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1. Nucleotide excision repair deficiency is a targetable therapeutic vulnerability in clear cell renal cell carcinoma

Author

Prosz, Aurel, Duan, Haohui, Tisza, Viktoria, Sahgal, Pranshu, Topka, Sabine, Klus, Gregory T., Börcsök, Judit, Sztupinszki, Zsofia, Hanlon, Timothy, Diossy, Miklos, Vizkeleti, Laura, Stormoen, Dag Rune, Csabai, Istvan, Pappot, Helle, Vijai, Joseph, Offit, Kenneth, Ried, Thomas, Sethi, Nilay, Mouw, Kent W., Spisak, Sandor, Pathania, Shailja, and Szallasi, Zoltan

Published
2023
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2. High-throughput and targeted drug screens identify pharmacological candidates against MiT-translocation renal cell carcinoma

Author

Lang, Martin, Schmidt, Laura S., Wilson, Kelli M., Ricketts, Christopher J., Sourbier, Carole, Vocke, Cathy D., Wei, Darmood, Crooks, Daniel R., Yang, Youfeng, Gibbs, Benjamin K., Zhang, Xiaohu, Klumpp-Thomas, Carleen, Chen, Lu, Guha, Rajarshi, Ferrer, Marc, McKnight, Crystal, Itkin, Zina, Wangsa, Darawalee, Wangsa, Danny, James, Amy, Difilippantonio, Simone, Karim, Baktir, Morís, Francisco, Ried, Thomas, Merino, Maria J., Srinivasan, Ramaprasad, Thomas, Craig J., and Linehan, W. Marston

Published
2023
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5. Increased frequency of CHD1 deletions in prostate cancers of African American men is associated with rapid disease progression without inducing homologous recombination deficiency

Author

Szallasi, Zoltan, primary, Diossy, Miklos, additional, Tisza, Viktoria, additional, Li, Hua, additional, Sahgal, Pranshu, additional, Zhou, Jia, additional, Sztupinszki, Zsofia, additional, Young, Denise, additional, Nuosome, Darryl, additional, Kuo, Claire, additional, Jiang, Jiji, additional, Chen, Yongmei, additional, Ebner, Reinhard, additional, Sesterhenn, Isabell, additional, Moncur, Joel, additional, Chesnut, Gregory, additional, Petrovics, Gyorgy, additional, T.Klus, Gregory, additional, Valcz, Gábor, additional, Nuzzo, Pier, additional, Ribli, Dezso, additional, Börcsök, Judit, additional, Prósz, Aurél, additional, Krzystanek, Marcin, additional, Ried, Thomas, additional, Szüts, Dávid, additional, Rizwan, Kinza, additional, Kaochar, Salma, additional, Pathania, Shailja, additional, D'Andrea, Alan, additional, Csabai, István, additional, Srivast, Shib, additional, Freedman, Matthew, additional, Dobi, Albert, additional, and Spisak, Sandor, additional

Published
2024
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7. Sex-chromosome dosage effects on gene expression in humans

Author

Raznahan, Armin, Parikshak, Neelroop N, Chandran, Vijay, Blumenthal, Jonathan D, Clasen, Liv S, Alexander-Bloch, Aaron F, Zinn, Andrew R, Wangsa, Danny, Wise, Jasen, Murphy, Declan GM, Bolton, Patrick F, Ried, Thomas, Ross, Judith, Giedd, Jay N, and Geschwind, Daniel H

Subjects
Clinical Research, Biotechnology, Genetics, Rare Diseases, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Aneuploidy, Animals, Chromosomes, Human, X, Chromosomes, Human, Y, Female, Gene Dosage, Gene Expression Regulation, Genome-Wide Association Study, Humans, Kruppel-Like Transcription Factors, Male, Mice, Mice, Knockout, Models, Genetic, sex chromosomes, X-inactivation, sex differences, Turner syndrome, Klinefelter syndrome
Abstract

A fundamental question in the biology of sex differences has eluded direct study in humans: How does sex-chromosome dosage (SCD) shape genome function? To address this, we developed a systematic map of SCD effects on gene function by analyzing genome-wide expression data in humans with diverse sex-chromosome aneuploidies (XO, XXX, XXY, XYY, and XXYY). For sex chromosomes, we demonstrate a pattern of obligate dosage sensitivity among evolutionarily preserved X-Y homologs and update prevailing theoretical models for SCD compensation by detecting X-linked genes that increase expression with decreasing X- and/or Y-chromosome dosage. We further show that SCD-sensitive sex-chromosome genes regulate specific coexpression networks of SCD-sensitive autosomal genes with critical cellular functions and a demonstrable potential to mediate previously documented SCD effects on disease. These gene coexpression results converge with analysis of transcription factor binding site enrichment and measures of gene expression in murine knockout models to spotlight the dosage-sensitive X-linked transcription factor ZFX as a key mediator of SCD effects on wider genome expression. Our findings characterize the effects of SCD broadly across the genome, with potential implications for human phenotypic variation.

