Zahrani, Khalid N., primary, Ma, Zhibo, primary, Liang, Minggao, primary, Uuskula-Reimand, Liis, primary, Espin, Roderic, primary, Teng, Katie, primary, Malik, Ahmad, primary, Bergholtz, Helga, primary, Ghamrasni, Samah El, primary, Afiuni-Zadeh, Somaieh, primary, Tsai, Ricky, primary, Alvi, Sana, primary, Elia, Andrew, primary, Lü, YiQing, primary, Oh, Robin H., primary, Kozma, Katelyn J., primary, Trcka, Daniel, primary, Narimatsu, Masahiro, primary, Liu, Jeff C., primary, Nguyen, Thomas, primary, Barutcu, Seda, primary, Loganathan, Sampath K., primary, Bremner, Rod, primary, Bader, Gary D., primary, Egan, Sean E., primary, Cescon, David W., primary, Sørlie, Therese, primary, Wrana, Jeffrey L., primary, Jackson, Hartland W., primary, Wilson, Michael D., primary, Witkiewicz, Agnieszka K., primary, Knudsen, Erik S., primary, Pujana, Miguel Angel, primary, Wahl, Geoffrey M., primary, and Schramek, Daniel, primary

Published
2023
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11. Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer

Author

Langille, Ellen, primary, Al-Zahrani, Khalid N., additional, Ma, Zhibo, additional, Liang, Minggao, additional, Uuskula-Reimand, Liis, additional, Espin, Roderic, additional, Teng, Katie, additional, Malik, Ahmad, additional, Bergholtz, Helga, additional, Ghamrasni, Samah El, additional, Afiuni-Zadeh, Somaieh, additional, Tsai, Ricky, additional, Alvi, Sana, additional, Elia, Andrew, additional, Lü, YiQing, additional, Oh, Robin H., additional, Kozma, Katelyn J., additional, Trcka, Daniel, additional, Narimatsu, Masahiro, additional, Liu, Jeff C., additional, Nguyen, Thomas, additional, Barutcu, Seda, additional, Loganathan, Sampath K., additional, Bremner, Rod, additional, Bader, Gary D., additional, Egan, Sean E., additional, Cescon, David W., additional, Sørlie, Therese, additional, Wrana, Jeffrey L., additional, Jackson, Hartland W., additional, Wilson, Michael D., additional, Witkiewicz, Agnieszka K., additional, Knudsen, Erik S., additional, Pujana, Miguel Angel, additional, Wahl, Geoffrey M., additional, and Schramek, Daniel, additional

Published
2022
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