Published
2018

8. Genomic and evolutionary classification of lung cancer in never smokers

Author

Zhang, Tongwu, Joubert, Philippe, Ansari-Pour, Naser, Zhao, Wei, Hoang, Phuc H., Lokanga, Rachel, Moye, Aaron L., Rosenbaum, Jennifer, Gonzalez-Perez, Abel, Martínez-Jiménez, Francisco, Castro, Andrea, Muscarella, Lucia Anna, Hofman, Paul, Consonni, Dario, Pesatori, Angela C., Kebede, Michael, Li, Mengying, Gould Rothberg, Bonnie E., Peneva, Iliana, Schabath, Matthew B., Poeta, Maria Luana, Costantini, Manuela, Hirsch, Daniela, Heselmeyer-Haddad, Kerstin, Hutchinson, Amy, Olanich, Mary, Lawrence, Scott M., Lenz, Petra, Duggan, Maire, Bhawsar, Praphulla M. S., Sang, Jian, Kim, Jung, Mendoza, Laura, Saini, Natalie, Klimczak, Leszek J., Islam, S. M. Ashiqul, Otlu, Burcak, Khandekar, Azhar, Cole, Nathan, Stewart, Douglas R., Choi, Jiyeon, Brown, Kevin M., Caporaso, Neil E., Wilson, Samuel H., Pommier, Yves, Lan, Qing, Rothman, Nathaniel, Almeida, Jonas S., Carter, Hannah, Ried, Thomas, Kim, Carla F., Lopez-Bigas, Nuria, Garcia-Closas, Montserrat, Shi, Jianxin, Bossé, Yohan, Zhu, Bin, Gordenin, Dmitry A., Alexandrov, Ludmil B., Chanock, Stephen J., Wedge, David C., and Landi, Maria Teresa

Published
2021
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12. Hard wiring of normal tissue-specific chromosome-wide gene expression levels is an additional factor driving cancer type-specific aneuploidies

Author

Patkar, Sushant, Heselmeyer-Haddad, Kerstin, Auslander, Noam, Hirsch, Daniela, Camps, Jordi, Bronder, Daniel, Brown, Markus, Chen, Wei-Dong, Lokanga, Rachel, Wangsa, Darawalee, Wangsa, Danny, Hu, Yue, Lischka, Annette, Braun, Rüdiger, Emons, Georg, Ghadimi, B. Michael, Gaedcke, Jochen, Grade, Marian, Montagna, Cristina, Lazebnik, Yuri, Difilippantonio, Michael J., Habermann, Jens K., Auer, Gert, Ruppin, Eytan, and Ried, Thomas

Published
2021
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13. Bile acid-induced “Minority MOMP” promotes esophageal carcinogenesis while maintaining apoptotic resistance via Mcl-1

Author

Xu, Yuan, Surman, Deborah R., Diggs, Laurence, Xi, Sichuan, Gao, Shaojian, Gurusamy, Devikala, McLoughlin, Kaitlin, Drake, Justin, Feingold, Paul, Brown, Kate, Wangsa, Danny, Wangsa, Darawalee, Zhang, Xi, Ried, Thomas, Davis, Jeremy L., Hernandez, Jonathan, Hoang, Chuong D., Souza, Rhonda F., Schrump, David S., and Taylor Ripley, R.

Published
2020
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17. Supplementary Figures S1-S6 and Tables S1-S5 from Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration

Author

Akagi, Keiko, primary, Symer, David E., primary, Mahmoud, Medhat, primary, Jiang, Bo, primary, Goodwin, Sara, primary, Wangsa, Darawalee, primary, Li, Zhengke, primary, Xiao, Weihong, primary, Dunn, Joe Dan, primary, Ried, Thomas, primary, Coombes, Kevin R., primary, Sedlazeck, Fritz J., primary, and Gillison, Maura L., primary

Published
2023
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18. Supplementary Video: HPV and Heterocateny from Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration

Author

Akagi, Keiko, primary, Symer, David E., primary, Mahmoud, Medhat, primary, Jiang, Bo, primary, Goodwin, Sara, primary, Wangsa, Darawalee, primary, Li, Zhengke, primary, Xiao, Weihong, primary, Dunn, Joe Dan, primary, Ried, Thomas, primary, Coombes, Kevin R., primary, Sedlazeck, Fritz J., primary, and Gillison, Maura L., primary

Published
2023
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20. Cancer Cytogenetics

Author

Ried, Thomas, Heselmeyer-Haddad, Kerstin, Camps, Jordi, Gaiser, Timo, Coleman, William B., editor, and Tsongalis, Gregory J., editor

Published
2017
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24. Figure S5 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes

Author

Pongor, Lőrinc Sándor, primary, Schultz, Christopher W., primary, Rinaldi, Lorenzo, primary, Wangsa, Darawalee, primary, Redon, Christophe E., primary, Takahashi, Nobuyuki, primary, Fialkoff, Gavriel, primary, Desai, Parth, primary, Zhang, Yang, primary, Burkett, Sandra, primary, Hermoni, Nadav, primary, Vilk, Noa, primary, Gutin, Jenia, primary, Gergely, Rona, primary, Zhao, Yongmei, primary, Nichols, Samantha, primary, Vilimas, Rasa, primary, Sciuto, Linda, primary, Graham, Chante, primary, Caravaca, Juan Manuel, primary, Turan, Sevilay, primary, Tsai-wei, Shen, primary, Rajapakse, Vinodh N., primary, Kumar, Rajesh, primary, Upadhyay, Deep, primary, Kumar, Suresh, primary, Kim, Yoo Sun, primary, Roper, Nitin, primary, Tran, Bao, primary, Hewitt, Stephen M., primary, Kleiner, David E., primary, Aladjem, Mirit I., primary, Friedman, Nir, primary, Hager, Gordon L., primary, Pommier, Yves, primary, Ried, Thomas, primary, and Thomas, Anish, primary

Published
2023
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25. Abstract 314: Intratumor genetic heterogeneity dictates metastatic subclones in stage II colon cancer

Author

Yaghoubi, Sanam, primary, Heselmeyer-Haddad, Kerstin, additional, Archilla, Ivan, additional, Parra, Carolina, additional, Wangsa, Darawalee, additional, Castellano, Giancarlo, additional, Lahoz, Sara, additional, Pablo-Fontecha, Veronica, additional, Hirsch, Daniela, additional, Chen, Wei-Dong, additional, Ried, Thomas, additional, Cuatrecasas, Miriam, additional, Meltzer, Paul S., additional, and Camps, Jordi, additional

Published
2023
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26. Table S6 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes

Author

Pongor, Lőrinc Sándor, primary, Schultz, Christopher W., primary, Rinaldi, Lorenzo, primary, Wangsa, Darawalee, primary, Redon, Christophe E., primary, Takahashi, Nobuyuki, primary, Fialkoff, Gavriel, primary, Desai, Parth, primary, Zhang, Yang, primary, Burkett, Sandra, primary, Hermoni, Nadav, primary, Vilk, Noa, primary, Gutin, Jenia, primary, Gergely, Rona, primary, Zhao, Yongmei, primary, Nichols, Samantha, primary, Vilimas, Rasa, primary, Sciuto, Linda, primary, Graham, Chante, primary, Caravaca, Juan Manuel, primary, Turan, Sevilay, primary, Tsai-wei, Shen, primary, Rajapakse, Vinodh N., primary, Kumar, Rajesh, primary, Upadhyay, Deep, primary, Kumar, Suresh, primary, Kim, Yoo Sun, primary, Roper, Nitin, primary, Tran, Bao, primary, Hewitt, Stephen M., primary, Kleiner, David E., primary, Aladjem, Mirit I., primary, Friedman, Nir, primary, Hager, Gordon L., primary, Pommier, Yves, primary, Ried, Thomas, primary, and Thomas, Anish, primary

Published
2023
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27. Figure 2 extended data from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes

Author

Pongor, Lőrinc Sándor, primary, Schultz, Christopher W., primary, Rinaldi, Lorenzo, primary, Wangsa, Darawalee, primary, Redon, Christophe E., primary, Takahashi, Nobuyuki, primary, Fialkoff, Gavriel, primary, Desai, Parth, primary, Zhang, Yang, primary, Burkett, Sandra, primary, Hermoni, Nadav, primary, Vilk, Noa, primary, Gutin, Jenia, primary, Gergely, Rona, primary, Zhao, Yongmei, primary, Nichols, Samantha, primary, Vilimas, Rasa, primary, Sciuto, Linda, primary, Graham, Chante, primary, Caravaca, Juan Manuel, primary, Turan, Sevilay, primary, Tsai-wei, Shen, primary, Rajapakse, Vinodh N., primary, Kumar, Rajesh, primary, Upadhyay, Deep, primary, Kumar, Suresh, primary, Kim, Yoo Sun, primary, Roper, Nitin, primary, Tran, Bao, primary, Hewitt, Stephen M., primary, Kleiner, David E., primary, Aladjem, Mirit I., primary, Friedman, Nir, primary, Hager, Gordon L., primary, Pommier, Yves, primary, Ried, Thomas, primary, and Thomas, Anish, primary

Published
2023
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28. Data from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes

Author

Pongor, Lőrinc Sándor, primary, Schultz, Christopher W., primary, Rinaldi, Lorenzo, primary, Wangsa, Darawalee, primary, Redon, Christophe E., primary, Takahashi, Nobuyuki, primary, Fialkoff, Gavriel, primary, Desai, Parth, primary, Zhang, Yang, primary, Burkett, Sandra, primary, Hermoni, Nadav, primary, Vilk, Noa, primary, Gutin, Jenia, primary, Gergely, Rona, primary, Zhao, Yongmei, primary, Nichols, Samantha, primary, Vilimas, Rasa, primary, Sciuto, Linda, primary, Graham, Chante, primary, Caravaca, Juan Manuel, primary, Turan, Sevilay, primary, Tsai-wei, Shen, primary, Rajapakse, Vinodh N., primary, Kumar, Rajesh, primary, Upadhyay, Deep, primary, Kumar, Suresh, primary, Kim, Yoo Sun, primary, Roper, Nitin, primary, Tran, Bao, primary, Hewitt, Stephen M., primary, Kleiner, David E., primary, Aladjem, Mirit I., primary, Friedman, Nir, primary, Hager, Gordon L., primary, Pommier, Yves, primary, Ried, Thomas, primary, and Thomas, Anish, primary

Published
2023
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29. Figure 1 extended data from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes

Author

Pongor, Lőrinc Sándor, primary, Schultz, Christopher W., primary, Rinaldi, Lorenzo, primary, Wangsa, Darawalee, primary, Redon, Christophe E., primary, Takahashi, Nobuyuki, primary, Fialkoff, Gavriel, primary, Desai, Parth, primary, Zhang, Yang, primary, Burkett, Sandra, primary, Hermoni, Nadav, primary, Vilk, Noa, primary, Gutin, Jenia, primary, Gergely, Rona, primary, Zhao, Yongmei, primary, Nichols, Samantha, primary, Vilimas, Rasa, primary, Sciuto, Linda, primary, Graham, Chante, primary, Caravaca, Juan Manuel, primary, Turan, Sevilay, primary, Tsai-wei, Shen, primary, Rajapakse, Vinodh N., primary, Kumar, Rajesh, primary, Upadhyay, Deep, primary, Kumar, Suresh, primary, Kim, Yoo Sun, primary, Roper, Nitin, primary, Tran, Bao, primary, Hewitt, Stephen M., primary, Kleiner, David E., primary, Aladjem, Mirit I., primary, Friedman, Nir, primary, Hager, Gordon L., primary, Pommier, Yves, primary, Ried, Thomas, primary, and Thomas, Anish, primary

Published
2023
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30. Figure S1 from Chemoradiotherapy Resistance in Colorectal Cancer Cells is Mediated by Wnt/β-catenin Signaling

Author

Emons, Georg, primary, Spitzner, Melanie, primary, Reineke, Sebastian, primary, Möller, Janneke, primary, Auslander, Noam, primary, Kramer, Frank, primary, Hu, Yue, primary, Beissbarth, Tim, primary, Wolff, Hendrik A., primary, Rave-Fränk, Margret, primary, Heßmann, Elisabeth, primary, Gaedcke, Jochen, primary, Ghadimi, B. Michael, primary, Johnsen, Steven A., primary, Ried, Thomas, primary, and Grade, Marian, primary

Published
2023
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33. Table S3 from Chemoradiotherapy Resistance in Colorectal Cancer Cells is Mediated by Wnt/β-catenin Signaling

Author

Emons, Georg, primary, Spitzner, Melanie, primary, Reineke, Sebastian, primary, Möller, Janneke, primary, Auslander, Noam, primary, Kramer, Frank, primary, Hu, Yue, primary, Beissbarth, Tim, primary, Wolff, Hendrik A., primary, Rave-Fränk, Margret, primary, Heßmann, Elisabeth, primary, Gaedcke, Jochen, primary, Ghadimi, B. Michael, primary, Johnsen, Steven A., primary, Ried, Thomas, primary, and Grade, Marian, primary

Published
2023
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35. Data from Chemoradiotherapy Resistance in Colorectal Cancer Cells is Mediated by Wnt/β-catenin Signaling

Author

Emons, Georg, primary, Spitzner, Melanie, primary, Reineke, Sebastian, primary, Möller, Janneke, primary, Auslander, Noam, primary, Kramer, Frank, primary, Hu, Yue, primary, Beissbarth, Tim, primary, Wolff, Hendrik A., primary, Rave-Fränk, Margret, primary, Heßmann, Elisabeth, primary, Gaedcke, Jochen, primary, Ghadimi, B. Michael, primary, Johnsen, Steven A., primary, Ried, Thomas, primary, and Grade, Marian, primary

Published
2023
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38. Supplementary Figure and Table Legends from Chemoradiotherapy Resistance in Colorectal Cancer Cells is Mediated by Wnt/β-catenin Signaling

Author

Emons, Georg, primary, Spitzner, Melanie, primary, Reineke, Sebastian, primary, Möller, Janneke, primary, Auslander, Noam, primary, Kramer, Frank, primary, Hu, Yue, primary, Beissbarth, Tim, primary, Wolff, Hendrik A., primary, Rave-Fränk, Margret, primary, Heßmann, Elisabeth, primary, Gaedcke, Jochen, primary, Ghadimi, B. Michael, primary, Johnsen, Steven A., primary, Ried, Thomas, primary, and Grade, Marian, primary

Published
2023
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46. Supplementary Table 3 from The Rectal Cancer microRNAome – microRNA Expression in Rectal Cancer and Matched Normal Mucosa

Author

Gaedcke, Jochen, primary, Grade, Marian, primary, Camps, Jordi, primary, Søkilde, Rolf, primary, Kaczkowski, Bogumil, primary, Schetter, Aaron J., primary, Difilippantonio, Michael J., primary, Harris, Curtis C., primary, Ghadimi, B. Michael, primary, Møller, Søren, primary, Beissbarth, Tim, primary, Ried, Thomas, primary, and Litman, Thomas, primary

Published
2023
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48. Supplementary Table S1 from ASXL3 Is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer

Author

Shukla, Vivek, primary, Rao, Mahadev, primary, Zhang, Hongen, primary, Beers, Jeanette, primary, Wangsa, Darawalee, primary, Wangsa, Danny, primary, Buishand, Floryne O., primary, Wang, Yonghong, primary, Yu, Zhiya, primary, Stevenson, Holly S., primary, Reardon, Emily S., primary, McLoughlin, Kaitlin C., primary, Kaufman, Andrew S., primary, Payabyab, Eden C., primary, Hong, Julie A., primary, Zhang, Mary, primary, Davis, Sean, primary, Edelman, Daniel, primary, Chen, Guokai, primary, Miettinen, Markku M., primary, Restifo, Nicholas P., primary, Ried, Thomas, primary, Meltzer, Paul A., primary, and Schrump, David S., primary

Published
2023
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49. Supplementary Table 2 from The Rectal Cancer microRNAome – microRNA Expression in Rectal Cancer and Matched Normal Mucosa

Author

Gaedcke, Jochen, primary, Grade, Marian, primary, Camps, Jordi, primary, Søkilde, Rolf, primary, Kaczkowski, Bogumil, primary, Schetter, Aaron J., primary, Difilippantonio, Michael J., primary, Harris, Curtis C., primary, Ghadimi, B. Michael, primary, Møller, Søren, primary, Beissbarth, Tim, primary, Ried, Thomas, primary, and Litman, Thomas, primary

Published
2023
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50. Supplementary Figure S1 from ASXL3 Is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer

Author

Shukla, Vivek, primary, Rao, Mahadev, primary, Zhang, Hongen, primary, Beers, Jeanette, primary, Wangsa, Darawalee, primary, Wangsa, Danny, primary, Buishand, Floryne O., primary, Wang, Yonghong, primary, Yu, Zhiya, primary, Stevenson, Holly S., primary, Reardon, Emily S., primary, McLoughlin, Kaitlin C., primary, Kaufman, Andrew S., primary, Payabyab, Eden C., primary, Hong, Julie A., primary, Zhang, Mary, primary, Davis, Sean, primary, Edelman, Daniel, primary, Chen, Guokai, primary, Miettinen, Markku M., primary, Restifo, Nicholas P., primary, Ried, Thomas, primary, Meltzer, Paul A., primary, and Schrump, David S., primary

Published
2023
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